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The buffalo was domesticated around 3000–6000 years ago and has substantial economic significance as a meat, dairy, and draught animal. The buffalo has remained underutilized in terms of the development of a well-annotated and assembled reference genome de novo. It is mandatory to explore the genetic architecture of a species to understand the biology that helps to manage its genetic variability, which is ultimately used for selective breeding and genomic selection. Morphological and molecular data have revealed that the swamp buffalo population has strong geographical genomic diversity with low gene flow but strong phenotypic consistency, while the river buffalo population has higher phenotypic diversity with a weak phylogeographic structure. The availability of recent high-quality reference genome and genotyping marker panels has invigorated many genome-based studies on evolutionary history, genetic diversity, functional elements, and performance traits. The increasing molecular knowledge syndicate with selective breeding should pave the way for genetic improvement in the climatic resilience, disease resistance, and production performance of water buffalo populations globally.

The integration of precision medicine in the care of hospitalized children is ever evolving. However, access to new genomic diagnostics such as rapid whole genome sequencing (rWGS) is hindered by barriers in implementation. Michigan’s Project Baby Deer (PBD) is a multi-center collaborative effort that sought to break down barriers to access by offering rWGS to critically ill neonatal and pediatric inpatients in Michigan. The clinical champion team used a standardized approach with inclusion and exclusion criteria, shared learning, and quality improvement evaluation of the project’s impact on the clinical outcomes and economics of inpatient rWGS. Hospitals, including those without on-site geneticists or genetic counselors, noted positive clinical impacts, accelerating time to definitive treatment for project patients. Between 95–214 hospital days were avoided, net savings of $4155 per patient, and family experience of care was improved. The project spurred policy advancement when Michigan became the first state in the United States to have a Medicaid policy with carve-out payment to hospitals for rWGS testing. This state project demonstrates how front-line clinician champions can directly improve access to new technology for pediatric patients and serves as a roadmap for expanding clinical implementation of evidence-based precision medicine technologies.

Genome sequencing is a powerful tool that can inform the management of threatened species. Koalas (Phascolarctos cinereus) are a globally recognized species that captured the hearts and minds of the world during the 2019/2020 Australian megafires. In 2022, koalas were listed as ‘Endangered’ in Queensland, New South Wales, and the Australian Capital Territory. Populations have declined because of various threats such as land clearing, habitat fragmentation, and disease, all of which are exacerbated by climate change. Here, we present the Koala Genome Survey, an open data resource that was developed after the Australian megafires. A systematic review conducted in 2020 demonstrated that our understanding of genomic diversity within koala populations was scant, with only a handful of SNP studies conducted. Interrogating data showed that only 6 of 49 New South Wales areas of regional koala significance had meaningful genome-wide data, with only 7 locations in Queensland with SNP data and 4 locations in Victoria. In 2021, we launched the Koala Genome Survey to generate resequenced genomes across the Australian east coast. We have publicly released 430 koala genomes (average coverage: 32.25X, range: 11.3–66.8X) on the Amazon Web Services Open Data platform to accelerate research that can inform current and future conservation planning.

Significant innovations in next-generation sequencing techniques and bioinformatics tools have impacted our appreciation and understanding of RNA. Practical RNASeq applications have evolved in conjunction with sequence technology and bioinformatic tool advances. In this review, we explained various computational resources, tools, and bioinformatics analyses advancement for small and large non-coding RNAs. These include non-coding RNAs (ncRNAs) such as piwi, micro, circular, and long ncRNAs. In addition, this article discusses future challenges, single-cell level sequencing for non-coding RNAs, and advantages of using long-read sequencing to annotate lncRNAs.

Legionellosis is an infection acquired through inhalation of aerosolized water droplets containing Legionella bacteria. In August 2018, public health officials in New Hampshire launched an investigation into a legionellosis outbreak. They identified 49 illnesses likely associated with the outbreak and implicated an improperly maintained hot tub at a hotel. The same strain of Legionella pneumophila serogroup 1 was found in both the hot tub and in samples from two patients with Legionnaires’ disease. The indoor hot tub vented to the outdoors, which is how some patients with confirmed legionellosis likely acquired the infection despite not entering the hotel during the incubation period. This outbreak is notable for 1) likely illness acquisition through the exterior vent of the hot tub room and 2) use of whole genome sequencing to link environmental and patient specimens. Collaboration among public health and environmental officials, laboratorians, and building managers was essential to determining the source of the outbreak and preventing further illness.

BackgroundPolycyclic aromatic hydrocarbon contamination presents significant environmental challenges, requiring effective bioremediation solutions.MethodsBacillus altitudinis DG4, isolated from the Damanganga River in Vapi, India, was investigated for its genomic characteristics and naphthalene degradation capabilities using whole genome sequencing and Gas Chromatography-Mass Spectrometry (GC–MS) analysis.ResultsGenome sequencing revealed a 3,831,796 base pair genome with 4120 protein-coding sequences. Genome annotation identified genes involved in diverse metabolic pathways including xenobiotic degradation. Pan-genome analysis of 122 B. altitudinis genomes revealed 2403 core genes, 1588 accessory genes, and 40 unique genes in strain DG4. Naphthalene degradation experiments showed that strain DG4 exhibited the highest degradation efficiency (90.0%) among five isolates tested, despite a moderate growth rate. GC–MS analysis confirmed the metabolism of naphthalene and formation of key intermediates, including 1-naphthalenol, 1,8-naphthalic anhydride, 1-acenaphthanone, and benzoic acid, suggesting a specific degradation pathway.ConclusionThe presence of genes associated with degradation pathways and the experimental validation of naphthalene degradation highlight the strong bioremoval potential of B. altitudinis DG4 for naphthalene-contaminated environments. These findings contribute to understanding microbial degradation mechanisms and support the development of effective bioremediation strategies for polycyclic aromatic hydrocarbon pollution.

We aimed to characterize knowledge and attitudes about rapid whole genome sequencing (rWGS) implementation of a broad constituency of healthcare professionals at hospitals participating in a statewide initiative to implement rWGS for hospitalized neonates and children up to 18 years of age meeting clinical criteria for testing. We surveyed 307 healthcare professionals from eight hospitals about their knowledge and attitudes regarding rWGS. We examined survey internal reliability using exploratory factor analysis and associations between respondent characteristics and attitudes toward rWGS with linear regression. We thematically analyzed free-text responses. Views about rWGS implementation in respondents’ own setting and respondents’ personal capability to implement rWGS were generally neutral (M = 3.44 (SD = 0.74); M = 3.30 (SD = 0.85), respectively). Views about the potential for rWGS in clinical practice were overall positive (M = 4.12 (SD = 0.57)). The degree of positivity of attitudes about rWGS was strongly influenced by perceived knowledge, clinical or non-clinical role, concerns about future insurance coverage for rWGS as a first-tier test, and future adverse impact of genomics health information on patients or families. We identified several actionable factors influencing attitudes toward rWGS of pediatric healthcare professionals. Expanded education and ongoing implementation research are needed for the full potential of rWGS in pediatrics to be realized.

Biomedical research is fundamental in developing preventive and therapeutic vaccines, serving as a cornerstone of global public health. This review explores the key concepts, methodologies, tools, and challenges in the vaccine development landscape, focusing on transitioning from basic biomedical sciences to clinical applications. Foundational disciplines such as virology, immunology, and molecular biology lay the groundwork for vaccine creation, while recent innovations like messenger RNA (mRNA) technology and reverse vaccinology have transformed the field. Additionally, it highlights the role of pharmaceutical advancements in translating lab discoveries into clinical solutions. Techniques like CRISPR-Cas9, genome sequencing, monoclonal antibodies, and computational modeling have significantly enhanced vaccine precision and efficacy, expediting the development of vaccines against infectious diseases. The review also discusses challenges that continue to hinder progress, including stringent regulatory pathways, vaccine hesitancy, and the rapid emergence of new pathogens. These obstacles underscore the need for interdisciplinary collaboration and the adoption of innovative strategies. Integrating personalized medicine, nanotechnology, and artificial intelligence is expected to revolutionize vaccine science further. By embracing these advancements, biomedical research has the potential to overcome existing challenges and usher in a new era of therapeutic and prophylactic vaccines, ultimately improving global health outcomes. This review emphasizes the critical role of vaccines in combating current and future health threats, advocating for continued investment in biomedical science and technology.

Structural variation of the human genome sequence is the insertion, deletion, or rearrangement of stretches of DNA sequence sized from around 1,000 to millions of base pairs. Over the past few years, structural variation has been shown to be far more common in human genomes than previously thought. Very little is currently known about the effects of structural variation on normal child development, but such effects could be of considerable significance. This review provides an overview of the phenomenon of structural variation in the human genome sequence, describing the novel genomics technologies that are revolutionizing the way structural variation is studied and giving examples of genomic structural variations that affect child development.

In 2007, with the help of DBT, a research project to create mutant resources for functional genomics in rice was launched through a national initiative involving ICAR-National Research Centre on Plant Biotechnology, New Delhi; ICAR-Indian Agricultural Research Institute, New Delhi; Tamil Nadu Agricultural University, Coimbatore; ICAR-Indian Institute of Rice Research, Hyderabad; University of Agricultural Sciences, Bangalore and Punjab Agricultural University, Ludhiana. Genetically well-defined material is a prerequisite for functional genomics. Thus, the project aimed to generate EMS mutants in the background of an upland and short duration aus genotype, Nagina22, characterize the mutants and use them in crop improvement. As of now, nearly 85,000 rice M2 mutant populations have been created under the project. Based on field phenotyping, gain and or loss of function mutants for tolerance to herbicide spray, drought, salinity and resistance to rice leaf and panicle blast, sheath blight and high phosphorus (P) use efficiency under low P field have been identified. Notably, the herbicide-tolerant mutant identified is under the process of registration for distribution to public and private rice breeders under appropriate material transfer agreement. Besides this, the project also aims to serve as a 'National Repository of rice EMS mutant resource' for the researchers involved in rice biology and improvement in the country.