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This document is a summary of a special issue of the journal "Genes" titled "Feature Papers in Population and Evolutionary Genetics and Genomics 2023." The special issue includes eight articles that cover a range of topics in population and evolutionary genetics. The articles explore subjects such as genetic diversity within human populations, the genetic impact of socioeconomic hardships, the effects of habitat loss on animal species, the genetic structure of marine species, the chromosomal characteristics of plant species, the accuracy of genotype imputation, and the population history of the Carpathian Basin. These studies contribute to our understanding of genetic diversity, evolutionary dynamics, and population structures, and highlight the importance of multidisciplinary approaches in genetic research. [Extracted from the article]

Background: Although, there is a wealth of information in the medical literature on the usefulness of genomic testing in assessing risk and its application in medical oncology decision making, there are no theoretical reflections in the nursing field. Aim: To understand the implications of molecular biology in nursing practice and highlight the role of Nursing Theory in guiding nurses' reasoning. Materials and Methods: Searching literature published between 2000 and 2022 in Medline and Google Scholar. Scientific evidence was analysed by the authors expert in different fields. Results: Based on the findings of the literature, concerns have been raised about the proper care of cancer patients who have a genomic risk profile determination. In particular, the absence of theoretical thinking and conceptual models that consider developments in molecular biology and their impact on nursing, in addition to the prevalence of heuristic thinking and the application of clinical patterns in nursing practice, could induce patient misjudgement with inadequate planning of preventive, curative, rehabilitative and educational nursing interventions. Nurses working in the field of oncology should be aware that the risk profile determined by genomics tests is merely the visible and stated portion of the cancer patient: the tip of iceberg. Discussion: This study demonstrates how genomic testing takes into account a fraction of genes discovered in tumour tissue to establish a risk profile. This subset differs, for example, from the social genome, which can determine the risk of dementia, cancer and cardiovascular disease, but in response to social adversity. Nursing theory, which views the environment as a metaparadigm, must consider a conceptual model that can integrate the findings of genomic testing with recommendations from studies on the social genome of humans to make it easier to build nursing treatments that can better reduce these risks. Conclusion: A nursing theoretical discourse on genomics is a paramount requirement for developing effective nursing care. [ABSTRACT FROM AUTHOR]

Despite significant advances in the diagnosis and treatment of cardiovascular diseases, recent calls have emphasized the unmet need to improve precision-based approaches in cardiovascular disease. Although some studies provide preliminary evidence of the diagnostic and prognostic potential of circulating coding and non-coding RNAs, the complex RNA biology and lack of standardization have hampered the translation of these markers into clinical practice. In this position paper of the CardioRNA COST action CA17129, we provide recommendations to standardize the RNA development process in order to catalyse efforts to investigate novel RNAs for clinical use. We list the unmet clinical needs in cardiovascular disease, such as the identification of high-risk patients with ischaemic heart disease or heart failure who require more intensive therapies. The advantages and pitfalls of the different sample types, including RNAs from plasma, extracellular vesicles, and whole blood, are discussed in the sample matrix, together with their respective analytical methods. The effect of patient demographics and highly prevalent comorbidities, such as metabolic disorders, on the expression of the candidate RNA is presented and should be reported in biomarker studies. We discuss the statistical and regulatory aspects to translate a candidate RNA from a research use only assay to an in-vitro diagnostic test for clinical use. Optimal planning of this development track is required, with input from the researcher, statistician, industry, and regulatory partners. [ABSTRACT FROM AUTHOR]

They describe the structure of the MRN Complex and its function in double-strand break (DSB) repair and analyze the different germline alterations of the MRN complex genes in autosomal recessive syndromes, as well as the association between heterozygous germline alterations in these genes and cancer predisposition. In the rapidly evolving landscape of molecular genetics and genomics, this Special Issue brings together a collection of insightful review articles that delve into the forefront of scientific exploration. The authors also propose a possible explanation of the discrepancies in the published results of the effects of the OXTR gene polymorphisms and methylation on different diseases [[2]]. [Extracted from the article]

Theodosius Dobzhansky famously wrote in 1973 that "nothing in biology makes sense except in the light of evolution" [[1]], laying the foundations for the Modern Synthesis that combined population genetics with evolutionary biology and bridged the gap between geneticists and naturalists. Population genetics study the genetic diversity and structure of populations and all the processes involved [[2]]. Today, population genetics theory is inarguably the theoretical backbone of the Modern Synthesis, and all this progress and the combination of population and evolutionary genetics and genomics have provided answers to biologically important questions in a wide range of areas of research. Finally, organelle genomes can also provide a better understanding of evolution, speciation, and population divergence, and mitochondrial DNA (mtDNA), with its intrinsic properties, is extremely valuable for evolutionary and population genetic studies. [Extracted from the article]

This article is an interview with Fay Cooper and Anestis Tsakiridis, who conducted a study on neuromesodermal progenitors (NMPs) and their role in the development of neural and mesodermal tissues. The study focused on the role of Notch signaling in NMP differentiation and Hox gene expression. The researchers found that Notch signaling plays a crucial role in the induction of pro-mesodermal and Hox genes in NMPs, as well as in determining cell fate decisions and positional identity acquisition. The study provides insights into the complex mechanisms involved in embryonic development. [Extracted from the article]

Background: Global estimates for cholera annually approximate 4 million cases worldwide with 95,000 deaths. Recent outbreaks, including Haiti and Yemen, are reminders that cholera is still a global health concern. Cholera outbreaks can rapidly induce high death tolls by overwhelming the capacity of health facilities, especially in remote areas or areas of civil unrest. Recent studies demonstrated that stool specimens preserved on filter paper facilitate molecular analysis of Vibrio cholerae in resource limited settings. Specimens preserved in a rapid, low-cost, safe and sustainable manner for sequencing provides previously unavailable data about circulating cholera strains. This may ultimately provide new information to shape public policy response on cholera control and elimination. Methodology/Principal findings: Whole genome sequencing (WGS) recovered close to a complete sequence of the V. cholerae O1 genome with satisfactory genome coverage from stool specimens enriched in alkaline peptone water (APW) and V. cholerae culture isolates, both spotted on filter paper. The minimum concentration of V. cholerae DNA sufficient to produce quality genomic information was 0.02 ng/μL. The genomic data confirmed the presence or absence of genes of epidemiological interest, including cholera toxin and pilus loci. WGS identified a variety of diarrheal pathogens from APW-enriched specimen spotted filter paper, highlighting the potential for this technique to explore the gut microbiome, potentially identifying co-infections, which may impact the severity of disease. WGS demonstrated that these specimens fit within the current global cholera phylogenetic tree, identifying the strains as the 7th pandemic El Tor. Conclusions: WGS results allowed for mapping of short reads from APW-enriched specimen and culture isolate spotted filter papers this provided valuable molecular epidemiological sequence information on V. cholerae strains from remote, low-resource settings. These results identified the presence of co-infecting pathogens while providing rare insight into the specific V. cholerae strains causing outbreaks in cholera-endemic areas. [ABSTRACT FROM AUTHOR]

Background Data papers have emerged as a powerful instrument for open data publishing, obtaining credit, and establishing priority for datasets generated in scientific experiments. Academic publishing improves data and metadata quality through peer review and increases the impact of datasets by enhancing their visibility, accessibility, and reusability. Objective We aimed to establish a new type of article structure and template for omics studies: the omics data paper. To improve data interoperability and further incentivize researchers to publish well-described datasets, we created a prototype workflow for streamlined import of genomics metadata from the European Nucleotide Archive directly into a data paper manuscript. Methods An omics data paper template was designed by defining key article sections that encourage the description of omics datasets and methodologies. A metadata import workflow, based on REpresentational State Transfer services and Xpath, was prototyped to extract information from the European Nucleotide Archive, ArrayExpress, and BioSamples databases. Findings The template and workflow for automatic import of standard-compliant metadata into an omics data paper manuscript provide a mechanism for enhancing existing metadata through publishing. Conclusion The omics data paper structure and workflow for import of genomics metadata will help to bring genomic and other omics datasets into the spotlight. Promoting enhanced metadata descriptions and enforcing manuscript peer review and data auditing of the underlying datasets brings additional quality to datasets. We hope that streamlined metadata reuse for scholarly publishing encourages authors to create enhanced metadata descriptions in the form of data papers to improve both the quality of their metadata and its findability and accessibility. [ABSTRACT FROM AUTHOR]

The Genetics Society of America is calling for submissions of papers on biobank-scale genomic data analyses. Biobanks, which are large collections of biological, medical, and genetic data on the same individuals, have revolutionized human genomics research. However, there is substantial heterogeneity between biobanks worldwide, creating both challenges and opportunities for data analysis. The series will focus on various topics, including population structures, selection bias, measurement errors, clinical observations, linkage with external data sources, meta-analysis, computational analysis methods, family-based analyses, ethical and privacy-related issues, and technological considerations. Manuscripts can be submitted until May 31, 2024, and the series will be an ongoing resource in this area. [Extracted from the article]

The coronavirus disease 2019 (COVID-19) pandemic has been as unprecedented as unexpected, affecting more than 105 million people worldwide as of 8 February 2020 and causing more than 2.3 million deaths according to the World Health Organization (WHO). Not only affecting the lungs but also provoking acute respiratory distress, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is able to infect multiple cell types including cardiac and vascular cells. Hence a significant proportion of infected patients develop cardiac events, such as arrhythmias and heart failure. Patients with cardiovascular comorbidities are at highest risk of cardiac death. To face the pandemic and limit its burden, health authorities have launched several fast-track calls for research projects aiming to develop rapid strategies to combat the disease, as well as longer-term projects to prepare for the future. Biomarkers have the possibility to aid in clinical decision-making and tailoring healthcare in order to improve patient quality of life. The biomarker potential of circulating RNAs has been recognized in several disease conditions, including cardiovascular disease. RNA biomarkers may be useful in the current COVID-19 situation. The discovery, validation, and marketing of novel biomarkers, including RNA biomarkers, require multi-centre studies by large and interdisciplinary collaborative networks, involving both the academia and the industry. Here, members of the EU-CardioRNA COST Action CA17129 summarize the current knowledge about the strain that COVID-19 places on the cardiovascular system and discuss how RNA biomarkers can aid to limit this burden. They present the benefits and challenges of the discovery of novel RNA biomarkers, the need for networking efforts, and the added value of artificial intelligence to achieve reliable advances. [ABSTRACT FROM AUTHOR]

In this cohort profile article we describe the lifetime major depressive disorder (MDD) database that has been established as part of the BIObanks Netherlands Internet Collaboration (BIONIC). Across the Netherlands we collected data on Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) lifetime MDD diagnosis in 132,850 Dutch individuals. Currently, N = 66,684 of these also have genomewide single nucleotide polymorphism (SNP) data. We initiated this project because the complex genetic basis of MDD requires large population-wide studies with uniform in-depth phenotyping. For standardized phenotyping we developed the LIDAS (LIfetime Depression Assessment Survey), which then was used to measure MDD in 11 Dutch cohorts. Data from these cohorts were combined with diagnostic interview depression data from 5 clinical cohorts to create a dataset of N = 29,650 lifetime MDD cases (22%) meeting DSM-5 criteria and 94,300 screened controls. In addition, genomewide genotype data from the cohorts were assembled into a genomewide association study (GWAS) dataset of N = 66,684 Dutch individuals (25.3% cases). Phenotype data include DSM-5 -based MDD diagnoses, sociodemographic variables, information on lifestyle and BMI, characteristics of depressive symptoms and episodes, and psychiatric diagnosis and treatment history. We describe the establishment and harmonization of the BIONIC phenotype and GWAS datasets and provide an overview of the available information and sample characteristics. Our next step is the GWAS of lifetime MDD in the Netherlands, with future plans including fine-grained genetic analyses of depression characteristics, international collaborations and multi-omics studies. [ABSTRACT FROM AUTHOR]

Paper mulberry (Broussonetia papyrifera) is a well-known woody tree historically used for Cai Lun papermaking, one of the four great inventions of ancient China. More recently, Paper mulberry has also been used as forage to address the shortage of feedstuff because of its digestible crude fiber and high protein contents. In this study, we obtained a chromosome-scale genome assembly for Paper mulberry using integrated approaches, including Illumina and PacBio sequencing platform as well as Hi-C, optical, and genetic maps. The assembled Paper mulberry genome consists of 386.83 Mb, which is close to the estimated size, and 99.25% (383.93 Mb) of the assembly was assigned to 13 pseudochromosomes. Comparative genomic analysis revealed the expansion and contraction in the flavonoid and lignin biosynthetic gene families, respectively, accounting for the enhanced flavonoid and decreased lignin biosynthesis in Paper mulberry. Moreover, the increased ratio of syringyl-lignin to guaiacyl-lignin in Paper mulberry underscores its suitability for use in medicine, forage, papermaking, and barkcloth making. We also identified the root-associated microbiota of Paper mulberry and found that Pseudomonas and Rhizobia were enriched in its roots and may provide the source of nitrogen for its stems and leaves via symbiotic nitrogen fixation. Collectively, these results suggest that Paper mulberry might have undergone adaptive evolution and recruited nitrogen-fixing microbes to promote growth by enhancing flavonoid production and altering lignin monomer composition. Our study provides significant insights into genetic basis of the usefulness of Paper mulberry in papermaking and barkcloth making, and as forage. These insights will facilitate further domestication and selection as well as industrial utilization of Paper mulberry worldwide. Analysis of the chromosome-scale genome (386.83 Mb) of paper mulberry revealed significant expansion and contraction in the flavonoid and lignin biosynthetic gene families, respectively, accounting for the enhanced flavonoid and decreased lignin biosynthesis in paper mulberry. Moreover, the increased ratio of syringyl-lignin to guaiacyl-lignin in paper mulberry underscores the genetic basis for its usefulness in medicine, forage, papermaking, and barkcloth making. [ABSTRACT FROM AUTHOR]

The incidence of pediatric drugs poses unique challenges due to the distinct corporal, pharmacokinetic, and pharmacodynamic characteristics of juveniles. Innovative methods are being developed to address these challenges and ensure the safety and efficacy of pediatric treatments. This paper investigates various approaches to improve pediatric drug handling, including the implementation of age-appropriate formulations, the use of advanced drug delivery systems, and the incorporation of real-world evidence and patient-centric models in clinical trials. Additionally, regulatory frameworks and procedures that support pediatric drug development are examined, emphasizing the roles of initiatives such as the Pediatric Research Equity Act (PREA) and the Best Pharmaceuticals for Children Act (BPCA) in the United States, as well as similar efforts in Europe and other regions. Emphasis is placed on collaborative efforts among key stakeholders: manufacturers, academia, regulatory bodies, and patient advocacy groups, to promote change and address unmet medical needs in pediatric populations. Furthermore, this paper discusses the potential of emerging technologies, particularly artificial intelligence and genomics, to transform pediatric drug development. By leveraging these innovative strategies, the pharmaceutical industry can enhance treatment outcomes for children and advance pediatric healthcare. [ABSTRACT FROM AUTHOR]

The paper mulberry is one of the multifunctional tree species in agroforestry systems and is also commonly utilized in traditional medicine in China and other Asian countries. However, little is known about its molecular genetics, which hinders research on and exploitation of this valuable resource. To discern the correlation between gene expression and the essential properties of the paper mulberry, we performed a transcriptomics analysis, assembling a total of 37,725 unigenes from 54,638,676 reads generated by RNA-seq. Among these, 22,692 unigenes showed greater than 60% similarity with genes from other species. The lengths of 13,566 annotated unigenes were longer than 1,000 bp. Functional clustering analysis with COG (Cluster of Orthologous Groups) revealed that 17,184 unigenes are primarily involved in transcription, translation, signal transduction, carbohydrate metabolism, secondary metabolism, and energy metabolism. GO (Gene Ontology) annotation suggests enrichment of genes encoding antioxidant activity, transporter activity, biosynthesis, metabolism and stress response, with a total of 30,659 unigenes falling in these categories. KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathway analysis showed that 7,199 unigenes are associated with 119 metabolic pathways. In addition to the basic metabolism, these genes are enriched for plant pathogen interaction, flavonoid metabolism and other secondary metabolic processes. Furthermore, differences in the transcriptomes of leaf, stem and root tissues were analyzed and 7,233 specifically expressed unigenes were identified. This global expression analysis provided novel insights about the molecular mechanisms of the biosynthesis of flavonoid, lignin and cellulose, as well as on the response to biotic and abiotic stresses including the remediation of contaminated soil by the paper mulberry. [ABSTRACT FROM AUTHOR]

Background In social groups, dominant individuals may socially inhibit reproduction of subordinates using aggressive interactions or, in the case of highly eusocial insects, pheromonal communication. It has been hypothesized these two modes of reproductive inhibition utilize conserved pathways. Here, we use a comparative framework to investigate the chemical and genomic underpinnings of reproductive dominance in the primitively eusocial wasp Polistes metricus. Our goals were to first characterize transcriptomic and chemical correlates of reproductive dominance and second, to test whether dominance-associated mechanisms in paper wasps overlapped with aggression or pheromone-related gene expression patterns in other species. To explore whether conserved molecular pathways relate to dominance, we compared wasp transcriptomic data to previous studies of gene expression associated with pheromonal communication and queen-worker differences in honey bees, and aggressive behavior in bees, Drosophila, and mice. Results By examining dominant and subordinate females from queen and worker castes in early and late season colonies, we found that cuticular hydrocarbon profiles and genome-wide patterns of brain gene expression were primarily associated with season/social environment rather than dominance status. In contrast, gene expression patterns in the ovaries were associated primarily with caste and ovary activation. Comparative analyses suggest genes identified as differentially expressed in wasp brains are not related to queen pheromonal communication or caste in bees, but were significantly more likely to be associated with aggression in other insects (bees, flies), and even a mammal (mice). Conclusions This study provides the first comprehensive chemical and molecular analysis of reproductive dominance in paper wasps. We found little evidence for a chemical basis for reproductive dominance in P. metricus, and our transcriptomic analyses suggest that different pathways regulate dominance in paper wasps and pheromone response in bees. Furthermore, there was a substantial impact of season/social environment on gene expression patterns, indicating the important role of external cues in shaping the molecular processes regulating behavior. Interestingly, genes associated with dominance in wasps were also associated with aggressive behavior in bees, solitary insects and mammals. Thus, genes involved in social regulation of reproduction in Polistes may have conserved functions associated with aggression in insects and other taxa. [ABSTRACT FROM AUTHOR]

Managing genetic disease using medically assisted reproductive technology is increasingly promoted as a feasible option, given revolutionary advances in genomics. Far less attention has been directed to the issue of whether there is equitable access to this option. Context and circumstance determine equitable access; however, reporting has drawn overwhelmingly from affluent Anglo-western populations in developed countries. The experiences of poorer, less educated subpopulations within affluent countries and populations in less developed countries are underreported. The ability of consumers to understand the opportunities and risks of medically assisted reproductive technology is likewise not well described in the literature despite significant technological complexity and evidence that genetic disease may be overrepresented within some disadvantaged population groups. Equity is achieved by identifying barriers and allocating appropriate resources to enable understanding and access. In the case of utilising medically assisted technology, social and power relationships, regulations, and the presumptions of authority figures and policymakers reduce equitable access. Physical or cultural marginalisation from mainstream health services may result in reduced access to genetic and prenatal testing, in-vitro fertilisation and genetic screening of embryos necessary for medically assisted reproduction. Cost and regulatory frameworks can likewise limit opportunities to engage with services. Moreover, the quality of the information provided to prospective users of the technology and how it is received governs understanding of prevention and inhibits adequately informed choice. Best practice care and adequately informed choice can only be achieved by conscientiously attending to these accessibility issues. Deep engagement with at-risk people and critical reflection on mainstream accepted standpoints is required. This paper outlines issues associated with engaging with medically assisted reproduction encountered by Aboriginal families living with Machado-Joseph Disease in some of the most remote areas of Australia. It is the right of these families to access such technologies regardless of where they live. Current barriers to access raise important questions for service providers with implications for practice as new technologies increasingly become part of standard medical care. [ABSTRACT FROM AUTHOR]

Fomitopsis betulina, as a macrofungus with both medicinal and dietary applications, is renowned for its rich content of bioactive substances. The recent advancements in research have significantly enhanced our understanding of its polysaccharides, cellulose-degrading enzymes, and wide range of secondary metabolites. This paper provides a comprehensive review of the artificial cultivation techniques and the chemical profiling of over 100 secondary metabolites identified in F. betulina, including terpenoids, phenols, and various other classes. These compounds exhibit notable pharmacological activities, such as anti-cancer, anti-inflammatory, antimicrobial, antiviral, and anti-malarial effects. Moreover, this review delves into the genomic analysis of F. betulina, focusing on the prediction and classification of terpene synthases, which play a crucial role in the biosynthesis of these bioactive compounds. This insight is instrumental for potentially facilitating future biochemical studies and pharmaceutical applications. Through this review, we aim to solidify the foundation for future in-depth studies and the development of new drugs derived from this promising natural resource. [ABSTRACT FROM AUTHOR]

Simple Summary: Wilms tumor is the most common pediatric primary renal malignancy globally but exhibits significant variations in epidemiological, clinical, and molecular aspects among different populations. Wilms tumor has been shown to occur at lower incidences, younger ages, and earlier stages of disease with higher incidences of favorable histology among Asians compared to Caucasians. Despite a worldwide convergence between the two main management approaches, it is not known if these are generalizable to all ethnic populations. This paper summarizes the current literature on the inter-ethnic variations in the clinical, pathological, and molecular characteristics of Wilms tumor. Wilms tumor is the commonest primary renal malignancy in children and demonstrates substantial inter-ethnic variation in clinical, pathological, and molecular characteristics. Wilms tumor occurs at a lower incidence and at a younger age in Asians compared to Caucasians and Africans. Asians also present at an earlier stage of disease, with a higher incidence of favorable histology tumors and a lower incidence of perilobar nephrogenic rests compared to Caucasians, while African children present with more advanced disease. Studies have implicated population differences in the incidence of WT1 mutations, loss of imprinting of the IGF2 locus, and loss of heterozygosity of 1p/16q, or 1q gain as possible bases for epidemiological differences in the disease profile of Wilms tumors in various ethnic groups. Yet, evidence to support these associations is confounded by differences in treatment protocols and inequalities in the availability of treatment resources and remains limited by the quality of population-based data, especially in resource-limited settings. [ABSTRACT FROM AUTHOR]

Oil palm is a versatile oil crop with numerous applications. Significant progress has been made in applying histological techniques in oil palm research in recent years. Whole genome sequencing of oil palm has been carried out to explain the function and structure of the order genome, facilitating the development of molecular markers and the construction of genetic maps, which are crucial for studying important traits and genetic resources in oil palm. Transcriptomics provides a powerful tool for studying various aspects of plant biology, including abiotic and biotic stresses, fatty acid composition and accumulation, and sexual reproduction, while proteomics and metabolomics provide opportunities to study lipid synthesis and stress responses, regulate fatty acid composition based on different gene and metabolite levels, elucidate the physiological mechanisms in response to abiotic stresses, and explain intriguing biological processes in oil palm. This paper summarizes the current status of oil palm research from a multi-omics perspective and hopes to provide a reference for further in-depth research on oil palm. [ABSTRACT FROM AUTHOR]

The current epoch in fisheries science has been driven by continual advances in laboratory techniques and increasingly sophisticated approaches to analysing datasets. We now have the scientific knowledge and tools to proactively identify obstacles to the sustainable management of marine resources. However, in addition to technological advances, there are predicted global environmental changes, each with inherent implications for fisheries. The 2023 symposium of the Fisheries Society of the British Isles called for "open and constructive knowledge exchange between scientists, stakeholders, managers and policymakers" (https://fsbi.org.uk/symposium-2023/), a nexus of collaborative groups best placed to identify issues and solutions. Arguably, the Centre of Environment, Aquaculture and Fisheries Science (Cefas) and their Scientific Advice for Fisheries Management (SAFM) Team sit at the centre of such a network. SAFM regularly engages with managers and stakeholders, undertakes scientific research, provides fisheries advice to the UK government, and are leading experts within the International Council for the Exploration of the Sea (ICES). As such, this paper is an opinion piece, linked to individual authors specialisms, that aims to highlight emerging issues affecting fisheries and suggest where research efforts could be focused that contribute to sustainable fisheries. [ABSTRACT FROM AUTHOR]

The clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein (Cas) system is a gene editing technology guided by RNA endonuclease. The CRISPR-Cas12a (also known as CRISPR-Cpf1) system is extensively utilized in genome editing research due to its accuracy and high efficiency. In this paper, we primarily focus on the application of CRISPR-Cpf1 technology in the construction of disease models and gene therapy. Firstly, the structure and mechanism of the CRISPR-Cas system are introduced. Secondly, the similarities and differences between CRISPR-Cpf1 and CRISPR-Cas9 technologies are compared. Thirdly, the main focus is on the application of the CRISPR-Cpf1 system in cell and animal genome editing. Finally, the challenges faced by CRISPR-Cpf1 technology and corresponding strategies are analyzed. Although CRISPR-Cpf1 technology has certain off-target effects, it can effectively and accurately edit cell and animal genomes, and has significant advantages in the preclinical research. [ABSTRACT FROM AUTHOR]

The number of genome assemblies has rapidly increased in recent history, with NCBI databases reaching over 41,000 eukaryotic genome assemblies across about 2,300 species. Increases in read length and improvements in assembly algorithms have led to increased contiguity and larger genome assemblies. While this number of assemblies is impressive, only about a third of these assemblies have corresponding genome size estimations for their respective species on publicly available databases. In this paper, genome assemblies are assessed regarding their total size compared to their respective publicly available genome size estimations. These deviations in size are assessed related to genome size, kingdom, sequencing platform, and standard assembly metrics, such as N50 and BUSCO values. A large proportion of assemblies deviate from their estimated genome size by more than 10%, with increasing deviations in size with increased genome size, suggesting nonprotein coding and structural DNA may be to blame. Modest differences in performance of sequencing platforms are noted as well. While standard metrics of genome assessment are more likely to indicate an assembly approaching the estimated genome size, much of the variation in this deviation in size is not explained with these raw metrics. A new, proportional N50 metric is proposed, in which N50 values are made relative to the average chromosome size of each species. This new metric has a stronger relationship with complete genome assemblies and, due to its proportional nature, allows for a more direct comparison across assemblies for genomes with variation in sizes and architectures. [ABSTRACT FROM AUTHOR]

Simple Summary: Immune checkpoint inhibitors have revolutionized cancer therapy and improved clinical outcomes. Immunotherapy is now increasingly combined with chemotherapy and other conventional treatments, such as radiation therapy, as part of the multimodal treatment of earlier-stage cancers. Although generally well tolerated and capable of inducing long-lasting responses, immunotherapy for thymic epithelial tumors can be challenging due to defects in immune self-tolerance, which increase the risk of immune-mediated toxicity. In order to improve the safety of immunotherapy and maximize clinical benefit in patients with thymic cancers, there is a pressing need to identify potential biomarkers of response and toxicity for this patient population. In this paper, we review the current role of immunotherapy for thymic cancers and discuss future applications across the spectrum of stage and histology of these diseases. Thymic epithelial tumors are a histologically diverse group of cancers arising from the epithelial compartment of the thymus. These tumors are characterized by a low tumor mutation burden, a lack of actionable genomic changes, and, especially with thymomas, defects in immune tolerance. Surgery is the mainstay of the management of resectable disease, whereas advanced, unresectable tumors are treated with platinum-based chemotherapy. Disease recurrence can occur months to years after frontline treatment. Although several options are available for conventional treatment of recurrent thymic tumors, response rates are generally low, and treatment-related toxicity can affect quality of life. A subset of patients benefit from biologic therapies, but there remains an unmet need for the development of new treatments. Immune checkpoint inhibitors are safe, clinically active, and have contributed to an improvement in survival for patients with a wide variety of cancers. However, the application of these revolutionary treatments for thymic cancers is limited to their use for the management of recurrent thymic carcinoma because of the risk of immune toxicity. In this paper, we review the current uses of immunotherapy for the management of thymic epithelial tumors and highlight potential strategies to improve safety and broaden the application of these treatments for patients with thymic cancers. [ABSTRACT FROM AUTHOR]

This paper problematizes the precision medicine approach embraced by the All of Us Research Program (US) and by Genomics England (UK) in terms of benefits distribution, by arguing that current "diversity and inclusion" efforts do not prevent exclusiveness, unless the framing and scope of the projects are revisited in public health terms. Grounded on document analysis and fieldwork interviews, this paper analyzes efforts to address potential patterns of exclusion upstream (from participating in precision medicine research) and downstream (from benefitting from precision medicine outputs). It argues that efforts for inclusion upstream are not corresponded downstream, and this unbalance jeopardizes the equitable capacities of the projects. It concludes that enhanced focus on socio-environmental determinants of health and aligned public health interventions as precision medicine outputs would be to the benefit of all and especially of those who are most at risk of (upstream as well as downstream) exclusion. [ABSTRACT FROM AUTHOR]

Simple Summary: Biliary tract malignancies, including cholangiocarcinoma (CCA) and gallbladder neoplasms, present intricate challenges in diagnosis and treatment. This comprehensive overview highlights the diversity of CCA subtypes, their genetic underpinnings, and the pivotal role of etiological factors. Despite diagnostic complexities, advancements in genomic sequencing reveal promising therapeutic targets, such as FGFR2 alterations and IDH1 mutations. Dr. James Cleary's insights underscore the potential of these targets in reshaping the treatment landscape. This paper provides insights into the conventional understanding of biliary tract malignancies and emphasizes the critical need for ongoing research to optimize outcomes in this challenging cancer subtype. By elucidating diverse FGFR2 alterations and the potential of IDH1 inhibition, the aim is to pave the way for targeted therapeutic interventions. As we delve deeper into understanding the intricate complexities of biliary tract malignancies, this research seeks to drive precision medicine forward, offering hope for improved treatment strategies and outcomes in the face of this formidable cancer. This paper provides insights into the conventional understanding of biliary tract malignancies, with a specific focus on cholangiocarcinoma (CCA). We then delve into the groundbreaking ideas presented by Dr. James Cleary. CCA, originating from biliary tree cells, manifests diverse subtypes contingent upon anatomical localization and differentiation status. These variants exhibit discrete genetic aberrations, yielding disparate clinical phenotypes and therapeutic modalities. Intrahepatic, perihilar, and distal CCAs intricately involve distinct segments of the biliary tree, further categorized as well-differentiated, moderately differentiated, or poorly differentiated adenocarcinomas based on their histological differentiation. Understanding the etiological factors contributing to CCA development assumes paramount importance. Stratifying these factors into two groups, those unrelated to fluke infestations (e.g., viral hepatitis and fatty liver conditions) and those associated with fluke infestations (e.g., chronic liver inflammation), facilitates predictive modeling. The epidemiology of CCA exhibits global variability, with Southeast Asia notably displaying higher incidences attributed primarily to liver fluke infestations. Jaundice resulting from bile duct obstruction constitutes a prevalent clinical manifestation of CCA, alongside symptoms like malaise, weight loss, and abdominal pain. Diagnostic challenges arise due to the symptomatic overlap with other biliary disorders. Employing comprehensive liver function tests and imaging modalities such as computed tomography assumes a pivotal role in ensuring accurate diagnosis and staging. However, the definitive confirmation of CCA necessitates a biopsy. Treatment modalities, predominantly encompassing surgical resection and radiation therapy, hold curative potential, although a considerable subset of patients is deemed unresectable upon exploration. Challenges intensify, particularly in cases classified as cancer of unknown origin, underscoring the imperative for early intervention. Advancements in genomic sequencing have revolutionized precision medicine in CCA. Distinct genomic markers, including fibroblast growth factor receptor 2 (FGFR2) alterations and isocitrate dehydrogenase 1 (IDH1) mutations, have emerged as promising therapeutic targets. FGFR2 alterations, encompassing mutations and rearrangements, play pivotal roles in oncogenesis, with FGFR inhibitors demonstrating promise despite identified resistance mechanisms. Similarly, IDH1 inhibitors face challenges with resistance, despite encouraging early clinical trial results, prompting exploration of novel irreversible inhibitors. Dr. James Cleary's illuminating discourse underscores the significance of diverse FGFR2 alterations and the potential of IDH1 inhibition in reshaping the treatment landscape for CCA. These findings unveil critical avenues for targeted therapeutic interventions, emphasizing the critical need for ongoing research to optimize outcomes in this challenging cancer subtype, incorporating innovative insights from Dr. Cleary. [ABSTRACT FROM AUTHOR]

Simple Summary: This paper delves into the latest developments in the emerging therapies for cholangiocarcinoma, with a focus on precision medicine, immunotherapy, and targeted therapies. We explore the potential of genomic profiling to tailor treatments to individual patients, as well as the promising results of immunotherapeutic agents in clinical trials. Furthermore, we examine the role of specific molecular targets and their inhibitors in slowing disease progression. The findings discussed in this paper offer hope for improved outcomes and prolonged survival in cholangiocarcinoma patients using more effective and personalized treatment strategies. Cholangiocarcinoma is a heterogeneous group of biliary tract cancers that has a poor prognosis and globally increasing incidence and mortality. While surgical resection remains the only curative option for the treatment of cholangiocarcinoma, the majority of cancers are unresectable at the time of diagnosis. Additionally, the prognosis of cholangiocarcinoma remains poor even with the current first-line systemic therapy regimens, highlighting the difficulty of treating locally advanced, metastatic, or unresectable cholangiocarcinoma. Through recent developments, targetable oncogenic driver mutations have been identified in the pathogenesis of cholangiocarcinoma, leading to the utilization of molecular targeted therapeutics. In this review, we comprehensively discuss the latest molecular therapeutics for the treatment of cholangiocarcinoma, including emerging immunotherapies, highlighting promising developments and strategies. [ABSTRACT FROM AUTHOR]

Endocrine disrupting compounds (EDCs) are chemicals that negatively impact endocrine system function, with effluent from paper mills one example of this class of chemicals. In Florida, female Eastern mosquitofish (Gambusia holbrooki) have been observed with male secondary sexual characteristics at three paper mill-impacted sites, indicative of EDC exposure, and are still found at one site on the Fenholloway River. The potential impacts that paper mill effluent exposure has on the G. holbrooki endocrine system and the stream ecosystem are unknown. The objective of this study was to use gene expression analysis to determine if exposure to an androgen receptor agonist was occurring and to couple this analysis with in vitro assays to evaluate the presence of androgen and progesterone receptor active chemicals in the Fenholloway River. Focused gene expression analyses of masculinized G. holbrooki from downstream of the Fenholloway River paper mill were indicative of androgen exposure, while genes related to reproduction indicated potential progesterone exposure. Hepatic microarray analysis revealed an increase in the expression of metabolic genes in Fenholloway River fish, with similarities in genes and biological processes compared to G. holbrooki exposed to androgens. Water samples collected downstream of the paper mill and at a reference site indicated that progesterone and androgen receptor active chemicals were present at both sites, which corroborates previous chemical analyses. Results indicate that G. holbrooki downstream of the Fenholloway River paper mill are impacted by a mixture of both androgens and progesterones. This research provides data on the mechanisms of how paper mill effluents in Florida are acting as endocrine disruptors. [ABSTRACT FROM AUTHOR]

Ischemic heart disease remains the leading cause of death worldwide. Ischemic pre-, post-, and remote conditionings trigger endogenous cardioprotection that renders the heart resistant to ischemic-reperfusion injury (IRI). Mimicking endogenous cardioprotection by modulating genes involved in cardioprotective signal transduction provides an opportunity to reproduce endogenous cardioprotection with better possibilities of translation into the clinical setting. Genes and signaling pathways by which conditioning maneuvers exert their effects on the heart are partially understood. This is due to the targeted approach that allowed identifying one or a few genes associated with IRI and cardioprotection. Genes critical for signaling pathways in cardioprotection include protectomiRs (e.g., microRNA 125b*), ZAC1 transcription factor, pro-inflammatory genes such as cycloxygenase (COX)-2 and inducible nitric oxide synthase (iNOS), antioxidant enzymes such as hemoxygenase (HO)-1, extracellular and manganese superoxidase dismutases (ec-SOD and Mg-SOD), heat shock proteins (HSPs), growth factors such as insulin like growth factor (IGF)-1 and hepatocyte growth factor (HGF), antiapoptotic proteins such as Bcl-2 and Bcl-xL, pro-apoptotic proteins such as FasL, Bcl-2, Bax, caspase-3 and p53, and proangiogenic genes such as TGFbeta, sphingosine kinase 1 (SPK1), and PI3K-Akt. By identifying the gene expression profiles of IRI and ischemic conditioning, one may reveal potential gene targets responsible for cardioprotection. In this manuscript, we review the current state of the art of gene therapy in cardioprotection and propose that gene expression analysis facilitates the identification of individual genes associated with cardioprotection. We discuss signaling pathways associated with cardioprotection that can be targeted by gene therapy to achieve cardioprotection. [ABSTRACT FROM AUTHOR]

Given the critical role of human papillomavirus (HPV) in the cause of cervical cancer and other malignancies, there is a need for innovative approaches to preventing this infection. It has been shown that immunoinformatics is an important strategy in computational vaccinology. It is used to design new multi-epitope vaccines against different types of HPV and subsequent cervical cancer. This paper reviews the scope of the entire computational pipeline of HPV vaccine design, starting from data analysis at the genomic and proteomic levels and continuing to epitope predictions of the innate and adaptive immune systems. The search strategy was based on investigating original articles published in “Google Scholar" and “PubMed" from 2015 to 2023-2024. The terms "Immunoinformatics", "Bioinformatics", "Human papillomavirus (HPV)", "Vaccine design", "In silico vaccine design", "Multi-epitope vaccine design", "Vaccinology" and "HPV vaccine" were used to for this purpose. We discussed various essential tools involved in the computational design of the vaccine process, e.g., sequence analysis, epitope prediction, conservancy analysis, tertiary structure modeling, refinement, molecular docking, molecular dynamics (MD) simulation, and in silico cloning. This review article describes immunoinformatics methods that facilitate the design of a multi-epitope vaccine against HPV. However, this pipeline can also be used to design novel chimeric vaccines for other pathogens. [ABSTRACT FROM AUTHOR]

The aim of this paper is to present methods for estimating inbreeding and inbreeding effects using genome data and to give an overview of previous results in dairy cattle populations. Arrays with 50,000 single nucleotide polymorphisms (SNPs) evenly distributed across the genome are predominantly used in cattle population studies. The genome-based methods make it possible to localize the clusters and size of the homozygous segments ("runs of homozygosity", ROH) created by inbreeding on the genome, which enables further analyses of the genomic inbreeding coefficient (FROH), the mapping of inbreeding effects, the allele effects in the ROH and the development of the ROH in ancestral generations. Another way to calculate genomic inbreeding coefficients is to use the individual SNPs. This method can lead to an overestimation of genomic inbreeding and inbreeding depression, as homozygous SNP genotypes are not necessarily identical-by-descent. If the ROH clusters and their detrimental effects on the breeding traits in a cattle population are known, then the expected distribution of ROH and their expected effects on performance depression can be predicted for each animal and its progeny. Most studies on genomic inbreeding have been performed in Holstein populations. A 1% increase in FROH was associated with an inbreeding depression in 305-day milk yield of 20 - 61 kg milk, while fat and protein yield showed an inbreeding depression of 1.3 - 1.7 kg and 1.2 - 2.5 kg, respectively. In phenotypic standard deviations of the traits, this corresponds to a decrease of 2.393%, 2.306% and 3.021%. The fertility traits experienced less inbreeding depression with 0.825% of the phenotypic standard deviation in comparison to milk performance. Disease incidences showed inbreeding depression with a 1% increase in FROH by 2.530% of the phenotypic standard deviation. The different lengths of the ROH segments showed very different trends for inbreeding depression depending on the traits and the respective population. The identified ROH regions with significant inbreeding depression were distributed across different chromosomal clusters and the effects varied greatly in size. A concentration on a few chromosomes or clusters was not found for any trait. Only a small number of loci in ROH exhibited pleiotropic effects on inbreeding depression. With the introduction of genomic selection, a faster fixation of loci and higher inbreeding increase occurs. Therefore, efficient inbreeding management is necessary for cattle populations. This can be improved by denser SNP sets. [ABSTRACT FROM AUTHOR]

Objective: This narrative review illuminates on the application of single‐cell RNA sequencing (scRNA‐seq) and spatial transcriptomics (ST) in periodontitis and highlights the probability of relating cell population and gene signatures to the pathogenesis of the disease for a better diagnosis. Methods: An electronic search of the literature in the PubMed database for the keywords, "single cell sequencing" OR "spatial transcriptomics" and "periodontitis" OR "gingiva" OR "oral mucosa" yielded 486 research articles and reviews. After filtering duplicates and careful curation, 22 papers conducted in humans were retained. Results: The molecular mechanisms underlying periodontitis are complex and involve the interaction of multiple cells and various gene expressions. Most residing cells in periodontal tissues participate in maintaining homeostasis and health, while in addition to infiltrating immune cells contribute to the fight against the bacterial insult. Conclusion: scRNA‐seq and ST have provided new insights into the cellular and molecular changes associated with periodontitis for a better diagnosis and clinical outcome. New functions of cells and genes are revealed with these techniques; however, no cells or gene signatures are attributed to periodontitis so far. [ABSTRACT FROM AUTHOR]

Simple Summary: Cancer arises through the accumulation of somatic mutations in key biological pathways. This paper aims to develop a probabilistic approach to delineate the temporal order of mutations during cancer development based on mutation profile data from a cohort of patients. A unique feature of our method is that it incorporates intra-tumor heterogeneity (ITH) information, which refers to the heterogeneous cell populations within a tumor and characterizes the evolutionary history of the tumor. We showed that by integrating ITH, pathways, and functional annotation information, our method yielded high accuracy in inferring the temporal order of pathway mutations during carcinogenesis. The development of cancer involves the accumulation of somatic mutations in several essential biological pathways. Delineating the temporal order of pathway mutations during tumorigenesis is crucial for comprehending the biological mechanisms underlying cancer development and identifying potential targets for therapeutic intervention. Several computational and statistical methods have been introduced for estimating the order of somatic mutations based on mutation profile data from a cohort of patients. However, one major issue of current methods is that they do not take into account intra-tumor heterogeneity (ITH), which limits their ability to accurately discern the order of pathway mutations. To address this problem, we propose PATOPAI, a probabilistic approach to estimate the temporal order of mutations at the pathway level by incorporating ITH information as well as pathway and functional annotation information of mutations. PATOPAI uses a maximum likelihood approach to estimate the probability of pathway mutational events occurring in a specific sequence, wherein it focuses on the orders that are consistent with the phylogenetic structure of the tumors. Applications to whole exome sequencing data from The Cancer Genome Atlas (TCGA) illustrate our method's ability to recover the temporal order of pathway mutations in several cancer types. [ABSTRACT FROM AUTHOR]

Simple Summary: Cancer remains one of the leading causes of death worldwide, which emphasizes the need for its early and accurate diagnosis and prognosis. Our review explores AI's potential in this field, analyzing 89 recent studies from 2020 through 2023. Specifically, these studies included AI applications for the analysis of multi-omics data: radiomics, pathomics, clinical records, and lab data. Notably, eight studies combined diverse omics data types (genomics, transcriptomics, epigenomics, and proteomics). Integration of AI for the analysis of clinical and omics data contributes to a significant advancement and is essential for safe clinical implementation. Cancer is one of the leading causes of death, making timely diagnosis and prognosis very important. Utilization of AI (artificial intelligence) enables providers to organize and process patient data in a way that can lead to better overall outcomes. This review paper aims to look at the varying uses of AI for diagnosis and prognosis and clinical utility. PubMed and EBSCO databases were utilized for finding publications from 1 January 2020 to 22 December 2023. Articles were collected using key search terms such as "artificial intelligence" and "machine learning." Included in the collection were studies of the application of AI in determining cancer diagnosis and prognosis using multi-omics data, radiomics, pathomics, and clinical and laboratory data. The resulting 89 studies were categorized into eight sections based on the type of data utilized and then further subdivided into two subsections focusing on cancer diagnosis and prognosis, respectively. Eight studies integrated more than one form of omics, namely genomics, transcriptomics, epigenomics, and proteomics. Incorporating AI into cancer diagnosis and prognosis alongside omics and clinical data represents a significant advancement. Given the considerable potential of AI in this domain, ongoing prospective studies are essential to enhance algorithm interpretability and to ensure safe clinical integration. [ABSTRACT FROM AUTHOR]

A crucial stage in eukaryote gene expression involves mRNA splicing by a protein assembly known as the spliceosome. This step significantly contributes to generating and properly operating the ultimate gene product. Since non-coding introns disrupt eukaryotic genes, splicing entails the elimination of introns and joining exons to create a functional mRNA molecule. Nevertheless, accurately finding splice sequence sites using various molecular biology techniques and other biological approaches is complex and time-consuming. This paper presents a precise and reliable computer-aided diagnosis (CAD) technique for the rapid and correct identification of splice site sequences. The proposed deep learning-based framework uses long short-term memory (LSTM) to extract distinct patterns from RNA sequences, enabling rapid and accurate point mutation sequence mapping. The proposed network employs one-hot encodings to find sequential patterns that effectively identify splicing sites. A thorough ablation study of traditional machine learning, one-dimensional convolutional neural networks (1D-CNNs), and recurrent neural networks (RNNs) models was conducted. The proposed LSTM network outperformed existing state-of-the-art approaches, improving accuracy by 3% and 2% for the acceptor and donor sites datasets. [ABSTRACT FROM AUTHOR]

Plant genomics plays a pivotal role in enhancing global food security and sustainability by offering innovative solutions for improving crop yield, disease resistance, and stress tolerance. As the number of sequenced genomes grows and the accuracy and contiguity of genome assemblies improve, structural annotation of plant genomes continues to be a significant challenge due to their large size, polyploidy, and rich repeat content. In this paper, we present an overview of the current landscape in crop genomics research, highlighting the diversity of genomic characteristics across various crop species. We also assessed the accuracy of popular gene prediction tools in identifying genes within crop genomes and examined the factors that impact their performance. Our findings highlight the strengths and limitations of BRAKER2 and Helixer as leading structural genome annotation tools and underscore the impact of genome complexity, fragmentation, and repeat content on their performance. Furthermore, we evaluated the suitability of the predicted proteins as a reliable search space in proteomics studies using mass spectrometry data. Our results provide valuable insights for future efforts to refine and advance the field of structural genome annotation. [ABSTRACT FROM AUTHOR]

This paper reports the results of gamma irradiation experiments and whole genome sequencing (WGS) performed on vegetative cells of two radiation resistant bacterial strains, Metabacillus halosaccharovorans (VITHBRA001) and Bacillus paralicheniformis (VITHBRA024) (D10 values 2.32 kGy and 1.42 kGy, respectively), inhabiting the top-ranking high background radiation area (HBRA) of Chavara-Neendakara placer deposit (Kerala, India). The present investigation has been carried out in the context that information on strategies of bacteria having mid-range resistance for gamma radiation is inadequate. WGS, annotation, COG and KEGG analyses and manual curation of genes helped us address the possible pathways involved in the major domains of radiation resistance, involving recombination repair, base excision repair, nucleotide excision repair and mismatch repair, and the antioxidant genes, which the candidate could activate to survive under ionizing radiation. Additionally, with the help of these data, we could compare the candidate strains with that of the extremely radiation resistant model bacterium Deinococccus radiodurans, so as to find the commonalities existing in their strategies of resistance on the one hand, and also the rationale behind the difference in D10, on the other. Genomic analysis of VITHBRA001 and VITHBRA024 has further helped us ascertain the difference in capability of radiation resistance between the two strains. Significantly, the genes such as uvsE (NER), frnE (protein protection), ppk1 and ppx (non-enzymatic metabolite production) and those for carotenoid biosynthesis, are endogenous to VITHBRA001, but absent in VITHBRA024, which could explain the former's better radiation resistance. Further, this is the first-time study performed on any bacterial population inhabiting an HBRA. This study also brings forward the two species whose radiation resistance has not been reported thus far, and add to the knowledge on radiation resistant capabilities of the phylum Firmicutes which are abundantly observed in extreme environment. [ABSTRACT FROM AUTHOR]

Homoploid hybrid speciation is challenging to document because hybridization can lead to outcomes other than speciation. Thus, some authors have argued that establishment of homoploid hybrid speciation should include evidence that reproductive barriers isolating the hybrid neo‐species from its parental species were derived from hybridization. While this criterion is difficult to satisfy, several recent papers have successfully employed a common pipeline to identify candidate genes underlying such barriers and (in one case) to validate their function. We describe this pipeline, its application to several plant and animal species and what we have learned about homoploid hybrid speciation as a consequence. We argue that – given the ubiquity of admixture and the polygenic basis of reproductive isolation – homoploid hybrid speciation could be much more common and more protracted than suggested by earlier conceptual arguments and theoretical studies. [ABSTRACT FROM AUTHOR]

Phylogenetic Trees are critical in human genome research for investigating human evolution and identifying disease-associated genetic markers. New high-throughput genome sequencing technologies raise an urgent need to develop statistical methods that can construct phylogenetic trees from long genome sequences with quick computation speeds, while considering various biological complexities. Though an ancestral mixture model has been proposed [Chen SC, Lindsay BG. Building mixture trees from binary sequence data. Biometrika. 2006;93(4):843–860. doi: 10.1093/biomet/93.4.843] to this end by allowing genetic mutations over generations, another essential evolution factor, genetic recombination, is missed. Therefore, in this paper, we develop a novel genetic recombination model for tree construction and propose to use Markov chain composite likelihood (MCCL) to make model estimation computationally feasible. To further reduce computation complexity, a hierarchical estimator is constructed to estimate unknown ancestral distributions through MCCL. Simulation studies and real data example show that our proposed methods perform well and fast, so have the potential for implementation in long sequence genome data. [ABSTRACT FROM AUTHOR]

Introduction/Objective. Ayocote bean (Phaseolus coccineus) has potential as a source of resistance in breeding programs because it exhibits greater tolerance to plant pathogens than P. vulgaris. However, its sanitary characterization is insipient; therefore, the purpose of this work was to carry out an etiological-epidemiological diagnosis, with emphasis on presumptive symptoms of viral and phytoplasmic organisms, and a typical fungal signs of powdery mildew. Materials and Methods: A plot (50 x 62 m) of flowering Ayocote bean was selected. It was divided into 80 (8 x 10) quadrats (6 x 6 m) and 720 subquadrats (2 x 2 m). From 25 plants with powdery-mildew-type leaf symptoms, mycelium was collected with adhesive tape for light microscopy observation and taxonomic identification. Length-width measurements were made on 60 conidia. Pure mycelium collected in situ and ex situ from 1-5 leaflets/plant was used for genomic analysis by PCR with universal primers ITS1 and ITS4. Samples were sequenced in Macrogen Inc. Korea. A total of 63 plants and 121 trifoliate leaves with viral and phytoplasmic symptoms were collected by direct sampling. In 88/121 samples, genomic analysis was performed by PCR with universal primers for Potyvirus (1), Begomovirus (2), and Phytoplasmas (1). Sequence editing and analysis were performed in SeqAssem and BLASTn/GenBank. Phylogenetic constructions were developed in Mega 11 with MUSCLE, Maximum Likelihood (ML), and HKY substitution model (1000-Bootstrap). Putative powdery mildew severity (%), flower damage (%), Macrodactylus sp. adult density, and plant vigor (%) were evaluated in 80 quadrats (3subquadrats/quadrat) with App-Monitor®v1.1 configured with a 5-class scale. In GoldenSurfer® v10, Kriging geostatistical analysis was performed to determine the spatial interrelationship between these variables. Results: Erysiphe vignae was identified as associated with powdery mildew of P. coccineus. The fungus, with hyaline, ovoid to ellipsoid conidia measuring 31.74 ± 0.3419 µm x 15.11 ± 0.1579 µm, without the presence of fibrosin bodies, had 100% genomic homology. This is the first report in Mexico. With average July-August temperature and relative humidity of 16.3 °C (±5.8) and 92.8 % (±10.7), respectively, powdery mildew leaf incidence and severity were 65.3 and 22.7 % (±16.9, range: 0 - 66.5 %), respectively. The most inductive focus (60-80 % severity) had an aggregate e 4-quadrat pattern (96 m2, lag = 4 and s2-s = 450). Inoculum dispersal was significantly associated with dominant North-South winds and plant vigor (lag = 4 and s2-s = 470). Flower damage was inconclusive in its spatial association with powdery mildew and Macrodactylus sp. suggesting uncorrelated events. No Potyvirus, Begomovirus, or Phytoplasmas were detected associated with yellowing, leaf distortion, mosaic, internode shortening, and other symptoms observed in situ. This confirms the relative tolerance/resistance reported for P. coccineus. Conclusion: E. vignae (Erysiphales: Erysiphaceae) associated with P. coccineus is reported for the first time in Mexico with moderate to intense epidemic level, which indicates its susceptible condition to this fungus. However, negative results for Potyvirus, Begomovirus, and Phytoplasmas, validate the apparent tolerance/resistance of P. coccineus to these organisms. [ABSTRACT FROM AUTHOR]

The landscape of scientific publishing is experiencing a transformative shift toward open access, a paradigm that mandates the availability of research outputs such as data, code, materials, and publications. Open access provides increased reproducibility and allows for reuse of these resources. This article provides guidance for best publishing practices of scientific research, data, and associated resources, including code, in The American Phytopathological Society journals. Key areas such as diagnostic assays, experimental design, data sharing, and code deposition are explored in detail. This guidance aligns with that observed by other leading journals. We hope the information assembled in this paper will raise awareness of best practices and enable greater appraisal of the true effects of biological phenomena in plant pathology. [ABSTRACT FROM AUTHOR]

In this study, four novel bacterial strains, USB13T, AW1T, GTP1T, and HM2T, were isolated from various environments in Busan and Jeju Island, Republic of Korea. The 16S rRNA sequencing results indicated that the four novel strains belong to the genus Ramlibacter. All four strains were tested for their potential cellulolytic properties, where strain USB13T was identified as the only novel bacterium and the first within its genus to show cellulolytic activity. When tested, the highest activities of endoglucanase, exoglucanase, β-glucosidase, and filter paper cellulase (FPCase) were 1.91 IU/mL, 1.77 IU/mL, 0.76 IU/mL, and 1.12 IU/mL, respectively at pH 6.0. Comparisons of draft whole genome sequences (WGS) were also made using average nucleotide identity, digital DNA-DNA hybridization values, and average amino acid identity values, while whole genome comparison was visualized using the BLAST Ring Image Generator. The G + C contents of the strains ranged from 67.9 to 69.9%, while genome sizes ranged from 4.31 to 6.15 Mbp. Based on polyphasic evidence, the novel strains represent four new species within the genus Ramlibacter, for which the names Ramlibacter cellulosilyticus sp. nov. (type strain, USB13T = KACC 21656T = NBRC 114839T) Ramlibacter aurantiacus sp. nov. (type strain, AW1T = KACC 21544T = NBRC 114862T), Ramlibacter albus sp. nov. (type strain, GTP1T = KACC 21702T = NBRC 114488T), and Ramlibacter pallidus sp. nov. (type strain, HM2T = KCTC 82557T = NBRC 114489T) are proposed. [ABSTRACT FROM AUTHOR]

Through their personal experience of having intrahepatic cholestasis of pregnancy (ICP), this paper covers the development of current understanding of ICP. It summarises how research and clinical practice was developed through clinicians and followed by the inception of an ICP research group in the 1990s. This group's work has led to a better understanding of the mechanisms behind ICP, the risk threshold for stillbirth, and a genomic understanding of the condition. It focuses on how collaborative work between the author and researchers led to the formation of a charity for ICP. Despite this, some obstetric healthcare professionals continue to provide misinformation about ICP to women and birthing people. Furthermore, the views of those affected by ICP, together with the research they present to clinicians, are being ignored. It highlights a need for those managing ICP to listen to their patients and to pay closer attention to the research being published. [ABSTRACT FROM AUTHOR]

The second ISCB-Asia conference of the International Society for Computational Biology took place December 17-19, 2012, in Shenzhen, China. The conference was co-hosted by BGI as the first Shenzhen Conference on Computational Genomics (SCCG). 45 talks were presented at ISCB-Asia/SCCG 2012. The topics covered included software tools, reproducible computing, next-generation sequencing data analysis, transcription and mRNA regulation, protein structure and function, cancer genomics and personalized medicine. Nine of the proceedings track talks are included as full papers in this supplement. In this report we first give a short overview of the conference by listing some statistics and visualizing the talk abstracts as word clouds. Then we group the talks by topic and briefly summarize each one, providing references to related publications whenever possible. Finally, we close with a few comments on the success of this conference [ABSTRACT FROM AUTHOR]

Objectives: The aim of this data paper is to describe a collection of 33 genomic, transcriptomic and epigenomic sequencing datasets of the B-cell acute lymphoblastic leukemia (ALL) cell line REH. REH is one of the most frequently used cell lines for functional studies of pediatric ALL, and these data provide a multi-faceted characterization of its molecular features. The datasets described herein, generated with short- and long-read sequencing technologies, can both provide insights into the complex aberrant karyotype of REH, and be used as reference datasets for sequencing data quality assessment or for methods development. Data description: This paper describes 33 datasets corresponding to 867 gigabases of raw sequencing data generated from the REH cell line. These datasets include five different approaches for whole genome sequencing (WGS) on four sequencing platforms, two RNA sequencing (RNA-seq) techniques on two different sequencing platforms, DNA methylation sequencing, and single-cell ATAC-sequencing. [ABSTRACT FROM AUTHOR]

Simple Summary: Cancer in all its forms of expression is a major cause of death. The bladder cancer is also causes the same. finding the biomarkers responsible for the cancer is a challenging task and in certain cases, such as disease progression and therapy response, it become more challenging. The advancements in technology provides latest machine learning methods that help to identify the genomic biomarkers computationally. In this paper, the genomic biomarkers are tracked for bladder cancer from Univeristy of Calgary cohort and different bioinformatics methods, such as differential gene expression, survival rate estimation, consensus gene selection approaches were optimally used. The elastic-net based regression method has been utilized as a machine learning method which shows satisfactory results. Cancer in all its forms of expression is a major cause of death. To identify the genomic reason behind cancer, discovery of biomarkers is needed. In this paper, genomic data of bladder cancer are examined for the purpose of biomarker discovery. Genomic biomarkers are indicators stemming from the study of the genome, either at a very low level based on the genome sequence itself, or more abstractly such as measuring the level of gene expression for different disease groups. The latter method is pivotal for this work, since the available datasets consist of RNA sequencing data, transformed to gene expression levels, as well as data on a multitude of clinical indicators. Based on this, various methods are utilized such as statistical modeling via logistic regression and regularization techniques (elastic-net), clustering, survival analysis through Kaplan–Meier curves, and heatmaps for the experiments leading to biomarker discovery. The experiments have led to the discovery of two gene signatures capable of predicting therapy response and disease progression with considerable accuracy for bladder cancer patients which correlates well with clinical indicators such as Therapy Response and T-Stage at surgery with Disease Progression in a time-to-event manner. [ABSTRACT FROM AUTHOR]

Simple Summary: Poultry meat is an affordable, lean source of animal protein. Where does it come from? Broilers (meat chickens) or turkeys raised on farms stem from core breeding families, which are crossed to generate commercial hybrids. It takes around four years for the birds from the core families to the birds on the farms. Over time, poultry breeding has developed from primarily looking at production (e.g., live weight and egg production) to balanced, holistic breeding, including a wide range of attributes (e.g., gait, leg health, robustness and cardiovascular health). All birds in the core breeding families are carefully measured for over forty items covering bird health and welfare, robustness, environmental impact, reproduction and production. Modern poultry breeding aims for the holistic improvement of all the traits included in a broad and balanced breeding goal. New and improved selection techniques and analytical tools are continuously developed to allow increases in the accuracy of selection's long-term progress. There are different broiler and turkey genotypes for different market requirements, and commercial portfolios will continue evolving with future markets and customer preferences. This paper provides a comprehensive overview of the history of commercial poultry breeding, from domestication to the development of science and commercial breeding structures. The development of breeding goals over time, from mainly focusing on production to broad goals, including bird welfare and health, robustness, environmental impact, biological efficiency and reproduction, is detailed. The paper outlines current breeding goals, including traits (e.g., on foot and leg health, contact dermatitis, gait, cardiovascular health, robustness and livability), recording techniques, their genetic basis and how trait these antagonisms, for example, between welfare and production, are managed. Novel areas like genomic selection and gut health research and their current and potential impact on breeding are highlighted. The environmental impact differences of various genotypes are explained. A future outlook shows that balanced, holistic breeding will continue to enable affordable lean animal protein to feed the world, with a focus on the welfare of the birds and a diversity of choice for the various preferences and cultures across the world. [ABSTRACT FROM AUTHOR]

This study analyzes the sustainability of the retail supply chain. The paper shows the integration of Artificial Intelligence (AI) with Mind Genomics to understand how ordinary people think about food sustainability. The combination reveals how people think about the topic, from the point of view of what information regarding sustainability in retail is attractive to the ordinary person, what information is believable, and finally, the nature of different ways of thinking about sustainabili ty in retail, namely mindsets. The paper closes with the PVI (personal viewpoint identifier) evaluation. [ABSTRACT FROM AUTHOR]