#Whole-genome sequencing (WGS)

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Mitochondrial Dysfunction in mtARS Disorders

Introduction

Mitochondria are indispensable organelles that facilitate cellular bioenergetics, predominantly through oxidative phosphorylation (OXPHOS). Mitochondrial aminoacyl-tRNA synthetases (mtARS) are essential for the fidelity of mitochondrial translation, catalyzing the ligation of amino acids to their cognate tRNAs. Mutations in mtARS genes precipitate a spectrum of mitochondrial disorders, culminating in dysfunctional protein synthesis and aberrant mitochondrial bioenergetics. This review delves into the molecular pathogenesis of mitochondrial dysfunction in mtARS disorders, elucidating their biochemical perturbations, clinical phenotypes, and emerging therapeutic paradigms.

Molecular Pathophysiology of mtARS Disorders

MtARS enzymes ensure translational accuracy by charging mitochondrial tRNAs with their respective amino acids, a prerequisite for mitochondrial protein biosynthesis. Pathogenic variants in mtARS genes result in defective aminoacylation, perturbing mitochondrial translation and compromising the integrity of the electron transport chain (ETC). These perturbations induce bioenergetic deficits, increased reactive oxygen species (ROS) production, and secondary mitochondrial stress responses, leading to cellular demise.

Genetic Etiology of mtARS Mutations

Dysfunctional mtARS genes such as DARS2, AARS2, RARS2, and YARS2 have been implicated in autosomal recessive mitochondrial disorders. These mutations exhibit tissue-specific phenotypic heterogeneity, with neurological, muscular, and systemic manifestations. For instance, DARS2 mutations drive leukoencephalopathy with brainstem and spinal cord involvement, whereas AARS2 defects result in a constellation of neurodegenerative and ovarian pathologies.

Biochemical and Cellular Consequences

Dysfunctional mtARS enzymes manifest in multifaceted mitochondrial deficits, including impaired translation, defective OXPHOS, and dysregulated mitochondrial proteostasis.

Disruption of Mitochondrial Translation

Impaired aminoacylation abrogates the synthesis of mitochondrially encoded proteins, undermining the assembly of ETC complexes. This translational arrest culminates in defective ATP synthesis and precipitates a systemic energy deficit.

Electron Transport Chain Dysfunction and Bioenergetic Failure

Pathogenic mtARS mutations lead to OXPHOS inefficiencies, reducing mitochondrial membrane potential (Δψm) and ATP output. Perturbed electron flux exacerbates ROS accumulation, instigating oxidative damage and apoptotic cascades.

Mitochondrial Unfolded Protein Response (UPRmt) Activation

Cellular compensatory mechanisms, including UPRmt, are upregulated in response to mitochondrial translation failure. UPRmt mitigates proteotoxic stress via chaperone-mediated protein refolding and degradation pathways. However, chronic UPRmt activation fosters maladaptive stress responses, contributing to progressive cellular degeneration.

Clinical Manifestations

mtARS disorders exhibit phenotypic variability, spanning from mild neuromuscular impairment to severe multisystemic involvement. The pathophysiological hallmark includes disrupted neurological, muscular, and cardiac function.

Neurological Dysfunction

Neurodegeneration is a predominant feature of mtARS disorders, manifesting as ataxia, seizures, intellectual disability, and progressive leukoencephalopathy. Magnetic resonance imaging (MRI) frequently reveals white matter abnormalities, indicative of compromised oligodendrocyte function.

Myopathy and Metabolic Dysregulation

Muscle tissue, with its high ATP demand, is particularly susceptible to mitochondrial dysfunction. Clinical hallmarks include hypotonia, muscle weakness, and exercise intolerance, often concomitant with metabolic anomalies such as lactic acidosis and elevated pyruvate-to-lactate ratios.

Cardiomyopathy and Mitochondrial Energetics

Hypertrophic cardiomyopathy has been observed in YARS2-associated mitochondrial disorders, wherein compromised ATP synthesis in cardiomyocytes disrupts contractile function and electrophysiological stability.

Diagnostic and Functional Evaluation

A combination of genomic, biochemical, and imaging modalities facilitates the diagnosis of mtARS disorders.

Genomic and Transcriptomic Analysis

Whole-exome sequencing (WES) and whole-genome sequencing (WGS) are pivotal for identifying pathogenic mtARS variants. Transcriptomic profiling elucidates perturbations in mitochondrial gene expression networks, further refining diagnostic accuracy.

Functional Mitochondrial Assays

Biochemical assays, including high-resolution respirometry, ATP quantification, and ETC enzymatic profiling, provide insights into mitochondrial bioenergetics. Patient-derived fibroblasts and induced pluripotent stem cells (iPSCs) serve as valuable models for functional interrogation.

Neuroimaging and Biomarker Identification

Advanced imaging modalities such as MR spectroscopy (MRS) detect metabolic derangements, including lactate accumulation in affected brain regions. Circulating mitochondrial-derived peptides and metabolomic signatures are emerging as potential diagnostic biomarkers.

Emerging Therapeutic Strategies

Despite the absence of curative therapies, multiple avenues are under investigation to ameliorate mitochondrial dysfunction in mtARS disorders.

Mitochondria-Directed Antioxidants

Therapeutic compounds such as MitoQ, idebenone, and edaravone aim to attenuate oxidative stress and preserve mitochondrial integrity.

Genetic and RNA-Based Interventions

Gene therapy strategies utilizing adeno-associated virus (AAV)-mediated delivery and CRISPR-based genome editing are being explored for genetic correction of mtARS mutations. Additionally, RNA-based approaches, including antisense oligonucleotides (ASOs) and mRNA replacement therapy, hold promise in restoring mtARS functionality.

Metabolic Modulation and Supportive Therapies

Ketogenic diets, NAD+ precursors (e.g., nicotinamide riboside), and mitochondrial biogenesis activators (e.g., PGC-1α modulators) are under investigation to enhance cellular energy metabolism. Supportive interventions, including physical therapy and neuromuscular rehabilitation, remain integral to patient management.

Conclusion and Future Directions

Mitochondrial dysfunction in mtARS disorders arises from defective mitochondrial translation, OXPHOS perturbation, and maladaptive stress responses. Advances in genomic medicine, mitochondrial therapeutics, and precision medicine approaches are poised to transform the diagnostic and therapeutic landscape. Continued research into mtARS pathobiology, coupled with translational innovations, will be instrumental in developing targeted interventions for affected individuals.

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Reference saved in our archive

Phylogenically tracing covid from the Wuhan outbreak through Ireland

[cbirt]

In order to establish standardized high-throughput whole-genome sequencing (WGS) for patients with cancer and rare diseases, the UK Government launched the groundbreaking 100,000 Genomes Project within the National Health Service (NHS) in England. This was accomplished through the use of an automated bioinformatics pipeline accredited by the International Organisation for Standardisation. Operating in conjunction with NHS England, Genomics England examined WGS data from 13,880 solid tumors representing 33 different cancer types, fusing genetic information with actual treatment and outcome data in a secure research environment. 

WGS and longitudinal life course clinical data were linked, enabling the evaluation of treatment results for patients categorized by pangenomic markers. The results of this study show how useful it is to connect genomic and practical clinical data in order to do survival analysis, locate cancer genes that influence prognosis, and deepen our knowledge of how cancer genomics affects patient outcomes.

Using an automated bioinformatics pipeline accredited by the International Organisation for Standardisation, the 100,000 Genomes Project was a ground-breaking UK Government initiative implemented within the National Health Service (NHS) in England with the goal of establishing standardized high-throughput whole-genome sequencing (WGS) for patients with cancer and rare diseases.

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[articlepublication]

MagBio Genomics’ Kits Simplify DNA Normalization in Next-Generation Sequencing

In modern genomics research, ensuring accurate and consistent DNA input is crucial for obtaining high-quality sequencing data. One of the most important steps in achieving this is DNA normalization, a process that ensures uniform DNA concentration across samples. With the increasing demand for precision in Next-Generation Sequencing (NGS), having a reliable method for DNA normalization is essential.

What is DNA Normalization and Why is it Important?

DNA normalization is the process of adjusting the concentration of DNA samples to a uniform level before sequencing or downstream applications. Unequal DNA input can lead to inconsistent sequencing coverage, impacting data quality and increasing variability in results. Effective normalization helps to:

Improve sequencing accuracy by maintaining uniform representation of all samples.

Reduce sample-to-sample variability, leading to more reliable results.

Optimize reagent usage, preventing waste and lowering costs.

Streamline workflows, making high-throughput sequencing more efficient.

Challenges in DNA Normalization

Traditional DNA normalization methods include spectrophotometry (NanoDrop), fluorometry (Qubit), and automated liquid handling. However, these approaches come with challenges:

Time-consuming and labor-intensive: Manual normalization can be tedious and error-prone.

Inconsistent measurements: Variability in DNA quantification methods can lead to inaccurate normalization.

High reagent costs: Some normalization methods require expensive reagents and equipment.

Given these challenges, researchers need an efficient, reproducible, and cost-effective solution.

MagBio’s DNA Normalization Kits: A Game-Changer for Genomic Research

MagBio Genomics has developed innovative DNA normalization kits that address the limitations of traditional methods. These kits utilize magnetic bead-based technology, ensuring accurate, scalable, and high-throughput DNA normalization for NGS and other applications.

Key Benefits of MagBio’s DNA Normalization Kits

Automated and Scalable: Ideal for high-throughput laboratories, reducing manual errors and hands-on time.

Highly Reproducible: Consistently delivers accurate DNA concentrations for improved sequencing performance.

Cost-Effective: Reduces reagent waste and the need for additional quantification steps.

Easy Integration: Compatible with liquid handling systems and standard laboratory workflows.

Non-Damaging to DNA: Ensures high-quality DNA with no degradation, making it suitable for sensitive applications like long-read sequencing.

How MagBio’s DNA Normalization Kits Work

MagBio’s kits utilize paramagnetic beads that selectively bind DNA molecules, allowing for precise concentration adjustments. The process involves:

Binding DNA to magnetic beads in a controlled manner.

Washing Steps to remove excess DNA and contaminants.

Elution in a defined volume, yielding normalized DNA ready for sequencing.

This simple, robust method eliminates the need for manual quantification, making it an efficient alternative to conventional normalization approaches.

Applications in Next-Generation Sequencing (NGS)

NGS platforms require uniform DNA input for optimal sequencing results. MagBio’s DNA normalization kits are designed to meet the needs of various sequencing applications, including:

Whole Genome Sequencing (WGS)

RNA-Seq and Transcriptomics

Targeted Sequencing Panels

Metagenomics and Microbiome Research

Amplicon-Based Sequencing

By ensuring consistent DNA input, researchers can achieve more accurate sequencing coverage, reducing variability and improving downstream data analysis.

Why Choose MagBio for DNA Normalization?

MagBio Genomics has a strong reputation for delivering high-quality magnetic bead-based solutions for nucleic acid purification and sequencing. Their DNA normalization kits are trusted by genomics researchers worldwide for their ease of use, efficiency, and reliability.

Whether you are running a small-scale study or handling high-throughput sequencing projects, MagBio’s DNA normalization kits provide the consistency and accuracy needed to optimize your workflows.

Conclusion

DNA normalization is a crucial step in NGS workflows, ensuring reproducibility and accuracy in sequencing results. MagBio’s DNA normalization kits offer a cutting-edge solution that simplifies the process, improves efficiency, and enhances data quality. By integrating these kits into your lab, you can streamline sequencing workflows while maintaining high standards of performance.

[evoldir]

Fwd: Postdoc: ColoradoStateU.PopGenomics

Begin forwarded message: > From: evoldir@evol.biology.mcmaster.ca > Subject: Postdoc: ColoradoStateU.PopGenomics > Date: 13 November 2024 at 06:31:23 GMT > To: rdmpage@gmail.com > > > > Postdoctoral Position: Population and Landscape Genomics to Inform > Host-Pathogen Co-evolution and Conservation Management > > A postdoctoral position focused on population and landscape genomics to > inform host-pathogen co-evolution of wild cervids and chronic wasting > disease (CWD) is available in the Funk Lab of Conservation Genomics > and Evolutionary Ecology at Colorado State University.  Funded by the > USDA National Wildlife Research Center, the postdoctoral scientist will > harness whole-genome sequence (WGS) data collected from mule deer to test > the landscape factors that influence connectivity and CWD transmission, > understand the roles of gene flow and pathogen-mediated selection in the > ecology and epidemiology of CWD, and investigate fitness consequences > of polymorphisms in the prion protein gene that influence the incubation > period of CWD, among other research question. In addition to publishing > their results in peer-reviewed scientific journals, the postdoctoral > scientist will communicate their results at scientific conferences > and with federal and state scientists and decision makers to improve > conservation management of wild cervid populations.  The postdoctoral > scientist will be part of a collaborative team from the USDA NWRC > (Dr. Jenn Malmberg) and Utah State University (Dr. Kezia Manlove). > > Required qualifications: > > -     Ph.D. by the time of start date in evolutionary biology, > population genetics, integrative biology, disease ecology and evolution, > or some equivalent. > > -     Excellent communication (verbal and written) and > organizational skills. > > -     Positive attitude and desire to work as part of a > dynamic, multi-disciplinary team. > > -     Strong expertise in bioinformatics, genomics, and the > application of genomics to evolutionary and conservation questions. > > -     Experience generating, analyzing, and/or integrating > large datasets – whole genome sequencing, RAD sequencing, and/or > transcriptome sequencing. > > Preferred qualifications: > > -     Fluency in Python or Perl, and R. > > -     Expertise in disease ecology. > > The successful candidate will work under the supervision of Professor > Dr. Chris Funk at Colorado State University, and in collaboration with > other team members. > > The appointment can be extended up to three years, pending satisfactory > performance. The salary will be commensurate with experience. Preferred > start date is approximately March 1, 2025. > > To apply: E-mail a single PDF including a cover letter, a CV, and the > names and contact information of three references to the Funk Laboratory > Manager, Mackenzie Woods (Mackenzie.Woods@colostate.edu), with the subject > line as "Postdoctoral application your name". Review of applications > will begin December 30, 2024, and continue until a suitable candidate > is identified. Informal inquiries prior to application are welcome and > can be directed to Chris Funk (Chris.Funk@colostate.edu). > > "Funk,Chris"

[businessmarketreports]

An Overview of Next Generation Sequencers Market: Trends and Insights

The Next-Generation Sequencers (NGS) market is witnessing rapid growth, driven by advancements in sequencing technology, declining costs, and increasing applications across healthcare, research, and agriculture. NGS enables high-throughput DNA sequencing, allowing for a more comprehensive analysis of genomes, transcriptomes, and epigenomes.

Buy Full Report for More Insights on the Next Generation Sequencers Market Forecast Download a Free Sample Report

This market encompasses various components, including instruments, software, and reagents, catering to a wide array of end-users, such as hospitals, research institutes, and biotechnology firms.

1. Market Overview

Market Size and Growth: The NGS market has shown robust growth due to rising demand for genomic analysis in personalized medicine, cancer research, and genetic diagnostics. Increasing adoption in clinical settings, along with advancements in technology, has driven accessibility and expanded market reach.

Regional Trends: North America and Europe currently dominate the market due to high healthcare expenditures, advanced infrastructure, and a significant focus on research and development. Meanwhile, Asia-Pacific is emerging as a promising market due to rising healthcare investments and increasing adoption of genomic medicine.

Key Applications: The major applications for NGS include oncology, infectious disease diagnostics, reproductive health, and hereditary disease screening, along with applications in agriculture and environmental studies.

2. Key Trends in the NGS Market

Declining Sequencing Costs: The costs of sequencing have significantly dropped since the advent of NGS technologies. The "thousand-dollar genome" has become a reality, making genetic testing more affordable and accessible, particularly in research and clinical diagnostics.

Shift Towards Clinical Applications: There is a growing demand for NGS in clinical settings, particularly in oncology for tumor profiling, hereditary disease detection, and pharmacogenomics. Clinical applications are gaining traction due to their potential for precision medicine, helping tailor treatments to individual genetic profiles.

Focus on Cancer Research: Oncology remains a major application area for NGS, as it enables detailed cancer genome analysis, leading to better understanding of mutations and tumor behavior. This technology supports both research and diagnostic applications, fueling demand among pharmaceutical companies and research institutes focused on oncology.

Rise of Liquid Biopsies: NGS is widely used in liquid biopsies, which offer a non-invasive method for cancer detection and monitoring by analyzing cell-free DNA (cfDNA) from blood samples. Liquid biopsies are gaining popularity as they allow real-time monitoring of tumor progression and treatment efficacy, reducing the need for invasive procedures.

Emergence of Long-Read Sequencing: Long-read sequencing technologies, such as those offered by Pacific Biosciences and Oxford Nanopore, are gaining traction due to their ability to provide more comprehensive genomic insights. These technologies are particularly valuable in detecting structural variants and resolving complex genomic regions.

Development of Companion Diagnostics: NGS-based companion diagnostics, used to determine the efficacy and safety of a specific drug for a targeted patient group, are expanding. These diagnostics guide treatment decisions in oncology, particularly for identifying biomarkers associated with certain therapies.

3. Market Segmentation

By Product: The NGS market includes sequencers, software, consumables, and services. Consumables, including reagents and kits, constitute the largest segment due to repeated purchases. However, software solutions are gaining traction as data analysis and interpretation become more complex.

By Technology:

Whole Genome Sequencing (WGS): WGS provides a comprehensive view of the entire genome, making it suitable for research and complex disease studies.

Targeted Sequencing: Targeted sequencing is cost-effective and focuses on specific regions of interest, widely used in oncology and clinical diagnostics.

RNA Sequencing: RNA sequencing enables transcriptome analysis and is valuable in cancer research, gene expression studies, and drug discovery.

Exome Sequencing: Exome sequencing, which targets protein-coding regions, is a more affordable alternative to WGS and is commonly used for diagnosing genetic disorders.

By Application: The NGS market serves several applications, including oncology, infectious disease diagnosis, reproductive health, genetic screening, and forensic analysis. Oncology holds the largest share, while infectious disease applications, particularly in tracking pathogens and outbreaks, are rapidly growing.

By End User: The primary end-users include academic and research institutions, hospitals and clinics, pharmaceutical and biotechnology companies, and government agencies. Hospitals and clinics are showing increasing demand as NGS technology moves from research into clinical diagnostics.

4. Key Drivers and Challenges

Drivers:

Increased Demand for Precision Medicine: The trend toward personalized medicine is a major driver, as NGS allows for tailored treatments based on genetic profiles, improving treatment outcomes.

Growing Investment in Genomic Research: Governments, healthcare institutions, and private companies are heavily investing in genomic research and infrastructure to support NGS applications across various fields.

Expansion of Genetic Screening Programs: Many countries are implementing large-scale genetic screening programs for early detection of genetic disorders and hereditary cancers, boosting demand for NGS.

Challenges:

Data Management and Analysis Complexity: The high volume of data generated by NGS requires advanced bioinformatics solutions for analysis, interpretation, and storage. This creates a need for skilled personnel and sophisticated software.

Regulatory and Ethical Concerns: The regulatory landscape for NGS is evolving, and concerns regarding data privacy and ethical issues are prevalent. Obtaining regulatory approval for clinical NGS applications can be time-consuming.

High Initial Investment: Although sequencing costs have decreased, the initial investment required for NGS platforms and bioinformatics infrastructure remains high, limiting adoption in resource-constrained regions.

5. Competitive Landscape

The NGS market is highly competitive, with established players as well as new entrants focusing on niche applications. Key players are investing in research and development, collaborations, and acquisitions to strengthen their market positions and expand product portfolios.

Illumina, Inc.: Illumina is the market leader, with a dominant position in sequencing instruments and consumables. Its sequencers, including the NovaSeq and NextSeq series, are widely used in research and clinical settings.

Thermo Fisher Scientific, Inc.: Known for its Ion Torrent platform, Thermo Fisher focuses on providing affordable, high-throughput sequencing solutions, with applications ranging from cancer research to infectious disease diagnostics.

Pacific Biosciences: PacBio specializes in long-read sequencing technology, particularly valuable for applications that require high accuracy in structural variant detection. Its Sequel system is popular among researchers in complex genomics.

Oxford Nanopore Technologies: Oxford Nanopore offers portable, real-time sequencing devices like the MinION and PromethION, which are particularly useful for field-based applications and rapid sequencing needs.

BGI Group: Based in China, BGI is a major player in genome sequencing services and provides a range of sequencers tailored for research and clinical applications. Its focus on affordability has helped it gain traction in emerging markets.

Qiagen N.V.: Qiagen provides NGS sample preparation and bioinformatics solutions, with a particular emphasis on clinical diagnostics. Its GeneReader NGS System is aimed at making NGS more accessible in clinical labs.

Agilent Technologies: Agilent offers NGS target enrichment and analysis solutions, focusing on workflows for oncology and hereditary disease testing.

6. Future Outlook

Advancements in Data Analysis Tools: Continued improvements in bioinformatics and artificial intelligence are expected to streamline data interpretation, making NGS more accessible to clinical users and reducing the time required for analysis.

Rise of Multi-Omics Approaches: Multi-omics, which combines genomics with proteomics, transcriptomics, and metabolomics, is expected to enhance the understanding of complex diseases. NGS will play a key role in integrating genomic data with other molecular insights.

Increased Focus on Rare Disease Research: NGS enables the identification of mutations associated with rare genetic disorders, facilitating research and development of targeted therapies. This area is likely to see continued growth, especially as pharmaceutical companies invest in precision medicine.

Expansion of Direct-to-Consumer (DTC) Testing: DTC genetic testing is gaining popularity, and as NGS becomes more affordable, companies may offer more comprehensive and affordable sequencing-based consumer tests.

Development of Point-of-Care Sequencing: Point-of-care NGS devices, offering rapid and portable sequencing capabilities, could find applications in emergency rooms and remote locations, particularly for infectious disease diagnosis.

Conclusion

The NGS market is positioned for substantial growth, driven by its expanding role in clinical diagnostics, advancements in sequencing technology, and increasing affordability. Applications in cancer research, infectious disease detection, and reproductive health are set to grow as the technology becomes more integrated into healthcare systems worldwide. However, challenges such as data complexity and regulatory hurdles will require ongoing innovation in bioinformatics and clear guidelines for clinical use. As technology advances, NGS has the potential to become a routine tool in personalized medicine, facilitating earlier diagnosis, better treatments, and improved patient outcomes across a range of medical fields.

[iammaevis]

Genome Sequencing Your Steak: “Where does your food come from?”

When I was about 14 years old, my family butchered our chickens. We had owned four chickens for about three years. The chickens had names, they played with our cat, we fed them dried maggots as a treat. But, after they stopped laying eggs, my parents told us that the next step would be to butcher them. “These animals provide us with food. We’ve eaten all the eggs they’ve given us, and now that they can’t produce eggs, we’ll eat them.” Pretty brutal.

My parents meant for this experience to be brutal. This was the first of many moments where they posed the question to us: “Where does your food come from?”. There’s a life behind the plastic packages we throw into our carts at the store, and remembering this can help us to be mindful of our consumption. This semester, I’ve had the opportunity to reflect on the intentional way my parents developed my relationship with food. I’m taking Food Systems and Policy and Food Security and Sustainability. I enjoy both of them despite how uncomfortable it is to shine a bright light behind the curtain of food production. As I attempt to understand the fundamental question, “Where does food come from?”, I can’t help but feel like my 14-year-old self again… watching a crimson creek of chicken blood make its way through my backyard.

My parents gave me a framework for questioning where my food has come from. I’ve always asked, “Who farmed this produce or raised this livestock?”, “Was the animal treated humanely?”, “What are the environmental impacts of this product?”. I think this line of questioning has been useful, but my recent formal education in food has opened a Pandora’s Box of questions about how food gets from farm to table, and, more importantly, all the things that can go wrong along the way.

I recently learned in Food Security and Sustainability that a staple practice in US agriculture and livestock practices is the employment of monocultures. “Monoculture” refers to the practice of specialization in farming. Farms that only produce one species of food or one species of animal are examples of monocultures. This practice is both wildly profitable and wildly dangerous for the environment, a recurring theme in modern-day markets. I’ve learned in my Evolutionary Biology classes that low genetic diversity has many side effects that almost always lead to population decline and collapse. Collapsing populations reduce global biodiversity which is a surefire way to make an uninhabitable planet. We don’t want that! The study I’ve selected examines how cattle ranchers can maintain genetic diversity in livestock populations and the cultural and ecological importance of said maintenance.

This Swedish study is a breath of fresh air amidst my harrowing discoveries about common practices in US food production (Prepare to read some Good News about some very responsible Swedes and their fluffy cow breeds). In recent years, indigenous cattle populations in Sweden have waned, creating a greater risk of decreased interspecific genetic diversity due to reduced mating options. A smaller gene pool can make populations vulnerable to genetic drift, genetic disorders, runaway mutations, and extinction by famine or disease. Researchers used whole-genome sequencing (WGS) to test the genetic variation between cattle breeds throughout Sweden to get a picture of the relative risk these populations are facing. After testing genomic DNA from 30 individuals, they found that genetic variation is high between species! In fact, genetic variation in indigenous cattle breeds in Sweden is higher compared to other cattle populations around Europe. This means that despite smaller populations, cattle farmers have prioritized smart breeding and isolation of species to maintain a diverse gene pool.

Through artificial breeding, Swedish cattle farmers have ensured that native populations are adapted to the local habitat and resistant to common diseases. They have kept populations isolated to keep species intact. The information gathered through Genome Sequencing is useful for continuing to conserve native breeds and for improving genomic selection programs. This means that native breeds can be mated with industrial breeds to foster genetic diversity.

While Swedish cattle remain on the right side of the sustainable farming tracks, this isn’t the case for most livestock or farming systems around the world. This study used WGS, an expensive and time-consuming genome sequencing technique that severely limits the quantity of samples that can be tested. If anyone in the US wanted to perform a similar test nationwide, major strides would have to be taken to optimize precise genome sequencing. The knowledge front in this study is twofold; the development of the genome sequencing technique and understanding of genetic diversity in livestock. If the efficiency and accessibility of WGS are improved, researchers will have a greater opportunity to understand the breadth of biodiversity in livestock populations and whether efforts to increase genetic diversity are making an impact. This will make it easier to practice smart breeding which keeps genetic diversity high and favors robust traits such as disease resistance.

I’ve never known how much I haven’t known about food production practices, and as I learn, I start to fear for the everyday consumer. As monopolies in agribusiness grow and devour smaller farms one by one, farming and livestock practices push the envelope on reasonable regulations. Pesticides and antibiotics fill our bellies in the form of unhealthy over-processed foods, mistreated livestock, and produce that is harvested by institutions contributing to the deterioration of the Earth. The study I’ve chosen describes a specific tool we can use to prioritize longevity in our livestock production. I hope that this study, among others, provides a basis for how we can improve food systems globally as the climate changes. I think a solid place to start is with questions. Maybe this essay can serve the same purpose as the sacrifice of four chickens in North Carolina around 2018, perhaps it can motivate you to start asking questions. Food doesn’t come from shelves. Food production practices have major adverse effects on the economic and ecological world. The next time you go grocery shopping, ask yourself, “Where does your food come from?”

References:

Harish, A., Lopes Pinto, F.A., Eriksson, S. et al. Genetic diversity and recent ancestry based on whole-genome sequencing of endangered Swedish cattle breeds. BMC Genomics 25, 89 (2024). https://doi.org/10.1186/s12864-024-09959-9

Acknowledgements:

Rio Kasunick’s peer review

Andrea Gonzalez’s peer review

Lori Chin’s Title Suggestions

Prof. Cecelia Musselman’s suggestions

NEU Food Security and Sustainability Fall 2024

NEU Food Systems and Policy Fall 2024

NEU Ecology Fall 2023

[trendingreportz]

Clinical Oncology Next Generation Sequencing Market - Forecast(2024 - 2030)

Clinical Oncology Next Generation Sequencing Market Overview

Clinical Oncology Next Generation Sequencing Market size was valued at $1.4 billion in 2020 and projected to grow at a CAGR of 13.6% during the forecast period 2021-2026. Next-generation sequencing is a technique that helps to simultaneously perform multiple reactions from which it is possible to sequence DNA or RNA. Biological sciences have been revolutionized by massively parallel sequencing technologies i.e. next-generation sequencing (NGS). Targeted sequencing and re-sequencing provides advantages such as high throughput and lower cost per sample of the process thereby enhancing its application Companion Diagnostics. It is a method of assessing the nucleotide sequence in a DNA section and is used for oncology research and enables researchers to carry out a wide range of applications and study biological systems with their ultra-high throughput, scalability, and speed at a level never before possible. In addition, sequencing of the next generation helps in the evaluation of several genes in a single assay, thus reducing the need to order numerous tests to evaluate the underlying mutation thereby driving the Clinical Oncology Next Generation Sequencing Market. In tumour science, a high implementation rate in whole-genome sequencing (WGS) has been seen in recent years driving the Clinical Oncology Next Generation Sequencing Market Industry. The emergence of next-generation sequencing clinical applications in precision oncology has accelerated key company’s efforts to create new platforms that can be used for genomic assays. In February 2021, for instance, Congenica partnered with Gabriel Precision Oncology Ltd. to create an automatic software interface for clinical oncology interpretation using biotechnology. In routine clinical practice, this product will promote NGS-based molecular diagnostics of tumours. 

Report Coverage

The report: “Clinical Oncology Next Generation Sequencing Market Forecast (2021-2026)”, by Industry ARC, covers an in-depth analysis of the following segments of the Clinical Oncology Next Generation Sequencing Market.

By Technology Type: Whole Genome Sequencing, Whole Exome Sequencing and Targeted Sequencing & Resequencing Centrifuges.

By Application: Screening - Sporadic Cancer and Inherited Cancer, Companion Diagnostics and Other Diagnostics.

By Workflow: NGS Pre-Sequencing, NGS Sequencing and NGS Data Analysis.

By End Use: Hospitals/Clinics, Laboratories and Research Labs.

By Geography: North America (U.S, Canada and Mexico), Europe (Germany, UK, France, Italy, Spain, Russia and Rest of Europe), Asia Pacific (China, Japan India, South Korea, Australia & New Zealand, and Rest of Asia Pacific), South America (Brazil, Argentina and Rest of South America) and RoW (Middle East and Africa).

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Key Takeaways

The increasing need for successful treatment of various cancer types and scientific developments in immunology, molecular biology and genetics are likely to contribute to the growth of the Clinical Oncology Next Generation Sequencing industry.

Geographically, North America Clinical Oncology Next Generation Sequencing Market held the largest revenue share of 36% in 2020 owing to an increased emphasis on cancer treatment by government agencies, a rise in healthcare spending and the presence of sufficient resources in the healthcare industry in this region.

The growth of the market is driven by rising research and development activities using NGS technologies, growing NGS applications in clinical diagnosis and discovery applications that demand NGS technology.

Detailed analysis on the Strength, Weakness and Opportunities of the prominent players operating in the market is provided in the Clinical Oncology Next Generation Sequencing Market.

Clinical Oncology Next Generation Sequencing Market Segment Analysis - By Technology Type

Based on Technology Type, Clinical Oncology Next Generation Sequencing Market is segmented into Whole Genome Sequencing, Whole Exome Sequencing and Targeted Sequencing & Resequencing Centrifuges. Targeted Sequencing & Resequencing Centrifuges accounted for the largest revenue market share in 2020 help reduce the expense, time, and volume of data analysed during tumour sample sequencing which is anticipated to favourably impact the segment growth. Targeted sequencing uses deep sequencing within an area of interest to identify recognized and novel variants. Illumina's 523-gene panel contains all the probable genes that have the ability to cause malignant tumours to develop. Medical laboratories have introduced the product to diagnose patients suffering from acute myeloid leukaemia. In addition, the efficacy of targeted panels for the identification of malignant tumors improves their clinical usefulness. In 64% of cancer cases, NGS panels are clinically beneficial, according to a report reported in JCO Precision Oncology, 2020 driving the Clinical Oncology Next Generation Sequencing Industry. Whole Genome Sequencing segment is anticipated to grow with the fastest CAGR of 8.3% in the forecast period 2021-2026 owing to the usefulness of this technology to discern and compare normal tissues from tumour tissues, segment growth. Moreover, whole-genome sequencing of cancer patients helps to identify therapies for existing mutations and also helps to target mutations ahead of time. It also helps analyse the prognosis of cancer and establish a treatment regimen depending on the genes affected aiding to the Clinical Oncology Next Generation Sequencing Market growth.

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Clinical Oncology Next Generation Sequencing Market Segment Analysis - By Application

Based on Application, Clinical Oncology Next Generation Sequencing Market is segmented into Screening - Sporadic Cancer and Inherited Cancer, Companion Diagnostics and Other Diagnostics. Screening accounted for the largest revenue market share in 2020. The most effective way to identify genetic alterations that can be targeted for clinical benefit in cancer patients is currently considered to be NGS-based testing. This technology enables clinicians to analyse several alterations of genes simultaneously. Moreover, as opposed to other pathology methods, technology needs less tumor tissues. An increase in the number of cancer sequencing projects is also increasing the growth of the segment. For instance, 38 different types of cancer were analysed by the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium by sequencing more than 2,600 tumour samples aiding to the market's growth. Companion Diagnostics segment is anticipated to grow with the fastest CAGR of 9.1% during the forecast period 2021-2026. Efforts taken by key market participants to develop advanced computational tools propel the segment growth. For instance, in January 2021, scientists from the MD Anderson Cancer Center created CopyKAT, a new computational tool to distinguish between normal as well as cancer cells in a tumour thus enhancing the Companion Diagnostics segment demand.

Clinical Oncology Next Generation Sequencing Market Segment Analysis - By Geography

Based on Geography, North America Clinical Oncology Next Generation Sequencing Market accounted for the 36% revenue share in 2020. This rise is accounted for by substantial efforts made by regulatory bodies to boost cancer screening detection in the U.S. For instance, the U.S.-initiated Cancer Genome Atlas programme, Next-generation sequencing has been conducted by the National Cancer Institute (NCI) of more than 20,000 primary cancer samples from 33 different cancer types. A consortium of 12 cancer centres, including Johns Hopkins University, Dana-Farber Cancer Institute, and others throughout the United States, is the NCI's Cancer Aim Discovery and Growth Network enhancing the Clinical Oncology Next Generation Sequencing Market. In January 2020, in the United States, the Intelligence Advanced Research Projects Activity provided $23 million to the Broad Institute and Harvard University, and DNA Script. In addition, the emergence of a range of laboratories, academic institutions and hospitals that provide early cancer detection and treatment services based on NGS is owing to the growth of the regional sector. For instance, EasyDNA Canada, a Toronto-based DNA Biotechnology testing company, provides Cancer Predisposition Panel tests that use NGS technology to recognise mutations in a total of 98 genes associated with 25 inherited cancers. The test helps to recognise people who at a later stage of their lives are at a high risk of developing cancer drive the regional growth. Asia-Pacific is predicted to be the fastest-growing region during the forecast period 2021- 2026 owing to the increasing automation in the pre-sequencing protocols in this particular region thereby aiding to regional growth.

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Clinical Oncology Next Generation Sequencing Market Drivers

Increasing Prevalence of Cancer:

Cancer is the second leading cause of death worldwide, according to the WHO, and was responsible for an estimated 9.6 million fatalities in 2018. Need for cancer therapies is rising with the increasing number of cancer cases and deaths caused by cancer. Thus government of various economies focus on drug development, targeted sequencing for the reduction of cancer cases have also increased. Rising biomedical research using next-generation clinical oncology sequencing is estimated to create a favourable environment in the near future for the growth of the next-generation clinical oncology sequencing industry. With substantial advances in genetic sequencing and biomedical science, much research into monoclonal antibodies is now focused on discovering new development targets and optimizing their effectiveness for clinical practice, demonstrating a significant effect on the need for the Clinical Oncology Next Generation Sequencing Market.

Decreasing Sequencing Costs Are Highly Likely To Lead To Market Growth:

In clinical oncology, research and academic institutions are generally interested in the characteristic features of next-generation targeted sequencing technology. The next-generation sequencing techniques in clinical oncology give a high percentage of reads and cost-effectiveness per read. The arrival of low-cost sequencing platforms on the market has made this possible. This increases the overall growth of the next-generation sequencing market for clinical oncology. Several industry players, such as Roche and Illumina, have launched sequencing techniques that have reduced the cost of next-generation sequencing for clinical oncology. Government support for life science research is also estimated to result in the availability of funding for the undertaking of different next-generation sequencing projects in clinical oncology, as well as for the jobs of the staff needed which further act as a driving factor for the growth of the Clinical Oncology Industry.

Clinical Oncology Next Generation Sequencing Market Challenges

Major Regulatory Concerns & Lack Skilled Professionals:

Regulatory concerns regarding usage of Clinical Oncology Next Generation Sequencing Analysis and growing stringent government policy and regulation towards the quantity of service being used in application is restraining growth of the market. Market restrain is also owing to the difficulty in the management of large data and complications, associated with Big Data management. In addition, some of the ethical issues associated with whole-genome sequencing, coupled with the lack of awareness among people are constraining the growth of the market. In addition, the lack of skilled professionals with the sequencing that could be serious for diagnosis purpose set to restrain the market growth. It gets difficult when in an emergency situation, the queue of patients have to wait for experts in the required field negatively impacting the growth.

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Clinical Oncology Next Generation Sequencing Industry Outlook:

Product launches, mergers and acquisitions, joint ventures and geographical expansions are key strategies adopted by players in the Clinical Oncology Next Generation Sequencing Market. Clinical Oncology Next Generation Sequencing Market top 10 companies are Illumina, Inc., Qiagen N.V., Pacific Biosciences of California, Inc., Takara Bio, Inc., Creative Biolabs, Mogene LC, F. Hoffmann-La Roche Ltd, Oxford Nanopore Technologies, Agilent Technologies and Thermo Fisher Scientific Inc.

Acquisitions/Product Launches:

In January 2021, 4baseCare, a start-up in precision oncology, partnered with the Advanced Centre for Cancer Treatment, Study and Education (ACTREC), India, to develop ClinOme, an AI-driven platform for clinical interpretation

In May 2020, Illumina, Inc., has partnered with Burning Rock Biotech Limited, a cancer test provider based in China, to promote the standardisation and development within China of the selection of NGS-based cancer therapy. The company has also signed an agreement to develop and commercialise myChoice tumour testing in China with Myriad Genetics, Inc.

In March 2019, Oxford Nanopore Technologies launched a new paradigm of smaller, on-demand DNA or RNA sequencing tests with the potential to transform a variety of applications where rapid insights are needed at a low cost.

[crimsonpublishers-medical]

Escherichia coli Harboring Mcr-1 on a Novel Plasmid in a Mink in Eastern China- Crimson Publishers

Escherichia coli Harboring Mcr-1 on a Novel Plasmid in a Mink in Eastern China- Crimson Publishers

In the current study, we described the characterization of an mcr-1-positive E. coli isolate from a dead mink in Dongping Lake, China. The molecular characterization of plasmids was also investigated. The strain was resistant to colistin, but it remained susceptible to several other agents, including amikacin, piperacillin-tazobactam, all carbapenems, and ESBLs. E. coli Mink_1 belonged to sequence type 140. Whole Genome Sequencing (WGS) showed that two plasmids, pM1mcr and pM1ctx, coexisted in the same bacterial. Blast and phylogenetic tree imply that Epidemic plasmids are vehicles for the dissemination of colistin resistance genes among the Enterobacterales. Restrictive use of antibiotics in animal husbandry should be taken to reduce the dissemination of mcr-1.

For more open access journals in crimson publishers Please click on link: https://crimsonpublishers.com

For more articles on Research in Medical & Engineering Sciences Please click on link: https://crimsonpublishers.com/rmes/

[covid-safer-hotties]

Analysis of SARS-CoV-2 genomic epidemiology reveals disease transmission coupled to variant emergence and allelic variation - Published April 1, 2021

TL;DR: The more covid spreads, the more variants we get and the more unpredictably they evolve. We've known that slowing the spread is the only viable way to control covid's evolution. Why are our leaders insisting that we allow unmitigated spread?

Abstract The spread of SARS-CoV-2 created a pandemic crisis with > 150,000 cumulative cases in > 65 countries within a few months. The reproductive number (R) is a metric to estimate the transmission of a pathogen during an outbreak. Preliminary published estimates were based on the initial outbreak in China. Whole genome sequences (WGS) analysis found mutational variations in the viral genome; however, previous comparisons failed to show a direct relationship between viral genome diversity, transmission, and the epidemic severity. COVID-19 incidences from different countries were modeled over the epidemic curve. Estimates of the instantaneous R (Wallinga and Teunis method) with a short and standard serial interval were done. WGS were used to determine the populations genomic variation and that underpinned creation of the pathogen genome identity (GENI) score, which was merged with the outbreak curve in four distinct phases. Inference of transmission time was based on a mutation rate of 2 mutations/month. R estimates revealed differences in the transmission and variable infection dynamics between and within outbreak progression for each country examined. Outside China, our R estimates observed propagating dynamics indicating that other countries were poised to move to the takeoff and exponential stages. Population density and local temperatures had no clear relationship to the outbreak progression. Integration of incidence data with the GENI score directly predicted increases in cases as the genome variation increased that led to new variants. Integrating the outbreak curve, dynamic R, and SNP variation found a direct association between increasing cases and transmission genome evolution. By defining the epidemic curve into four stages and integrating the instantaneous country-specific R with the GENI score, we directly connected changes in individual outbreaks based on changes in the virus genome via SNPs. This resulted in the ability to forecast potential increases in cases as well as mutations that may defeat PCR screening and the infection process. By using instantaneous R estimations and WGS, outbreak dynamics were defined to be linked to viral mutations, indicating that WGS, as a surveillance tool, is required to predict shifts in each outbreak that will provide actionable decision making information. Integrating epidemiology with genome sequencing and modeling allows for evidence-based disease outbreak tracking with predictive therapeutically valuable insights in near real time.

[rnomics]

IJMS, Vol. 25, Pages 7793: An Integrated Transcriptomics and Genomics Approach Detects an X/Autosome Translocation in a Female with Duchenne Muscular Dystrophy

Duchenne and Becker muscular dystrophies, caused by pathogenic variants in DMD, are the most common inherited neuromuscular conditions in childhood. These diseases follow an X-linked recessive inheritance pattern, and mainly males are affected. The most prevalent pathogenic variants in the DMD gene are copy number variants (CNVs), and most patients achieve their genetic diagnosis through Multiplex Ligation-dependent Probe Amplification (MLPA) or exome sequencing. Here, we investigated a female patient presenting with muscular dystrophy who remained genetically undiagnosed after MLPA and exome sequencing. #RNA sequencing (#RNAseq) from the patient’s muscle biopsy identified an 85% reduction in DMD expression compared to 116 muscle samples included in the cohort. A de novo balanced translocation between chromosome 17 and the X chromosome (t(X;17)(p21.1;q23.2)) disrupting the DMD and BCAS3 genes was identified through trio whole genome sequencing (WGS). The combined analysis of #RNAseq and WGS played a crucial role in the detection and characterisation of the disease-causing variant in this patient, who had been undiagnosed for over two decades. This case illustrates the diagnostic odyssey of female DMD patients with complex structural variants that are not detected by current panel or exome sequencing analysis. https://www.mdpi.com/1422-0067/25/14/7793?utm_source=dlvr.it&utm_medium=tumblr

[leedsomics]

Whole genome sequence and 16S rRNA gene amplicon metagenomics of enhanced in-situ reductive dechlorination at a tetrachloroethene-contaminated superfund site

The application of environmental DNA analysis techniques to guide the bioremediation strategy for tetrachloroethene-contaminated groundwater is exemplified by the North Railroad Avenue Plume (NRAP) Superfund site located in New Mexico, USA. Enhanced reductive dechlorination (ERD) was selected as the remedy due to the presence of tetrachloroethene biodegradation byproducts, organohalide respiring genera Dehalococcoides and Dehalobacter, and associated reductive dehalogenase genes detected prior to remediation. DNA extracted from groundwater samples collected prior to remedy application and after four, 23 and 39 months was subjected to 16SrRNA gene amplicon and whole genome sequencing (WGS). The goals were to compare the potential of these methods as tools for environmental engineers and to highlight how advancements in DNA techniques can be used to understand ERD. The response of the indigenous NRAP microbiome to the injection and recirculation of electron donors and hydrogen sources is consistent with results obtained from microcosms, dechlorinating consortia, and other contaminated sites. WGS detects three times as many phyla and six times as many genera as 16S rRNA gene amplicons. Both techniques reveal abundance changes in Dehalococcoides and Dehalobacter that reflect organohalide form and availability. No methane was detected before remediation, its appearance after biostimulation corresponds to the increase in methanogenic Archaea. Assembly of WGS reads produced scaffolds containing reductive dehalogenase genes from Dehalococcoides, Dehalobacter, Dehalogenimonas, Desulfocarbo, and Desulfobacula. Anaerobic and aerobic cometabolic organohalide degrading microbes that increase in abundance at NRAP include methanogenic Archaea, methanotrophs, Dechloromonas, and Xanthobacter, some of which contain hydrolytic dehalogenase genes. Aerobic cometabolism may be supported by oxygen gradients existing at the aquifer-soil interface or by microbes that have the potential to produce O2 via chlorite dismutation. Results from next-generation sequencing-based methods are consistent with current hypotheses regarding syntrophy in environmental microbiomes and reveals novel taxa and genes that may contribute to ERD. http://dlvr.it/T8kS3l

[evoldir]

Fwd: Postdoc: UOldenburg.EvolutionAntibioticResistance

Begin forwarded message: > From: evoldir@evol.biology.mcmaster.ca > Subject: Postdoc: UOldenburg.EvolutionAntibioticResistance > Date: 24 January 2025 at 05:54:32 GMT > To: rdmpage@gmail.com > > > > Postdoctoral fellow in the Institute of Medical Microbiology and Virology > > The School VI of Medicine and Health Sciences comprises the fields of > human medicine, medical physics and acoustics, neurosciences, psychology > and health services research. Together with the four regional hospitals, > School VI forms the University Medicine Oldenburg. Furthermore, the > university cooperates closely with the University Medicine of the > University of Groningen. > > In the research laboratory (location: Philosophenweg) of the Institute of > Medical Microbiology and Virology (Director: Prof. Dr. Axel Hamprecht), > Medical Campus of the University of Oldenburg, we are engaged in > clinically-oriented and fundamental microbiological research with a focus > on antibiotic resistance, resistance mechanisms and multidrug-resistant > pathogens in human and veterinary medicine and the environment. > > Your tasks > > � The scientific activity includes the supervision of research projects > from conception, acquisition of third-party funding to the publication > of results. > > � You will actively participate in the development and organization of > the research laboratory. > > � Active participation in the planning and implementation of teaching. > > Your profile > > Required qualifications: > > � Completed university degree (Master or equivalent) in biology, > biochemistry, human biology, human or veterinary medicine or a related > field with completion of a PhD, MD or equivalent. > > � Expertise in microbiological and biomolecular methods. > > � Experience in documentation of research results, data management > and analysis. > > � Ability to prepare, present and publish scientific data. > > � Excellent communication skills in English, knowledge of German > (B2-level) > > � High level of commitment, an independent way of working and the > ability to work in a team. > > Preferred qualifications: > > � Knowledge of bioinformatic methods and whole genome sequencing (WGS). > > � Experience in genetic engineering work > > We offer > > � A friendly environment with opportunities to develop your own research > focus and projects. > > � Active participation in the development of our research unit. > > � Payment in accordance with collective bargaining law (special annual > payment, public service pension scheme, asset-related benefits) incl. > 30 days annual leave > > � Support and guidance during your onboarding phase > > � A family-friendly environment with flexible working hours (flexitime) > and the possibility of pro-rata mobile work > > � Benefits from the university's health promotion programme > > � The possibility of personal scientific qualification (post-doctoral > thesis/habilitation) > > � An extensive and free further education programme as well as > programmes geared toward the promotion of early career researchers > (https://ift.tt/yBfMrRW) > > Our standards > > The University of Oldenburg is dedicated to increase the percentage of > female employees in the field of science. Therefore, female candidates > are strongly encouraged to apply.  In accordance to � 21 Section 3 > NHG, female candidates with equal qualifications will be preferentially > considered. Applicants with disabilities will be given preference in > case of equal qualification. > > Further information > > There is the possibility of personal scientific qualification > (post-doctoral thesis). > > Contact > > For further information please contact Prof. Dr. Axel Hamprecht, > sandra.schoebel@uol.de, 0441/403 2160. > > Apply now > > Please send your application via e-mail by 22.02.2025 to > > sandra.schoebel@uol.de > > Please send your application documents (description of your motivation, > curriculum vitae, references) as one PDF document. > > Timo van Eldijk