Search

Australian elapid snake venoms are uniquely procoagulant, utilizing blood clotting enzyme Factor Xa (FXa) as a toxin, which evolved as a basal trait in this clade. The subsequent recruitment of Factor Va (FVa) as a toxin occurred in the last common ancestor of taipans (Oxyuranus species) and brown snakes (Pseudonaja species). Factor II (prothrombin) activation has been stated as the primary mechanism for the lethal coagulopathy, but this hypothesis has never been tested. The additional activation of Factor VII (FVII) by Oxyuranus/Pseudonaja venoms has historically been considered as a minor, unimportant novelty. This study aimed to investigate the significance of toxic FVII activation relative to prothrombin activation by testing a wide taxonomical range of Australian elapid species with procoagulant venoms. The activation of FVII or prothrombin, with and without the Factor Va as a cofactor, was assessed, along with the structural changes involved in these processes. All procoagulant species could activate FVII, establishing this as a basal trait. In contrast, only some lineages could activate prothrombin, indicating that this is a derived trait. For species able to activate both zymogens, Factor VII was consistently more strongly activated than prothrombin. FVa was revealed as an essential cofactor for FVII activation, a mechanism previously undocumented. Species lacking FVa in their venom utilized endogenous plasma FVa to exert this activity. The ability of the human FXa:FVa complex to activate FVII was also revealed as a new feedback loop in the endogenous clotting cascade. Toxin sequence analyses identified structural changes essential for the derived trait of prothrombin activation. This study presents a paradigm shift in understanding how elapid venoms activate coagulation factors, highlighting the critical role of FVII activation in the pathophysiological effects upon the coagulation cascade produced by Australian elapid snake venoms. It also documented the novel use of Factor Va as a cofactor for FVII activation for both venom and endogenous forms of FXa. These findings are crucial for developing better antivenoms and treatments for snakebite victims and have broader implications for drug design and the treatment of coagulation disorders. The research also advances the evolutionary biology knowledge of snake venoms. [ABSTRACT FROM AUTHOR]

Life on Earth comprises prokaryotes and a broad assemblage of endosymbioses. The pages of Molecular Biology and Evolution and Genome Biology and Evolution have provided an essential window into how these endosymbiotic interactions have evolved and shaped biological diversity. Here, we provide a current perspective on this knowledge by drawing on decades of revelatory research published in Molecular Biology and Evolution and Genome Biology and Evolution , and insights from the field at large. The accumulated work illustrates how endosymbioses provide hosts with novel phenotypes that allow them to transition between adaptive landscapes to access environmental resources. Such endosymbiotic relationships have shaped and reshaped life on Earth. The early serial establishment of mitochondria and chloroplasts through endosymbioses permitted massive upscaling of cellular energetics, multicellularity, and terrestrial planetary greening. These endosymbioses are also the foundation upon which all later ones are built, including everything from land–plant endosymbioses with fungi and bacteria to nutritional endosymbioses found in invertebrate animals. Common evolutionary mechanisms have shaped this broad range of interactions. Endosymbionts generally experience adaptive and stochastic genome streamlining, the extent of which depends on several key factors (e.g. mode of transmission). Hosts, in contrast, adapt complex mechanisms of resource exchange, cellular integration and regulation, and genetic support mechanisms to prop up degraded symbionts. However, there are significant differences between endosymbiotic interactions not only in how partners have evolved with each other but also in the scope of their influence on biological diversity. These differences are important considerations for predicting how endosymbioses will persist and adapt to a changing planet. [ABSTRACT FROM AUTHOR]

Background: A major challenge of evolutionary biology is making underlying concepts accessible to wide audiences. One method for doing so is to utilise multi-media formats that have potential to engage and inform through entertainment. This pilot study outlines and discusses a sonification concert that integrated musical performance with a range of evolutionary concepts and ideas fundamental to an understanding of evolution, such as protein sequences. We aimed to showcase sound-art objects and live-coding performances created using sonification as a mechanism for presenting complex biological processes to both researcher and non-researchers. We sought to evaluate the effectiveness of this art-adjacent practice for public engagement with evolutionary biology research, and also to gather feedback to guide future events. Toward this end, we held a live concert showcasing biologically-based algorithmic music exploring links between evolutionary biology research, sound art, and musical performance. The event had three main acts: a generative audio-visual piece giving an artistic representation of SARS coronavirus based on a parameter-mapping sonification of protein sequence of the replicase polyprotein; a pre-recorded string ensemble demonstrating the effects of codon selection on translation speed using parameter-mapping sonification; and a live-coded music piece interactively sonifying protein structures. Results: Our event attracted 90 attendees. We evaluated success using direct observation and written feedback forms with a 58% response rate: 95% of respondents stated they had enjoyed the event and 63% indicated they were inspired by it. Conclusions: Presenting the sonic outputs of sonification research in a concert format showed good potential for the pursuit of public engagement with evolutionary biology research, demonstrating the ability to engage curiosity and inspire an audience while also conveying scientific content alongside the nuanced and complex world of modern evolutionary biology. [ABSTRACT FROM AUTHOR]

Simple Summary: The mitochondrial genome of insects has been widely used in studies of molecular evolution, population genetics, phylogenetics, and species identification due to its small size (approximately 14–20 kb), relatively high evolutionary rate, low levels of recombination, and high genome copy numbers. In this study, 13 complete mitogenomes of Chiasmini, a diverse group of grassland leafhoppers, were sequenced and analyzed for the first time. The phylogenetic position of Chiasmini within leafhoppers and the phylogenetic relationships among Chiasmini genera were reconstructed. The results show that all 13 mitogenomes are composed of a circular, double-stranded molecule that consists of 37 genes with a total length ranging from 14,805 to 16,269 bp and a variable number of non-coding A + T-rich regions. The gene size, order, arrangement, base composition, codon usage, and secondary structure of tRNAs in these newly sequenced mitogenomes of 13 species are highly conserved in Chiasmini. Phylogenetic analysis of the newly sequenced genomes plus representatives of other tribes and subfamilies of Cicadellidae recover all included subfamilies of Cicadellidae and tribes of Deltocephalinae as monophyletic, except Athysanini and Opsiini in Deltocephalinae, which are paraphyletic in agreement with some other recent studies. Chiasmini form a monophyletic group consisting of seven monophyletic genera arranged as follows: ((Zahniserius + (Gurawa + (Doratura + Aconurella))) + (Leofa + (Exitianus + Nephotettix))). The grassland leafhopper tribe Chiasmini (Cicadellidae: Deltocephalinae) presently comprises 324 described species worldwide, with the highest species diversity occurring in the Nearctic region but a greater diversity of genera occurring in the Old World. In China, this tribe comprises 39 described species in 11 genera, but the fauna remains understudied. The complete mitogenomes of three species of this tribe have been sequenced previously. In order to better understand the phylogenetic position of Chiasmini within the subfamily Deltocephalinae and to investigate relationships among Chiasmini genera and species, we sequenced and analyzed the complete mitogenomes of 13 species belonging to seven genera from China. Comparison of the newly sequenced mitogenomes reveals a closed circular double-stranded structure containing 37 genes with a total length of 14,805 to 16,269 bp and a variable number of non-coding A + T-rich regions. The gene size, gene order, gene arrangement, base composition, codon usage, and secondary structure of tRNAs of the newly sequenced mitogenomes of these 13 species are highly conserved in Chiasmini. The ATN codon is commonly used as the start codon in protein-coding genes (PCGs), except for ND5 in Doratura sp. and ATP6 in Nephotettix nigropictus, which use the rare GTG start codon. Most protein-coding genes have TAA or TAG as the stop codon, but some genes have an incomplete T stop codon. Except for the tRNA for serine (trnS1(AGN)), the secondary structure of the other 21 tRNAs is a typical cloverleaf structure. In addition to the primary type of G–U mismatch, five other types of tRNA mismatches were observed: A–A, A–C, A–G, U–C, and U–U. Chiasmini mitochondrial genomes exhibit gene overlaps with three relatively stable regions: the overlapping sequence between trnW and trnC is AAGTCTTA, the overlapping sequence between ATP8 and ATP6 is generally ATGATTA, and the overlapping sequence between ND4 and ND4L is generally TTATCAT. The largest non-coding region is the control region, which exhibits significant length and compositional variation among species. Some Chiasmini have tandem repeat structures within their control regions. Unlike some other deltocephaline leafhoppers, the sequenced Chiasmini lack mitochondrial gene rearrangements. Phylogenetic analyses of different combinations of protein-coding and ribosomal genes using maximum likelihood and Bayesian methods under different models, using either amino acid or nucleotide sequences, are generally consistent and also agree with results of prior analyses of nuclear and partial mitochondrial gene sequence data, indicating that complete mitochondrial genomes are phylogenetically informative at different levels of divergence within Chiasmini and among leafhoppers in general. Apart from Athysanini and Opsiini, most of the deltocephaline tribes are recovered as monophyletic. The results of ML and BI analyses show that Chiasmini is a monophyletic group with seven monophyletic genera arranged as follows: ((Zahniserius + (Gurawa + (Doratura + Aconurella))) + (Leofa + (Exitianus + Nephotettix))). [ABSTRACT FROM AUTHOR]

Introduction: Oral carcinogenetic is based on a variety of genomic imbalances (gross chromosome or specific gene alterations) that drive the normal oral mucosa to its neoplastic/dysplastic epithelial form and finally to a totally malignant tissue transformation. In this multi-step procedure, down-regulation of suppressor genes combined with overactivation of oncogenes are two crucial and partially early genetic events involved in the onset and progression of neoplastic/malignant epithelia transformation. More specifically, deregulation of strong transcription factors negatively affects the normal expression of a broad spectrum of genes that are involved in cell proliferation and signalling transduction to the nucleus. Objective: The purpose of the current molecular review was to explore the c-Jun (chromosome location: 1p32-p31) transcription factor transformation mechanisms to oncogene in oral squamous cell carcinoma (OSCC). Material and method: A systematic review of the literature was carried out by searching in PubMed international database. The year 2010 was set as a prominent time limit for the publication date of the articles in the majority of them, whereas specific references of great importance and historical value in the field of the c-Jun gene discovery and analysis were also included. The following keywords were used: c-Jun, oncogene, signaling pathway, oral, carcinoma, transcription. A pool of 45 important articles were selected for the present study at the basis of combining molecular knowledge with new targeted therapeutic strategies. Results: C-Jun -- as a part of the c-Jun/c-Fos transcription factors' complex --critically regulates the expression levels in a variety of genes inside the cellular microenvironment. A broad spectrum of malignancies, including OSCC, demonstrate c-Jun alterations driving the gene to its oncogenic phenotype. Interestingly, c-Jun oncogenic activation is mediated by high-risk human papilloma virus (HR-HPV) persistent infection in significant subsets of these malignancies. Conclusions: C-Jun was the first oncogene -- acting as a strong transcription factor -- that was discovered and cloned 35 years ago. C-Jun is the living history of oncogenes and its discovery marks a significant step in the evolution of molecular biology. [ABSTRACT FROM AUTHOR]

This document is a correction to a previously published article titled "The Evolution of Temperature and Desiccation-Related Protein Families in Tardigrada Reveals a Complex Acquisition of Extremotolerance." The correction addresses errors in the original publication, including a mistake in the coloring of Halechiniscus, which should be depicted as a marine species instead of a terrestrial one. Additionally, there are corrections to Figure 1 and Figure 7, as well as the addition of Table S3 to the supplementary data. These corrections have been made to the article. [Extracted from the article]

Modern humans originated in Africa 300,000 yr ago, and before leaving their continent of origin, they underwent a process of intense diversification involving complex demographic dynamics. Upon exiting Africa, different populations emerged on the four other inhabited continents, shaped by the interplay of various evolutionary processes, such as migrations, founder effects, and natural selection. Within each region, continental populations, in turn, diversified and evolved almost independently for millennia. As a backdrop to this diversification, introgressions from archaic species contributed to establishing different patterns of genetic diversity in different geographic regions, reshaping our understanding of our species' variability. With the increasing availability of genomic data, it has become possible to delineate the subcontinental human population structure precisely. However, the bias toward the genomic research focused on populations from the global North has limited our understanding of the real diversity of our species and the processes and events that guided different human groups throughout their evolutionary history. This perspective is part of a series of articles celebrating 40 yr since our journal, Molecular Biology and Evolution , was founded (Russo et al. 2024). The perspective is accompanied by virtual issues, a selection of papers on human diversification published by Genome Biology and Evolution and Molecular Biology and Evolution. [ABSTRACT FROM AUTHOR]

Prostate cancer (PC) is the second most diagnosed cancer among men. It was observed that early diagnosis of disease is highly beneficial for the survival of cancer patients. Therefore, the extension and increasing quality of life of PC patients can be achieved by broadening the cancer screening programs that are aimed at the identification of cancer manifestation in patients at earlier stages, before they demonstrate well-understood signs of the disease. Therefore, there is an urgent need for standard, sensitive, robust, and commonly available screening and diagnosis tools for the identification of early signs of cancer pathologies. In this respect, the "Holy Grail" of cancer researchers and bioengineers for decades has been molecular sensing probes that would allow for the diagnosis, prognosis, and monitoring of cancer diseases via their interaction with cell-secreted and cell-associated PC biomarkers, e.g., PSA and PSMA, respectively. At present, most PSA tests are performed at centralized laboratories using high-throughput total PSA immune analyzers, which are suitable for dedicated laboratories and are not readily available for broad health screenings. Therefore, the current trend in the detection of PC is the development of portable biosensors for mobile laboratories and individual use. Phage display, since its conception by George Smith in 1985, has emerged as a premier tool in molecular biology with widespread application. This review describes the role of the molecular evolution and phage display paradigm in revolutionizing the methods for the early diagnosis and monitoring of PC. [ABSTRACT FROM AUTHOR]

We are launching a series to celebrate the 40th anniversary of the first issue of Molecular Biology and Evolution. In 2024, we will publish virtual issues containing selected papers published in the Society for Molecular Biology and Evolution journals, Molecular Biology and Evolution and Genome Biology and Evolution. Each virtual issue will be accompanied by a perspective that highlights the historic and contemporary contributions of our journals to a specific topic in molecular evolution. This perspective, the first in the series, presents an account of the broad array of methods that have been published in the Society for Molecular Biology and Evolution journals, including methods to infer phylogenies, to test hypotheses in a phylogenetic framework, and to infer population genetic processes. We also mention many of the software implementations that make methods tractable for empiricists. In short, the Society for Molecular Biology and Evolution community has much to celebrate after four decades of publishing high-quality science including numerous important inferential methods. [ABSTRACT FROM AUTHOR]

Few animal groups can claim the level of wonder that cephalopods instill in the minds of researchers and the general public. Much of cephalopod biology, however, remains unexplored: the largest invertebrate brain, difficult husbandry conditions, and complex (meta-)genomes, among many other things, have hindered progress in addressing key questions. However, recent technological advancements in sequencing, imaging, and genetic manipulation have opened new avenues for exploring the biology of these extraordinary animals. The cephalopod molecular biology community is thus experiencing a large influx of researchers, emerging from different fields, accelerating the pace of research in this clade. In the first post-pandemic event at the Cephalopod International Advisory Council (CIAC) conference in April 2022, over 40 participants from all over the world met and discussed key challenges and perspectives for current cephalopod molecular biology and evolution. Our particular focus was on the fields of comparative and regulatory genomics, gene manipulation, single-cell transcriptomics, metagenomics, and microbial interactions. This article is a result of this joint effort, summarizing the latest insights from these emerging fields, their bottlenecks, and potential solutions. The article highlights the interdisciplinary nature of the cephalopod-omics community and provides an emphasis on continuous consolidation of efforts and collaboration in this rapidly evolving field. [ABSTRACT FROM AUTHOR]

Class IV genes were present in both chlorophyte and charophyte algae, while class III was found to be land plant specific. Conclusions We performed a phylogenetic analysis of 863 land plant genes and 26 algal genes identified by orthogroup analysis as belonging to I bHLH i classes III and IV. Keywords: basic helix-loop-helix; evolution; genomes; plants; transcription factor EN basic helix-loop-helix evolution genomes plants transcription factor 1717 1721 5 11/06/23 20231201 NES 231201 Data availability The genomes analysed in the present study are publicly available, as detailed in Table S1. [Extracted from the article]

Various ML algorithms are currently being developed to enhance the prediction of single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) from both short- and long-read sequences, thereby reducing the occurrence of false positives and enabling the detection of high-quality single nucleotide variants in a timely manner [[38]]. These methods allow the reduction of genome complexity and generation of genome-wide high-density markers. While microsatellites maintained a fair balance in terms of abundance across the genome, polymorphism, and automation [[15]], Single Nucleotide Polymorphisms (SNPs) have made a breakthrough in plant genotyping [[16]]. The era of plant genotyping began in the early 1980s with the progress in molecular biology and nucleic acid research and the advent of molecular marker technology. [Extracted from the article]

Agneesh Barua is a postdoctoral researcher who has received several awards and fellowships for his work in molecular biology and evolution. He is the first author of a paper on the gene regulatory network behind oral venom systems in snakes. Barua completed his PhD at the Okinawa Institute of Science and Technology, focusing on the evolution genetics of snake venoms. He is now interested in the field of evolutionary developmental biology (EvoDevo) and the challenges it presents for research projects. As a postdoc, Barua faces the challenge of balancing high-impact research, independence, and developing new research directions. He also believes that the academic discipline needs to address issues such as reliance on summary metrics for hiring decisions and the need for more comprehensive evaluation methods. [Extracted from the article]

Researchers have called for undergraduate courses to update teaching frameworks based on the Modern Synthesis with insights from molecular biology, by stressing the molecular underpinnings of variation and adaptation. To support this goal, we developed a modified version of the widely used Assessing Conceptual Reasoning of Natural Selection (ACORNS) instrument. The expanded tool, called the E‐ACORNS, is explicitly designed to test student understanding of the connections among genotypes, phenotypes, and fitness. E‐ACORNS comprises a slight modification to the ACORNS open‐response prompts and a new scoring rubric. The rubric is based on five core concepts in evolution by natural selection, with each concept broken into elements at the novice, intermediate, and expert‐level understanding. Initial tests of the E‐ACORNS showed that (1) upper‐level undergraduates can score responses reliably and quickly, and (2) students who were just starting an introductory biology series for majors do not yet grasp the molecular basis of phenotypic variation and its connection to fitness. [ABSTRACT FROM AUTHOR]

Relative to model plants, ornamental plants have many special characteristics, such as their flower color and shape, and a floral fragrance. Zhang et al. were involved in regulating plant branching and development to provide candidate genes for improving crop architecture through gene editing or directed breeding [[7]]. Cheng et al. developed an efficient virus-induced gene silencing (VIGS) system using the leaf tip needle injection method, which could effectively silence genes in I Lycoris chinensis i , providing a powerful tool for gene function studies [[16]]. With the development of sequencing technology and omics tools, core regulatory networks and genes related to specific traits were discovered in a variety of ornamental plants. [Extracted from the article]

Cystatin plays a crucial role in immune evasion by parasites. It regulates diverse immune response processes, such as antigen presentation, cytokine and NO production, and phagocytosis. In recent years, an increasing number of parasite cystatins have been identified and studied for the treatment of inflammatory diseases. In contrast, cystatin from Spirometra erinaceieuropaei has received limited research attention. The objective of this study was to utilize bioinformatics tools and molecular biology techniques to predict the biological properties and obtain a recombinant cystatin analogue from Spirometra erinaceieuropaei (SeCystatin). The SeCystatin gene consists of 417 bp and encodes a putative 100-amino acid protein. The predicted molecular weight and isoelectric point of SeCystatin were 10.89 kDa and 6.82, respectively; SeCystatin possesses 12 phosphorylation sites and five post-translational modification sites but has no signal peptide and transmembrane region. The secondary structure of SeCystatin consists of one α-helix, four β-folds and six coils. It also possesses a cystatin-specific conserved domain, QxVxG, which is positioned at the boundary between the first and second β-folds, thereby demonstrating the characteristic features of type I cystatin. In the context of molecular evolution, SeCystatin demonstrates the highest level of evolutionary similarity to Schistocephalus solidus. The SeCystatin gene was fully synthesized, and the recombinant plasmid pET-30a (+)-SeCystatin was constructed to express the target protein in Escherichia coli BL 21. Recombinant SeCystatin was successfully induced for expression by IPTG and subsequently purified using affinity chromatography (Ni-IDA). Our study provides a solid foundation for further studies on the biological functions of SeCystatin. [ABSTRACT FROM AUTHOR]

The Society for Molecular Biology and Evolution (SMBE) is celebrating the 40th anniversary of the first issue of Molecular Biology and Evolution by publishing a series of virtual issues in 2024. These virtual issues feature selected papers from the society's journals, Molecular Biology and Evolution and Genome Biology and Evolution. Each virtual issue is accompanied by a Perspective article that highlights the historical and contemporary contributions of the journals to a specific topic in molecular evolution. The September Perspective, titled "Epigenetics Research in Evolutionary Biology: Perspectives on Timescales and Mechanisms," was written by Soojin Yi and can be found in Molecular Biology and Evolution. The virtual issues include notable papers on Epigenetics and Evolution and can be accessed on SMBE's 40th anniversary site. [Extracted from the article]

Autophagy plays an intricate role in paradigmatic human pathologies such as cancer, and neurodegenerative, cardiovascular, and autoimmune disorders. Autophagy regulation is performed by a set of autophagy-related (ATG) genes, first recognized in yeast genome and subsequently identified in other species, including humans. Several other genes have been identified to be involved in the process of autophagy either directly or indirectly. Studying the codon usage bias (CUB) of genes is crucial for understanding their genome biology and molecular evolution. Here, we examined the usage pattern of nucleotide and synonymous codons and the influence of evolutionary forces in genes involved in human autophagy. The coding sequences (CDS) of the protein coding human autophagy genes were retrieved from the NCBI nucleotide database and analyzed using various web tools and software to understand their nucleotide composition and codon usage pattern. The effective number of codons (ENC) in all genes involved in human autophagy ranges between 33.26 and 54.6 with a mean value of 45.05, indicating an overall low CUB. The nucleotide composition analysis of the autophagy genes revealed that the genes were marginally rich in GC content that significantly influenced the codon usage pattern. The relative synonymous codon usage (RSCU) revealed 3 over-represented and 10 under-represented codons. Both natural selection and mutational pressure were the key forces influencing the codon usage pattern of the genes involved in human autophagy. [ABSTRACT FROM AUTHOR]

As a member of the Alphavirus, Getah virus (GETV) was becoming more serious and posing a serious threat to animal safety and public health. However, the circulation, distribution and evolution of GETV is not well understood. Hence, we integrated a variety of bioinformatic methodologies, from genomic alterations to systematic analysis, phylogeography, selection, adaptive analysis, prediction of protein modification, structural biology and molecular dynamics simulations to understand the characteristics of GETV. The results of phylogeography and molecular evolution show that due to the lack of vaccine, GETV is rapidly expanding its host range and geographical distribution at a high evolutionary rate. We also predicted the important modification sites, and identified the adaptive and active selection sites. Finally, the analysis of spatial structure and function showed that six adaptive sites may be related to the structural stability, receptor binding ability, immunogenicity and immune evasion of the virus, respectively. The data from this study have important implications for the understanding of ongoing GETV outbreaks worldwide and will guide future efforts to develop effective preventive and control measures against GETV. In particular, biosafety measures should be strengthened immediately to prevent GETV from becoming a pandemic, especially in China, South Korea and Japan. [ABSTRACT FROM AUTHOR]

To celebrate the 40th anniversary of Molecular Biology and Evolution, the Society for Molecular Biology and Evolution (SMBE) is publishing a series of virtual issues in 2024. These virtual issues feature selected papers from the society's journals, Molecular Biology and Evolution and Genome Biology and Evolution. Each virtual issue is accompanied by a Perspective that highlights the contributions of the journals to a specific topic in molecular evolution. The August Perspective, titled "Lessons from extremophiles: genomic innovations and functional adaptations across the eukaryotic tree of life," was written by H.B. Rappaport and Angela M. Oliverio and appears in Genome Biology and Evolution. The virtual issues include noteworthy papers on Genomic Innovations in Extremophiles and can be found on SMBE's 40th anniversary site. [Extracted from the article]

The Society for Molecular Biology and Evolution (SMBE) is celebrating the 40th anniversary of Molecular Biology and Evolution by publishing a series of virtual issues in 2024. These virtual issues feature selected papers from the society's journals, Molecular Biology and Evolution and Genome Biology and Evolution. Each virtual issue is accompanied by a Perspective that highlights the historical and contemporary contributions of the journals to a specific topic in molecular evolution. The July Perspective, titled "Understanding the genetic basis of variation in meiotic recombination: past, present, and future," was written by Susan E. Johnston and can be found in Molecular Biology and Evolution. The virtual issues include notable papers on Recombination and Meiosis and can be accessed on SMBE's 40th anniversary site. [Extracted from the article]

This is a correction to: Petri Kemppainen, Rhiannon Schembri, Paolo Momigliano, Boundary Effects Cause False Signals of Range Expansions in Population Genomic Data, Molecular Biology and Evolution, Volume 41, Issue 5, May 2024, msae091, https://doi.org/10.1093/molbev/msae091.In the originally published version of this manuscript, the link to the data given in the Data Availability section was incorrect.This has been corrected. [Extracted from the article]

The Society for Molecular Biology and Evolution (SMBE) is celebrating the 40th anniversary of Molecular Biology and Evolution by publishing a series of virtual issues in 2024. These virtual issues feature selected papers from the society's journals, Molecular Biology and Evolution and Genome Biology and Evolution. Each virtual issue is accompanied by a Perspective article that highlights the contributions of the journals to a specific topic in molecular evolution. The June Perspective, titled "Endosymbioses have shaped the evolution of biological diversity and complexity time and time again," was written by Gordon M. Bennett, Younghwan Kwak, and Reo Maynard and appears in Genome Biology and Evolution. The virtual issues include noteworthy papers on the Evolutionary Impacts of Endosymbiosis and can be found on SMBE's 40th anniversary site. [Extracted from the article]

The history of rDNA research started almost 90 years ago when the geneticist, Barbara McClintock observed that in interphase nuclei of maize the nucleolus was formed in association with a specific region normally located near the end of a chromosome, which she called the nucleolar organizer region (NOR). Cytologists in the twentieth century recognized the nucleolus as a common structure in all eukaryotic cells, using both light and electron microscopy and biochemical and genetic studies identified ribosomes as the subcellular sites of protein synthesis. In the mid- to late 1960s, the synthesis of nuclear-encoded rRNA was the only system in multicellular organisms where transcripts of known function could be isolated, and their synthesis and processing could be studied. Cytogenetic observations of NOR regions with altered structure in plant interspecific hybrids and detailed knowledge of structure and function of rDNA were prerequisites for studies of nucleolar dominance, epistatic interactions of rDNA loci, and epigenetic silencing. In this article, we focus on the early rDNA research in plants, performed mainly at the dawn of molecular biology in the 60 to 80-ties of the last century which presented a prequel to the modern genomic era. We discuss – from a personal view – the topics such as synthesis of rRNA precursor (35S pre-rRNA in plants), processing, and the organization of 35S and 5S rDNA. Cloning and sequencing led to the observation that the transcribed and processed regions of the rRNA genes vary enormously, even between populations and species, in comparison with the more conserved regions coding for the mature rRNAs. Epigenetic phenomena and the impact of hybridization and allopolyploidy on rDNA expression and homogenization are discussed. This historical view of scientific progress and achievements sets the scene for the other articles highlighting the immense progress in rDNA research published in this special issue of Frontiers in Plant Science on "Molecular organization, evolution, and function of ribosomal DNA." [ABSTRACT FROM AUTHOR]

Paleontology in the 21st century is a field with high interdisciplinary cooperation. Aside from the traditional morphology analysis, modern paleontologists and taxonomists can also leverage novel technical breakthroughs in molecular biology to peek into the evolutionary past. Irregular echinoids, which comprise the extant members of heart urchins (Atelostomata), sand dollars (Scutelloida), and sea biscuits (Clypeasteroida), is a subgroup of echinoids exhibiting a secondary bilateral symmetry body plan. This clade's evolution history and development remain a realm of intensive investigation that benefits profoundly from the progress of Next Generation Sequencing (NGS) technology. In this study, we reviewed the methodology and theoretical basis of molecular evolution and conducted a case study on the Taiwanese endemic sand dollar species Sinaechinocyamus mai. We exemplified the value of sequence analysis in phylogeny study and the prospect of incorporating molecular data in future investigations to shed light on the enigmatic phylogenetic relationship and body plan establishment of Scutelloida and Clypeasteroida. [ABSTRACT FROM AUTHOR]

Auxin response factors (ARFs) influence plant growth and development via the coupling of basic biological processes. However, the evolution, expansion, and regulatory mechanisms of ARFs in the domesticated crop quinoa after artificial selection remain elusive. In this study, we systematically identified 30 Chenopodium quinoa ARFs (CqARFs). In this typical domesticated crop, ARFs divided into three subfamilies are subjected to strong purification selection and have a highly conserved evolutionary pattern. Polyploidy is the primary reason for the expansion of the ARF family after quinoa domestication. The expression patterns of CqARFs in different tissues have been differentiated, and CqARF2, 5, 9 and 10 from class A have the characteristics of local heterogeneous expression in different regions of roots, which may be the key factors for crops to respond in complex environments. Overall, we examined the evolution and expansion of ARFs in representative domesticated crops using the genome, transcriptome, and molecular biology and discovered a class A ARF-centered heterogeneous expression network that played an important role in auxin signaling and environmental responses. We provide new insights into how ARFs promote domesticated crop adaptation to artificial selection by polyploid expansion. [ABSTRACT FROM AUTHOR]

The Society for Molecular Biology and Evolution (SMBE) is celebrating the 40th anniversary of Molecular Biology and Evolution by publishing a series of virtual issues in 2024. These virtual issues feature selected papers from the society's journals, Molecular Biology and Evolution and Genome Biology and Evolution. Each virtual issue is accompanied by a Perspective that highlights the journals' contributions to a specific topic in molecular evolution. The May Perspective, titled "Wright's hierarchical F-statistics," written by Marcy K. Uyenoyama, can be found in Molecular Biology and Evolution. The virtual issues include notable papers on F-statistics and Population Structure and can be accessed on SMBE's 40th anniversary site. [Extracted from the article]

Due to the extreme living conditions, extremophiles have unique characteristics in morphology, structure, physiology, biochemistry, molecular evolution mechanism and so on. Extremophiles have superior growth and synthesis capabilities under harsh conditions compared to conventional microorganisms, allowing for unsterilized fermentation processes and thus better performance in low-cost production. In recent years, due to the development and optimization of molecular biology, synthetic biology and fermentation technology, the identification and screening technology of extremophiles has been greatly improved. In this review, we summarize techniques for the identification and screening of extremophiles and review their applications in industrial biotechnology in recent years. In addition, the facts and perspectives gathered in this review suggest that next-generation industrial biotechnology (NGIBs) based on engineered extremophiles holds the promise of simplifying biofuturing processes, establishing open, non-sterilized continuous fermentation production systems, and utilizing low-cost substrates to make NGIBs attractive and cost-effective bioprocessing technologies for sustainable manufacturing. • The development of screening techniques for extremophile strains was reviewed. • The advantages and disadvantages of conventional identification, bacterial identification system and molecular biological identification methods were compared. • Extremophiles have better growth and synthesis ability in harsh industrial conditions. • The application of extremophiles to the next generation industrial biotechnology (NGIBs) is expected to establish an open, non-sterile continuous fermentation production system. [ABSTRACT FROM AUTHOR]

The Society for Molecular Biology and Evolution (SMBE) journals are releasing a series of virtual issues to commemorate the 40th anniversary of Molecular Biology and Evolution. These virtual issues feature selected papers from the society's journals, Molecular Biology and Evolution and Genome Biology and Evolution. Each virtual issue is accompanied by a Perspective article that highlights the historical and contemporary contributions of the journals to a specific topic in molecular evolution. The April Perspective, titled "Microbial diversity and open questions about the deep Tree of Life," was written by Laura Eme and Daniel Tamarit and can be found in Genome Biology and Evolution. The virtual issues, available on SMBE's 40th anniversary site, include notable papers on microbial diversity and the Tree of Life from both journals. [Extracted from the article]

The Society for Molecular Biology and Evolution (SMBE) journals are releasing a series of virtual issues to commemorate the 40th anniversary of the first issue of Molecular Biology and Evolution. These virtual issues feature selected papers from the society's journals, Molecular Biology and Evolution and Genome Biology and Evolution. Each virtual issue is accompanied by a Perspective article that highlights the historical and contemporary contributions of the journals to a specific topic in molecular evolution. The March Perspective, titled "Biogeographic Perspectives on Our Species' Genetic Diversification," written by Tábita Hünemeier, can be found in Molecular Biology and Evolution. The virtual issues include notable papers on Human Genetic Diversification and can be accessed on SMBE's 40th anniversary site. [Extracted from the article]

Copyright of Revista Electrónica de Enseñanza de las Ciencias is the property of Revista Electronica de Ensenanza de las Ciencias and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Medicago arabica (Linnaeus, 1762) Huds. is an important annual legume forage that grows in a wide range of climates, from subtropical to temperate. This study aimed to sequence the chloroplast genome of M. arabica and compare it with other legumes. In this study, we sequenced the entire chloroplast genome of M. arabica, which has 125,056 base pairs. The total GC content of the chloroplast genome of M. arabica was 34.4%. From the 110 unique genes of the circular genome, 30 tRNA genes, four rRNA genes, and 76 protein-coding genes were successfully annotated. A maximum likelihood (ML) tree was constructed using the model species and 17 species of the Medicago genus. M. arabica was shown to be phylogenetically closely related to M. polymorpha. The nucleotide diversity of the chloroplast genome may provide valuable molecular markers to study chloroplast, genetic breeding, and plant molecular evolution. These findings provide a solid foundation for future research on the molecular biology of the chloroplast. [ABSTRACT FROM AUTHOR]

Tomato (Lycopersicon esculentum Mill [ Solanum lycopersicum L.].) is an important food material and cash crop, as well as a model plant for genetic evolution and molecular biology research. However, as a cold-sensitive crop originating from the tropics, the growth and development of tomato is often affected by low temperature stress. Therefore, how processing tomatoes resist this type of stress has important theoretical and practical significance. In this study, the LeCOLD1 gene was cloned from processing tomato. Subcellular localization analysis showed that LeCOLD1 was located in the plasma membrane. Real-time quantitative PCR analysis showed that LeCOLD1 was highly expressed in roots. Drought, salt and low temperatures induced the expression of COLD1. Overexpression and RNA interference vectors of LeCOLD1 were constructed and were transformed into tomato by the Agrobacterium-mediated method, and then obtaining transgenic tomato plants. It was found that LeCOLD1 increased the height of processing tomato plants and increased the length of their roots. In addition, overexpression of LeCOLD1 significantly improved the cold resistance of the plants. Overexpressing LeCOLD1 in tomato plants reduced the damage to the cell membrane, accumulation of ROS and photoinhibition of PSII, and maintained the high activity of antioxidant enzymes and the content of osmotic regulators. Further analysis revealed that during low temperature stress, the cells maintained high levels of antioxidant enzyme activity by regulating the transcription of the genes encoding these enzymes. The results show that overexpressing LeCOLD1 in tomato increases the plants' resistance to low temperatures, and that reducing LeCOLD1 expression makes the plants more sensitive to low temperatures. • Overexpression of LeCOLD1 enhances the cold tolerance of transgenic tomato plants. • LeCOLD1 overexpression decreases membrane damage and the production of reactive oxygen species. • LeCOLD1 overexpression increases the levels of osmotic regulators and the activities of antioxidant enzymes. • Suppression of LeCOLD1 by RNAi decreases the cold tolerance of tomato plants. [ABSTRACT FROM AUTHOR]

This paper presents the survey of three algorithms to transform atomic-level molecular snapshots from molecular dynamics (MD) simulations into metadata representations that are suitable for in situ analytics based on machine learning methods. MD simulations studying the classical time evolution of a molecular system at atomic resolution are widely recognized in the fields of chemistry, material sciences, molecular biology and drug design; these simulations are one of the most common simulations on supercomputers. Next-generation supercomputers will have a dramatically higher performance than current systems, generating more data that needs to be analysed (e.g. in terms of number and length of MD trajectories). In the future, the coordination of data generation and analysis can no longer rely on manual, centralized analysis traditionally performed after the simulation is completed or on current data representations that have been defined for traditional visualization tools. Powerful data preparation phases (i.e. phases in which original row data is transformed to concise and still meaningful representations) will need to proceed data analysis phases. Here, we discuss three algorithms for transforming traditionally used molecular representations into concise and meaningful metadata representations. The transformations can be performed locally. The newmetadata can be fed into machine learningmethods for runtime in situ analysis of largerMDtrajectories supported by high-performance computing. In this paper, we provide an overview of the three algorithms and their use for three different applications: protein-ligand docking in drug design; protein folding simulations; and protein engineering based on analytics of protein functions depending on proteins' three-dimensional structures. [ABSTRACT FROM AUTHOR]

Background: Eukaryotic genes typically form independent evolutionary lineages through either speciation or gene duplication events. Generally, gene copies resulting from speciation events (orthologs) are expected to maintain similarity over time with regard to sequence, structure and function. After a duplication event, however, resulting gene copies (paralogs) may experience a broader set of possible fates, including partial (subfunctionalization) or complete loss of function, as well as gain of new function (neofunctionalization). This assumption, known as the Ortholog Conjecture, is prevalent throughout molecular biology and notably plays an important role in many functional annotation methods. Unfortunately, studies that explicitly compare evolutionary processes between speciation and duplication events are rare and conflicting. Methods: To provide an empirical assessment of ortholog/paralog evolution, we estimated ratios of nonsynonymous to synonymous substitutions (ω = dN/dS) for 251,044 lineages in 6,244 gene trees across 77 vertebrate taxa. Results: Overall, we found ω to be more similar between lineages descended from speciation events (p < 0.001) than lineages descended from duplication events, providing strong support for the Ortholog Conjecture. The asymmetry in ω following duplication events appears to be largely driven by an increase along one of the paralogous lineages, while the other remains similar to the parent. This trend is commonly associated with neofunctionalization, suggesting that gene duplication is a significant mechanism for generating novel gene functions. [ABSTRACT FROM AUTHOR]