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  • Researchers create genetic atlas detailing early stages of zebrafish development

    Researchers create genetic atlas detailing early stages of zebrafish development
    19th December 2023

    Credit: J. Swan and K. Tabor, NICHD/NIH

    Researchers at the National Institutes of Health have published an atlas of zebrafish development, detailing the gene expression programs that are activated within nearly every cell type during the first five days of development, a period in which embryos mature from a single cell into distinct cell types. These diverse cells become tissues and organs that form juvenile fish capable of swimming and looking for food. The findings are published in Developmental Cell.

    “Perhaps surprisingly, tiny zebrafish provide us with significant insight into human development and disease. Many of the gene expression programs that direct embryonic growth are similar across fish, people, and other animals,” said Christopher McBain, Ph.D., scientific director of the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), which conducted the work. “Since zebrafish are visibly transparent, fertilize eggs externally, and are easy to study genetically, they represent a unique and effective way to model human disease.”

    The process of embryonic development is orchestrated by instructions in DNA that direct different programs of gene expression within individual cells, which give different cell types their unique functional characteristics. To create the atlas, the study team used a method called single-cell RNA sequencing to identify gene expression programs over the course of five days, with samples taken every two to 12 hours.

    By NIH/Eunice Kennedy Shriver National Institute of Child Health and Human Development

    Article can be accessed on: MedicalXpress

  • Peroxidase gene found to confer drought tolerance in soybean

    Peroxidase gene found to confer drought tolerance in soybean
    1st December 2023

    Credit: IGDB

    A research team led by Prof. Tian Zhixi of the Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Sciences, in collaboration with Prof. Ma Junkui from the Industrial Crop Institute of Shanxi Agriculture University/Shanxi Academy of Agricultural Sciences, identified the drought tolerance value of 585 soybean accessions covering the major growing areas of the world to mine the genes and corresponding beneficial alleles in soybean germplasm.

    The paper entitled “Natural allelic diversities of GmPrx16 confer drought tolerance in soybean” was published in Plant Biotechnology Journal on Nov. 22. A significant locus on chromosomes 16 was detected by genome-wide association study (GWAS). Further analysis showed that a peroxidase harboring a nonsynonymous SNP was the occasional gene in the locus, and the nonsynonymous mutations resulted in peroxidase activity differences between the two GmPrx16 haplotypes. Furthermore, overexpression of GmPrx16 in Dongnong No.50 could improve the peroxidase activity and enhance the drought tolerance in soybean, but GmPrx16 RNAi transgenic lines reduced the peroxidase activity and showed a drought-sensitive phenotype. Interestingly, overexpression of GmPrx16 could improve salt tolerance in soybean at the same time, suggesting multiple applications of GmPrx16 in breading abiotic tolerant soybean.

    GmDRF1 and GmDRF2 could bind to the promoter of GmPrx16 and regulate the expression level of GmPrx16, proposing the working model of GmPrx16: drought stress induces the expression of GmDRF1 and GmDRF2, GmDRF1 and GmDRF2 physically interact with the promoter of GmPrx16, and promote its expression, thereby influencing the accumulation of ROS and regulating drought tolerance in soybean.

    By Zhang Nannan, Chinese Academy of Sciences

    Article can be accessed on: phys.org

  • Potential new treatment for COVID-19 is made from plants

    Potential new treatment for COVID-19 is made from plants
    1st December 2023

    The novel coronavirus SARS CoV-2 is responsible for the COVID-19 global pandemic. A new form of monoclonal antibody therapeutic to treat the disease is described in a new study, which graces the cover of Plant Biology Journal. Credit: Jason Drees

    In new research, Shawn Chen, a researcher with Arizona State University’s Biodesign Center for Immunotherapy, Vaccines and Virotherapy and School of Life Sciences, describes an innovative therapy for COVID-19. The method highlighted in the study uses transient expression in tobacco plants to develop and produce a monoclonal antibody, or mAb. The study highlights the potential of synergizing antibody cocktails with the addition of monoclonal antibodies that do not directly hinder ACE2 binding to the receptor-binding domain. The study also underscores the potential of plant-based monoclonal antibody expression platforms in therapeutic development against the ever-evolving SARS-CoV-2 pandemic. Plant-made COVID-19 therapies have several advantages over other production platforms. Plants can produce large quantities of therapeutic proteins in a relatively short amount of time, making them ideal for scaling up production. They are inexpensive to grow and maintain, making them a cost-effective alternative to traditional protein expression systems. Because plants are not natural hosts for human pathogens, their use reduces the risk of contamination with infectious agents.

    Finally, plant-based expression systems can be rapidly reprogrammed to produce new therapeutics in response to emerging pathogens such as SARS-CoV-2, making them an attractive option for pandemic response.

    By Richard Harth, Arizona State University

    Article can be accessed on: MedicalXpress

  • CAR-T cell therapy leads to long-term remission in lupus while maintaining vaccine response

    CAR-T cell therapy leads to long-term remission in lupus while maintaining vaccine response
    8th November 2023

    Credit: CC0 Public Domain

    New research at ACR Convergence 2023, the American College of Rheumatology’s annual meeting, demonstrates that CAR-T cell therapy could lead to sustained suppression of autoantibodies in treatment-resistant lupus while maintaining a robust response to vaccines. Systemic lupus erythematosus (SLE, lupus) is a complex autoimmune disease marked by the production of autoantibodies to nucleic acid DNA and nuclear protein autoantigens and is associated with dysfunctional B cells. It mainly affects women and is more common and severe in people who are Black, Hispanic, or Asian. Lupus can lead to a wide range of systemic problems varying in severity, including skin, kidney, lung, joints, and heart disease and complications during pregnancy. The disease often requires lifelong treatment with immunosuppressive or immunomodulatory drugs, and a considerable number of patients don’t respond to them. One theoretical option for these patients is chimeric antigen receptor (CAR)-T cell therapy, which is successfully used to treat refractory blood cancers by destroying malignant cells. “We were intrigued by the possibility that a deep B cells depletion exerted by CAR-T cells could lead to permanent eradication of the autoimmune disease,” says Georg Schett, MD, a rheumatologist at the University Hospital Erlangen in Germany. CAR-T cells are created by removing some of a patient’s white blood cells, including immune system T cells, and genetically altering them in a lab to produce chimeric antigen receptors (CARs). The modifications allow the treated T cells to recognize and destroy antigens on the surface of target pathogenic cells after they are infused back into the patient.

    By American College of Rheumatology

    Article can be accessed on: MedicalXpress

  • A comprehensive database for the study of protein aggregation

    A comprehensive database for the study of protein aggregation
    8th November 2023

    Credit: Autonomous University of Barcelona

    Researchers at the IBB-UAB have developed the most comprehensive database available to date to help understand the basis of protein aggregation, a phenomenon associated with aging and several pathologies. The new resource, A3D-MOBD, brings together the proteomes of 12 of the most studied model organisms, which cover distant biological clades, and contains more than half a million predictions of protein regions with a propensity to form aggregates. The A3D-MOBD was developed by the Protein Folding and Computational Diseases Group at the Institut de Biotecnologia i de Biomedicina of the Universitat Autònoma de Barcelona (IBB-UAB), which is directed by Biochemistry and Molecular Biology Professor Salvador Ventura. In collaboration with scientists from the University of Warsaw, the study was recently published in the journal Nucleic Acids Research. It provides pre-calculated aggregation propensity analyses and tools for the study of this phenomenon on a proteomic scale as well as evolutionary comparison between different species.

    The new resource builds on the method that the same research group designed in 2015, Aggrescan 3D, but significantly expands the obtainable data. In total, it contains more than 500,000 structural predictions for more than 160,000 proteins from 12 highly characterized model organisms widely used in biology, biotechnology and biomedicine research.

    It includes the herbaceous plant Arabidopsis thaliana,  nematode worm Caenorhabditis elegans, zebrafish Danio rerio, enteric bacterium Escherichia coli, minimal genome bacteria Mycoplasma genitalium, mouse Mus musculus, fusion and fission yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, human Homo sapiens, rat Rattus norvegicus, fruit fly Drosophila melanogaster and  COVID-19 causative virus SARS-CoV-2.

     

    By Autonomous University of Barcelona

    Article can be accessed on: phys.org

  • Study shows the microbiome of fruit and vegetables positively influences diversity in the gut

    Study shows the microbiome of fruit and vegetables positively influences diversity in the gut
    27th October 2023

    Overview of the bioinformatic workflow for the recovery of metagenome-assembled genomes (MAGs) from fruits and vegetables and the detection of their presence in the gut. Credit: DOI: 10.1080/19490976.2023.2258565

    It is known that an important part of the maternal microbiome is transferred to the baby at birth, and the same happens during the breastfeeding period via breast milk. Further sources were yet to be discovered. However, a team led by Wisnu Adi Wicaksono and Gabriele Berg from the Institute of Environmental Biotechnology at Graz University of Technology (TU Graz) has now succeeded in proving that plant microorganisms from fruit and vegetables contribute to the human microbiome. They report this in a study published in the journal Gut Microbes. The authors were able to demonstrate that the frequency of fruit and vegetable consumption and the variety of plants consumed influences the amount of fruit- and vegetable-associated bacteria in the human gut. Early childhood in particular represents a window of opportunity for colonization with plant-associated bacteria. It was also demonstrated that the microorganisms of plant origin have probiotic and health-promoting properties. A microbiome is the totality of all microorganisms that colonize a macroorganism (human, animal, plant) or a part of it, for example the intestine or a fruit. While the individual microbiomes are becoming better understood, little is known about their connections.

    “The proof that microorganisms from fruits and vegetables can colonize the human gut has now been established for the first time,” explains first author Wisnu Adi Wicaksono.

     

    By Falko Schoklitsch, Graz University of Technology

    Article can be accessed on: MedicalXpress

  • Scientists use custom genome assembly and editing method to improve sheepgrass

    Scientists use custom genome assembly and editing method to improve sheepgrass
    27th October 2023

    Morphological view and genomic profile of forage Sheepgrass. Credit: IGDB

    A research team led by Dr. Cao Xiaofeng at the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences has improved biomass-related traits in sheepgrass using its own custom genome editing system while increasing understanding of sheepgrass genomics. The team’s genome assembly and innovative gene editing system, characterized by the fusion of big data and biotechnology, reveals the potential for intelligent and rapid genomic breeding of sheepgrass. The study was published in PNAS on Oct. 24.

    Leymus chinensis (sheepgrass), a member of the Triticeae family, is a prominent grass species throughout the Eurasian steppe. This species, which is known for its robust rhizomes, has impressive attributes such as frost tolerance, drought tolerance, salt tolerance, and good soil stabilization capacity, etc.

    Sheepgrass is widely recognized as a high quality forage that provides both ecological and economic benefits due to its exceptional nutritional value and palatability. However, due to the sheepgrass genome’s large size and high heterozygosity, studying it and elucidating its outstanding properties is challenging.

    In this study, the researchers selected L. chinensis Lc6-5, a type of sheepgrass from the grasslands of Northeast China with strong rhizomes. They performed genome assembly using cutting-edge sequencing and assembly techniques. The assembled genome size was approximately eight Gb, with a contig N50 of more than 300 Mb and repetitive sequences accounting for 87.76% of the genome.

     

    By Zhang Nannan, Chinese Academy of Sciences

    Article can be accessed on: phys.org
  • Regenerative cell therapy for epilepsy

    Regenerative cell therapy for epilepsy
    16th October 2023

    Credit: Cell Stem Cell (2023). DOI: 10.1016/j.stem.2023.08.013

    Together with colleagues, veterinarian and neuroscientist Sonja Bröer has researched how regenerative cell therapies can contribute to curing or alleviating epilepsy. The work was carried out at biotechnology start-up Neurona Therapeutics, Inc. in San Francisco, where Bröer led a team in preclinical research, before she moved to Freie Universität Berlin. The company is developing a cell therapy (NRTX-1001) for treatment-resistant epilepsy and has now published the results from preclinical studies in Cell Stem Cell. Based on these data, the cell therapy is now being evaluated in human patients as part of an ongoing phase 1/2 clinical trial. On October 6, 2023, Bröer will present both the preclinical and the first clinical data at the Einstein Center for Neurosciences’ Berlin Neuroscience Meeting. Approximately 50 million people worldwide suffer from epilepsy; in about one-third of patients, epileptic seizures do not respond to drug treatment, reducing patients’ quality of life as well as their life expectancy. Epilepsy occurs when excessive electrical discharges occur in nerve cells of the brain. The neurotransmitter gamma-aminobutyric acid (GABA) can block this overexcitation. However, the nerve cells that secrete this neurotransmitter can degenerate in patients with epilepsy, creating an imbalance between inhibition and excitation in the brain that is thought to pave the way for epileptic seizure activity. In their recent publication in Cell Stem Cell, Bröer and her colleagues report on the transplantation of inhibitory GABA-secreting neurons that can potentially restore the balance in the brain and suppress epileptic seizures.

    By Japhet Johnstone, Free University of Berlin

    Article can be accessed on: MedicalXpress

  • Researchers develop new open-source method to improve decoding of single-cell data

    Researchers develop new open-source method to improve decoding of single-cell data
    16th October 2023

    Credit: Nature Biotechnology (2023). DOI: 10.1038/s41587-023-01940-3

    Researchers at Memorial Sloan Kettering Cancer Center (MSK) have developed a new open-source computational method, dubbed Spectra, which improves the analysis of single-cell transcriptomic data. By guiding data analysis in a unique way, Spectra can offer new insights into the complex interplay between cells-like the interactions between cancer cells and immune cells, which are critical to improving immunotherapy treatments. The team’s approach and findings were recently published in Nature Biotechnology. Spectra, the researchers note, can cut through technical “noise” to identify functionally relevant gene expression programs, including those that are novel or highly specific to a particular biological context. The algorithm is well suited to study data from large patient cohorts and to suss out clinically meaningful patient characteristics, the MSK team writes in a research briefing that accompanies the study, adding that Spectra is ideal for identifying biomarkers and drug targets in the burgeoning field of immuno-oncology. Additionally, the MSK team has made Spectra freely available to researchers around the world.

    “I’m trained as a computer scientist,” says study senior author Dana Pe’er, Ph.D., who chairs the Computational and Systems Biology Program at MSK’s Sloan Kettering Institute. “Every single tool I build, I strive to make robust so it can be used in many contexts, not just one. I also try and make them as accessible as possible.”

    By Ian Demsky, Memorial Sloan Kettering Cancer Center

    Article can be accessed on: MedicalXpress

     

  • Gates Foundation funding $40 million effort to help develop mRNA vaccines in Africa in coming years

    Gates Foundation funding $40 million effort to help develop mRNA vaccines in Africa in coming years
    10th October 2023

    Bill Gates speaks to The Associated Press during a visit of the Institut Pasteur in dakar, Senegal, Sunday, Oct. 8, 2023. Credit: AP Photo

    A $40 million investment will help several African manufacturers produce new messenger RNA vaccines on the continent where people were last in line to receive jabs during the COVID-19 pandemic, the Bill & Melinda Gates Foundation announced Monday. While it could still take at least three more years before any of the vaccines are approved and on the market, the foundation said that its mRNA investment marks an important step forward in improving vaccine equity.

    “Whether it’s for local diseases in Africa like Rift Valley (fever) or for global diseases like TB, mRNA looks like a very promising approach,” Bill Gates told The Associated Press on Sunday after visiting one of the facilities involved, the Institut Pasteur in Dakar, Senegal. “And so it allows us to bring in lots of African capabilities to work on these vaccines, and then this can be scaled up. The announcement comes as the foundation opens its annual three-day Grand Challenges event, which brings together scientists and public health researchers from around the world.

    Institut Pasteur, along with the South Africa-based company Biovac, will be using an mRNA research and manufacturing platform that was developed by Quantoom Biosciences in Belgium. The two Africa-based vaccine manufacturers are receiving $5 million each in funding from the foundation, while another $10 million is earmarked for other companies that have not yet been named. The remaining $20 million is going to Quantoom “to further advance the technology and lower costs.”

    By Krista Larson

    Article can be accessed on: MedicalXpress