Biological Research Research Articles

Sequential trait evolution did not drive deep-time diversification in sharks.

Estimating how traits evolved and impacted diversification across the tree of life represents a critical topic in ecology and evolution. Although there has been considerable research in comparative biology, large parts of the tree of life remain underexplored. Sharks are an iconic clade of marine vertebrates, and key components of marine ecosystems since the early Mesozoic. However, few studies have addressed how traits evolved or whether they impacted their extant diversity patterns. Our study aimed to fill this gap by reconstructing the largest time-calibrated species-level phylogeny of sharks and compiling an exhaustive database for ecological (diet, habitat) and biological (reproduction, maximum body length) traits. Using state-of-the-art models of evolution and diversification, we outlined the major character shifts and modes of trait evolution across shark species. We found support for sequential models of trait evolution and estimated a small to medium-sized lecithotrophic and coastal-dwelling most recent common ancestor for extant sharks. However, our exhaustive hidden traits analyses do not support trait-dependent diversification for any examined traits, challenging previous works. This suggests that the role of traits in shaping sharks' diversification dynamics might have been previously overestimated and should motivate future macroevolutionary studies to investigate other drivers of diversification in this clade.

Important antiviral properties of Streptomyces species compounds

species, a subgroup of Actinomycetes bacteria, have been analysed for their antiviral properties. These bioactive secondary metabolites, which have a broad spectrum of chemical structures and strong biological activity, offer a promising opportunity for new antiviral therapeutics against various viral infections. These metabolites target different stages of viral replication or interactions with host cells, making them important for biological research and pharmaceutical development. bacteria contain numerous antiviral mechanisms that inhibit viral infections at different stages of the viral life cycle. and other actinomycetes can improve the health of people with viruses, and recent research suggests that combining with other bacterial species could improve overall health and regulate infections. This emphasises the importance of comprehensive approaches to combating viral infections and research into natural products. Further research into multispecies combinations of and other bacterial species is needed to fully utilise their therapeutic potential against viral diseases.

Editorial: Developmental biology and endocrine research for a successful pregnancy

Editorial: Developmental biology and endocrine research for a successful pregnancy

The biophysics of water in cell biology: perspectives on a keystone for both marine sciences and cancer research

The biophysics of water, has been debated over more than a century. Although its importance is still underestimated, significant breakthroughs occurred in recent years. The influence of protein condensation on water availability control was documented, new findings on water-transport proteins emerged, and the way water molecules rearrange to minimize free energy at interfaces was deciphered, influencing membrane thermodynamics. The state of knowledge continued to progress in the field of deep-sea marine biology, highlighting unknown effects of high hydrostatic pressure and/or temperature on interactions between proteins and ligands in extreme environments, and membrane structure adaptations. The role of osmolytes in protein stability control under stress is also discussed here in relation to fish egg hydration/buoyancy. The complexity of water movements within the cell is updated, all these findings leading to a better view of their impact on many cellular processes. The way water flow and osmotic gradients generated by ion transport work together to produce the driving force behind cell migration is also relevant to both marine biology and cancer research. Additional common points concern water dynamic changes during the neoplastic transformation of cells and tissues, or embryo development. This could improve imaging techniques, early cancer diagnosis, and understanding of the molecular and physiological basis of buoyancy for many marine species.

Why more biologists must embrace quantitative modeling.

Biology as a field has transformed since the time of its foundation from an organized enterprise cataloging the diversity of the natural world to a quantitatively rigorous science seeking to answer complex questions about the functions of organisms and their interactions with each other and their environments. As the mathematical rigor of biological analyses has improved, quantitative models have been developed to describe multi-mechanistic systems and to test complex hypotheses. However, applications of quantitative models have been uneven across fields, and many biologists lack the foundational training necessary to apply them in their research or to interpret their results to inform biological problem-solving efforts. This gap in scientific training has created a false dichotomy of "biologists'' and "modelers" that only exacerbates the barriers to working biologists seeking additional training in quantitative modeling. Here, we make the argument that all biologists are modelers, and are capable of using sophisticated quantitative modeling in their work. We highlight four benefits of conducting biological research within the framework of quantitative models, identify the potential producers and consumers of information produced by such models, and make recommendations for strategies to overcome barriers to their widespread implementation. Improved understanding of quantitative modeling could guide the producers of biological information to better apply biological measurements through analyses that evaluate mechanisms, and allow consumers of biological information to better judge the quality and applications of the information they receive. As our explanations of biological phenomena increase in complexity, so too must we embrace modeling as a foundational skill.

Discovery of the Lysosome-Inhibiting Function of Acremolactone B

Lysosome inhibitors have garnered considerable interest for their utility in lysosome biology research and potential therapeutic applications. We discovered the lysosome-inhibiting function of acremolactone B (1), a scarce azaphilone-type polyketide, leveraging our previous scalable synthesis. This compound significantly reduces lysosomal acidity and impairs the maturation of the lysosomal protease cathepsin D (CTSD) in triple-negative breast cancer cells (MDA-MB-231) and human lung cancer cells (A549). Furthermore, we found that compound 1 suppresses downstream autophagy, as revealed by monitoring autophagic flux and conducting transmission electron microscopy (TEM) analysis. This study unveils the previously unrecognized biological role of 1 and introduces a new scaffold for lysosome inhibitors.

Identification and validation of stable reference genes for RT-qPCR analyses of Kobresia littledalei seedlings

BackgroundKobreisa littledalei, belonging to the Cyperaceae family is the first Kobresia species with a reference genome and the most dominant species in Qinghai-Tibet Plateau alpine meadows. It has several resistance genes which could be used to breed improved crop varieties. Reverse Transcription Quantitative Real-Time Polymerase Chain Reaction (RT-qPCR) is a popular and accurate gene expression analysis method. Its reliability depends on the expression levels of reference genes, which vary by species, tissues and environments. However, K.littledalei lacks a stable and normalized reference gene for RT-qPCR analysis.ResultsThe stability of 13 potential reference genes was tested and the stable reference genes were selected for RT-qPCR normalization for the expression analysis in the different tissues of K. littledalei under two abiotic stresses (salt and drought) and two hormonal treatments (abscisic acid (ABA) and gibberellin (GA)). Five algorithms were used to assess the stability of putative reference genes. The results showed a variation amongst the methods, and the same reference genes showed tissue expression differences under the same conditions. The stability of combining two reference genes was better than a single one. The expression levels of ACTIN were stable in leaves and stems under normal conditions, in leaves under drought stress and in roots under ABA treatment. The expression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) expression was stable in the roots under the control conditions and salt stress and in stems exposed to drought stress. Expression levels of superoxide dismutase (SOD) were stable in stems of ABA-treated plants and in the roots under drought stress. Moreover, RPL6 expression was stable in the leaves and stems under salt stress and in the stems of the GA-treated plants. EF1-alpha expression was stable in leaves under ABA and GA treatments. The expression levels of 28 S were stable in the roots under GA treatment. In general, ACTIN and GAPDH could be employed as housekeeping genes for K. littledalei under different treatments.ConclusionThis study identified the best RT-qPCR reference genes for different K. littledalei tissues under five experimental conditions. ACTIN and GAPDH genes can be employed as the ideal housekeeping genes for expression analysis under different conditions. This is the first study to investigate the stable reference genes for normalized gene expression analysis of K. littledalei under different conditions. The results could aid molecular biology and gene function research on Kobresia and other related species.

A Psychological, Historical Analysis of Post-Slavery Trauma and Post-Slavery Growth: Are They Viable Constructs?

Around the turn of the 20th century, two sociologists, W. E. B. Du Bois, and E. Franklin Frazier, produced separate narratives depicting the legacy of slavery. Du Bois documented both the apparent negative consequences as well the way many ex-slaves achieved “uplift” within a short period of time, following Emancipation. Frazier claimed that exiting slavery the ex-slaves were a broken and damaged community in dire need of assimilation. In the 1930s, when Black psychologists entered the picture, their contribution tended to favor and extend Frazier’s work, resulting in a series of studies documenting racial self-hatred and damage to the self-concept. Inspired by contemporary biological and genealogical research showing trauma can become embedded in DNA structures and transmitted from one generation to another, Joy DeGruy theorized that most African Americans suffer from a Post-Traumatic Slave Syndrome [PTSS]. Missing from DeGruy’s theorizing was mention of theory and research on the way trauma can result in positive psychological outcomes or Post-Traumatic Growth [PTG]. The current work attempts to summarize theory and research for both PTSS and PTG, as each may apply to an analysis of the psychological legacy of slavery.

Biocompatible plasma-treated liquids: A sustainable approach for decontaminating gastrointestinal-infection causing pathogens

Nosocomial infections are a serious threat and difficult to cure due to rising antibiotic resistance in pathogens and biofilms. Direct exposure to cold atmospheric plasma (CAP) has been widely employed in numerous biological research endeavors. Nonetheless, plasma-treated liquids (PTLs) formulated with physiological solutions may offer additional benefits such as enhanced portability, and biocompatibility. Additionally, CAP-infused long-lived reactive oxygen and nitrogen species (RONS) such as nitrite (NO2−), nitrate (NO3−), and hydrogen peroxide (H2O2) can synergistically induce their antibacterial activity. Herein, we investigated those argon-plasma jet-treated liquids, including Ringer’s lactate (RL), phosphate-buffered saline (PBS), and physiological saline, have significant antibacterial activity against nosocomial/gastrointestinal-causing pathogens, which might be due to ROS-mediated lipid peroxidation. Combining the conventional culture-based method with propidium iodide monoazide quantitative PCR (PMAxx™-qPCR) indicated that PTLs induce a minimal viable but non-culturable (VBNC) state and moderately affect culturable counts. Specifically, the PTL exposure resulted in pathogenicity dysfunction via controlling T3SS-related effector genes of S. enterica. Overall, this study provides insights into the effectiveness of PTLs for inducing ROS-mediated damage, controlling the virulence of diarrheagenic bacteria, and modulating homeostatic genes.

Dimethyl Sulfoxide (DMSO) as a Potential Source of Interference in Research Related to Sulfur Metabolism—A Preliminary Study

Dimethyl sulfoxide (DMSO), an organosulfur compound, is widely used as the gold standard solvent in biological research. It is used in cell culture experiments and as a component of formulations in in vivo studies. Unfortunately, parameters related to sulfur metabolism are often not taken into account when using DMSO. Therefore, in this work we aim to show that the addition of DMSO to the culture medium (even in amounts commonly considered acceptable) alters some parameters of sulfur metabolism. For this study, we used three cell lines: a commercially available Caco-2 line (HTB-37, ATCC) and two lines created as part of our early studies (likewise previously described in the literature) to investigate the anomalies of sulfur metabolism in mucopolysaccharidosis. As the negative effects of DMSO on the cell membrane are well known, additional experiments with the partial loading of DMSO into polymerosomes (poly(ethylene glycol) methyl ether-block-poly(lactide-co-glycolide), PEG-PLGA) were performed to eliminate these potentially disruptive effects. The results show that DMSO is a source of interference in studies related to sulfur metabolism and that there are not just simple effects that can be corrected in the final result by subtracting control values, since complex synergisms are also observed.

Deciphering male influence in gynogenetic Pengze crucian carp (Carassius auratus var. pengsenensis): insights from Nanopore sequencing of structural variations

In this study, we investigate gynogenetic reproduction in Pengze Crucian Carp (Carassius auratus var. pengsenensis) using third-generation Nanopore sequencing to uncover structural variations (SVs) in offspring. Our objective was to understand the role of male genetic material in gynogenesis by examining the genomes of both parents and their offspring. We discovered a notable number of male-specific structural variations (MSSVs): 1,195 to 1,709 MSSVs in homologous offspring, accounting for approximately 0.52%–0.60% of their detected SVs, and 236 to 350 MSSVs in heterologous offspring, making up about 0.10%–0.13%. These results highlight the significant influence of male genetic material on the genetic composition of offspring, particularly in homologous pairs, challenging the traditional view of asexual reproduction. The gene annotation of MSSVs revealed their presence in critical gene regions, indicating potential functional impacts. Specifically, we found 5 MSSVs in the exonic regions of protein-coding genes in homologous offspring, suggesting possible direct effects on protein structure and function. Validation of an MSSV in the exonic region of the polyunsaturated fatty acid 5-lipoxygenase gene confirmed male genetic material transmission in some offspring. This study underscores the importance of further research on the genetic diversity and gynogenesis mechanisms, providing valuable insights for reproductive biology, aquaculture, and fostering innovation in biological research and aquaculture practices.

The m6A reader IGF2BP2 promotes esophageal cell carcinoma progression by enhancing EIF4A1 translation

Esophageal squamous cell carcinoma (ESCC) is one of most prevalent cancers worldwide, especially in China. Lacking in depth mechanism study, effective targets and therapeutics are desperately needed in the clinic. RNA-binding proteins (RBPs) mediate the localization, stability, and translation of the target transcripts and fine-tune the physiological functions of the proteins encoded. Bioinformatics analysis revealed that IGF2BPs were highly expressed in ESCC tissues and at least participated in the regulation of cell proliferation of ESCC cells. Biological researches demonstrated that IGF2BP2 promoted the cell proliferation, migration and invasion of ESCC KYSE30 and KYSE450 cells. IGF2BP2 could bind to EIF4A1 mRNA by recognition of m6A sites and enhanced translation of EIF4A1. IGF2BPs, as m6A reader, IGF2BPs were oncogenic genes in ESCC by regulating the expression of EIF4A1 through m6A sites. IGF2BP2, EIF4A1 and their targets could serve as potential biomarkers and therapeutic targets for ESCC, offering promising novel approaches for the diagnosis and treatment of ESCC.

Mass Transport and Energy Conversion of Magnetic Nanofluids from Nanoparticles’ Movement and Liquid Manipulation

Magnetic nanofluids, also referred to as ferromagnetic particle levitation systems, are materials with highly responsive magnetic properties. Due to their magnetic responsiveness, excellent controllability, favorable thermal characteristics, and versatility, magnetic nanofluids have sparked considerable interest in both industrial manufacturing and scientific research. Magnetic nanofluids have been used and developed in diverse areas such as materials science, physics, chemistry and engineering due to their remarkable characteristics such as rapid magnetic reaction, elastic flow capacities, and tunable thermal and optical properties. This paper provides a full and in-depth introduction to the diverse uses of ferrofluids including material fabrication, fluid droplet manipulation, and biomedicine for the power and machinery sectors. As a result, magnetic nanofluids have shown promising applications and have provided innovative ideas for multidisciplinary research in biology, chemistry, physics and materials science. This paper also presents an overview of the device construction and the latest developments in magnetic-nanofluid-related equipment, as well as possible challenging issues and promising future scenarios.

Biological Underpinnings of Criminal Behavior: A Comprehensive Review

Background: Traditional criminological theories often emphasize social and environmental factors in criminal behavior. However, early biological research, which was initially reductionist and focused on physical traits, has evolved significantly with advancements in genetics and neuroimaging techniques. This evolution has led to a more nuanced understanding of the role of biological factors in criminal behavior. Objective: This review aims to critically examine how genetic, neurobiological, and psychophysiological factors contribute to criminal behavior, and to explore the interplay between these biological predispositions and environmental influences. Methods: We systematically analyzed empirical studies that investigate the impact of abnormalities in brain structures, neurotransmitter systems, and genetic predispositions on antisocial behaviors, integrating these findings with socio-environmental conditions. Results: Findings from recent studies indicate significant contributions of abnormalities in brain areas such as the prefrontal cortex and amygdala, and dysregulation in neurotransmitter systems to antisocial behaviors. These biological factors, when combined with environmental influences, enhance our understanding of criminal tendencies. Conclusion: The integration of biological perspectives into criminological theories marks a significant shift towards a more holistic approach in the study of criminal behavior. This review advocates for the development of targeted intervention strategies and ethical policy formulations, emphasizing the potential of biological research to improve the efficacy and humanity of the criminal justice system. Ongoing interdisciplinary research and collaboration are essential to continue advancing our understanding and management of criminal behavior.

A new framework for exploratory network mediator analysis in omics data.

Omics methods are widely used in basic biology and translational medicine research. More and more omics data are collected to explain the impact of certain risk factors on clinical outcomes. To explain the mechanism of the risk factors, a core question is how to find the genes/proteins/metabolites that mediate their effects on the clinical outcome. Mediation analysis is a modeling framework to study the relationship between risk factors and pathological outcomes, via mediator variables. However, high-dimensional omics data are far more challenging than traditional data: (1) From tens of thousands of genes, can we overcome the curse of dimensionality to reliably select a set of mediators? (2) How do we ensure that the selected mediators are functionally consistent? (3) Many biological mechanisms contain nonlinear effects. How do we include nonlinear effects in the high-dimensional mediation analysis? (4) How do we consider multiple risk factors at the same time? To meet these challenges, we propose a new exploratory mediation analysis framework, medNet, which focuses on finding mediators through predictive modeling. We propose new definitions for predictive exposure, predictive mediator, and predictive network mediator, using a statistical hypothesis testing framework to identify predictive exposures and mediators. Additionally, two heuristic search algorithms are proposed to identify network mediators, essentially subnetworks in the genome-scale biological network that mediate the effects of single or multiple exposures. We applied medNet on a breast cancer data set and a metabolomics data set combined with food intake questionnaire data. It identified functionally consistent network mediators for the exposures' impact on the outcome, facilitating data interpretation.

Ecological perspectives on female and male reproductive success with competition in two Serapias species.

The deceptive strategies by which orchids are pollinated and how these are capable of attracting pollinators remain understudied with regard to their implications on plant fitness. Despite its ecological importance, limited investigations have been conducted on sexual deception and shelter mimicry in orchid species, making it a compelling avenue in orchid biology research. To expand the knowledge of these reproductive mechanisms, we studied the pollination of Serapias lingua and S. parviflora, in co-occurring and isolated sites in Balearic Islands (Spain), further accentuated by the presence of a hybrid, indicating shared pollinators. We employed bagging and hand pollination experiments to examine their reproductive biology. Furthermore, we evaluated the influence of phenotypical and ecological factors on reproductive success, including biometric measurements, reproductive performance and neighborhood diversity (co-flowering and pollinator communities). Reproductive mechanisms between these two orchid species exhibit substantial disparities. Serapias lingua relies primarily on insect-mediated pollination, while S. parviflora demonstrates self-reproduction capacity. Although events of open pollination are rare, hybridization occurs predominantly when S. lingua is the pollen donor. Fruit set in S. parviflora was positively correlated with plant height, while in S. lingua it was negatively associated with flower size. The coexistence of both species positively affected pollinia removal in S. parviflora, but did not exert an influence on reproductive traits in S. lingua. Overall, biometric parameters were diminished in isolated compared to co-occurring sites. At the community level, the increased diversity of co-flowering species in the vicinity exhibited an inhibitory effect on pollinia removal in S. parviflora. Under a context of pollinator loss or phenological mismatch between pollinator presence and flowering, the selfing capacity of S. parviflora would guarantee reproduction whereas S. lingua survival would be compromised. Furthers studies are needed to assess the effects of phenotypical and ecological factors on reproductive success of S. lingua in pollinator-decline scenarios.

From synthesis to applications of biomolecule-protected luminescent gold nanoclusters.

Gold nanoclusters (AuNCs) are a class of novel luminescent nanomaterials that exhibit unique properties of ultra-small size, featuring strong anti-photo-bleaching ability, substantial Stokes shift, good biocompatibility, and low toxicity. Various biomolecules have been developed as templates or ligands to protect AuNCs with enhanced stability and luminescent properties for biomedical applications. In this review, the synthesis of AuNCs based on biomolecules including amino acids, peptides, proteins and DNA are summarized. Owing to the advantages of biomolecule-protected AuNCs, they have been employed extensively for diverse applications. The biological applications, particularly in bioimaging, biosensing, disease therapy and biocatalysis have been described in detail herein. Finally, current challenges and future potential prospects of bio-templated AuNCs in biological research are briefly discussed.

User-Friendly Multifunctional Red-Emissive Carbon Dots for Rapid Cell Nucleus Staining via Targeting Nuclear Proteins.

Cytoarchitectural staining is of great importance in disease diagnosis and cell biology research. This study developed user-friendly multifunctional red-emissive carbon dots (R-CDs) for rapid cell nucleus staining via targeting nuclear proteins. R-CDs, simply prepared by electrochemical treatment of 1,2,4-benzenetriamine, exhibit strong emission at 635 nm when excited at 507 nm. The R-CDs can rapidly stain the nucleus of human SH-SY5Y, HepG2, and HUH-7 cells with a high signal-to-noise ratio owing to fluorescence enhancement after entering the nucleus. Compared to conventional cytosolic dyes such as Hoechst and DAPI, R-CDs are cheaper, more highly dispersed in water, and more stable (requiring no stringent storage conditions). The R-CDs show stable optical properties with insignificant photobleaching over 7 days and salt resistance up to 2 M of NaCl. More importantly, R-CDs, possessing a positive charge, allow rapid staining of live cells (3 min) and dead cells (10 s) in saline. According to kinetic variation, R-CDs can distinguish live cells from dead cells. Staining exhibits high efficiency in onion epidermal cells, Aspergillus niger, Caenorhabditis elegans, and human spermatozoa. The mechanism for efficient staining is based on their fast accumulation in the nucleus due to their small size and positive charge and strong interaction with nuclear proteins at amino acid residues of histidine and arginine, resulting in fluorescence enhancement by dozens of times. The developed R-CDs do not bind to DNA and would not cause genetic damage and will find various safe applications in biological and medical fields.

Physiology Brings Relevance to Biological Research: A Vision for Function

Physiology Brings Relevance to Biological Research: A Vision for Function

Pangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks

BackgroundThe genetic diversity of yak, a key domestic animal on the Qinghai-Tibetan Plateau (QTP), is a vital resource for domestication and breeding efforts. This study presents the first yak pangenome obtained through the de novo assembly of 16 yak genomes.ResultsWe discovered 290 Mb of nonreference sequences and 504 new genes. Our pangenome-wide presence and absence variation (PAV) analysis revealed 5,120 PAV-related genes, highlighting a wide range of variety-specific genes and genes with varying frequencies across yak populations. Principal component analysis (PCA) based on binary gene PAV data classified yaks into three new groups: wild, domestic, and Jinchuan. Moreover, we proposed a ‘two-haplotype genomic hybridization model’ for understanding the hybridization patterns among breeds by integrating gene frequency, heterozygosity, and gene PAV data. A gene PAV-GWAS identified a novel gene (BosGru3G009179) that may be associated with the multirib trait in Jinchuan yaks. Furthermore, an integrated transcriptome and pangenome analysis highlighted the significant differences in the expression of core genes and the mutational burden of differentially expressed genes between yaks from high and low altitudes. Transcriptome analysis across multiple species revealed that yaks have the most unique differentially expressed mRNAs and lncRNAs (between high- and low-altitude regions), especially in the heart and lungs, when comparing high- and low-altitude adaptations.ConclusionsThe yak pangenome offers a comprehensive resource and new insights for functional genomic studies, supporting future biological research and breeding strategies.