Biology doi: 10.3390/biology13110926

Authors: Yuyin Huang Hongying Cai Yunsheng Han Peilong Yang

Heat stress (HS) due to high temperatures has adverse effects on poultry, including decreased feed intake, lower feed efficiency, decreased body weight, and higher mortality. There are complex mechanisms behind heat stress in poultry involving the neuroendocrine system, organ damage, and other physiological systems. HS activates endocrine glands, such as the pituitary, adrenal, thyroid, and gonadal, by the action of the hypothalamus and sympathetic nerves, ultimately causing changes in hormone levels: HS leads to increased corticosterone levels, changes in triiodothyronine and thyroxine levels, decreased gonadotropin levels, reduced ovarian function, and the promotion of catecholamine release, which ultimately affects the normal productive performance of poultry. Meanwhile, heat stress also causes damage to the liver, lungs, intestines, and various immune organs, severely impairing organ function in poultry. Nutrient additives to feed are important measures of prevention and treatment, including natural plants and extracts, probiotics, amino acids, and other nutrients, which are effective in alleviating heat stress in poultry. Future studies need to explore the specific mechanisms through which heat stress impacts the neuroendocrine system in poultry and the interrelationships between the axes and organ damage so as to provide an effective theoretical basis for the development of preventive and treatment measures.

Biology doi: 10.3390/biology13110925

Authors: Diana Reznikova Nikita Kochetkov Alexey Vatlin Dmitry Nikiforov-Nikishin Olesya Galanova Anastasia Klimuk Svetlana Smorodinskaya Daria Matyushkina Alexey Kovalenko Ivan Butenko Maria Marsova Valery Danilenko

Agricultural and industrial activities are increasing pollution of water bodies with low doses of xenobiotics that have detrimental effects on aquaculture. The aim of this work was to determine the possibility of using Levilactobacillus brevis 47f culture in fish aquaculture under the influence of low doses of xenobiotics as an adaptogen. An increase in the survival of Danio rerio individuals exposed to the xenobiotic bisphenol A solution and fed with the L. brevis 47f was shown compared to control groups and, at the same time, the cytokine profile in the intestinal tissues of Danio rerio was also investigated. Analysis of differential gene expression of the L. brevis 47f grown under the action of high concentrations of bisphenol A showed changes in mRNA levels of a number of genes, including genes of various transport proteins, genes involved in fatty acid synthesis, genes of transcriptional regulators, genes of the arabinose operon, and the oppA gene. The identification of L. brevis 47f proteins from polyacrylamide gel by mass spectrometry revealed L-arabinose isomerase, Clp chaperone subunit, ATP synthase subunits, pentose phosphate pathway and glycolysis enzyme proteins, which are likely part of the L. brevis 47f strain’s anti-stress response, but probably do not affect its adaptogenic activity toward Danio rerio.

Biology doi: 10.3390/biology13110924

Authors: Dinara R. Dikaeva Alexander G. Dvoretsky

The Barents Sea region is influenced by an increased inflow of warm Atlantic water, which impacts all components of the local ecosystem. Information on the state of benthic communities is required to predict alterations in the food web’s structure and functioning. The spatial distribution of polychaete communities was investigated in relation to environmental conditions at nine stations along the Kola Transect (70°00′–74°00′ N, 33°30′ E) in April 2019. A taxonomically diverse fauna containing 114 taxa was found, with 95 identified at the species level. The fauna was composed predominantly of boreo-Arctic species (63%), followed by boreal (22%) and Arctic species (13%). The polychaete abundance and biomass exhibited considerable variability, ranging from 910 to 3546 ind. m−2 and from 3.4 to 72.7 g m−2, with average values of 1900 ind. m−2 and 18.7 g m−2, respectively. Cluster analysis revealed three distinct polychaete communities differing in dominant species composition, abundance, and biomass. The southern region featured the most abundant community, the middle part exhibited the highest diversity, and the northern area presented the community with the highest biomass. These spatial variations in community structure corresponded closely to the distribution and properties of water masses within the study area. Multivariate analysis identified depth as the primary driver of diversity indices, with higher values observed at shallow water sites. Salinity and water temperature together explained 46% of the variation in abundance, reflecting warming effects and showing positive or negative effects, depending on the taxa. Furthermore, an increase in water temperature had a positive impact on the contribution of boreal species to the total material, while exerting a strong negative effect on the overall community biomass, underscoring the potential of polychaetes in biological indication.

Biology doi: 10.3390/biology13110923

Authors: Alejandra Gutiérrez-González Irene Del Hierro Ariel Ernesto Cariaga-Martínez

Multiple myeloma is a complex and challenging type of blood cancer that affects plasma cells in the bone marrow. In recent years, the development of advanced research techniques, such as omics approaches—which involve studying large sets of biological data like genes and proteins—and high-throughput sequencing technologies, has allowed researchers to analyze vast amounts of genetic information rapidly and gain new insights into the disease. Additionally, the advent of artificial intelligence tools has accelerated data analysis, enabling more accurate predictions and improved treatment strategies. This review aims to highlight recent research advances in multiple myeloma made possible by these novel techniques and to provide guidance for researchers seeking effective approaches in this field.

Biology doi: 10.3390/biology13110922

Authors: Sara Wighard Ralf J. Sommer

Polyphenisms, the capability of organisms to form two or more alternative phenotypes in response to environmental variation, are prevalent in nature. However, associated molecular mechanisms and potential general principles of polyphenisms among major organismal groups remain currently unknown. This review focuses on an emerging model system for developmental plasticity and polyphenism research, the nematode Pristionchus pacificus and explores mechanistic insight obtained through unbiased genetic, experimental and natural variation studies. Resulting findings identify a central role for epigenetic switches in the environmental control of alternative phenotypes and their micro–and macroevolution. Several features observed in P. pacificus are shared with insects and plants and might become general principles for the control of polyphenisms during development.

Biology doi: 10.3390/biology13110921

Authors: Olga Maria Manna Stefano Burgio Domiziana Picone Adelaide Carista Alessandro Pitruzzella Alberto Fucarino Fabio Bucchieri

In recent years, the increasing number of long-duration space missions has prompted the scientific community to undertake a more comprehensive examination of the impact of microgravity on the human body during spaceflight. This review aims to assess the current knowledge regarding the consequences of exposure to an extreme environment, like microgravity, on the human body, focusing on the role of heat-shock proteins (HSPs). Previous studies have demonstrated that long-term exposure to microgravity during spaceflight can cause various changes in the human body, such as muscle atrophy, changes in muscle fiber composition, cardiovascular function, bone density, and even immune system functions. It has been postulated that heat-shock proteins (HSPs) may play a role in mitigating the harmful effects of microgravity-induced stress. According to past studies, heat-shock proteins (HSPs) are upregulated under simulated microgravity conditions. This upregulation assists in the maintenance of the proper folding and function of other proteins during stressful conditions, thereby safeguarding the physiological systems of organisms from the detrimental effects of microgravity. HSPs could also be used as biomarkers to assess the level of cellular stress in tissues and cells exposed to microgravity. Therefore, modulation of HSPs by drugs and genetic or environmental techniques could prove to be a potential therapeutic strategy to reduce the negative physiological consequences of long-duration spaceflight in astronauts.

Biology doi: 10.3390/biology13110920

Authors: Thérèse Dix-Peek Caroline Dickens Juan Valcárcel Raquel A. B. Duarte

Fibroblast growth factor receptor 2 (FGFR2) has been associated with breast cancer. We performed in silico analyses to investigate the FGFR2 mRNA expression and splice variants associated with breast cancer subtypes. Online databases, including cBioPortal and TCGA SpliceSeq, were used to examine the association between the FGFR2 expression and splice variants with breast cancer subtypes. A higher FGFR2 mRNA was significantly associated with luminal, oestrogen receptor (ER)-positive breast cancers, and invasive lobular carcinomas, whereas a lower FGFR2 was associated with human epidermal growth factor receptor 2 (HER2)-positive breast cancer and invasive ductal carcinomas. The epithelial alternatively spliced FGFR2 IIIb isoform was significantly enriched in ER+ breast cancer, while the mesenchymal FGFR2 IIIc isoform was significantly prevalent in HER2+ cancer. Increased levels of FGFR2 and IIIb splice isoforms are associated with less aggressive breast cancer phenotypes, while decreased levels of FGFR2 and increased IIIc splice isoform are associated with more aggressive phenotypes.

Biology doi: 10.3390/biology13110919

Authors: Helene Sánchez-Zelaia Irene Maja Nanni Ivano Oggiano Mónica Hernández Ana María Díez-Navajas Marina Collina

Plasmopara viticola is the causal agent of Grapevine Downy Mildew (GDM), which is a devastating disease of grapevines in humid temperate regions. The most employed method for protecting grapevines against GDM is the application of chemical fungicides. In Spain, Carboxylic Acid Amides (CAAs) are a fungicide group currently utilized in GDM control. In P. viticola, resistance to CAAs is conferred by G1105S and G1105V mutations in the CesA3 gene. Droplet digital polymerase chain reaction (ddPCR) is an innovative technique that combines PCR and droplet microfluidics to disperse the sample into thousands of water-in-oil droplets in which an amplification reaction is individually performed. In this study, we set up a ddPCR protocol to quantify S1105 and V1105 mutations conferring resistance to CAAs in P. viticola. The optimal PCR conditions were established, and the sensitivity and precision of the protocol were assessed. Four P. viticola populations coming from commercial vineyards in northern Spain were analyzed, and different allele frequencies were found in the analyzed samples corresponding to the different fungicide management strategies, ranging from 7.72% to 100%. Knowing the level of mutated alleles allows for designing resistance management strategies suited for each location. This suggests that similar ddPCR assays could be developed for studying mutations implicated in fungicide resistance in other fungicide groups and plant pathogens.

Biology doi: 10.3390/biology13110918

Authors: Osayd Zohud Iqbal M. Lone Kareem Midlej Aysar Nashef Fuad A. Iraqi

Smad4, a critical tumor suppressor gene, plays a significant role in pancreatic biology and tumorigenesis. Genetic background and sex are known to influence phenotypic outcomes, but their impact on pancreatic weight in Smad4-deficient mice remains unclear. This study investigates the impact of Smad4 deficiency on pancreatic weight in first-generation (F1) mice from diverse collaborative cross (CC) lines, focusing on the influence of genetic background and sex. F1 mice were generated by crossbreeding female CC mice with C57BL/6J-Smad4tm1Mak males. Genotyping confirmed the presence of Smad4 knockout alleles. Mice were housed under standard conditions, euthanized at 80 weeks, and their pancreatic weights were measured, adjusted for body weight, and analyzed for effects of Smad4 deficiency, sex, and genetic background. The overall population of F1 mice showed a slight but non-significant increase in adjusted pancreatic weights in heterozygous knockout mice compared to wild-type mice. Sex-specific analysis revealed no significant difference in males but a significant increase in adjusted pancreatic weights in heterozygous knockout females. Genetic background analysis showed that lines CC018 and CC025 substantially increased adjusted pancreatic weights in heterozygous knockout mice. In contrast, other lines showed no significant difference or varied non-significant changes. The interplay between genetic background and sex further influenced these outcomes. Smad4 deficiency affects pancreatic weight in a manner significantly modulated by genetic background and sex. This study highlights the necessity of considering these factors in genetic research and therapeutic development, demonstrating the value of the collaborative cross mouse population in dissecting complex genetic interactions.

Biology doi: 10.3390/biology13110917

Authors: Maksim Lyubomudrov Anastasiya Babkina Zoya Tsokolaeva Mikhail Yadgarov Sergey Shigeev Dmitriy Sundukov Arkady Golubev

Hemorrhagic stroke is the deadliest type of stroke. Cellular and molecular biomarkers are important for understanding the pathophysiology of stroke. Microglia are among the most promising biological markers. However, the morphological and physiological characteristics of microglia, as well as the structural and functional aspects of their interactions with neurons and other cells, are largely unknown. Due to the large number of different morphological phenotypes and very limited information on microglial changes in subarachnoid hemorrhage (SAH), we performed this study aimed at identifying the features of the distribution of various microglial phenotypes in the layers of the cerebral cortex in the hyperacute phase of non-traumatic SAH. We studied the distribution of various microglial phenotypes in the layers of the cerebral cortex of SAH non-survivors with a control group (coronary heart disease and sudden cardiac death were the underlying causes of death). An immunohistochemical study using antibodies to iba-1 (a marker of microglia) revealed changes in the morphological phenotypes of microglia in the cerebral cortex after subarachnoid hemorrhage. Significant differences between the groups indicate a rapid microglial response to injury. The findings indicate that there are quantitative and phenotypic changes in microglia in the cerebral cortex during early SAH in the human cortex.

Biology doi: 10.3390/biology13110916

Authors: Kano Matsuo Masaki Ikemoto Kohki Okada

S100A8 is a protein that is abundant in neutrophils and macrophages (MΦ), but its role in inflammation remains unclear. This study aimed to assess the immunological role(s) of S100A8 in acute intestinal inflammation in rats and its role in MΦ. Rat recombinant S100A8 (rr-S100A8, 1.0 mg/kg) was intraperitoneally administered daily to rats with 3% dextran sulfate sodium (DSS) (DSS + A8 group)-induced experimental acute colitis. The histological severity score (6.50 ± 0.51, p = 0.038) in the DSS + A8 group rats remained lower than that (9.75 ± 1.48) of the rats without S100A8 (DSS group) administration. The tumor necrosis factor-alpha (TNF-α) production in the colon tissues of the rats in the DSS + A8 group (4.76 ± 0.90 pg/mL/g, p = 0.042) was significantly suppressed, compared with that of the DSS group (10.45 ± 2.04 pg/mL/g). To stimulate rat peritoneal MΦ, rr-S100A8, the anti-rat S100A8 antibody, and a lipopolysaccharide (LPS) were used in the in vitro experiments. In the MΦ stimulated with rr-S100A8 for 2 h, the mRNA level of intracellular S100A8 (47.41 ± 24.44, p = 0.002) increased in an autocrine manner, whereas that of S100A9 (0.24 ± 0.43, p = 0.782) was not significant. The TNF-α mRNA level in the MΦ treated with LPS and the anti-rat S100A8 antibody significantly increased (102.26 ± 18.60, p = 0.001) compared to that with LPS alone (16.9 ± 8.56). These results indicate that S100A8 can serve as an anti-inflammatory protein in acute inflammation by negatively regulating S100A9 and TNF-α production through inflammatory signaling pathways in MΦ.

Biology doi: 10.3390/biology13110915

Authors: Emilie C. Baker David G. Riley Rodolfo C. Cardoso Thomas B. Hairgrove Charles R. Long Ronald D. Randel Thomas H. Welsh

As the amygdala is associated with fear and anxiety, it is important to determine the potential effects of gestational stressors on behavior and stress responses in offspring. The objective of this study was to investigate the effects of prenatal transportation stress on amygdala gene expression in 25-day-old Brahman calves, focusing on sex-specific differences. Amygdala tissue samples from prenatally stressed (PNS) and control bull and heifer calves were analyzed using RNA sequencing. A thorough outlier detection process, utilizing visual inspection of multidimensional scaling plots, robust principal component analysis, and PCAGrid methods, led to the exclusion of 5 of 32 samples from subsequent analyses. Differential expression analysis revealed no significant treatment differences between the control and PNS groups within either sex. However, sex-specific differences in gene expression were identified in both the control and PNS groups. The control group showed seven differentially expressed genes between sexes, while ten were identified between PNS males and females, with seven located on the X chromosome. Among these was the ubiquitin-specific peptidase 9 X-linked gene, which plays a role in neurodevelopmental pathways. When comparing males to females, regardless of treatment, a total of 58 genes were differentially expressed, with 45 showing increased expression in females. Gene enrichment analysis indicated that many differentially expressed genes are associated with infectious disease-related pathways. Future research should explore amygdala size and functional responses to various postnatal stimuli.

Biology doi: 10.3390/biology13110914

Authors: Ebtsam Sayed Hassan Abdallah Walaa Gomaa Mohamed Metwally Mootaz Ahmed Mohamed Abdel-Rahman Marco Albano Mahmoud Mostafa Mahmoud

Streptococcus agalactiae (Group B Lancefield) has emerged as a significant pathogen affecting both humans and animals, including aquatic species. Infections caused by S. agalactiae are becoming a growing concern in aquaculture and have been reported globally in various freshwater and marine fish species, particularly those inhabiting warm water environments. This has led to numerous outbreaks with high morbidity and mortality in fish. Nile tilapia (Oreochromis niloticus), a member of the Cichlid family, is one of the severely affected fish species by S. agalactiae. The current study aims to focus on S. agalactiae infection in cultured O. niloticus with reference to its transmission and sources of infection; risk factors influencing GBS infection, disease clinical signs, lesions, and pathogenesis; S. agalactiae virulence factors; and how to diagnose, treat, control, and prevent infection including vaccination and herbal extract medication.

Biology doi: 10.3390/biology13110913

Authors: Guy Beauchamp

In many species of animals, males aggregate in particular locations and produce calls to attract searching females for reproduction. One striking feature of such choruses is synchronization. On a scale of hours, choruses are often concentrated at particular times of day, such as dawn or dusk. On a scale of seconds, males may also synchronize the rhythm of their calls with one another. While synchronized calling at this scale suggests benefits acting at the collective level, competitive interactions between males to attract females can also lead to synchronized calling as an epiphenomenon. Why males in some species synchronize the rhythm of their calls is still debated, and more work is needed to understand the evolution of this behavior. I investigated chorus organization in the Emerald cicada (Zammara smaragdula), a Neotropical forest cicada in southern Belize, to explore these issues. Choruses in this species occurred at dawn and dusk and, occasionally, during daytime. There was no evidence for synchronization in the rhythm of calls among males, as bouts of collective calling occurred after quiet intervals of variable rather than fixed durations. The temporal aggregation of calls in this species thus probably emerged from competitive interactions among males to attract females. The degree of temporal overlap in the calls of males during a chorus varied as a function of chorus phase and time of day, suggesting flexibility in chorus organization, perhaps in relation to temporal variations in factors such as the number of calling cicadas, the number of predators present or ambient temperature during a chorus.

Biology doi: 10.3390/biology13110912

Authors: Bing Bai Meihui Wang Zhongguo Zhang Qingyun Guo Jingjing Yao

To solve the problem of large-scale growth of wetland reeds, wood vinegar, a by-product of pyrolysed reed wood vinegar, can be used as a natural antimicrobial agent. In this study, we compare the changes in growth and bacterial morphology of Escherichia coli (E. coli) treated with reed wood vinegar at different pyrolysis temperatures (300 °C, 500 °C and 700 °C) and reveal the bacterial inhibition mechanism of reed wood vinegar by RNA-Seq. The results of bacteria inhibitory activity showed that 1/2MIC 500 °C wood vinegar had the most prominent bacteria inhibitory activity. qPCR results showed that reed wood vinegar was able to significantly inhibit the expression of E. coli biofilm and genes related to the cell membrane transporter proteins. Electron microscopy observed that the wood vinegar disrupted the cellular morphology of E. coli, resulting in the crumpling of E. coli cell membranes. RNA-Seq showed the multifaceted antimicrobial effects of wood vinegar and demonstrated that the inhibitory effect of wood vinegar on E. coli was mainly realized through the inhibition of the expression of malE, which is an ATP-binding cassette (ABC) transporter complex of E. coli. In conclusion, our study provides an effective method and a theoretical basis for the mechanism of reed wood vinegar as a natural antimicrobial agent and its pathway of bacterial inhibition.

Biology doi: 10.3390/biology13110911

Authors: Jorge L. Cervantes-Salazar Nonanzit Pérez-Hernández Juan Calderón-Colmenero José Manuel Rodríguez-Pérez María G. González-Pacheco Clara Villamil-Castañeda Angel A. Rosas-Tlaque Diego B. Ortega-Zhindón

Congenital heart diseases (CHDs) are a group of complex diseases characterized by structural and functional malformations during development in the human heart; they represent an important problem for public health worldwide. Within these malformations, septal defects such as ventricular (VSD) and atrial septal defects (ASD) are the most common forms of CHDs. Studies have reported that CHDs are the result of genetic and environmental factors. Here, we review and summarize the role of genetics involved in cardiogenesis and congenital cardiac septal defects. Moreover, treatment regarding these congenital cardiac septal defects is also addressed.

Biology doi: 10.3390/biology13110910

Authors: Panagiotis Ntavaroukas Konstantinos Michail Rafaela Tsiakalidou Eleni Stampouloglou Katerina Tsiggene Dimitrios Komiotis Nikitas Georgiou Thomas Mavromoustakos Stella Manta Danielle Aje Panagiotis Michael Barry J. Campbell Stamatia Papoutsopoulou

The NF-κB family of transcription factors is a master regulator of cellular responses during inflammation, and its dysregulation has been linked to chronic inflammatory diseases, such as inflammatory bowel disease. It is therefore of vital importance to design and test new effective NF-κB inhibitors that have the potential to be utilized in clinical practice. In this study, we used a commercial transgenic HeLa cell line as an NF-κB activation reporter to test a novel quinoline molecule, Q3, as a potential inhibitor of the canonical NF-κB pathway. Q3 inhibited NF-κB-induced luciferase in concentrations as low as 5 μM and did not interfere with cell survival or induced cell death. A real-time PCR analysis revealed that Q3 could inhibit the TNF-induced transcription of the luciferase gene, as well as the TNF gene, a known downstream target gene. Immunocytochemistry studies revealed that Q3 moderately interferes with TNF-induced NF-κB nuclear translocation. Moreover, docking and molecular dynamics analyses confirmed that Q3 could potentially modulate transcriptional activity by inhibiting the interaction of NF-κB and DNA. Therefore, Q3 could be potentially developed for further in vivo studies as an NF-κB inhibitor.

Biology doi: 10.3390/biology13110909

Authors: Mary Clare McKenna Jana Kleinerova Alan Power Angela Garcia-Gallardo Ee Ling Tan Peter Bede

Introduction: Quantitative spinal cord imaging has facilitated the objective appraisal of spinal cord pathology in a range of neurological conditions both in the academic and clinical setting. Diverse methodological approaches have been implemented, encompassing a range of morphometric, diffusivity, susceptibility, magnetization transfer, and spectroscopy techniques. Advances have been fueled both by new MRI platforms and acquisition protocols as well as novel analysis pipelines. The quantitative evaluation of specific spinal tracts and grey matter indices has the potential to be used in diagnostic and monitoring applications. The comprehensive characterization of spinal disease burden in pre-symptomatic cohorts, in carriers of specific genetic mutations, and in conditions primarily associated with cerebral disease, has contributed important academic insights. Methods: A narrative review was conducted to examine the clinical and academic role of quantitative spinal cord imaging in a range of neurodegenerative and acquired spinal cord disorders, including hereditary spastic paraparesis, hereditary ataxias, motor neuron diseases, Huntington’s disease, and post-infectious or vascular disorders. Results: The clinical utility of specific methods, sample size considerations, academic role of spinal imaging, key radiological findings, and relevant clinical correlates are presented in each disease group. Conclusions: Quantitative spinal cord imaging studies have demonstrated the feasibility to reliably appraise structural, microstructural, diffusivity, and metabolic spinal cord alterations. Despite the notable academic advances, novel acquisition protocols and analysis pipelines are yet to be implemented in the clinical setting.

Biology doi: 10.3390/biology13110908

Authors: José Armando L. da Silva

A few trace elements are absolutely essential for the human metabolism, despite their low levels in the organism [...]

Biology doi: 10.3390/biology13110907

Authors: Carla Petrella Giampiero Ferraguti Luigi Tarani Francesca Tarani Marisa Patrizia Messina Marco Fiore

Neurotrophins (NTs) constitute a family of small protein messengers that play a fundamental role in both the central and peripheral nervous systems. In particular, the nerve growth factor (NGF) and the brain-derived neurotrophic factor (BDNF) play a subtle role in the survival, differentiation, and functioning of neuronal populations, as well as in the fine regulation of immune functions. The SARS-CoV-2 infection was characterized by a sequela of symptoms (serious respiratory pathology, inflammatory storm, neurological discomfort, up to the less serious flu-like symptoms), which caused, at the end of 2023, more than 7 million deaths worldwide. Despite the official end of the pandemic, the physical and psychological consequences are currently the object of scientific research, both acute and chronic/long-lasting (Long-COVID-19). Given the multifactorial nature of the outcomes of SARS-CoV-2 infection in adults and children, several studies have investigated the potential involvement of the NGF and BDNF systems in the pathology. This narrative review aims to summarize the most recent evidence on this crucial topic.

Biology doi: 10.3390/biology13110906

Authors: Camila C. Furlan Alexandre R. Freire Beatriz C. Ferreira-Pileggi Luciane N. O. Watanabe Paulo R. Botacin Felippe B. Prado Ana Cláudia Rossi

The aim of this study was to evaluate the mechanical effect of ovariectomy, diet, and tooth extraction on the bone structure of the mandible of Wistar rats. Mandibles from 40 female Wistar rats were used, divided into rats with ovariectomy surgery or surgical simulation. Half of the rats had the right upper incisor extracted and a soft diet was introduced for half of the animals for 30 days. After euthanasia, microtomography of the mandibles was performed for bone segmentation to construct three-dimensional models. Each mandible was subjected to a three-point bending test. The simulation by finite element method was configured according to the protocol for positioning the part on the support and force action by the load cell defined in the mechanical tests. Stress dissipation was described qualitatively on a color scale distributed in ranges of stress values. All models showed a higher concentration of stresses in the regions of force action and in the support regions, with differences in stress values and locations. Diet and dental condition interfered in the distribution of stresses, with the lateral surface of the mandible being more influenced by diet and the medial surface of the mandible by diet and dental condition.

Biology doi: 10.3390/biology13110905

Authors: Nasserdine Papa Mze Houssein Yonis Arreh Rahma Abdi Moussa Mahdi Bachir Elmi Mohamed Ahmed Waiss Mohamed Migane Abdi Hassan Ibrahim Robleh Samatar Kayad Guelleh Abdoul-ilah Ahmed Abdi Hervé Bogreau Leonardo K. Basco Bouh Abdi Khaireh

Djibouti is confronted with malaria resurgence, with malaria having been occurring in epidemic proportions since a decade ago. The current epidemiology of drug-resistant Plasmodium falciparum is not well known. Molecular markers were analyzed by targeted sequencing in 79 P. falciparum clinical isolates collected in Djibouti city in 2023 using the Miseq Illumina platform newly installed in the country. The objective of the study was to analyze the key codons in these molecular markers associated with antimalarial drug resistance. The prevalence of the mutant Pfcrt CVIET haplotype (92%) associated with chloroquine resistance and mutant Pfdhps-Pfdhfr haplotypes (7.4% SGEA and 53.5% IRN, respectively) associated with sulfadoxine-pyrimethamine resistance was high. By contrast, Pfmdr1 haplotypes associated with amodiaquine (YYY) or lumefantrine (NFD) resistance were not observed in any of the isolates. Although the “Asian-type” PfK13 mutations associated with artemisinin resistance were not observed, the “African-type” PfK13 substitution, R622I, was found in a single isolate (1.4%) for the first time in Djibouti. Our genotyping data suggest that most Djiboutian P. falciparum isolates are resistant to chloroquine and sulfadoxine-pyrimethamine but are sensitive to amodiaquine, lumefantrine, and artemisinin. Nonetheless, the presence of an isolate with the R622I PfK13 substitution is a warning signal that calls for a regular surveillance of molecular markers of antimalarial drug resistance.

Biology doi: 10.3390/biology13110904

Authors: Aijun Tong Dengwei Wang Nan Jia Ying Zheng Yusong Qiu Weichao Chen Hesham R. El-Seed Chao Zhao

Diabetes mellitus (DM) is becoming increasingly prominent, posing a serious threat to human health. Its prevalence is rising every year, and often affects young people. In the past few decades, research on marine algae has been recognized as a major field of drug discovery. Seaweed active substances, including algal polysaccharides, algal polyphenols, algal unsaturated fatty acids, and algal dietary fiber, have unique biological activities. This article reviews the effects and mechanisms of the types, structures, and compositions of seaweed on inhibiting glucose and lipid metabolism disorders, with a focus on the inhibitory effect of active substances on blood glucose reduction. The aim is to provide a basis for the development of seaweed active substance hypoglycemic drugs.

Biology doi: 10.3390/biology13110903

Authors: Yu Chen Rui Yang Haojie Wang Xianghui Xiao Baoguang Xing Yanfang Li Qiankun Liu Quanwei Lu Renhai Peng Guodong Chen Yongbo Wang Pengtao Li

Oxidative Stress 3 (OXS3) encodes a plant-specific protein that makes great contributions to a plant’s stress tolerance. However, reports on genome-wide identification and expression pattern analyses of OXS3 were only found for Arabidopsis, wheat, and rice. The genus Gossypium (cotton) serves as an ideal model for studying allopolyploidy. Therefore, two diploid species (G. raimondii and G. arboreum) and two tetraploid species (G. hirsutum and G. barbadense) were chosen in this study for a bioinformatics analysis, resulting in 12, 12, 22, and 23 OXS3 members, respectively. A phylogenetic tree was constructed using 69 cotton OXS3 genes alongside 8 Arabidopsis, 10 rice, and 9 wheat genes, which were classified into three groups (Group 1–3). A consistent evolutionary relationship with the phylogenetic tree was observed in our structural analysis of the cotton OXS3 genes and the clustering of six conserved motifs. Gene duplication analysis across the four representative Gossypium species suggested that whole-genome duplication, segmental duplication, and tandem duplication might play significant roles in the expansion of the OXS3 gene family. Some existing elements responsive to salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA) were identified by cis-regulatory element analysis in the promoter regions, which could influence the expression levels of cotton OXS3 genes. Furthermore, the expression patterns of the GhOXS3 gene were examined in different tissues or organs, as well as in developing ovules and fibers, with the highest expression observed in ovules. GhOXS3 genes exhibited a more pronounced regulatory response to abiotic stresses, of which ten GhOXS3 genes showed similar expression patterns under cold, heat, salt, and drought treatments. These observations were verified by quantitative real-time PCR experiments. These findings enhance our understanding of the evolutionary relationships and expression patterns of the OXS3 gene family and provide valuable insights for the identification of vital candidate genes for trait improvement in cotton breeding.

Biology doi: 10.3390/biology13110902

Authors: Imon Abedin Hilloljyoti Singha Hye-Eun Kang Hyun-Woo Kim Shantanu Kundu

Terrestrial carnivores, such as the clouded leopard (Neofelis nebulosa), are ‘vulnerable’ and experiencing significant population declines in mainland Asia. Considering the assessed threats, the IUCN has repetitively revised the range of this felid and now characterized it into four distinct categories (extant, possibly extant, possibly extinct, and extinct). Although several ecological works have been accomplished on this enigmatic carnivore, the overall view of its habitat suitability, fragmentation, and corridor connectivity in both present and historical ranges is lacking. Thus, achieving this ecological information under present and future climate scenarios is crucial. The model identified merely 44,033 sq. km falling within the extant range (representing 31.66%) and 20,034 sq. km (8.13%) in the possibly extant range. Fascinatingly, within the historical ranges, an additional 15,264 sq. km (6.58%) has been identified as suitable habitat in the possibly extinct range and 14,022 sq. km (2.38%) in the extinct range. Notably, a total of 25,614 sq. km of suitable habitat is found within designated protected areas across the entire range. Nevertheless, climate change is expected to drive habitat loss of up to 41% (overall IUCN range) for N. nebulosa in both present and historical extent, with habitat patches becoming increasingly fragmented. This is reflected in a projected decline in the number of viable habitat patches (NP) by up to 23.29% in the future. This study also identified 18 transboundary biological corridors for N. nebulosa, with Southeast Asian countries expected to experience the most significant declines in corridor connectivity. In contrast, the South Asian countries (Bhutan, Nepal, and India) are projected to maintain relatively higher connectivity in the future. Nevertheless, a substantial decline in overall mean corridor connectivity is projected in the near future due to the impacts of climate change. This study underscores the urgent need for a coordinated and multifaceted conservation strategy for N. nebulosa, focusing on mitigating habitat loss and fragmentation. Practical measures must be implemented to protect the species’ shrinking range, considering its declining corridor networks and heightened vulnerability to inbreeding depression. Moreover, the assessment of habitat suitability both within and beyond the extant range, alongside corridor connectivity measures, provides valuable insights into potential translocation and reintroduction sites for this species. These findings provide a critical foundation for developing a strategic conservation plan tailored to the specific needs of this felid species across South and Southeast Asia, ensuring enhanced climate resilience and mitigating associated threats.

Biology doi: 10.3390/biology13110901

Authors: Xiaosong Tian Xiaoai Lin Qing Xie Jinping Liu Longzao Luo

The aim of this study was to explore the effects of temperature and light on microalgal growth and nutrient removal in turtle aquaculture wastewater using a single-factor experiment method. Results showed that the growth process of Desmodesmus sp. CHX1 in turtle aquaculture wastewater exhibited three stages, namely adaptation, logarithmic, and stable periods. Temperature and light significantly influenced the growth and protein and lipid accumulation of Desmodesmus sp. CHX1. The optimal conditions for the growth and biomass accumulation of Desmodesmus sp. CHX1 included a temperature of 30 °C, a photoperiod of 24L:0D, and a light intensity of 180 μmol photon/(m2·s). Increased temperature, photoperiod, and light intensity enhanced nutrient removal efficiency. Maximum nitrogen removal was achieved at a temperature of 30 °C, a photoperiod of 24L:0D, and a light intensity of 180 μmol photon/(m2·s), with the removal efficiency of 86.53%, 97.94%, 99.57%, and 99.15% for ammonia, nitrate, nitrite, and total phosphorus (TP), respectively. Temperature did not significantly affect TP removal, but increased photoperiod and light intensity improved the removal efficiency of TP. The development of microalgae biomass as a feed rich in protein and lipids could address feed shortages and meet the nutritional needs of turtles, offering a feasible solution for large-scale production.

Biology doi: 10.3390/biology13110900

Authors: Yu Cao Ye Li Zhong-Yan Gao Xian-Guang Zhang Bo-Tao Jiang Hong-Bao Wang

Species of the family Prosthogonimidae are considered the most pathogenic trematodes of poultry and wild birds worldwide, causing heavy economic losses in many countries. Prosthogonimosis was a common parasitic disease of Grus japonensis (Müller, 1776) which caused inflammation of the cloaca and bursa of Fabricius and even death. Morphological identifications of Prosthogonimus species are easily confusing; therefore, molecular characterization is used for discrimination. The present study was conducted to identify Prosthogonimus species at Zhalong National Nature Reserve, northeast of China. Considering the morphological variability and wide host range of individual Prosthogonimus species, a combination of both morphological and molecular analyses is indispensable for the valid identification of this parasite and the internal transcribed spacer (ITS) region was amplified for the sequence analysis and phylogenetic analysis. The results of molecular analysis together with phylogenetic reconstruction indicated that the Prosthogonimus pellucidus (von Linstow, 1873) in this study form a single cluster with P. pellucidus, revealing potentially high diversity within the genus Prosthogonimus. Classification of Prosthogonimus species seems to be unrelated to the host and may be related to geographical location. These data provide a significant resource of molecular markers for studying the taxonomy, population genetics, and systematics of Prosthogonimidae.

Biology doi: 10.3390/biology13110899

Authors: Ge Song Dan Song Yongwei Wang Li Wang Weiwei Wang

The ketogenic diet is becoming an assisted treatment to control weight, obesity, and even type 2 diabetes. However, there has been no scientific proof supporting that the ketogenic diet is absolutely safe and sustainable. In this study, Sprague–Dawley (SD) rats were fed different ratios of fat to carbohydrates under the same apparent metabolizable energy level to evaluate the effects of a ketogenic diet on healthy subjects. The results showed that the ketogenic diet could relatively sustain body weight and enhance the levels of serum alanine aminotransferase (ALT) and serum alkaline phosphatase (SAP), leading to more moderate lipoidosis and milder local non-specific inflammation in the liver compared with the high-carbohydrate diet. In addition, the abundance of probiotic strains such as Lactobacillus, Lactococcus, and Faecalitalea were reduced with the ketogenic diet in rats, while an abundance of pathogenic strains such as Anaerotruncus, Enterococcus, Rothia, and Enterorhabdus were increased with both the ketogenic diet and the high-carbohydrate diet. This study suggests that the ketogenic diet can lead to impairments of liver function and changed composition of the gut microbiota in rats, which to some extent indicates the danger of consuming a generalized ketogenic diet.

Biology doi: 10.3390/biology13110898

Authors: Sheila Spada Sumit Mukherjee

There exists a long-standing research interest to understand the molecular and signaling interactions between tumor cells and the innate and adaptive immune cells such as dendritic cells, macrophages, NK cells, and B and T cells that occur in the tumor microenvironment (TME) [...]

Biology doi: 10.3390/biology13110897

Authors: Nejib Doss Aldo Morrone Patrizia Forgione Giusto Trevisan Serena Bonin

Lyme borreliosis (LB) is more common in the Northern Hemisphere. It is endemic mainly in North America, where the vectors are Ixodes scapularis and Ixodes pacificus, and in Eurasia, where the vectors are Ixodes ricinus and Ixodes persulcatus. Both tick-borne diseases and LB are influenced by climate change. Africa and South America are crossed by the equator and are situated in both the Northern and Southern Hemispheres. In Africa, the LB is present on the Mediterranean and the Indian Ocean coasts. Borrelia lusitaniae is prevalent in countries bordering the Mediterranean Sea, such as Tunisia, Morocco, Algeria, and Egypt. Ticks were detected in the Ixodes Ricinus, which are carried by migratory birds and the Ixodes inopinatus and captured by the Psammodromus algirus lizards. The Borreliae Lyme Group (LG) and, in particular, Borrelia garinii, have been reported in countries bordering the Indian Ocean, such as Kenya, Tanzania, and Mozambique, transported by migratory birds from North African countries, where the vector was identified as Hyalomma rufipes ticks. This review aims to document the presence of Borreliae LG and LB in Africa.

Biology doi: 10.3390/biology13110895

Authors: Chaoyong Wang Qianjin Che Bin Luo Yuxuan Zhu Jie Liu Mengmeng Tang

The impact of volcanic activity on microorganisms has always been a hot topic of discussion during geological history. Further studies are needed on the effects of volcanic activity on microbial growth in shale and the differences in nutrients provided by volcanic ash and other weathered rocks. This study’s results indicated that TOC contents at the bottom of the shale layer are 1.93–4.44% and 3.0% on average. The TOC contents at the top of the layer are 3.38–5.13% and 4.0% on average. It indicated that TOC contents at the bottom of the shale layer are smaller than the TOC contents at the top of the layer, suggesting that volcanic activity posed a long-term effect on biological growth. Seven different leachate concentrations were set in this experiment as follows: 1/10, 1/100, 1/500, 1/1000, 1/1500, 1/2000, and 1/2500. The results showed that the growth status of Pseudourostyla crassipes was affected by the addition of leachates with different concentrations compared to the control group. Additionally, the synthesis of chlorophyll a by Anabaena pseudoichthyoides was the most efficient with the 1/10 volcanic ash leachate. Through the analysis of major and trace elements in the solution before labeland after cultivation, the main elemental content of Ca2+, Mg2+, Na+, and K+ decreased by 3.8~87.24%, 75.96~92.70%, 86.56~95.67%, and 5.42~20.52% in the solution after microbial growth respectively. The trace elements B, Ba, Zn, and Fe decreased by 27.54~94.39%, 20~82.03%, 70.45~98.29%, and 99%. It was found that the B, Ba, Fe, and Zn elements decreased significantly. The nutrients from volcanic ash are the main factor promoting microbial growth. It can be indicated that the volcanic ash soaking solution has a higher content of nutrients when compared to the solubility of nutrients in volcanic ash compared to that of granite. A higher content of nutrients promotes microbial growth. The calculation results indicate that a volcanic eruption with a quantity of several 1010 m3 has a significant impact on microorganisms, lasting from tens of thousands to hundreds of thousands of years.

Biology doi: 10.3390/biology13110896

Authors: Takoua Ben Attia Sana Bahri Sonia Ben Younes Afef Nahdi Ridha Ben Ali Linda Bel Haj Kacem Michèle Véronique El May Eduardo Alberto López-Maldonado Abada Mhamdi

The primary objective of this study was to investigate the pulmonary damage resulting from isolated or combined exposure to inhaled toluene (300 ppm) and noise 85 dB (A), with a focus on evaluating the potential protective effects of Olea europaea L. leaf extract (OLE). Forty-eight male Wistar rats were divided into eight groups: control (C), OLE treatment (O), noise exposure (N), noise exposure with OLE treatment (N+OLE), toluene exposure (T), toluene exposure with OLE treatment (T + OLE), co-exposure to toluene and noise (NT), and co-exposure with OLE treatment (NT + OLE). OLE (40 mg/kg/day) was administered daily for six weeks via oral gavage. Exposure to toluene and noise resulted in significant disruption of the pulmonary tissue structure, accompanied by oxidative stress, as evidenced by increased lipid peroxidation, diminished catalase and superoxide dismutase activities, and elevated pro-inflammatory cytokines IL6, IL-β, and TNF-α. Notably, the administration of OLE effectively mitigated oxidative stress and inflammation and preserved pulmonary histology. In conclusion, exposure to toluene and its combination with noise significantly elevated oxidative stress, inflammatory responses, and histological disruptions in the lung tissue. In contrast, noise exposure alone is characterized by minimal effects, although it is still associated with an inflammatory response. Notably, Olea europaea L. leaf extract (OLE) exhibits a substantial protective role, effectively mitigating the adverse effects of combined exposure and highlighting its potential as a therapeutic agent for lung health.

Biology doi: 10.3390/biology13110894

Authors: Yingxuan Xu Shifeng Wang Yongcan Zhou Zhenyu Xie Bei Wang Zhangding Zhao Wenlong Cai Peibo Wang Weiliang Guo Dongdong Zhang Zhi Ye

Flavobacterium davisii is one of the causative agents of columnaris disease, significantly impacting Nile tilapia aquaculture. This study examines the invasion and immune evasion mechanisms of a highly virulent F. davisii strain through transcriptomic profiling of tilapia gills following acute immersion. We identified 8192 differentially expressed genes (DEGs) at 2 h, 6 h, and 12 h post-infection. They are enriched in pathways related to oxidative stress, immune suppression, tissue necrosis, and bacterial infection. Notably, early overexpression of rhamnose-binding lectin and mucin genes facilitated bacterial adhesion. Key immune genes, including those encoding major histocompatibility complex (MHC), immunoglobulins (Ig), Toll-like receptors (TLRs), and chemokines, were downregulated, indicating immune suppression. Conversely, immune evasion genes such as Fc receptor-like (FcRL) and programmed death-ligand 1 (PDL1) were upregulated, along with genes associated with reactive oxygen species (ROS) production, leading to increased tissue damage. Additionally, the upregulation of fibroblast growth factor and collagen genes suggested active tissue repair. In conclusion, F. davisii rapidly invades its host by enhancing adhesion to gill tissues, suppressing immune function, and inducing tissue damage. These findings enhance our understanding of F. davisii infection mechanisms and support the future breeding of disease-resistant tilapia and the development of sustainable control strategies.

Biology doi: 10.3390/biology13110893

Authors: Oyedele J. Olaoye Asya Esin Aksoy Santeri V. Hyytiäinen Aia A. Narits Miriam A. Hickey

Parkinson’s disease (PD) is the second-most common neurodegenerative disease worldwide. Patients are diagnosed based upon movement disorders, including bradykinesia, tremor and stiffness of movement. However, non-motor signs, including constipation, rapid eye movement sleep behavior disorder, smell deficits and pain are well recognized. Peripheral neuropathy is also increasingly recognized, as the vast majority of patients show reduced intraepidermal nerve fibers, and sensory nerve conduction and sensory function is also impaired. Many case studies in the literature show that high-dose levodopa may induce or exacerbate neuropathy in PD, which is thought to involve levodopa’s metabolism to homocysteine. Here, we treated primary cultures of dorsal root ganglia and a sensory neuronal cell line with levodopa to examine effects on cell morphology, mitochondrial content and physiology, and lysosomal function. High-dose levodopa reduced mitochondrial membrane potential. At concentrations observed in the patient, levodopa enhanced immunoreactivity to beta III tubulin. Critically, levodopa reduced lysosomal content and also reduced the proportion of lysosomes that were acidic, thereby impairing their function, whereas homocysteine tended to increase lysosome content. Levodopa is a critically important drug for the treatment of PD. However, our data suggest that at concentrations observed in the patient, it has deleterious effects on sensory neurons that are not related to homocysteine.

Biology doi: 10.3390/biology13110892

Authors: Yanxia Duan Jiaxin Liu Ailin Li Chang Liu Guang Shu Gang Yin

Along with abnormalities in glucose metabolism, disturbances in the balance of lipid catabolism and synthesis have emerged as a new area of cancer metabolism that needs to be studied in depth. Disturbances in lipid metabolic homeostasis, represented by fatty acid oxidation (FAO) imbalance, leading to activation of pro-cancer signals and abnormalities in the expression and activity of related metabolically critical rate-limiting enzymes, have become an important part of metabolic remodeling in cancer. The FAO process is a metabolic pathway that facilitates the breakdown of fatty acids into CO2 and H2O and releases large amounts of energy in the body under aerobic conditions. More and more studies have shown that FAO provides an important energy supply for the development of cancer cells. At the same time, the CPT family, including carnitine palmitoyltransferase 1 (CPT1) and carnitine palmitoyltransferase 2 (CPT2), are key rate-limiting enzymes for FAO that exert a pivotal influence on the genesis and progression of neoplastic growth. Therefore, we look at molecular structural properties of the CPT family, the roles they play in tumorigenesis and development, the target drugs, and the possible regulatory roles of CPTs in energy metabolism reprogramming to help understand the current state of CPT family research and to search for new therapeutic strategies.

Biology doi: 10.3390/biology13110891

Authors: María Botía María Martín-Cuervo Silvia Martínez-Subiela José Joaquín Cerón Ignacio Ayala Sanni Hansen Alberto Muñoz-Prieto

Equine Gastric Ulcer Syndrome (EGUS) is a widespread disease with a very high prevalence and importance in horses. It includes two conditions: Equine squamous gastric disease (ESGD), linked to acid disturbances, and Equine Glandular Gastric Disease (EGGD), associated with inflammation and immune system issues. In saliva, increased levels of immunological markers have been observed in this disease, indicating immune system involvement. In addition, changes in biomarkers of oxidative stress have been described. In horses, IgG and IgA are proteins that appear in saliva and serum and are considered to be the major proteins in specific immunity; however, their levels in horses with EGUS have not been previously studied. This report aims to evaluate IgG and IgA concentrations in the saliva and serum of horses with EGUS, measured by automated assays, and compare them with other biomarkers of the immune and oxidative stress system. This work validated the IgG and IgA assays in saliva and showed that IgA significantly increased in the saliva of horses with EGUS. When the correlation between IgG and IgA and other biomarkers of immune system issues and oxidative stress such as ADA, S100 A8-A9 (calprotectin), S100 A12 (calgranulin), uric acid, FRAS, and AOPP was studied, IgA in saliva showed a significant moderate correlation with adenosine deaminase, indicating its possible involvement in the immune reaction occurring in EGUS.

Biology doi: 10.3390/biology13110890

Authors: Chin-Yu Liu Yi-Wen Chen Tsung-Yu Tsai Te-Hua Liu Ting-Chia Chang Chih-Wei Tsao

Our study was designed to investigate the Lactiplantibacillus plantarum 1008 (LP1008) on testicular antioxidant capacity, spermatogenesis, apoptosis, autophagy, and metabolic function in male mice with high-fat-diet-induced obesity. A total of thirty-six male C57BL/6 mice were fed a normal diet (denoted as the NC group) or a high-fat control diet (denoted as the HFC group) for 16 weeks, then half of the HFC group was randomly chosen and subsequently fed with LP1008 for the final 8 weeks (high-fat diet + LP1008; denoted as the HFP group). The HFP group expressed improved blood cholesterol, insulin resistance, hepatic function, and lipopolysaccharide (LPS) levels compared to the HFC group. Meanwhile, the HFC group displayed decreased testicular testosterone levels, sperm quality, and 17β-HSD protein expression, which were rescued after LP1008 treatment. Moreover, the HFC group had lower superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPX) enzyme activities. After LP1008 treatment, enhanced antioxidative activities and decreased lipid peroxidation were observed. The HFC group also exhibited aggravated apoptosis, inflammation, and autophagy proteins in the testis, which were ameliorated by LP1008 supplementation. Furthermore, the gut microbiota analysis results revealed that the Firmicutes/Bacteroidetes ratio was significantly elevated in the HFC and HFP groups compared to the NC group and that LP1008 treatment diminished Ruminococcaceae and enhanced Bifidobacteriaceae diversity. In summary, LP1008 treatment strengthened antioxidative enzyme levels and regulated microbiota-ameliorated HFC-induced oxidative stress, apoptosis, inflammation, and autophagy, and thus improved testicular function and semen quality.

Biology doi: 10.3390/biology13110889

Authors: Jin-Young Jeong Junsik Kim Minji Kim Sungkwon Park

Deoxynivalenol (DON) is a common mycotoxin observed in cereal grains, and feed contamination poses health risks to pigs. Biological antidotes, such as synbiotics (SYNs), have garnered attention for mitigating DON toxicity. This study aimed to assess the efficacy of SYNs by comparing the blood biochemistry, histology, and gut microbiome of weaned piglets. A 4-week trial was conducted on 32 weaned piglets. After a week of diet and environmental adaptation, the pigs were divided into four groups: (1) control (CON, n = 8); (2) SYN (n = 8); (3) DON (n = 8); and (4) DON+SYN (n = 8). The SYN supplementation of weaned piglets increased the final body weight (21.71 ± 0.93 vs. 20.73 ± 0.84), average daily gain (0.38 ± 0.02 vs. 0.34 ± 0.02), and gain-to-feed ratio (0.49 ± 0.04 vs. 0.43 ± 0.02), and decreased the feed conversion ratio (2.14 ± 0.14 vs. 2.39 ± 0.13) compared to the DON group. A high dose of DON induced liver and colon fibrosis and liver and cecum apoptosis, which were alleviated by SYNs. Glucose in the DON group (84.9 ± 3.7) was significantly lower than in the control (101.3 ± 4.2). Additionally, both the DON and DON+SYN groups exhibited higher creatine (0.9 ± 0.0 and 0.9 ± 0.1) and lower cholesterol (88.3 ± 3.2 and 90.0 ± 4.8) levels (p < 0.05). In conclusion, SYNs alleviated DON toxicity, indicating its potential as an antidote for specific biomarkers.

Biology doi: 10.3390/biology13110888

Authors: Kumar Uddipto Julie A. Quinlivan George L. Mendz

The existence of intra-amniotic and placental microbiomes during pregnancy has been the source of considerable debate, with research yielding conflicting evidence. This study evaluated investigations into the putative presence of these microbiomes in healthy pregnancies by identifying design and data interpretation issues, particularly concerning contamination in samples with low-density bacterial DNA. Positive findings from diverse populations suggest a consistent presence of microbiota in the intra-amniotic space. Negative conclusions regarding the existence of these prenatal microbiomes emphasise the impact of contamination in the analysis of samples with low-density bacterial DNA. This study concluded that there is no definitive evidence to refute the existence of intra-amniotic microbiomes in healthy pregnancies. Also, it provides suggestions for controlling potential contamination factors in future research on intra-amniotic and placental microbial populations.

Biology doi: 10.3390/biology13110887

Authors: Musallam Kashoob Afshan Masood Assim A. Alfadda Salini Scaria Joy Wed Alluhaim Shahid Nawaz Mashal Abaalkhail Omar Alotaibi Saad Alsaleh Hicham Benabdelkamel

(1) Background: Chronic rhinosinusitis (CRS) is a common chronic inflammation of the nasal mucosa and the paranasal sinuses. The pathogenesis of chronic rhinosinusitis (CRS) is multifactorial and, as of yet, not well understood. (2) Methods: Nasal lavage fluid samples were collected from patients diagnosed with chronic sinusitis with nasal polyposis (CRSwNP) (n = 10) and individuals without sinusitis (control group) (n = 10) who had no nasal complaints. In the present study, we used an untargeted label-free LC-MS/MS mass spectrometric approach combined with bioinformatics and network pathway analysis to compare the changes in the proteomic profiles of the CRSwNP group and the control group. Data from LC-MS/MS underwent univariate and multivariate analyses. (3) Results: The proteomic analyses revealed distinct differences in the abundances of nasal lavage fluid proteins between the CRSwNP and control groups: a total of 234 proteins, 151 up- and 83 down-regulated in CRSwNP. Functional Gene Ontology (GO) analysis showed that dysregulated proteins were involved in airway inflammatory reaction, immune response, and oxidative stress. The biomarkers were evaluated using the Receiver Operating Characteristic (ROC) curve; an Area Under the Curve (AUC) of 0.999 (95% CI) identified potential biomarkers between the CRSwNP and control group. EMILIN-3 and RAB11-binding protein RELCH were down-regulated, and Macrophage migration inhibitory factor and deoxyribonuclease-1 were up-regulated, in CRSwNP compared to the control group. (4) Conclusions: These differentially expressed proteins identified in CRSwNP are involved in airway inflammatory reaction, immune response, and oxidative stress. In particular, the identification of increased interleukin-36 gamma (IL-36γ), which contributes to inflammatory response, and a decrease in SOD, in this group are notable findings. In the future, several of these proteins may prove useful for exploring the pathogenesis of nasal polyps and chronic sinusitis or as objective biomarkers for quantitatively monitoring disease progression or response to therapy.

Biology doi: 10.3390/biology13110886

Authors: Chuan-Sheng Song Qi-Cong Xu Cui-Ping Wan De-Zhi Kong Cai-Li Lin Shao-Shuai Yu

The thymidylate kinase (tmk) gene is indispensable for the proliferation and survival of phytoplasma. To reveal the molecular variation and phylogeny of the tmk genes of Candidatus phytoplasma ziziphi, in this study, the tmk genes of 50 phytoplasma strains infecting different resistant and susceptible jujube cultivars from different regions in China were amplified and analyzed. Two sequence types, tmk-x and tmk-y, were identified using clone-based sequencing. The JWB phytoplasma strains were classified into three types, type-X, type-Y, and type-XY, based on the sequencing chromatograms of the tmk genes. The type-X and type-Y strains contained only tmk-x and tmk-y genes, respectively. The type-XY strain contained both tmk-x and tmk-y genes. The type-X, type-Y, and type-XY strains comprised 42%, 12%, and 46% of all the strains, respectively. The type-X and type-XY strains were identified in both susceptible and resistant jujube cultivars, while type-Y strain was only identified in susceptible cultivars. Phylogenetic analysis indicated that the tmk genes of the phytoplasmas were divided into two categories: phylo-S and phylo-M. The phylo-S tmk gene was single-copied in the genome, with an evolutionary pattern similar to the 16S rRNA gene; the phylo-M tmk gene was multi-copied, related to PMU-mediated within-genome transposition and between-genome transfer. Furthermore, the phylogenetic tree suggested that the tmk genes shuttled between the genomes of the Paulownia witches’ broom phytoplasma and JWB phytoplasma. These findings provide insights into the evolutionary and adaptive mechanisms of phytoplasmas.

Biology doi: 10.3390/biology13110885

Authors: Kristian A. Choate Evan P. S. Pratt Matthew J. Jennings Robert J. Winn Paul B. Mann

In 2021, the World Health Organization classified isocitrate dehydrogenase (IDH) mutant gliomas as a distinct subgroup of tumors with genetic changes sufficient to enable a complete diagnosis. Patients with an IDH mutant glioma have improved survival which has been further enhanced by the advent of targeted therapies. IDH enzymes contribute to cellular metabolism, and mutations to specific catalytic residues result in the neomorphic production of D-2-hydroxyglutarate (D-2-HG). The accumulation of D-2-HG results in epigenetic alterations, oncogenesis and impacts the tumor microenvironment via immunological modulations. Here, we summarize the molecular, cellular, and clinical implications of IDH mutations in gliomas as well as current diagnostic techniques.

Biology doi: 10.3390/biology13110884

Authors: Mustafa Al-gafari Sasi Kumar Jagadeesan Thomas David Daniel Kazmirchuk Sarah Takallou Jiashu Wang Maryam Hajikarimlou Nishka Beersing Ramessur Waleed Darwish Calvin Bradbury-Jost Houman Moteshareie Kamaledin B. Said Bahram Samanfar Ashkan Golshani

Translation is a fundamental process in biology, and understanding its mechanisms is crucial to comprehending cellular functions and diseases. The regulation of this process is closely linked to the structure of mRNA, as these regions prove vital to modulating translation efficiency and control. Thus, identifying and investigating these fundamental factors that influence the processing and unwinding of structured mRNAs would be of interest due to the widespread impact in various fields of biology. To this end, we employed a computational approach and identified genes that may be involved in the translation of structured mRNAs. The approach is based on the enrichment of interactions and co-expression of genes with those that are known to influence translation and helicase activity. The in silico prediction found CAF20 and ECM32 to be highly ranked candidates that may play a role in unwinding mRNA. The activities of neither CAF20 nor ECM32 have previously been linked to the translation of PGM2 mRNA or other structured mRNAs. Our follow-up investigations with these two genes provided evidence of their participation in the translation of PGM2 mRNA and several other synthetic structured mRNAs.

Biology doi: 10.3390/biology13110883

Authors: Larry A. Tucker Carson J. Bates

Telomere length is an index of cellular aging. Healthy lifestyles are associated with reduced oxidative stress and longer telomeres, whereas unhealthy behaviors are related to shorter telomeres and greater biological aging. This investigation was designed to determine if strength training accounted for differences in telomere length in a random sample of 4814 US adults. Data from the National Health and Nutrition Examination Survey (NHANES) were employed to answer the research questions using a cross-sectional design. Time spent strength training was calculated by multiplying days of strength training per week by minutes per session. Participation in other forms of physical activity was also calculated based on reported involvement in 47 other activities. Weighted multiple regression and partial correlation were used to calculate the mean differences in telomere length across levels of strength training, adjusting for differences in potential confounders. With the demographic covariates controlled, strength training and telomere length were linearly related (F = 14.7, p = 0.0006). Likewise, after adjusting for all the covariates, the linear association remained strong and significant (F = 14.7, p = 0.0006). In this national sample, 90 min per week of strength training was associated with 3.9 years less biological aging, on average. Regular strength training was strongly related to longer telomeres and less biological aging in 4814 US adults.

Biology doi: 10.3390/biology13110882

Authors: Yi-Chen Chen Ryoya Oga Takahiro Furumi Koki Nakagawa Yoshihiro Nita Hiroyuki Tamaki

Electrical stimulation-induced muscle contraction (ESMC) has demonstrated various physiological benefits, but its effects on the secretion of undercarboxylated osteocalcin (ucOC), a bone-derived cytokine, remain unclear. This study explored the relationship between ESMC, bone strain, and ucOC secretion through two experiments. In the first, young male Fischer 344 rats were divided into three groups: low-frequency ES (LF, 10 Hz), high-frequency ES (HF, 100 Hz), and control (CON). Acute 30-min transcutaneous ES was applied, and both bone strain and ucOC levels were measured. In the second experiment, rats underwent LF or HF long-term ES (two sessions per week for 4 weeks), with ucOC and insulin levels monitored. Results revealed a significant peak in ucOC at 6 h post-acute LF-ESMC. Despite HF-ESMC generating greater bone strain, LF-ESMC, with smaller but repetitive bone strain, proved more effective in stimulating ucOC secretion. In the long-term study, both ESMC groups exhibited early increases in ucOC, with a positive correlation to insulin levels. In conclusion, bone strain induced by ES-mediated muscle contraction promotes ucOC secretion, with both the magnitude and frequency of strain playing critical roles.

Biology doi: 10.3390/biology13110881

Authors: Quanquan Cao Mohamed S. Kisha Alkhateib Gaafar Abdelgayed Metwaly Younes Haifeng Liu Jun Jiang

The yellow catfish is an economically significant freshwater fish with increasing importance in aquaculture. However, the low temperature environments prevalent in certain regions pose challenges to its growth, development, and overall health. This study aimed to explore the impact of dietary arginine (Arg) addition on the growth, digestive capacity, and intestinal antioxidant response in fish under low temperature acclimation (18 °C). Total 720 fish were randomly distributed into six groups, each containing 120 fish. Over the course of eight weeks, each group was fed with diets about varying Arg concentrations (1.79–3.26 g/kg). The results indicated that Arg supplementation resulted in an increase in specific growth rate (SGR), feed intake (FI), feed efficiency (FE), as well as pancreatic enzyme activities in both pancreas and intestine. Conversely, malondialdehyde (MDA) and protein carbonyl (PC) contents initially decreased but increased with higher Arg concentrations. Glutathione peroxidase 1a (GPX1a) showed a positive correlation with nuclear factor-erythroid 2-related factor-2 (Nrf2), showing its role in antioxidative capacity. Furthermore, this study revealed that Arg significantly enhanced the activities of anti-superoxide anion, anti-hydroxyl radical, and anti-oxidative enzymes, along with the relative mRNA abundance of Copper-Zinc superoxide dismutase (CuZnSOD), catalase, GPX1a, glutamate-cysteine ligase catalytic subunit (GCLC), and Nrf2 in the intestine. It was determined that yellow catfish weighing between 61.0 g and 89.0 g require an intake of 26.8 g of Arg per kilogram of diet based on polynomial regression analysis of specific growth rate (SGR), which is equivalent to 37.0 g of dietary protein, under sub-low temperature conditions of 18 °C.

Biology doi: 10.3390/biology13110880

Authors: Jintao Lu Senzhe Zhang Jiaxin Liu Yuhua Zhang Lijuan Hu Zhende Yang Ping Hu

Monochamus alternatus, a pest posing a serious threat to coniferous species, such as Pinus massoniana, has had devastating effects on pine forests due to its association with Bursaphelenchus xylophilus. The creation of unique simple sequence repeat (SSR) primers for M. alternatus is crucial, as there has been little study of the species’ phylogeography. The aim of this study was to identify and create polymorphic SSR primers by sequencing samples of M. alternatus obtained from three different sampling points using the restriction site-associated DNA sequencing (Red-seq) approach. Subsequently, supplementary samples were integrated, and genetic typing was performed utilizing the identified polymorphic primers. Through comprehensive analysis, a total of 95,612 SSR loci were identified. Among these, mononucleotide repeats (51.43%), dinucleotide repeats (28.79%), and trinucleotide repeats (16.74%) predominated among the SSR motif types. Ultimately, 18 pairs of SSR primers were screened out, demonstrating stable amplification and high polymorphism. Genetic typing revealed that the mean number of alleles (Na) for these primer pairs ranged from 3 to 8, observed heterozygosity (Ho) ranged from 0.133 to 0.733, polymorphic information content (PIC) ranged from 0.294 and 0.783, and Shannon’s index (I) ranged from 0.590 to 1.802. This study effectively produced 16 pairs of SSR primers that can be applied to different populations of M. alternatus. As a result, important tools for furthering studies on the phylogeography of pine wood nematodes, creating genetic maps, gene mapping, and carrying out in-depth investigations into gene function have been made available.

Biology doi: 10.3390/biology13110879

Authors: Paul G. Holhorea Fernando Naya-Català Ricardo Domingo-Bretón Federico Moroni Álvaro Belenguer Josep À. Calduch-Giner Jaume Pérez-Sánchez

A confinement stress test with 75% tank space reduction and behavioural monitoring through tri-axial accelerometers externally attached to the operculum was designed. This procedure was validated by demonstrating the less pronounced stress response in gilthead sea bream than in European sea bass (950–1200 g). Our study aimed to assess habituation to high stocking densities with such procedure in gilthead sea bream. Animals (420–450 g) were reared (June–August) in a flow-through system at two stocking densities (CTRL: 10–15 kg/m3; HD: 18–24 kg/m3), with natural photoperiod and temperature (21–29 °C), and oxygen levels at 5.2–4.2 (CTRL) and 4.2–3.2 ppm (HD). At the end, blood and muscle were sampled for haematology and transcriptomic analyses, and external tissue damage was assessed by image-based scoring. Four days later, fish underwent a 45 min confinement stress test over two consecutive days. HD fish showed reduced feed intake, growth rates and haematopoietic activity. Muscle transcriptome changes indicated a shift from systemic to local growth regulation and a primed muscle regeneration over protein accretion in HD animals with slight external injuries. After stress testing, HD fish exhibited a decreased recovery time in activity and respiration rates, which was shorter after a second stressor exposure, confirming habituation to high densities.

Biology doi: 10.3390/biology13110878

Authors: Meghan M. Holst Catharine J. Wheaton Alexandra N. Schoen Jill V. Spangenberg Kevin T. McEligot Melissa L. Schouest Charlene M. Burns Natalie D. Mylniczenko

Background: Leopard sharks (Triakis semifasciata) are abundant, coastal, eastern Pacific, mesopredatory sharks and are frequently managed in aquariums and zoos. Medical examinations are a routine part of good husbandry practices, but the handling protocols vary greatly between facilities. In this study, we compared the physiological stress responses of T. semifasciata associated with manual restraint and sedated handling under parallel holding and handling procedures in a 10 min interval. Methods: Blood was collected and analyzed for the hematocrit (Hct), lactate, glucose, beta-hydroxybutyrate (β-HB), pH, blood gasses, 1α-hydroxycorticosterone (1α-OHB), and corticosterone (B). Results: Overall, a minimal physiological stress response was observed in both groups. However, statistically significant increases in the PCO2, β-HB and lactate occurred, while the pHTC, SO2, and BE decreased over time in the manual-restraint group. In the sedated group, the B, PCO2, and lactate increased while the pHTC, SO2, and base excess (BE) decreased over time. When comparing treatments, the sedated group had a higher B and PCO2 TC and a lower pHTC, BE, and SO2 than the manual-restraint group at the second time point. Conclusions: This study indicates that manual restraint is comparable to the described sedation in T. semifasciata for minimally invasive procedures. The overall results show that this species had low physiological stress responses to both methods.

Biology doi: 10.3390/biology13110877

Authors: Kristine McLellan Sima Sabbagh Momoko Takahashi Hui Hong Yuan Wang Jason Tait Sanchez

Neurotrophins are proteins that mediate neuronal development using spatiotemporal signaling gradients. The chicken nucleus magnocellularis (NM), an analogous structure to the mammalian anteroventral cochlear nucleus, provides a model system in which signaling between the brain-derived neurotrophic factor (BDNF) and tyrosine receptor kinase B (TrkB) is temporally regulated. In the NM, TrkB expression is high early in development (embryonic [E] day 9) and is downregulated until maturity (E18–21). It is currently unknown how BDNF–TrkB signaling affects neuronal properties throughout development and across a spatial (i.e., frequency) axis. To investigate this, we exogenously applied BDNF onto NM neurons ex vivo and studied intrinsic properties using whole-cell patch clamp electrophysiology. Early in development (E13), when TrkB expression is detectable with immunohistochemistry, BDNF application slowed the firing of high-frequency NM neurons, resembling an immature phenotype. Current measurements and biophysical modeling revealed that this was mediated by a decreased conductance of the voltage-dependent potassium channels. Interestingly, this effect was seen only in high-frequency neurons and not in low-frequency neurons. BDNF–TrkB signaling induced minimal changes in late-developing NM neurons (E20–21) of high and low frequencies. Our results indicate that normal developmental downregulation of BDNF–TrkB signaling promotes neuronal maturation tonotopically in the auditory brainstem, encouraging the appropriate development of neuronal properties.

Biology doi: 10.3390/biology13110876

Authors: Guoqing Bai Ruiwen Ding Qizhen Su Xiaomin Ge Shasha Li Huiying Shang Aiguo Zhao Chen Chen

Lacquer trees (Toxicodendron vernicifluum), economically vital, face high-temperature stress in summer. Transcriptomic, proteomic, and metabolomic analyses were employed to investigate the mechanisms by which lacquer trees respond to high temperatures. High-temperature treatment led to notable metabolite changes with 224 upregulated and 69 downregulated. Indole-3-acetic acid remained stable while abscisic acid decreased, with increases in jasmonic acid and jasmonoyl-L-isoleucine indicating complex hormonal responses. JAR1 and ABA 8′-hydroxylase encoding genes were upregulated. The rise in JAs boosted the alkaloid content and activated nitrogen transport. High temperatures also increased specific amino acids and upregulated aminotransferase and protease-encoding genes. Metabolomic analysis showed elevated flavonoid glycosides and the upregulation of glycosyltransferase genes. WPCNA found 35 protein modules involved in secondary metabolite biosynthesis, protein phosphorylation, and signal transduction. Protein–protein interaction analysis revealed MYC6’s link with flavonoid biosynthesis, indicating its role in promoting flavonoids.

Biology doi: 10.3390/biology13110875

Authors: Jiaze Gu Haifeng Mi Mingchun Ren Dongyu Huang Ahmed Mohamed Aboseif Hualiang Liang Lu Zhang

The aim of this study was to investigate the effects of S6K1α and β on the expression of glycolysis- and gluconeogenesis-related genes in juvenile blunt snout bream. Two isoforms, α and β, of ribosomal protein S6 kinase 1 in blunt snout bream were cloned and characterized, and their expression patterns were examined in vivo. The sequence analysis showed that s6k1α and s6k1β contain open reading frames of 2217 and 1497 bp, encoding 738 and 498 amino acids, respectively. Both S6K1α and S6K1β consist of an S_TKc domain and an extended S_TK_X domain. s6k1α and s6k1β were abundantly expressed in the heart and gonads. siRNAs were designed, and the experiment showed that α-siRNA inhibited s6k1α and s6k1β expression, but β-siRNA exclusively inhibited s6k1α expression (p < 0.05). α-siRNA upregulated the expression levels of gk and pk, while β-siRNA upregulated pepck and g6p expression (p < 0.05). The expression of g6pdh was found to be downregulated, but the gs mRNA level was overexpressed after treatment with α-siRNA and β-siRNA (p < 0.05). In the present experiment, S6K1α was more intimately involved in the regulation of gluconeogenesis when only S6K1α was inhibited, whereas the inhibition of both S6K1α and S6K1β collectively co-regulated glycolysis.

Biology doi: 10.3390/biology13110874

Authors: Anna K. Zalota Polina Yu. Dgebuadze Alexander D. Kiselev Margarita V. Chikina Alexey A. Udalov Daria V. Kondar Alexey V. Mishin Sergey M. Tsurikov

The introduction of a large predatory snow crab, Chionoecetes opilio, into the Kara Sea is a unique situation where the impact of an invasive species affecting an otherwise undisturbed ecosystem can be observed unhindered by other ecosystem stressors. Trophic interactions are one of the principal relationships between animals and can help assess an ecosystem’s stability. The trophic positions and sources of organic material for the most common benthic species of Blagopoluchiya Bay sampled at different stages of the invasion were calculated using stable isotope analysis. The most pronounced changes in the trophic web occurred amongst the megabenthic species, where previously most abundant deposit-feeding ophiuroids have disappeared. However, the benthic species’ trophic position and primary production source preference did not change. A sea star, Urasterias lincki, remained the highest carnivore in the bay, and the invasive crab remained at a lower trophic level, showing higher omnivory in its diet. Any changes in the consumers’ prey items were within the same trophic level. Overall, active predators became one of the most abundant feeding mode groups. The average weighted trophic position of all megabenthic species increased to the third trophic level, where mostly secondary consumers remained.

Biology doi: 10.3390/biology13110873

Authors: Yuqing Long Yuxi Dan Yao Jiang Jing Ma Tao Zhou Liaoqiong Fang Zhibiao Wang

Background: Angiogenesis plays a crucial role in the growth of colorectal cancer (CRC). Recent studies have identified extracellular vesicles (EVs) in the tumor microenvironment as important mediators of cell-to-cell communication. However, the specific role and mechanisms of CRC-derived EVs in regulating tumor angiogenesis remain to be further investigated. Methods: EVs were isolated from the conditioned medium of the CRC cells using ultracentrifugation. We investigated the effects of HT-29-derived EVs on tumor growth and angiogenesis in a subcutaneous HT-29 CRC tumor model in mice. Additionally, we evaluated the impact of HT-29-derived EVs on the proliferation, migration, and tube formation of human umbilical vein endothelial cells (HUVECs). Subsequently, bioinformatics analysis was performed to identify relevant signaling pathways, and pathway inhibitors were used to block the activation of these pathways, aiming to elucidate their roles in angiogenesis. Results: We found that HT-29-derived EVs can promote tumor growth and angiogenesis in vivo, as well as significantly enhance the proliferation, migration, and tube formation of HUVECs. Bioinformatics analysis revealed that HT-29-derived EVs may regulate angiogenesis through the JAK/STAT3 signaling pathway. Specifically, we observed that CRC-derived EVs promoted the phosphorylation of STAT3 (p-STAT3) and the expression of VEGFA in the nucleus of HUVECs. Treatment with the STAT3 inhibitor Stattic reduced the nuclear expression of p-STAT3, which impaired its function as a transcription factor, thereby inhibiting VEGFA expression and the pro-angiogenic effects of CRC-derived EVs. Conclusions: EVs derived from CRC cells promote CRC tumor angiogenesis by regulating VEGFA through the JAK/STAT3 pathway in endothelial cells.

Biology doi: 10.3390/biology13110872

Authors: Jiayao He Ke Chen Peishan Sun Han Xu Xubin Pan

The impact of invasive alien species (IAS) on nature and society is increasing globally. It is crucial to utilize information systems for evidence-based management, enabling the assessment and supporting survey and control actions. However, the lack of accessible and comprehensive baseline IAS data often impedes the ability to prioritize and allocate resources efficiently. Despite the increased public awareness of biological invasions in China over the past decades, the critical importance of data requirements has not been fully recognized, leading to gaps in available data. Here, we outline the key data demands for the management of biological invasions and highlight the current lack of high-quality data for invasion management in China, and critically assess data gaps in IAS distribution, inventory, and impact. Additionally, we propose a conceptual framework to illustrate the data requirements throughout the invasion management process, along with indicators to assess data quality within three dimensions: relevance, resolution, and reliability.

Biology doi: 10.3390/biology13110871

Authors: Mingrui Zou Mingmei Lin Kai-Lun Hu Rong Li

Endometriosis (EMT) is a common gynecological disease with a strong genetic component, while its precise etiology remains elusive. This study aims to integrate transcriptome-wide association study (TWAS), Mendelian randomization (MR), and bioinformatics analyses to reveal novel putatively causal genes and potential mechanisms. We obtained summary-level data of the Genotype-Tissue Expression Project (GTEx), v8 expression quantitative loci (eQTL) data, and the genome-wide association study (GWAS) data of EMT and its subtypes from the R11 release results of the FinnGen consortium for analysis. GWAS data of modifiable risk factors were collected from IEU Open GWAS. Cross-tissue TWAS analyses were performed using the unified test for molecular signature (UTMOST), while functional summary-based imputation (FUSION) was employed for single-tissue TWAS analyses. Furthermore, we also conducted multi-marker analysis of genomic annotation (MAGMA) analyses to validate the significant associations. Subsequent Mendelian randomization (MR) and colocalization analysis elucidated the causal associations between the identified genes across various tissues and EMT. To further delve into mechanisms, two-sample network MR analyses were conducted. At last, bioinformatics analyses were employed to enhance our understanding of the functional implications and expression patterns of these identified genes. For EMT, 22 significant gene signals were identified by UTMOST, 615 by FUSION, and 354 by MAGMA. Ultimately, six genes, including CISD2, EFRB, GREB1, IMMT, SULT1E1, and UBE2D3, were identified as candidate susceptibility genes for EMT. Through similar procedures, we identified GREB1, IL1A, and SULT1E1 for EMT of the ovary, and we identified GREB1 for EMT of the pelvic peritoneum, EMT of rectovaginal septum and vagina, and deep EMT. In MR analyses, the expression of IMMT in 21 tissues, EFR3B in the adrenal gland, CISD2 in 17 tissues, and UBE2D3 in 7 tissues demonstrated causal relationships with EMT risk. In addition, CISD2, IMMT, and UBE2D3, across different tissues, exhibited strong colocalization with EMT (PPH4 > 0.7). Two-sample network MR analyses revealed that CISD2, EFR3B, and UBE2D3 could potentially regulate the levels of blood lipids and hip circumference so as to influence the risk of EMT. Furthermore, bioinformatics analyses confirmed our findings and delved into the biological functions of the identified genes. Our study unveiled seven novel candidate genes whose predicted expression was associated with the risk of EMT, providing new insights into the underlying genetic framework of EMT. These findings will facilitate a deeper comprehension of the tissue-specific transcriptional regulatory mechanisms associated with EMT, paving the way for optimizing the management and treatment of EMT.

Biology doi: 10.3390/biology13110870

Authors: Xiujun Sun Xi Chen Biao Wu Liqing Zhou Yancui Chen Sichen Zheng Songlin Wang Zhihong Liu

Bivalve mollusks, comprising animals enclosed in two shell valves, are well-adapted to benthic life in many intertidal zones. Clams have evolved the buried lifestyle, which depends on their unique soft tissue structure and their wedge-shaped muscular foot and long extendible siphons. However, molecular mechanisms of adaptative phenotype evolution remain largely unknown. In the present study, we obtain the high-quality chromosome-level genome of Manila clam R. philippinarum, an economically important marine bivalve in many coastal areas. The genome is constructed by the Hi-C assisted assembly, which yields 19 chromosomes with a total of 1.17 Gb and BUSCO integrity of 92.23%. The de novo assembled genome has a contig N50 length of 307.7 kb and scaffold N50 of 59.5 Mb. Gene family expansion analysis reveals that a total of 24 single-copy gene families have undergone the significant expansion or contraction, including E3 ubiquitin ligase and dynein heavy chain. The significant expansion of transposable elements has been also identified, including long terminal repeats (LTR) and non-LTR retrotransposons. The comparative transcriptomics among different clam tissues reveals that extracellular matrix (ECM) receptors and neuroactive ligand receptors may play the important roles in tissue structural support and neurotransmission during their infaunal life. These findings of gene family expansion and tissue-specific expression may reflect the unique soft tissue structure of clams, suggesting the evolution of lineage-specific morphological novelties. The high-quality genome and transcriptome data of R. philippinarum will not only facilitate the genetic studies on clams but will also provide valuable information on morphological novelties in mollusks.

Biology doi: 10.3390/biology13110869

Authors: Qi Deng Zhifeng Feng Jin Xiang Hao Wu Xin Yang Zhou Zhang Cheng Li Xiaofei Cheng Min Xie Shaoming Li

Fish gut health is influenced by various factors, with the environment being a significant one. S. sinensis is a key aquaculture species in China, yet research on the impact of different aquaculture systems on its intestinal health remains limited. This study aims to explore the changes in intestinal morphology and gut microbiota of S. sinensis under two aquaculture systems. The juveniles of S. sinensis were divided into two groups and cultured in traditional ponds (CT) and an in-pond tank culture system (JY), with equal amounts of feed provided daily over a 72-day experimental period. The results showed no significant differences in growth performance metrics, including the specific growth rate, weight gain rate, hepatosomatic index, and viscerosomatic index between the two groups. In terms of intestinal morphology, the JY group villus width was significantly wider than the CT group, and the number of goblet cells in the CT group was significantly higher than that of the JY group (p < 0.05), which suggested that the fish in the JY group may have better intestinal nutrient absorption capacity, while the water quality in the CT group may be worse. The 16S rRNA gene sequencing analysis of the gut microbiota showed that the JY group had a significantly higher Shannon index compared to the CT group (p < 0.05), indicating greater species richness and evenness. Principal Coordinates Analysis (PCoA) revealed a distinct clustering of gut microbiota between the two groups. At the phylum level, the relative abundance of Fusobacteriota was significantly higher in the CT group, whereas Bacteroidota and Proteobacteria were significantly higher in the JY group (p < 0.05). Furthermore, KEGG pathway predictions indicated differences in the potential metabolic capabilities of the gut microbiota between the two groups (p < 0.05). Overall, this study is the first to conduct a comparative analysis of the growth performance, intestinal tissue morphology, and gut microbiota of S. sinensis under two different aquaculture systems, which has valuable implications for the further optimization of aquaculture practices.

Biology doi: 10.3390/biology13110868

Authors: Zhihui Sun Limei Yuan Yulin Wang Ran Fang Xiaoya Lin Haiyang Li Liyu Chen Yichun Wu Xin Huang Fanjiang Kong Baohui Liu Sijia Lu Lingping Kong

The development of soybean (Glycine max) is regulated by the photoperiod, with genes related to photoperiod sensitivity primarily focused on the flowering time. However, their roles in post-flowering reproductive development and the mechanisms by which the photoperiod affects them are not yet determined. In this study, we found that pod formation is sensitive to the photoperiod. Long-day conditions tended to extend the time from flowering to pod formation, and the first wave of flowers tended to fall off. Additionally, the photoperiod affected the pistil morphology; under short-day conditions, the stigma had a curved hook-like structure that facilitated better interaction with the filaments when pollen was released, ultimately influencing the timing of pod formation. Photoperiod-insensitive mutants, lacking E1 family and Evening Complex (EC) genes, showed no difference in the pod formation time under long-day or short-day conditions. Hormone content analysis and transcriptome data analysis indicated that various hormones, reactive oxygen species (ROS) burst pathway signals, and the application of sucrose solution in vitro might influence floral organ abscission.

Biology doi: 10.3390/biology13110867

Authors: Hajed Obaid A. Alharbi Asifa Khan Arshad Husain Rahmani

Atherosclerosis (AS) is a chronic inflammatory condition of the arteries, characterized by plaque formation that can restrict blood flow and lead to potentially fatal cardiovascular events. Given that AS is responsible for a quarter of global deaths, this study aimed to develop a systematic bioinformatics approach to identify biomarkers and regulatory targets involved in plaque development, with the goal of reducing cardiovascular disease risk. AS-specific mRNA expression profiles were retrieved from a publicly accessible database, followed by differentially expressed genes (DEGs) identification and AS-specific weighted gene co-expression network (WGCN) construction. Thereafter, calcification and atherosclerosis-specific (CASS) DEGs were utilized for protein–protein interaction network (PPIN) formation, followed by gene ontology (GO) term and pathway enrichment analyses. Lastly, AS-specific 3-node miRNA feed-forward loop (FFL) construction and analysis was performed. Microarray datasets GSE43292 and GSE28829 were obtained from gene expression omnibus (GEO). A total of 3785 and 6176 DEGs were obtained in case of GSE28829 and GSE43292; 3256 and 5962 module DEGs corresponding to GSE28829 and GSE43292 were obtained from WGCN. From a total of 54 vascular calcification (VC) genes, 20 and 29 CASS-DEGs corresponding to GSE28829 and GSE43292 were overlapped. As observed from FFL centrality measures, the highest-order subnetwork motif comprised one TF (SOX7), one miRNA (miR-484), and one mRNA (SPARC) in the case of GSE28829. Also, in the case of GSE43292, the highest-order subnetwork motif comprised one TF (ESR2), one miRNA (miR-214-3p), and one mRNA (MEF2C). These findings have important implications for developing new therapeutic strategies for AS. The identified TFs and miRNAs may serve as potential therapeutic targets for treating atherosclerotic plaques, offering insights into the molecular mechanisms underlying the pathogenesis and highlighting new avenues for research and treatment.

Biology doi: 10.3390/biology13110866

Authors: Abdurrahman Basol Gulsum Yaldiz Mahmut Camlica

In this study, 119 different coriander genotypes (38 different countries), including 114 genotypes and five cultivars, were undertaken to characterize the genotypes based on phenotypic, morphological, yield, and International Union for the Protection of New Varieties of Plants (UPOV) properties, along with some chemical properties. The yield components were between 1.34 and 21.49 g for thousand-grain weight, 0.02–9.58 g/plant for fruit yield, 0.01–50.78 g/plant for biological yield, and 8.48–73.36% for harvest index. Similarly, the results of this study revealed significant variations in essential oil (0.05–1.86%v/w) and fixed oil content (10.22–34.03%v/w). The main components of the essential oil were determined as linalool (3.13–45.70%v/v), p-cymene (0.10–15.77%v/v), ɣ-terpinene (0.04–13.80%v/v), while the fixed oil main acids were determined as petroselinic (24.47–87.70%v/v), palmitic (7.13–23.04%v/v), elaidic (1.55–47.44%v/v), and behenic acids (3.17–12.56%v/v). The cluster, heat map, correlation, and principal coordinate (PCA) analyses were conducted to determine the genetic diversity and relationship among the genotypes based on the examined properties. The cluster and heat map analyses showed differences in the same origin genotypes. Petroselinic acid was the major contributing factor for PCA. As a result of this study, Ames 13900 and Ames 18595 genotypes had high values for fruit yield, fixed oil content, and essential oil content.

Biology doi: 10.3390/biology13110865

Authors: Haiwei Wang Zhuping Chen Lin Ma Yifan Wu Xianzhi Zhao Keshan Zhang Jiajia Xue Yi Luo Chao Wang Zuohua Liu Youhui Xie Ying Chen Guangliang Gao Qigui Wang

The genetic regulation of goose meat quality traits remains relatively unexplored, and the underlying mechanisms are yet to be elucidated. This study aims to employ single nucleotide polymorphism (SNP) genotyping in conjunction with genome-wide association studies (GWAS) to investigate critical candidate regions and genes associated with the pH trait of meat in Sichuan white geese. A cohort of 203 healthy male Sichuan white geese was randomly selected and slaughtered at 70 days of age. Measurements were taken of meat pH, growth parameters, body dimensions, and post-slaughter traits. High-throughput sequencing on the Illumina HiSeq X Ten platform facilitated gene resequencing and SNP evaluation, and GWAS was employed to detect key genes within quantitative trait loci (QTL) intervals. The sequencing of 203 individuals yielded a total of 2601.19 Gb of genomic data, with an average sequencing depth of 10.89×. Through GWAS analysis, a total of 30 SNPs associated with pH were identified. These SNPs were identified on multiple chromosomes, including on chromosome 17 (chr: 23.57–23.68 Mb) and chromosome 13 (chr13: 31.52–31.61 Mb). By annotating these associated SNPs, nine candidate genes (including C19L2, AMFR, POL, RERGL, ZN484, GMDS, WAC) associated with the pH of goose meat were identified. The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) genotyping of 10 SNPs centered on these nine candidate genes was confirmed. GO enrichment analysis revealed that genes within 1 Mb of the associated SNPs are significantly enriched in pathways involved in lymphocyte activation, in response to hydrogen peroxide, Salmonella infection, and other metabolic processes. This study explores the gene regulatory pathways influencing pH traits in goose meat and provides molecular markers for enhancing meat quality. These findings are expected to facilitate the advancement of molecular breeding programs in geese.

Biology doi: 10.3390/biology13110864

Authors: Michiyo Suzuki

Charged-particle microbeam irradiation devices, which can convert heavy-ion or proton beams into microbeams and irradiate individual animal cells and tissues, have been developed and used for bioirradiation in Japan, the United States, China, and France. Microbeam irradiation technology has been used to analyze the effects of irradiation on mammalian cancer cells, especially bystander effects. In 2006, individual-level microbeam irradiation of the nematode Caenorhabditis elegans was first realized using JAEA-Takasaki’s (now QST-TIAQS’s) TIARA collimated microbeam irradiation device. As of 2023, microbeam irradiation of C. elegans has been achieved at five sites worldwide (one in Japan, one in the United States, one in China, and two in France). This paper summarizes the global progress in the field of microbeam biology using C. elegans, while focusing on issues unique to microbeam irradiation of live C. elegans, such as the method of immobilizing C. elegans for microbeam experiments.

Biology doi: 10.3390/biology13110863

Authors: Yanli Yang Ni Zhang Zhiyun Zhou Lin Li Kelong Chen Wei Ji Xia Zhao

Global climate warming has led to the deepening of the active layer of permafrost on the Tibetan Plateau, further triggering thermal subsidence phenomena, which have profound effects on the carbon cycle of regional ecosystems. This study conducted warming (W) and thermal subsidence (RR) control experiments using an Open-Top Chamber (OTC) device in the river source wetlands of the Qinghai Lake basin. The aim was to assess the impacts of warming and thermal subsidence on soil temperature, volumetric water content, biomass, microbial diversity, and soil respiration (both autotrophic and heterotrophic respiration). The results indicate that warming significantly increased soil temperature, especially during the colder seasons, and thermal subsidence treatment further exacerbated this effect. Soil volumetric water content significantly decreased under thermal subsidence, with the RRW treatment having the most pronounced impact on moisture. Additionally, a microbial diversity analysis revealed that warming promoted bacterial richness in the surface soil, while thermal subsidence suppressed fungal community diversity. Soil respiration rates exhibited a unimodal curve during the growing season. Warming treatment significantly reduced autotrophic respiration rates, while thermal subsidence inhibited heterotrophic respiration. Further analysis indicated that under thermal subsidence treatment, soil respiration was most sensitive to temperature changes, with a Q10 value reaching 7.39, reflecting a strong response to climate warming. In summary, this study provides new scientific evidence for understanding the response mechanisms of soil carbon cycling in Tibetan Plateau wetlands to climate warming.

Biology doi: 10.3390/biology13110862

Authors: Nazli Karimi Vahid Ahmadi

This study examines the critical role of aquaporins (AQPs) in skin physiology and aging pathophysiology. The skin plays a vital role in maintaining homeostasis by acting as a protective barrier against external pathogens and excessive water loss, while also contributing to the appearance and self-esteem of individuals. Key physiological features, such as elasticity and repair capability, are essential for its proper function. However, with aging, these characteristics deteriorate, reducing the skin’s ability to tolerate environmental stressors which contribute to external aging as well as internal aging processes, which negatively affect barrier function, immune response, and overall well-being. AQPs, primarily known for facilitating water transport, are significant for normal skin functions, including hydration and the movement of molecules like glycerol and hydrogen peroxide, which influence various cellular processes and functions. In this context, we categorized aquaporin dysfunction into several hallmarks of aging, including mitochondrial dysfunction, cellular senescence, stem cell depletion, impaired macroautophagy, dysbiosis, and inflamm-aging. Eight aquaporins (AQP1, 3, 5, 7, 8, 9, 10, and 11) are expressed in various skin cells, regulating essential processes such as cell migration, proliferation, differentiation, and also immune response. Dysregulation or altered expression of these proteins can enhance skin aging and related pathologies by activating these hallmarks. This study provides valuable insights into the potential of targeting aquaporins to mitigate skin aging and improve skin physiologic functions.

Biology doi: 10.3390/biology13110861

Authors: Setsuko Komatsu Takumi Nishiuchi

Finding solutions to mitigate the impact of salinity on crops is important for global food security because soil salinity significantly reduces plant growth and grain yield. Ethanol may play an important role in mitigating the negative salt-induced effects on crops. Soybean root growth was significantly reduced under salt stress; however, it was restored and comparable to control values by ethanol application even under stress. To study the positive mechanism of ethanol on soybean growth, a proteomic approach was carried out. The categories with the greatest changes in protein numbers were protein metabolism, transport, and cell organization in biological processes, nucleus and cytosol in cellular components, and nucleic acid binding activity in molecular functions. Proteomic data were confirmed using immunoblot analysis. Reactive oxygen species enzymes increased under salt stress; among them, mitochondrial ascorbate peroxidase was further accumulated by ethanol application. Among the cell wall and membrane-associated proteins, xyloglucan xyloglucosyl transferase and H+-ATPase increased and decreased, respectively, under salt stress; however, they were restored to control levels by ethanol application. These results suggest that soybeans were adversely affected by salt stress and recovered with ethanol application via the regulation of cell wall and membrane functions through the detoxification of reactive oxygen species.

Biology doi: 10.3390/biology13110860

Authors: Marta Mastrogiovanni Emmanuel Donnadieu Rajiv Pathak Vincenzo Di Bartolo

Cell adhesion regulates specific migratory patterns, location, communication with other cells, physical interactions with the extracellular matrix, and the establishment of effector programs. Proper immune control of cancer strongly depends on all these events occurring in a highly accurate spatiotemporal sequence. In response to cancer-associated inflammatory signals, effector immune cells navigating the bloodstream shift from their patrolling exploratory migration mode to establish adhesive interactions with vascular endothelial cells. This interaction enables them to extravasate through the blood vessel walls and access the cancer site. Further adhesive interactions within the tumor microenvironment (TME) are crucial for coordinating their distribution in situ and for mounting an effective anti-tumor immune response. In this review, we examine how alterations of adhesion cues in the tumor context favor tumor escape by affecting effector immune cell infiltration and trafficking within the TME. We discuss the mechanisms by which tumors directly modulate immune cell adhesion and migration patterns to affect anti-tumor immunity and favor tumor evasion. We also explore indirect immune escape mechanisms that involve modifications of TME characteristics, such as vascularization, immunogenicity, and structural topography. Finally, we highlight the significance of these aspects in designing more effective drug treatments and cellular immunotherapies.

Biology doi: 10.3390/biology13110859

Authors: Yossi Wein Ofri Vaidenfeld Chris Sabastian Enav Bar Shira Sameer J. Mabjeesh Haim Tagari Aharon Friedman

Homeostasis preservation is essential for animal survival, and any event that causes a disturbance in homeostasis is defined as a stressor. Here, we aimed to evaluate the effect of scratch brushes and stages as an environmental enrichment to alleviate stress in dairy goats. Twenty-four mixed-breed goats were divided into two groups according to common physiological conditions in breeding farms: milking and dry (milk-producing and non-milk-producing, respectively). Ten days after exposure to environmental enrichment treatment or not (control), blood was sampled. Following the enrichment, we observed a reduction in reactive oxidative stress metabolites, advanced glycation end products (AGEs), and their binding protein (transferrin) in the dry goats, as determined by an ELISA. In contrast, no change in AGEs, along with an increase in transferrin levels, was observed in the milking goats. Moreover, oxytocin levels decreased in the dry and increased in the milking goats, while serotonin levels increased in the dry and remained unchanged in the milking goats. Additionally, gene expression of the cytokines, IL-6 and IL-1ß, and anti-oxidative proteins, lysozyme and transferrin (in peripheral blood leukocytes), as determined by qPCR, presented the same pattern: down-regulation in the dry or up-regulation in the milking goats. In conclusion, a reliable methodology was developed for measuring husbandry stress in goats and to improve dairy goats’ husbandry practice. Current environmental enrichment produced different responsiveness in goats correlated to their physiological status: beneficial effect in dry goats, detrimental effect in milking goats.

Biology doi: 10.3390/biology13110858

Authors: Boris Krznar Marijan Vilenica Frank Rühli Nicole Bender

Humans adapt their life history strategy and lifestyle behavior to the environment. The social restrictions during the COVID-19 pandemic in the years 2020–2021 led to changes in diet and physical activity habits in large parts of populations worldwide. Additionally, many people reported an increase in body weight during the pandemic. We investigated how diet quality, physical activity, and BMI changed since the end of the COVID-19 restrictions in Switzerland (2019–2023). We assessed diet and physical activity using a standardized questionnaire. We measured anthropometry and BMI using a stadiometer and a balance of a medical bioimpedance analyzer. Our results show a stable BMI in men and women during the pandemic. In both sexes, diet quality and physical activity levels did not change significantly during this time. Among women, physical activity and age were associated with BMI, while in men, apart from physical activity, high diet quality and living in the agglomeration were associated with BMI. Overall, we did not find evidence for a transient “unhealthier” lifestyle immediately after the COVID-19 pandemic. However, we found constituent sex differences in BMI determinants. Our results could indicate a higher resilience in highly educated persons and might contribute to more personalized approaches to prevent obesity.

Biology doi: 10.3390/biology13110857

Authors: Rakhim Kanat Malika Shamekova Zagipa Sapakhova Maxat Toishimanov Dias Daurov Nurgul Raissova Zhanar Abilda Ainash Daurova Kabyl Zhambakin

Drought has increasingly affected the yield of Solanum tuberosum L. (potato) every year over the last decade, posing serious economic problems for the global agricultural industry. Therefore, it is important to research drought tolerance in plants and obtain more robust varieties of crops. The aim of the present work was to study the expression of drought-upregulated genes in drought-tolerant and drought-sensitive varieties of potato. Bioreactors were used to identify whether each variety was drought-tolerant or drought-sensitive; then, expression analysis was performed according to the morphological characteristics of the plantlets in two different media: Murashige and Skoog (MS) medium and MS medium with 20% PEG-6000 to simulate osmotic stress. Based on the quantitative parameters of six initial varieties, two varieties were selected (Gala and Aksor) for further gene expression analysis. The expression of genes commonly upregulated in drought (ER24, TAS14, DREB147315, PP2C, 102605413 and NF-YC4) was higher in the drought-tolerant variety than in the sensitive one. Therefore, the expression of these genes can be used to determine the drought tolerance of a potato variety in vitro in the early plant development stage. Moreover, comparative analysis showed that some of the targeted genes used to identify drought tolerance in this study are conserved across different plant species.

Biology doi: 10.3390/biology13110856

Authors: Xiulin Liu Chunlei Zhang Sobhi F. Lamlom Kezhen Zhao Ahmed M. Abdelghany Xueyang Wang Fengyi Zhang Rongqiang Yuan Dezhi Han Bire Zha Wencheng Lu Honglei Ren Bixian Zhang

Low temperatures greatly restrict the development, growth, and productivity of soybeans, with their effects differing across various cultivars. The present work investigated the transcriptome and physiological reactions of two soybean cultivars, namely “KD52” exhibiting cold tolerance and “DS17” displaying cold sensitivity, to cold stress across a precisely defined period. The soybean plants were subjected to cold treatment at 6 °C for durations of 0, 2, 4, and 8 h. A comparative physiological marker study revealed distinct reactions to cold stress in the two cultivars. The findings showed that increased malondialdehyde levels provided evidence of DS17’s heightened vulnerability to lipid peroxidation and membrane degradation. In contrast, the KD52 cultivar exhibited increased activities of antioxidant enzymes, including peroxidase and superoxide dismutase, in response to cold exposure, suggesting a strong antioxidant defense system against oxidative stress. The transcriptomic analysis revealed dynamic responses, mapping 54,532 genes. Within this group, a total of 234 differentially expressed genes (DEGs) were found to be consistently changed at several time intervals, showing unique expression patterns across the two cultivars. Analysis of the association between these important DEGs and the physiological indicators revealed candidate genes that may be involved in controlling oxidative damage and antioxidant defenses. Some key genes showed a progressive rise in expression over time in both cultivars, with a more significant acceleration in KD52, and are probably involved in promoting adaptation processes during extended periods of cold exposure. The identification of improved defense mechanisms in KD52, together with the identification of crucial genes, offers great prospects for enhancing the cold stress resilience of soybean.

Biology doi: 10.3390/biology13110855

Authors: Yu Wang Yu-Ping Huang Mana Rogers Heidi Leskinen Päivi Soppela Anne Tuomivaara Juha Hyvönen Daniela Barile

Milk oligosaccharides are complex carbohydrates composed of various monosaccharide units linked together by glycosidic bonds. They play an essential role in promoting gut health by fostering beneficial bacteria, supporting the development of the immune system, and protecting against infections and diseases. This work compared the oligosaccharide profiles in widely utilized breeds such as Holstein and Ayrshire (Nordic Red), with the native Northern Finncattle, which is considered an endangered breed. Oligosaccharides were extracted from milk and analyzed by liquid chromatography–mass spectrometry. The composition and relative abundance of the identified oligosaccharides were characterized and compared. The statistical analyses showed that neutral, sialylated, and fucosylated oligosaccharides vary among the breeds. Ayrshire and Northern Finncattle oligosaccharides formed a cluster, while Holstein’s profile shared features with both Ayrshire and Northern Finncattle. Holstein had the lowest abundance of fucosylated OS among the three breeds, with Ayrshire having the highest content followed by Northern Finncattle. The relatively higher sialylated over neutral content of Northern Finncattle is an important feature that should be preserved. Ayrshire is a good candidate to recover more diverse oligosaccharides with potential gut health implications for consumers.

Biology doi: 10.3390/biology13110853

Authors: Maiara Taffarel Bianca Sulzbacher da Silva Angélica Macedo Borgês Paulino Luciana Ortega Telles Sabrina Trigueiro Mendonça Cintia Vieira dos Santos Morenna Alana Giordani André Ferreira Nascimento Danilo Henrique Aguiar Valéria Dornelles Gindri Sinhorin Carla Regina Andrighetti Renata de Azevedo Melo Luvizotto Gisele Facholi Bomfim

Copaifera sp. is a native tree in the Amazon region. Copaiba oleoresin has components such as sesquiterpenes, which have anti-inflammatory and antioxidant potential. Liver cirrhosis is the end stage of liver disease with limited therapeutic options. We aimed to evaluate the effect of copaiba oleoresin supplementation on the liver of animals with thioacetamide (TAA)-induced cirrhosis. For the induction of liver cirrhosis, 100 mg/kg of TAA was administered intraperitoneally twice a week for 8 weeks. A total of 200 mg/kg/day of copaiba oleoresin was administered via gavage for the same period. Copaiba oleoresin supplementation improved cirrhosis-associated cachexia by increasing weight gain and body fat. In addition, copaiba oleoresin attenuated systemic inflammation, as shown by the decrease in the circulating C-reactive protein. In the liver, the copaiba oleoresin decreased carbonyl proteins and increased IL-10 compared with TAA-treated rats. TAA groups demonstrated increased SOD, catalase, GST, and GSH activity in the liver. In conclusion, the supplementation of copaiba oleoresin demonstrated a beneficial systemic effect in alleviating cirrhotic cachexia and antioxidant and anti-inflammatory action in the liver. However, it failed to improve the serological and histological markers of liver damage, which could be associated with the advanced stage of the disease.

Biology doi: 10.3390/biology13110854

Authors: Emma M. Palmer Caleb A. Snoddy Peyton M. York Sydney M. Davis Madelyn F. Hunter Natraj Krishnan

Over the past two decades, Drosophila melanogaster has proven to be successful in modeling the polyglutamine (polyQ) (caused by CAG repeats) family of neurodegenerative disorders, including the faithful recapitulation of pathological features such as polyQ length-dependent formation of protein aggregates and progressive neuronal degeneration. In this study, pan-neuronal expression of human Ataxin-1 with long polyQ repeat of 82 amino acids was driven using an elav-GAL4 driver line. This would essentially model the polyQ disease spinocerebellar ataxia type 1 (SCA1). Longevity and behavioral analysis of male flies expressing human Ataxin-1 revealed compromised lifespan and accelerated locomotor activity deficits both in diurnal activity and negative geotaxis response compared to control flies. Interestingly, this decline in motor response was coupled to an enhancement of matrix metalloproteinase 1 (dMMP1) expression together with declining expression of extracellular matrix (ECM) fibroblast growth factor (FGF) signaling by hedgehog (Hh) and branchless (bnl) and a significant decrease in expression of survival motor neuron gene (dsmn) in old (30 d) flies. Taken together, our results indicate a role for dysregulation of matrix metalloproteinase in polyQ disease with consequent impact on ECM signaling factors, as well as SMN at the neuromuscular junction causing overt physiological and behavioral deficits.

Biology doi: 10.3390/biology13110852

Authors: Lei Yang Hui Yang Ganggang Sun Xueqin Wang Tianli Zheng

Fe-OC is crucial for SOC preservation in the global ecosystem. However, there is still significant uncertainty in the determination methods of Fe-OC, and these methods are often not calibrated to each other, making the Fe-OC content by different methods impossible to compare. Here, Fe-OC is analyzed by the CBD method and the SD method from 45 soils from different land types (e.g., wetland, grassland, and forest) to compare and analyze the uncertainty and influencing factors between the two methods. Our results showed that the Fe-OC contributions to SOC (fFe-OC) measured by CBD and SD methods were significantly lower in the wetland ecosystem than in grassland and forest ecosystems. The Fe-OC content and fFe-OC in the grassland ecosystem was significantly higher using the CBD method compared to the SD method, with no significant difference between the methods in wetland and forest ecosystems. The random forest model revealed that Fe-OCCBD content was mainly affected by C/N, Clay%, and TC, whereas SOC, total nitrogen, and soil inorganic carbon were the main influences on Fe-OCSD. Taken together, our findings highlight the importance of incorporating ecosystem types and soil properties into soil carbon estimation models when predicting and estimating Fe-OC and its contribution to SOC.

Biology doi: 10.3390/biology13110851

Authors: Eleftherios Kasiouras Peter C. Hubbard Albin Gräns Lynne U. Sneddon

Nociceptors are receptors that detect injurious stimuli and are necessary to convey such information from the periphery to the central nervous system. While nociception has been extensively studied in various taxa, there is relatively little electrophysiological evidence for the existence of nociceptors in decapod crustaceans. This study investigated putative nociceptive responses in the shore crabs, specifically their response to mechanical and noxious chemical stimuli. Extracellular multi-unit electrophysiological recordings were conducted from the anterior ganglion and the circumesophageal connective ganglia to assess nociceptive responses. Soft tissues at the joints of the chelae, antennae, and walking legs were stimulated using acetic acid (noxious stimulus) and von Frey hairs (mechanical stimulus), while nearby ganglion activity was recorded. The results indicate the existence of nociceptors in the tested areas, with mechanical stimuli eliciting shorter, more intense neural activity compared with acetic acid. Although acetic acid triggered responses in all areas, the antennae and antennules did not respond to mechanical stimuli. Though we acknowledge the challenges of conducting in vivo electrophysiological recordings, future research should focus on further characterizing nociceptor activity because the results suggest the presence of nociceptors.

Biology doi: 10.3390/biology13110850

Authors: Qun Wan Brad C. Bennett

Hydrogen is the lightest atom and composes approximately half of the atomic content in macromolecules, yet their location can only be inferred or predicted in most macromolecular structures. This is because hydrogen can rarely be directly observed by the most common structure determination techniques (such as X-ray crystallography and electron cryomicroscopy). However, knowledge of hydrogen atom positions, especially for enzymes, can reveal protonation states of titratable active site residues, hydrogen bonding patterns, and the orientation of water molecules. Though we know they are present, this vital layer of information, which can inform a myriad of biological processes, is frustratingly invisible to us. The good news is that, even at modest resolution, neutron crystallography (NC) can reveal this layer and has emerged this century as a powerful tool to elucidate enzyme catalytic mechanisms. Due to its strong and coherent scattering of neutrons, incorporation of deuterium into the protein crystal amplifies the power of NC. This is especially true when solvation and the specific participation of key water molecules are crucial for catalysis. Neutron data allow the modeling of all three atoms in water molecules and have even revealed previously unobserved and unique species such as hydronium (D3O+) and deuteroxide (OD−) ions as well as lone deuterons (D+). Herein, we briefly review why neutrons are ideal probes for identifying catalytically important water molecules and these unique water-like species, limitations in interpretation, and four vignettes of enzyme success stories from disparate research groups. One of these groups was that of Dr. Chris G. Dealwis, who died unexpectedly in 2022. As a memorial appreciation of his scientific career, we will also highlight his interest and contributions to the neutron crystallography field. As both the authors were mentored by Chris, we feel we have a unique perspective on his love of molecular structure and admiration for neutrons as a tool to query those structures.

Biology doi: 10.3390/biology13110849

Authors: Tania Koning Gloria M. Calaf

Breast cancer is a major global health concern as it is the primary cause of cancer death for women. Environmental radiation exposure and endogenous factors such as hormones increase breast cancer risk, and its development and spread depend on cell motility and migration. The expression of genes associated with cell motility, such as ADAM12, CYR61, FLRT2, SLIT2, VNN1, MYLK, MAP1B, and TUBA1A, was analyzed in an experimental breast cancer model induced by radiation and estrogen. The results showed that TUBA1A, SLIT2, MAP1B, MYLK, and ADAM12 gene expression increased in the irradiated Alpha3 cell line but not in the control or the malignant Tumor2 cell line. Bioinformatic analysis indicated that FLERT2, SLIT2, VNN1, MAP1B, MYLK, and TUBA1A gene expressions were found to be higher in normal tissue than in tumor tissue of breast cancer patients. However, ADAM12 and CYR61 expressions were found to be higher in tumors than in normal tissues, and they had a negative correlation with ESR1 gene expression. Concerning ESR2 gene expression, there was a negative correlation with CYR61, but there was a positive correlation with FLRT2, MYLK, MAP1B, and VNN1. Finally, a decreased survival rate was observed in patients exhibiting high expression levels of TUBA1A and MAP1B. These genes also showed a negative ER status, an important parameter for endocrine therapy. The genes related to motility were affected by ionizing radiation, confirming its role in the initiation process of breast carcinogenesis. In conclusion, the relationship between the patient’s expression of hormone receptors and genes associated with cell motility presents a novel prospect for exploring therapeutic strategies.

Biology doi: 10.3390/biology13110848

Authors: Pedro H. Godoy Sanches Nicolly Clemente de Melo Andreia M. Porcari Lucas Miguel de Carvalho

With the advent of high-throughput technologies, the field of omics has made significant strides in characterizing biological systems at various levels of complexity. Transcriptomics, proteomics, and metabolomics are the three most widely used omics technologies, each providing unique insights into different layers of a biological system. However, analyzing each omics data set separately may not provide a comprehensive understanding of the subject under study. Therefore, integrating multi-omics data has become increasingly important in bioinformatics research. In this article, we review strategies for integrating transcriptomics, proteomics, and metabolomics data, including co-expression analysis, metabolite–gene networks, constraint-based models, pathway enrichment analysis, and interactome analysis. We discuss combined omics integration approaches, correlation-based strategies, and machine learning techniques that utilize one or more types of omics data. By presenting these methods, we aim to provide researchers with a better understanding of how to integrate omics data to gain a more comprehensive view of a biological system, facilitating the identification of complex patterns and interactions that might be missed by single-omics analyses.

Biology doi: 10.3390/biology13100847

Authors: Kuo Yang Yue Yang Jie Wang Xiaomeng Huang Daizong Cui Min Zhao

This study investigated the impact of CdS nanoparticles (NPs) on Escherichia coli growth and metabolism under varying conditions. Under illumination, CdS NPs significantly enhanced bacterial growth, glucose assimilation, and biomass accumulation. Key metabolic and stress response genes showed increased expression, indicating improved ATP synthesis and oxidative stress resistance. Additionally, CdS NPs enhanced the electrochemical properties of E. coli, promoting efficient electron transfer. No significant changes were observed in the dark. These findings suggest that light-activated CdS NPs promote E. coli growth and metabolic efficiency by upregulating crucial genes involved in growth and oxidative stress management.

Biology doi: 10.3390/biology13100846

Authors: Laiba Noor Arun Upadhyay Vibhuti Joshi

Glioma is known for its immunosuppressive microenvironment, which makes it challenging to target through immunotherapies. Immune cells like macrophages, microglia, myeloid-derived suppressor cells, and T lymphocytes are known to infiltrate the glioma tumor microenvironment and regulate immune response distinctively. Among the variety of immune cells, T lymphocytes have highly complex and multifaceted roles in the glioma immune landscape. T lymphocytes, which include CD4+ helper and CD8+ cytotoxic T cells, are known for their pivotal roles in anti-tumor responses. However, these cells may behave differently in the highly dynamic glioma microenvironment, for example, via an immune invasion mechanism enforced by tumor cells. Therefore, T lymphocytes play dual roles in glioma immunity, firstly by their anti-tumor responses, and secondly by exploiting gliomas to promote immune invasion. As an immunosuppression strategy, glioma induces T-cell exhaustion and suppression of effector T cells by regulatory T cells (Tregs) or by altering their signaling pathways. Further, the expression of immune checkpoint inhibitors on the glioma cell surface leads to T cell anergy and dysfunction. Overall, this dynamic interplay between T lymphocytes and glioma is crucial for designing more effective immunotherapies. The current review provides detailed knowledge on the roles of T lymphocytes in the glioma immune microenvironment and helps to explore novel therapeutic approaches to reinvigorate T lymphocytes.

Biology doi: 10.3390/biology13100845

Authors: Thippawan Yasanga Sineenart Santidherakul Klintean Wunnapuk Rochana Phuackchantuck Lakkana Thaikruea Thunyaporn Achalawitkun Purinat Rungraung

Nematocysts, specialized stinging cells in cnidarians, play a crucial role in both defense and prey capture, containing venomous, coiled tubes within a capsule. While box jellyfish are recognized as a medical threat, information on the nematocysts of species like Gershwinia thailandensis and Morbakka sp. from Thai waters remains sparse. This study explores the types and morphology of nematocysts found in the tentacles of these species using light and scanning electron microscopy. We identified three nematocyst types: club-shaped microbasic p-mastigophores, oval isorhizas, and oval microbasic p-rhopaloids. Notably, significant differences in capsule sizes were observed, especially in the microbasic p-mastigophores and isorhizas. The discharge tubules tapered from the proximal to the distal ends, featuring arrow-shaped spines in a helical pattern. A distinct lancet structure was present in both microbasic p-mastigophores and p-rhopaloids. These findings suggest that variations in nematocyst size and morphology may be linked to evolutionary adaptations, functional roles, and venom toxicity. Further research into venom discharge mechanisms could offer valuable insights into the ecological and medical importance of these cnidarians.

Biology doi: 10.3390/biology13100844

Authors: Callan D. Wesley Annarita Sansonetti Cedric H. G. Neutel Dustin N. Krüger Guido R. Y. De Meyer Wim Martinet Pieter-Jan Guns

Proteasome inhibitors such as bortezomib and carfilzomib induce apoptosis and are a cornerstone in the treatment of relapsed or refractory multiple myeloma. However, concerns have emerged concerning their link to cancer therapy-related cardiovascular dysfunction (CTRCD). Bortezomib, a reversible first-generation inhibitor, and carfilzomib, a second-generation irreversible inhibitor, are associated with hypertension, heart failure, and cardiac arrhythmias. The current study investigated the effects of bortezomib and carfilzomib on cardiac (left ventricular ejection fraction, LVEF) and vascular (arterial stiffness, vascular reactivity) function. Cardiac function assessment aimed to build upon existing evidence of proteasome inhibitors CTRCD, while arterial stiffness served as an early indicator of potential vascular remodeling. Groups of 12-week-old C57BL/6J male mice (n = 8 per group) were randomly assigned to receive vehicle, carfilzomib (8 mg/kg I.P.), or bortezomib (0.5 mg/kg I.P.). Additionally, proteasome inhibition was assessed in mice treated with L-NAME (0.5 mg/kg) to induce hypertension. Cardiac and vascular parameters were evaluated via echocardiography on days 0 and 3. On day 6, mice were sacrificed for ex vivo analysis of arterial stiffness and vascular reactivity. Overall, no changes in arterial stiffness were detected either in vivo or ex vivo at basal pressures. However, a steeper pressure–stiffness curve was observed for carfilzomib in normotensive (p < 0.01) and hypertensive (p < 0.0001) mice ex vivo. Additionally, in hypertensive mice, carfilzomib decreased LVEF (p = 0.06), with bortezomib exhibiting similar trends. Vascular reactivity remained largely unchanged, but proteasome inhibition tended to enhance endothelial-independent relaxations in both control and hypertensive mice. In conclusion, short-term treatment with carfilzomib and bortezomib is considered relatively safe for the protocols assessed in the study.

Biology doi: 10.3390/biology13100843

Authors: Jinyun Jiang Lingyao Xu Yizheng Zhuang Xingyu Wei Zhenyang Zhang Wei Zhao Qingyu Wang Xiaowei Ye Jiamin Gu Caiyun Cao Jiabao Sun Kan He Zhe Zhang Qishan Wang Yuchun Pan Zhen Wang

Intensively farmed animals such as pigs inevitably experience a certain degree of psychological stress, which leads to a reduction in production performance. Mental health traits are currently difficult to measure, resulting in a gap in understanding their genetic basis. To address this challenge, we propose a computational framework called mental health of animals (MeHA), capable of revealing genes related to animal mental health traits. Using MeHA, we identified 109 candidate genes associated with pig mental health and discovered their intricate connections with critical functions, such as memory, cognition, and neural development, which are essential components of mental health and cognitive performance. Importantly, our findings provide evidence of the potential impact of these genes on economically important traits, including meat quality and piglet survival. This research underscores the importance of genetic studies in enhancing our understanding of animal behavior and cognition, as well as promoting agricultural practices. By applying our approach to study the genetic basis of mental health in pigs as a case, we confirmed that our framework is an effective way to reveal genetic factors affecting animal mental health traits, which contributes to animal welfare and has potential implications for understanding human mental disorders.

Biology doi: 10.3390/biology13100842

Authors: He-Li Zhang Xi-Xi Qiu Xin-Hua Liao

As an appendage of the skin, hair protects against ultraviolet radiation and mechanical damage and regulates body temperature. It also reflects an individual’s health status and serves as an important method of expressing personality. Hair loss and graying are significant psychosocial burdens for many people. Hair is produced from hair follicles, which are exclusively controlled by the dermal papilla (DP) at their base. The dermal papilla cells (DPCs) comprise a cluster of specialized mesenchymal cells that induce the formation of hair follicles during early embryonic development through interaction with epithelial precursor cells. They continue to regulate the growth cycle, color, size, and type of hair after the hair follicle matures by secreting various factors. DPCs possess stem cell characteristics and can be cultured and expanded in vitro. DPCs express numerous stemness-related factors, enabling them to be reprogrammed into induced pluripotent stem cells (iPSCs) using only two, or even one, Yamanaka factor. DPCs are an important source of skin-derived precursors (SKPs). When combined with epithelial stem cells, they can reconstitute skin and hair follicles, participating in the regeneration of the dermis, including the DP and dermal sheath. When implanted between the epidermis and dermis, DPCs can induce the formation of new hair follicles on hairless skin. Subcutaneous injection of DPCs and their exosomes can promote hair growth. This review summarizes the in vivo functions of the DP; highlights the potential of DPCs in cell therapy, particularly for the treatment of hair loss; and discusses the challenges and recent advances in the field, from basic research to translational applications.

Biology doi: 10.3390/biology13100841

Authors: Karen Sanmartín-Vivar Jessica Guachizaca-Macas Diego Marín-Armijos

This study sheds light on the complex relationship between land use, biodiversity, and the functional traits of dung beetles in Ecuador. The results indicate that the richness and abundance of dung beetles vary across different land uses and regions, with forests generally having a positive impact, while eucalyptus and pine plantations have a negative effect in certain areas. Specific indicator species, such as Homocopris buckleyi for forest areas and Onthophagus curvicornis for eucalyptus plantations, were identified. This study also found that functional diversity analysis, based on morphological traits, revealed that certain traits, such as biomass, pronotum width, head width, and elytra length, were significant contributors to differences in dung beetle communities across various land uses and regions. This study highlights the potential conservation value of certain modified habitats and emphasizes the importance of considering both taxonomic and functional diversity when assessing the impact of land use on the ecosystem services provided by dung beetles. It underscores the potential value of plantations as refuges for dung beetle communities and the need for long-term assessments to better understand biodiversity changes over time.

Biology doi: 10.3390/biology13100840

Authors: Evgenii Balakin Ksenia Yurku Viacheslav Kuropatkin Alexander Izotov Valeriya Nakhod Vasiliy Pustovoyt

Physical overexertion surpassing the functional capacity of the nervous system causes the hyperactivation of the neural structures of the cerebellum. In turn, it causes the depletion of intracellular resources and progressive structural changes in cerebellar cells and fibers. These degenerative changes may lead to cerebellar dysfunction, including the worsening of coordination, balance, and motor functions. In order to maintain the health and functioning of the cerebellum and the nervous system in general, one needs to avoid physical overexertion and have enough time to recover. Three major types of Purkinje cells were identified in control group animals. After the forced swimming test, animals had significant morphological changes in pyriform cells, granule cells, internuncial neurons, and neuroglial cells. In particular, the extreme degeneration of granule cells was manifested via their fusion into conglomerates. These changes demonstrate that neurodegeneration in the cerebellum takes place in response to physical overexertion.

Biology doi: 10.3390/biology13100839

Authors: Wenhua Wu Funing Ma Xiaoyan Zhang Yuxin Tan Te Han Jing Ding Juyou Wu Wenting Xing Bin Wu Dongmei Huang Shaoling Zhang Yi Xu Shun Song

Passiflora edulis, also known as passion fruit, is celebrated for its rich nutritional content, distinctive flavour, and significant medicinal benefits. At present, viral diseases pose a major challenge to the passion fruit industry, affecting both the production and quality of the fruit. These diseases impede the sustainable and healthy growth of the passion fruit sector. In recent years, with the expansion of P. edulis cultivation areas, virus mutations, and advances in virus detection technology, an increasing number of virus species infecting P. edulis have been discovered. To date, more than 40 different virus species have been identified; however, there are different strains within the same virus. This poses a challenge for the control and prevention of P. edulis virus disease. Therefore, this review discusses the different types of viruses and their characteristics, modes of transmission, and effects on the growth of the passion fruit plant, as well as the mechanisms of virus generation and preventive measures, with the hope that these discussions will provide a comprehensive understanding of and countermeasures for viruses in passion fruit.

Biology doi: 10.3390/biology13100838

Authors: Yundong Li Juan Chen Song Jiang Qibin Yang Lishi Yang Jianhua Huang Jianzhi Shi Yan Zhang Zhibin Lu Falin Zhou

Due to its high tolerance to salinity and temperature, as well as its strong adaptability, Metapenaeus ensis holds an important position in the Chinese aquaculture industry. However, studies on the evaluation of its germplasm resources remain insufficient. This research conducted an in-depth comparative evaluation of M. ensis from three representative farming regions in China: Sanya, Zhuhai, and Raoping. The nutritional analysis of muscle tissue showed no statistically significant differences in crude ash, moisture, and crude protein content among the populations (p > 0.05). However, significant differences were observed in crude fat and total sugar content (p < 0.05). The MeSY and MeRP populations had higher crude fat content than the MeZH population (p < 0.05), while the MeZH population exhibited the highest total sugar content. In terms of amino acid composition, the MeSY population had relatively higher total essential amino acid content and proportion, as well as higher total amino acid content, both of which were statistically significant (p < 0.05). A fatty acid composition analysis further highlighted the advantages of the MeRP population in several key fatty acids (p < 0.05). Physiological and biochemical analyses showed no significant differences among the three populations in total antioxidant capacity, superoxide dismutase activity, or catalase activity (p > 0.05). A genetic diversity analysis indicated that M. ensis has relatively low diversity, with the MeSY population showing higher SNP density and nucleotide diversity. A genetic differentiation analysis revealed significant genetic differentiation between the MeSY and MeZH populations, while differentiation between the MeZH and MeRP populations was relatively smaller. This comprehensive assessment of nutritional components, amino acids, fatty acids, antioxidant capacity, and genetic diversity highlights the advantages of germplasm resources from different regions. These findings provide valuable insights for future research on the genetic characteristics and breeding potential of M. ensis.

Biology doi: 10.3390/biology13100837

Authors: Weitao Li Jiongying Yu Yanfu Que Xingkun Hu Ezhou Wang Xiaolin Liao Bin Zhu

The Bighead carp (Hypophthalmichthys nobilis), a primary freshwater aquaculture species in China, faces challenges due to over-exploitation and environmental changes. We leveraged RAD-seq to perform a comprehensive population genetic analysis on 14 H. nobilis populations sampled from the Yangtze River (13 populations) and the Marseilles Reach of the Illinois River (one population). Analysis of genetic diversity showed that different parameters demonstrated varied inferences, and notably, Zhongxian (ZX2), Wanhzou (WZ2), Yangzhou hatchery (YZYZ), Yangzhou (YZ), and Taihu (TH) populations showed apparent heterozygote deficiency. Linkage disequilibrium (LD) analysis exhibited a trend of higher linkage disequilibrium in populations from the upper reaches of the Yangtze River, followed by those from the middle reaches and then those from the lower reaches. Additionally, the reconstructed polygenetic tree and PCA plot clustered all populations into 2 major subgroups, while the results of structure analysis indicated 4 ancestors. The pairwise FST values ranged from 0 to 0.5530. Among these, high FST values (0.1931–0.5530) were only observed between populations WZ2, YZ, YZYZ, and the remaining 11 populations. Furthermore, genetic bottlenecks were observed in all populations 20–30 thousand years ago. Overall, the research offers insights essential for genetic management practices for sustainable aquaculture and biodiversity conservation of bighead carp.

Biology doi: 10.3390/biology13100836

Authors: Jin-Young Jeong Junsik Kim Minji Kim Seong-Hoon Shim Cheolju Park Sungju Jung Hyunjung Jung

Mycotoxin-contaminated feed or food can affect physiological responses and cause illnesses in humans and animals. In this study, we evaluated the effects of deoxynivalenol (DON) toxicity on the growth performance, blood biochemistry, histology, microbiome, and metabolism of rats fed with different toxin concentrations. After 1 week of acclimatization, seven-week-old male rats received 0.9% saline as a control, 0.02 mg/kg DON as T1, and 0.2 mg/kg DON as T2 via oral gavage for 4 weeks. The final body weight of the T2 group was significantly lower than that of the control and T1; however, the average daily gain, feed intake, and feed conversion ratio did not differ. Fibrosis and apoptosis were observed in various tissues as DON concentration increased. Creatinine and alkaline phosphatase levels were significantly lower in the DON-treated group than in the control. Firmicutes and Desulfobacterota phyla dominated the cecum, whereas those in the feces were Proteobacteria and Bacteroidetes. Metabolomic profiling showed phenylalanine, tyrosine, and tryptophan biosynthesis as the most prominent pathways. Overall, our results suggest that low-dose and short-term DON exposure can trigger several adverse effects in rats. Dietary toxicants in rats may explain the physiological effects associated with the metabolism commonly reported in animals.

Biology doi: 10.3390/biology13100835

Authors: María Ramírez-delaCruz Alfredo Bravo-Sánchez Jorge Sánchez-Infante Pablo Abián Javier Abián-Vicén

The neurocognitive response following hypoxia has received special interest. However, it is necessary to understand the impact of acute hypoxic exposure induced by simulated altitude on cognitive performance. This study aimed to determine the effects of acute hypoxic exposure in simulated altitude in healthy adults on reaction time, response accuracy, memory, and attention. Five electronic databases were searched. The inclusion criteria were: (1) Experimental studies involving a hypoxia intervention induced by a hypoxic air generator to determine the effects on cognitive performance; and (2) Conducted in adults (males and/or females; aged 18–50 years) without pathologies or health/mental problems. Four meta-analyses were performed: (1) reaction time, (2) response accuracy, (3) memory, and (4) attention. Finally, 37 studies were included in the meta-analysis. Hypoxia exposure induced detrimental effects on reaction time (standard mean difference (SMD) −0.23; 95% confidence interval (CI) −0.38–−0.07; p = 0.004), response accuracy (SMD −0.20; 95% CI −0.38–−0.03; p = 0.02), and memory (SMD −0.93; 95% CI: −1.68–−0.17; p = 0.02). Nevertheless, attention was not affected during hypoxia exposure (SMD −0.06; 95% CI: −0.23–0.11; p = 0.47). Acute exposure to hypoxia in controlled lab conditions appears to be detrimental to cognitive performance, specifically in reaction time, response accuracy, and memory.

Biology doi: 10.3390/biology13100834

Authors: David Eilam Zohar Hagbi

Hatching captive barn owl chicks underwent four developmental phases. In the first 10 days (phase 1), behavior consisted of lateral movements that gradually changed to forward progression and peaked a few days before and after eye-opening. This behavior resembled a general developmental pattern that characterizes other vertebrates. Chicks also underwent a postural change, from head bent underneath the ventrum to resting on the rear end of the trunk with the head lifted in the air. Then, once their eyes were opened, chicks became more stationary and preoccupied with visual exploration, manifested in lateral head movements and peering episodes (phase 2, until day 20). The latter behavior, which is also typical of mature owls when not on the wing, characterized the chicks’ behavior after post-hatching day 20 (phase 3), when their flight and contour feathers grew, along with shedding the down plumage and standing tall. Development culminated in active flight, first observed by days 50–60 (phase 4). Altogether, during post-hatching development, barn owl chicks gradually shifted from egg posture to the adult upright body posture. At the same time, their behavior consisted of speciation from the general developmental pattern to the typical stationary barn owl behavior, and, finally, flight was incorporated.

Biology doi: 10.3390/biology13100833

Authors: Naiéle Sartori Patias Eveline Aparecida Isquierdo Fonseca de Queiroz Stela Regina Ferrarini Gisele Facholi Bomfim Danilo Henrique Aguiar Adilson Paulo Sinhorin Alexandre Aymberé Bello Geovana Vicentini Fazolo da Silva Larissa Cavalheiro Valéria Dornelles Gindri Sinhorin

In the original publication [...]

Biology doi: 10.3390/biology13100832

Authors: Carmen Celis-Giraldo Carlos F. Suárez William Agudelo Nieves Ibarrola Rosa Degano Jaime Díaz Raúl Manzano-Román Manuel A. Patarroyo

Salmonellosis is a zoonotic infection that has a major impact on human health; consuming contaminated pork products is the main source of such infection. Vaccination responses to classic vaccines have been unsatisfactory; that is why peptide subunit-based vaccines represent an excellent alternative. Immunopeptidomics was used in this study as a novel approach for identifying antigens coupled to major histocompatibility complex class II molecules. Three homozygous individuals having three different haplotypes (Lr-0.23, Lr-0.12, and Lr-0.21) were thus selected as donors; peripheral blood macrophages were then obtained and stimulated with Salmonella typhimurium (MOI 1:40). Although similarities were observed regarding peptide length distribution, elution patterns varied between individuals; in total, 1990 unique peptides were identified as follows: 372 for Pig 1 (Lr-0.23), 438 for Pig 2 (Lr.0.12) and 1180 for Pig 3 (Lr.0.21). Thirty-one S. typhimurium unique peptides were identified; most of the identified peptides belonged to outer membrane protein A and chaperonin GroEL. Notably, 87% of the identified bacterial peptides were predicted in silico to be elution ligands. These results encourage further in vivo studies to assess the immunogenicity of the identified peptides, as well as their usefulness as possible protective vaccine candidates.

Biology doi: 10.3390/biology13100831

Authors: Sunil J. Wimalawansa

The interaction of the SARS-CoV-2 spike protein with membrane-bound angiotensin-converting enzyme-2 (ACE-2) receptors in epithelial cells facilitates viral entry into human cells. Despite this, ACE-2 exerts significant protective effects against coronaviruses by neutralizing viruses in circulation and mitigating inflammation. While SARS-CoV-2 reduces ACE-2 expression, vitamin D increases it, counteracting the virus’s harmful effects. Vitamin D’s beneficial actions are mediated through complex molecular mechanisms involving innate and adaptive immune systems. Meanwhile, vitamin D status [25(OH)D concentration] is inversely correlated with severity, complications, and mortality rates from COVID-19. This study explores mechanisms through which vitamin D inhibits SARS-CoV-2 replication, including the suppression of transcription enzymes, reduced inflammation and oxidative stress, and increased expression of neutralizing antibodies and antimicrobial peptides. Both hypovitaminosis D and SARS-CoV-2 elevate renin levels, the rate-limiting step in the renin-angiotensin-aldosterone system (RAS); it increases ACE-1 but reduces ACE-2 expression. This imbalance leads to elevated levels of the pro-inflammatory, pro-coagulatory, and vasoconstricting peptide angiotensin-II (Ang-II), leading to widespread inflammation. It also causes increased membrane permeability, allowing fluid and viruses to infiltrate soft tissues, lungs, and the vascular system. In contrast, sufficient vitamin D levels suppress renin expression, reducing RAS activity, lowering ACE-1, and increasing ACE-2 levels. ACE-2 cleaves Ang-II to generate Ang(1–7), a vasodilatory, anti-inflammatory, and anti-thrombotic peptide that mitigates oxidative stress and counteracts the harmful effects of SARS-CoV-2. Excess ACE-2 molecules spill into the bloodstream as soluble receptors, neutralizing and facilitating the destruction of the virus. These combined mechanisms reduce viral replication, load, and spread. Hence, vitamin D facilitates rapid recovery and minimizes transmission to others. Overall, vitamin D enhances the immune response and counteracts the pathological effects of SARS-CoV-2. Additionally, data suggests that widely used anti-hypertensive agents—angiotensin receptor blockers and ACE inhibitors—may lessen the adverse impacts of SARS-CoV-2, although they are less potent than vitamin D.

Biology doi: 10.3390/biology13100830

Authors: Yaron Ilan

Uncertainty in biology refers to situations in which information is imperfect or unknown. Variability, on the other hand, is measured by the frequency distribution of observed data. Biological variability adds to the uncertainty. The Constrained Disorder Principle (CDP) defines all systems in the universe by their inherent variability. According to the CDP, systems exhibit a degree of variability necessary for their proper function, allowing them to adapt to changes in their environments. Per the CDP, while variability differs from uncertainty, it can be viewed as a regulated mechanism for efficient functionality rather than uncertainty. This paper explores the various aspects of un-certainties in biology. It focuses on using CDP-based platforms for refining fuzzy algorithms to address some of the challenges associated with biological and medical uncertainties. Developing a fuzzy decision tree that considers the natural variability of systems can help minimize uncertainty. This method can reveal previously unidentified classes, reduce the number of unknowns, improve the accuracy of modeling results, and generate algorithm outputs that are more biologically and clinically relevant.

Biology doi: 10.3390/biology13100829

Authors: María Botía Damián Escribano Eva Mainau Alberto Muñoz-Prieto José J. Cerón

Colostrum is a mammary secretion released from the time of farrowing to 36 h post-farrowing. After this time and during all the rest of lactation, the mammary secretion is considered milk. The objectives of this study were: (1) to perform an analytical validation in the colostrum and milk of sows of assays for four analytes related to immunity: total ADA (tADA) and its isoenzymes (ADA1 and ADA2), myeloperoxidase (Mpx), calprotectin, and calgranulin, and two analytes related to welfare: cortisol and alpha-amylase. (2) To evaluate the changes in these analytes during lactation (3) To assess the correlations between these new analytes, as well as with IgG and IgA. In the analytical validation, all the assays were precise and accurate. When changes during lactation were evaluated, the concentration of tADA and ADA2 was found to be higher in colostrum than in milk (p < 0.02), while the activity of Mpx was observed to be higher in mature milk than in colostrum (p < 0.03). Furthermore, cortisol and alpha-amylase activity were found to be higher in colostrum compared to mature milk (p < 0.04 and p < 0.0001, respectively). Regarding the relation between analytes, alpha-amylase showed a significant correlation with both IgG and IgA and calprotectin was correlated with calgranulin and Mpx. Further studies should be performed to elucidate the possible practical application of the analytes evaluated in this study as biomarkers of colostrum and milk in sows.

Biology doi: 10.3390/biology13100827

Authors: Franco F. Roldán Gallardo Daniel E. Martínez Piñerez Kevin F. Reinarz Torrado Gabriela A. Berg Jael D. Herzfeld Vanina G. Da Ros Manuel López Seoane Cristina A. Maldonado Amado A. Quintar

Background: Clinical and experimental evidence has linked Benign Prostatic Hyperplasia (BPH) with dyslipidemic and hypercholesterolemic conditions, though the underlying cellular mechanisms remain unclear. This study investigates the impact of dyslipidemia, specifically oxidized LDL (OxLDL), on prostatic stromal cell proliferation and the release of extracellular vesicles (EVs). Methods: Mice were fed a high-fat diet, and human prostatic stromal cells (HPSCs) were treated with OxLDL. Proliferation assays and EV characterization were performed to assess the role of EVs in BPH progression. Results: Pro-atherogenic conditions significantly increased cell proliferation in both murine prostatic cells and HPSCs. Treatment with metformin effectively inhibited OxLDL-induced proliferation. Additionally, OxLDL stimulated the production and release of pro-proliferative EVs by HPSCs, which further promoted cellular proliferation. Conclusions: The findings suggest that dyslipidemia drives prostatic stromal cell proliferation and EV secretion, contributing to BPH progression. Metformin demonstrates potential as a therapeutic agent to mitigate these effects, offering insight into novel strategies for BPH management. This study highlights the complex interaction between dyslipidemia, cell proliferation, and extracellular communication in the context of BPH pathogenesis.

Biology doi: 10.3390/biology13100828

Authors: Daniel Puppe Jacqueline Busse Mathias Stein Danuta Kaczorek Christian Buhtz Jörg Schaller

The potato is the most important non-cereal food crop, and thus improving potato growth and yield is the focus of agricultural researchers and practitioners worldwide. Several studies reported beneficial effects of silicon (Si) fertilization on potato performance, although plant species from the family Solanaceae are generally considered to be non-Si-accumulating. We used results from two field experiments in the temperate zone to gain insight into silica accumulation in potato plants, as well as corresponding long-term potato yield performance. We found relatively low Si contents in potato leaves and roots (up to 0.08% and 0.3% in the dry mass, respectively) and negligible Si contents in potato tuber skin and tuber flesh for plants grown in soils with different concentrations of plant-available Si (field experiment 1). Moreover, potato yield was not correlated to plant-available Si concentrations in soils in the long term (1965–2015, field experiment 2). Based on our results, we ascribe the beneficial effects of Si fertilization on potato growth and yield performance reported in previous studies mainly to antifungal/osmotic effects of foliar-applied Si fertilizers and to changes in physicochemical soil properties (e.g., enhanced phosphorus availability and water-holding capacity) caused by soil-applied Si fertilizers.