Innovations In Bioinformatics Research Articles

Harnessing Multi-Omics Strategies and Bioinformatics Innovations for Advancing Soybean Improvement: A Comprehensive Review.

Soybean improvement has entered a new era with the advent of multi-omics strategies and bioinformatics innovations, enabling more precise and efficient breeding practices. This comprehensive review examines the application of multi-omics approaches in soybean-encompassing genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics. We first explore pre-breeding and genomic selection as tools that have laid the groundwork for advanced trait improvement. Subsequently, we dig into the specific contributions of each -omics field, highlighting how bioinformatics tools and resources have facilitated the generation and integration of multifaceted data. The review emphasizes the power of integrating multi-omics datasets to elucidate complex traits and drive the development of superior soybean cultivars. Emerging trends, including novel computational techniques and high-throughput technologies, are discussed in the context of their potential to revolutionize soybean breeding. Finally, we address the challenges associated with multi-omics integration and propose future directions to overcome these hurdles, aiming to accelerate the pace of soybean improvement. This review serves as a crucial resource for researchers and breeders seeking to leverage multi-omics strategies for enhanced soybean productivity and resilience.

Monoclonal antibodies to the circumsporozoite proteins as an emerging tool for malaria prevention.

Despite various public health strategies, malaria caused by Plasmodium falciparum parasites remains a major global health challenge that requires development of new interventions. Extended half-life human monoclonal antibodies targeting the P. falciparum circumsporozoite protein on sporozoites, the infective form of malaria parasites, prevent malaria in rodents and humans and have been advanced into clinical development. The protective epitopes on the circumsporozoite protein targeted by monoclonal antibodies have been defined. Cryogenic electron and multiphoton microscopy have enabled mechanistic structural and functional investigations of how antibodies bind to the circumsporozoite protein and neutralize sporozoites. Moreover, innovations in bioinformatics and antibody engineering have facilitated enhancement of antibody potency and durability. Here, we summarize the latest scientific advances in understanding how monoclonal antibodies to the circumsporozoite protein prevent malaria and highlight existing clinical data and future plans for how this emerging intervention can be used alone or alongside existing antimalarial interventions to control malaria across at-risk populations.

Bettercallsal: better calling of Salmonella serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting.

Most current Salmonella subtyping analyses rely on whole genome sequencing (WGS), which focuses on the high-resolution analysis of single genomes or multiple single genomes from the isolated colonies on microbiological agar plates. In this study, we introduce bioinformatics innovations for a metagenomic outbreak response workflow that accurately identifies multiple Salmonella serovars at the same time. bettercallsal is one of the first analysis tools to identify multiple Salmonella enterica serotypes from metagenomic or quasi-metagenomic datasets with high accuracy, allowing these isolate-independent methods to be incorporated into surveillance and root cause investigations. It was tested on an in silico benchmark dataset comprising 29 unique Salmonella serovars, 46 non-Salmonella bacterial genomes, and 10 viral genomes at varying read depths and on previously well-characterized and sequenced non-selective primary and selective enrichments of papaya and peach samples from separate outbreak investigations that resulted in the identification of multiple Salmonella serovars using traditional isolate culturing and WGS as well as nucleic acid assays. Analyses were also conducted on these datasets using a custom-built k-mer tool, SeqSero2, and Kallisto to compare serotype calling to bettercallsal. The in silico dataset analyzed with bettercallsal achieved the maximum precision, recall, and accuracy of 100, 83, and 94%, respectively. In the papaya outbreak samples, bettercallsal identified the presence of multiple serovars in agreement with the Luminex® xMAP assay results and also identified more serovars per sample, as evidenced by NCBI SNP clustering. In peach outbreak samples, bettercallsal identified two serovars in concordance with k-mer analysis and the Luminex xMAP assay. The genome hit reported by bettercallsal clustered with the chicken isolate genome, as reported by the FDA peach outbreak investigation from sequenced isolates (WGS). Overall, bettercallsal outperformed k-mer, Seqsero2, and Kallisto in identifying multiple serovars from enrichment cultures using shotgun metagenomic sequencing.

Resistance that stacks up: engineering rust and mildew disease control in the cereal crops wheat and barley.

Staying ahead of the arms race against rust and mildew diseases in cereal crops is essential to maintain and preserve food security. The methodological challenges associated with conventional resistance breeding are major bottlenecks for deploying resistance (R) genes in high-yielding crop varieties. Advancements in our knowledge of plant genomes, structural mechanisms, innovations in bioinformatics, and improved plant transformation techniques have alleviated this bottleneck by permitting rapid gene isolation, functional studies, directed engineering of synthetic resistance and precise genome manipulation in elite crop cultivars. Most cloned cereal R genes encode canonical immune receptors which, on their own, are prone to being overcome through selection for resistance-evading pathogenic strains. However, the increasingly large repertoire of cloned R genes permits multi-gene stacking that, in principle, should provide longer-lasting resistance. This review discusses how these genomics-enabled developments are leading to new breeding and biotechnological opportunities to achieve durable rust and powdery mildew control in cereals.

The Current Therapeutic Role of Chromatin Remodeling for the Prognosis and Treatment of Heart Failure.

Cardiovascular diseases are a major cause of death globally, with no cure to date. Many interventions have been studied and suggested, of which epigenetics and chromatin remodeling have been the most promising. Over the last decade, major advancements have been made in the field of chromatin remodeling, particularly for the treatment of heart failure, because of innovations in bioinformatics and gene therapy. Specifically, understanding changes to the chromatin architecture have been shown to alter cardiac disease progression via variations in genomic sequencing, targeting cardiac genes, using RNA molecules, and utilizing chromatin remodeler complexes. By understanding these chromatin remodeling mechanisms in an injured heart, treatments for heart failure have been suggested through individualized pharmaceutical interventions as well as biomarkers for major disease states. By understanding the current roles of chromatin remodeling in heart failure, a potential therapeutic approach may be discovered in the future.

Peptide-Based Vaccines for Tuberculosis.

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis. As a result of the coronavirus disease 2019 (COVID-19) pandemic, the global TB mortality rate in 2020 is rising, making TB prevention and control more challenging. Vaccination has been considered the best approach to reduce the TB burden. Unfortunately, BCG, the only TB vaccine currently approved for use, offers some protection against childhood TB but is less effective in adults. Therefore, it is urgent to develop new TB vaccines that are more effective than BCG. Accumulating data indicated that peptides or epitopes play essential roles in bridging innate and adaptive immunity and triggering adaptive immunity. Furthermore, innovations in bioinformatics, immunoinformatics, synthetic technologies, new materials, and transgenic animal models have put wings on the research of peptide-based vaccines for TB. Hence, this review seeks to give an overview of current tools that can be used to design a peptide-based vaccine, the research status of peptide-based vaccines for TB, protein-based bacterial vaccine delivery systems, and animal models for the peptide-based vaccines. These explorations will provide approaches and strategies for developing safer and more effective peptide-based vaccines and contribute to achieving the WHO’s End TB Strategy.

Bioinformatics innovations and patent eligibility

Bioinformatics technology (combination of biology and information technology) is worthy of special consideration in terms of intellectual property. Bioinformatics inventions have brought up many uncertainties over the issue of patent eligibility. There is neither any specific bioinformatics law nor any court has adjudicated any disputes related to bioinformatics. This paper critically examines bioinformatics‐related patent laws and practices and analyzes whether patent laws protect bioinformatics innovations particularly software which analyze DNA sequences.

Patenting Bioinformatics Innovations: Emerging Trends and Challenges in the United States

Bioinformatics tools and techniques are useful not only to manage and analyze the vast amount of raw biological data generated from various genomics research but also to understand the phenomena of the biological system at the macromolecular level. The development of bioinformatics has come a long way from DNA sequencing tools of the Human Genome Project (HGP) era to DNA circuits and programmable synthetic biological devices in the twenty-first century. The present article attempts to analyze and reveal the emerging trends in bioinformatics and computational biology research and innovation and challenges in patenting them under the current US patent regime.

PATENTING BIOINFORMATICS INNOVATIONS: EMERGING TRENDS AND CHALLENGES IN THE UNITED STATES.

31May 2017 PATENTING BIOINFORMATICS INNOVATIONS: EMERGING TRENDS AND CHALLENGES IN THE UNITED STATES. TuhinChatterjee. Ph.D. candidate, The West Bengal National University of Juridical Sciences (WB NUJS) and Indian Patent Attorney.

Bioinformatics Materials and Issue of Patentability

This summery of research critically examines the patentable aspects of bioinformatics materials, i. e., biological sequences, sequences database, and software. It surveys related patent laws and practices of Japan, the US, Europe, Canada and Australia, and it analyzes whether bioinformatics innovations are protected by patent in these jurisdictions; similarity and contradictions of patentability aspects of bioinformatics materials between different jurisdictions; its interrelationship with the open source policy; and the issues of harmonization of this subject matter.

Copyright versus Database Right of Protection in the UK: The Bioinformatics Bone of Contention

Bioinformatics is the development and use of databases for storing and interpreting genomic information. The information explosion in these databases has raised a plethora of intellectual property issues for the scientists who depend on them. Copyright and database protection are two notable and significant methods of exploiting innovations in bioinformatics. This article makes an in‐depth analysis of the scope and utility of copyright and database protection laws in bioinformatics. This article focuses initially on the working of bioinformatics databases, and then delves into the issues and implications of copyright and database protection in bioinformatics. The article concludes that copyright in comparison to database laws serves as a better platform in keeping the balance between the interests of bioinformatics database makers and its users.

An update of the HLA genomic region, locus information and disease associations: 2004

The human major histocompatibility (MHC) genomic region at chromosomal position 6p21 encodes the six classical transplantation HLA genes and many other genes that have important roles in the regulation of the immune system as well as in some fundamental cellular processes. This small segment of the human genome has been associated with more than 100 diseases, including common diseases--such as diabetes, rheumatoid arthritis, psoriasis, asthma and various autoimmune disorders. The MHC 3.6 Mb genomic sequence was first reported in 1999 with the annotation of 224 gene loci. The locus and allelic information of the MHC continue to be updated by identifying newly mapped expressed genes and pseudogenes based on comparative genomics, SNP analysis and cDNA projects. Since 1999, new innovations in bioinformatics and gene-specific functional databases and studies on the MHC genes have resulted in numerous changes to gene names and better ways to update and link the MHC gene symbols, names and sequences together with function, variation and disease associations. In this study, we present a brief overview of the MHC genomic structure and the recent information that we have gathered on the MHC gene loci via LocusLink at the National Centre for Biological Information (http://www.ncbi.nih.gov/.) and the MHC genes' association with various diseases taken from publications and records in public databases, such as the Online Mendelian Inheritance in Man and the Genetic Association Database.