How genomics can help biodiversity conservation

Trends in Genetics, Journal Year: 2023, Volume and Issue: 39(7), P. 545 - 559

Published: Feb. 16, 2023

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches applications in conservation genomics, considering practical factors, such as cost, time, prerequisite skills, current shortcomings applications. Most perform best combination with reference genomes from target species or closely related species. We review case studies to illustrate how facilitate research across tree life. conclude that time is ripe view fundamental integrate their use a practice genomics.

Language: Английский

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High-Throughput Transcriptome Profiling in Drug and Biomarker Discovery

Frontiers in Genetics, Journal Year: 2020, Volume and Issue: 11

Published: Feb. 5, 2020

The development of new drugs is multidisciplinary and systematic work. High-throughput techniques based on ‘-omics’ have driven the discovery biomarkers in diseases therapeutic targets drugs. A transcriptome complete set all RNAs transcribed by certain tissues or cells at a specific stage physiological condition. Transcriptome research can demonstrate gene functions structures from whole level reveal molecular mechanism biological processes diseases. Currently, expression microarray high-throughput RNA-sequencing been widely used biological, medical, clinical drug research. former has applied screening biomarker detection due to its high throughput, fast speed, simple analysis relatively low price. With further technology improvement analytical methods, flux RNA-seq much higher but price lower, hence it powerful advantages detecting discovery. Compared with traditional RNA-seq, scRNA-seq accuracy efficiency, especially single-cell pattern provide more information for Therefore, (sc)RNA-seq broader application prospects, field In this overview, we will review these technologies drug, natural development. Emerging applications third generation tools are also discussed.

Language: Английский

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Aspergillus derived mycotoxins in food and the environment: Prevalence, detection, and toxicity

Toxicology Reports, Journal Year: 2021, Volume and Issue: 8, P. 1008 - 1030

Published: Jan. 1, 2021

Aspergillus species are the paramount ubiquitous fungi that contaminate various food substrates and produce biochemicals known as mycotoxins. Aflatoxins (AFTs), ochratoxin A (OTA), patulin (PAT), citrinin (CIT), aflatrem (AT), secalonic acids (SA), cyclopiazonic acid (CPA), terrein (TR), sterigmatocystin (ST) gliotoxin (GT), other toxins produced by of plays a major role in human health. Mycotoxins exhibited wide range toxicity to humans animal models even at nanomolar (nM) concentration. Consumption detrimental mycotoxins adulterated foodstuffs affects health trace amounts. Bioaerosols consisting spores hyphal fragments active elicitors bronchial irritation allergy, challenging public is furthermost predominant environmental contaminant unswervingly defile lives with 40–90 % mortality risk patients conceded immunity. Genomics, proteomics, transcriptomics, metabolomics approaches useful for mycotoxins' detection which expensive. Antibody based chemotypes may result cross-reactivity uncertainty. Aptamers (APT) single stranded DNA (ssDNA/RNA), specifically binds target molecules can be generated systematic evolution ligands through exponential enrichment (SELEX). APT fast, sensitive, simple, in-expensive, field-deployable rapid point care (POC) toxins, better alternative antibodies.

Language: Английский

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Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing

Cell Reports, Journal Year: 2021, Volume and Issue: 37(7), P. 110022 - 110022

Published: Nov. 1, 2021

Alternative splicing is a post-transcriptional regulatory mechanism producing distinct mRNA molecules from single pre-mRNA with prominent role in the development and function of central nervous system. We used long-read isoform sequencing to generate full-length transcript sequences human mouse cortex. identify novel transcripts not present existing genome annotations, including mapping putative (unannotated) genes fusion incorporating exons multiple genes. Global patterns diversity are similar between cortex, although certain characterized by striking differences species. also developmental changes alternative splicing, differential usage fetal adult Our data confirm importance dramatically increasing transcriptional representing an important underpinning gene regulation brain. provide transcript-level for cortex as resource scientific community.

Language: Английский

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Mitochondrial dysfunction and oxidative stress in Alzheimer’s disease, and Parkinson’s disease, Huntington’s disease and Amyotrophic Lateral Sclerosis -An updated review

Mitochondrion, Journal Year: 2023, Volume and Issue: 71, P. 83 - 92

Published: June 1, 2023

Language: Английский

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Molecular Breeding and Drought Tolerance in Chickpea

Life, Journal Year: 2022, Volume and Issue: 12(11), P. 1846 - 1846

Published: Nov. 11, 2022

L. is the third greatest widely planted imperative pulse crop worldwide, and it belongs to Leguminosae family. Drought utmost common abiotic factor on plants, distressing their water status limiting growth development. Chickpea genotypes have natural ability fight drought stress using certain strategies viz., escape, avoidance tolerance. Assorted breeding methods, including hybridization, mutation, marker-aided breeding, genome sequencing along with omics approaches, could be used improve chickpea germplasm lines(s) against stress. Root features, for instance depth root biomass, been recognized as beneficial morphological factors managing terminal tolerance in chickpea. Marker-aided selection, example, a genomics-assisted (GAB) strategy that can considerably increase accuracy competence. These technologies, notably marker-assisted omics, plant physiology knowledge, underlined importance of future improvement programmes generate drought-tolerant cultivars(s).

Language: Английский

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RNA sequencing and its applications in cancer and rare diseases

Molecular Biology Reports, Journal Year: 2022, Volume and Issue: 49(3), P. 2325 - 2333

Published: Jan. 6, 2022

Language: Английский

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Protein tyrosine phosphatase 1B (PTP1B) function, structure, and inhibition strategies to develop antidiabetic drugs

FEBS Letters, Journal Year: 2024, Volume and Issue: unknown

Published: May 9, 2024

Tyrosine protein phosphatase non‐receptor type 1 (PTP1B; also known as tyrosine 1B) is a member of the (PTP) family and soluble enzyme that plays an essential role in different physiological processes, including regulation metabolism, specifically insulin leptin sensitivity. PTP1B crucial pathogenesis 2 diabetes mellitus obesity. These biological functions have made validated antidiabetic anti‐obesity, potentially anticancer, molecular target. Four main approaches aim to inhibit PTP1B: orthosteric, allosteric, bidentate inhibition, PTPN1 gene silencing. Developing potent selective inhibitor still challenging due enzyme's ubiquitous expression, subcellular location, structural properties. This article reviews advances study since it was first isolated 1988, well recent contextual information related PTP which this belongs. Furthermore, we offer overview obesity, challenges developing selective, effective, potent, bioavailable, cell‐permeable compounds can enzyme.

Language: Английский

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Twelve quick steps for genome assembly and annotation in the classroom

PLoS Computational Biology, Journal Year: 2020, Volume and Issue: 16(11), P. e1008325 - e1008325

Published: Nov. 12, 2020

Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting budgets individual research groups. Third-generation long-read DNA technologies are used, providing extensive genomic toolkits that were reserved for a few select model organisms. Generating high-quality assemblies annotations many aquatic species still presents significant challenges due to their large sizes, complexity, high chromosome numbers. Indeed, selecting most appropriate software platforms annotation pipelines new project can be daunting because tools often only work in limited contexts. In genomics, generating assembly/annotation has an indispensable tool better understanding biology any species. Herein, we state 12 steps help researchers get started projects by presenting guidelines broadly applicable (to species), sustainable over time, cover all aspects assembly from start finish. We review some commonly used approaches, including practical methods extract choices best library preparations. addition, discuss range potential bioinformatics pipelines, structural functional (e.g., transposable elements repetitive sequences). This paper also includes information on how build wide community project, importance data management, make results Findable, Accessible, Interoperable, Reusable (FAIR) submitting them public repository sharing with community.

Language: Английский

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Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish

Genome Research, Journal Year: 2021, Volume and Issue: 31(8), P. 1486 - 1497

Published: June 15, 2021

Alternate isoforms are important contributors to phenotypic diversity across eukaryotes. Although short-read RNA-sequencing has increased our understanding of isoform diversity, it is challenging accurately detect full-length transcripts, preventing the identification many alternate isoforms. Long-read sequencing technologies have made possible sequence alternative characterizing splicing events, transcription start and end sites, differences in UTR regions. Here, we use Pacific Biosciences (PacBio) long-read (Iso-Seq) examine transcriptomes five organs threespine stickleback fish (

Language: Английский

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