Tag: bioRxiv
DeepMind’s AlphaFold Seeing Uptake for Protein-Protein Interaction Work
NEW YORK – Since its introduction in 2018, DeepMind’s AlphaFold program has become a key tool in biological research, allowing scientists to predict protein structures with high accuracy based on their amino acid sequences. More recently, researchers have begun using AlphaFold and its newer iteration, AlphaFold2, for protein-protein interaction (PPI)…
Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants
Awasthi MK, Singh E, Binod P, Sindhu R, Sarsaiya S, Kumar A, et al. Biotechnological strategies for bio-transforming biosolid into resources toward circular bio-economy: a review. Renew Sustain Energy Rev. 2022;156:111987. Article CAS Google Scholar Diamantis V, Eftaxias A, Stamatelatou K, Noutsopoulos C, Vlachokostas C, Aivasidis A. Bioenergy in the…
Transcriptomics and the origin of obligate parthenogenesis
Avise J (2008) Clonality: the genetics, ecology, and evolution of sexual abstinence in vertebrate animals. Oxford University Press, USA Book Google Scholar Avise JC (2015) Evolutionary perspectives on clonal reproduction in vertebrate animals. Proc Natl Acad Sci USA 112(29):8867–8873 Article CAS PubMed PubMed Central Google Scholar Andrews S (2010) FastQC:…
Fine-scale genomic tracking of Ross River virus using nanopore sequencing | Parasites & Vectors
Flaxman JP, Smith DW, Mackenzie JS, Fraser JRE, Bass SP, Hueston L, et al. A comparison of the diseases caused by Ross River virus and Barmah Forest virus. Med J Aust. 1998;169:159–63. Article Google Scholar El-Hage CM, Bamford NJ, Gilkerson JR, Lynch SE. Ross River virus infection of horses: appraisal…
The Biostar Herald for Monday, June 05, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
Long-read genome sequencing identifies cryptic structural variants in congenital aniridia cases | Human Genomics
Hingorani M, Hanson I, van Heyningen V. Aniridia. Eur J Hum Genet. 2012;20:1011–7. Article CAS PubMed PubMed Central Google Scholar Lima Cunha D, Arno G, Corton M, Moosajee M. The spectrum of PAX6 mutations and genotype-phenotype correlations in the eye. Genes. 2019;10:1050. Article PubMed PubMed Central Google Scholar Cvekl A,…
Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes
Johnson, W. E. Endogenous retroviruses in the genomics era. Annu. Rev. Virol. 2, 135–159 (2015). Article CAS PubMed Google Scholar Johnson, W. E. Origins and evolutionary consequences of ancient endogenous retroviruses. Nat. Rev. Microbiol. 17, 355–370 (2019). Article CAS PubMed Google Scholar Johnson, W. E. Endless forms most viral. PLoS…
Transfer learning enables predictions in network biology
Vaswani, A. et al. Attention is all you need. Preprint at doi.org/10.48550/arXiv.1706.03762 (2017). Devlin, J., Chang, M. W., Lee, K. & Toutanova, K. BERT: pre-training of deep bidirectional transformers for language understanding. In Proc. 2019 Conference North American Chapter of the Association for Computational Linguistics: Human Language Technologies Vol. 1…
Nuclear export of pre-60S particles through the nuclear pore complex
Hampoelz, B., Andres-Pons, A., Kastritis, P. & Beck, M. Structure and assembly of the nuclear pore complex. Annu. Rev. Biophys. 48, 515–536 (2019). Article CAS PubMed Google Scholar Lin, D. H. & Hoelz, A. The structure of the nuclear pore complex (an update). Annu. Rev. Biochem. 88, 725–783 (2019). Article …
Reduced trace gas oxidizers as a response to organic carbon availability linked to oligotrophs in desert fertile islands
Makhalanyane TP, Valverde A, Gunnigle E, Frossard A, Ramond JB, Cowan DA. Microbial ecology of hot desert edaphic systems. FEMS Microbiol Rev. 2015;39:203–21. Article CAS PubMed Google Scholar Pointing SB, Belnap J. Microbial colonization and controls in dryland systems. Nat Rev Microbiol. 2012;10:551–62. Article CAS PubMed Google Scholar Ji M,…
A non-coding variant linked to metabolic obesity with normal weight affects actin remodelling in subcutaneous adipocytes
Cho, N. H. et al. IDF Diabetes Atlas: global estimates of diabetes prevalence for 2017 and projections for 2045. Diabetes Res. Clin. Pract. 138, 271–281 (2018). Article CAS PubMed Google Scholar Lu, Y. et al. New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk. Nat….
Deep exome sequencing identifies enrichment of deleterious mosaic variants in neurodevelopmental disorder genes and mitochondrial tRNA regions in bipolar disorder
GBD 2016 Disease Injury Incidence Prevalence Collaborators. Global, regional, and national incidence, prevalence, and years lived with disability for 328 diseases and injuries for 195 countries, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet. 2017;390:1211–59. Article Google Scholar Kato T. Current understanding of bipolar disorder:…
ImmuneBuilder: Deep-Learning models for predicting the structures of immune proteins
Kingwell, K. T cell receptor therapeutics hit the immuno-oncology stage. Nat. reviews. Drug Discov. www.nature.com/articles/d41573-022-00073-7 (2022). Kaplon, H., Chenoweth, A., Crescioli, S. & Reichert, J. M. Antibodies to watch in 2022. mAbs 14, 2014296 (2022). Article PubMed PubMed Central Google Scholar Lu, R.-M. et al. Development of therapeutic antibodies for…
The RNA-DNA World And The Emergence Of DNA-encoded Heritable Traits
Origin & Evolution of Life Status Report biorxiv.org May 28, 2023 Stochastic simulation of a population of water-in-oil droplets containing strands. Heatmaps for A: average fraction of replicase ribozymes per droplet; B: fraction of droplets containing both replicase (R) and replicase encoding DNA template (TdR); C: average reaction propensity of…
Genomelink’s global ancestry – XGMix algorithm for deeper DNA analysis
Genomelink’s global ancestry (New): Uses the XGMix algorithm for deeper DNA analysis (at the Chromosome level) that shows how the ancestry breaks down at the chromosome level and also shows the overalls ethnicity estimate. Backed by Carlos D. Bustamante, Alexander Ioanidis, Razib Khan. see:genomelink.io/product/global…try-dna-reportwww.biorxiv.org/content/10.1…876v1.full.pdf My overall ethnicity: chromosome level (examples…
Targeted adaptive long-read sequencing for discovery of complex phased variants in inherited retinal disease patients
Bessant, D. A., Ali, R. R. & Bhattacharya, S. S. Molecular genetics and prospects for therapy of the inherited retinal dystrophies. Curr. Opin. Genet. Dev. 11, 307–316 (2001). Article CAS PubMed Google Scholar Berger, W., Kloeckener-Gruissem, B. & Neidhardt, J. The molecular basis of human retinal and vitreoretinal diseases. Prog….
Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds
Asalone KC, Ryan KM, Yamadi M, Cohen AL, Farmer WG, George DJ, Joppert C, Kim K, Mughal MF, Said R, Toksoz-Exley M, Bisk E, Bracht JR (2020) Regional sequence expansion or collapse in heterozygous genome assemblies. PLoS Comput Biol. doi.org/10.1371/journal.pcbi.1008104 Article PubMed PubMed Central Google Scholar Bankevich A, Nurk S,…
Pangenomics of the death cap mushroom Amanita phalloides, and of Agaricales, reveals dynamic evolution of toxin genes in an invasive range
Sakai AK, Allendorf FW, Holt JS, Lodge DM, Molofsky J, With KA, et al. The population biology of invasive species. Annu Rev Ecol Syst. 2001;32:305–32. Article Google Scholar Allendorf FW, Lundquist LL. Introduction: population biology, evolution, and control of invasive species. Conserv Biol. 2003;17:24–30. Article Google Scholar Erickson AB. The…
New vaccine concept against SARS-CoV-2 successfully tested
Single-cycle vaccine concept and viral characterization. Credit: bioRxiv (2023). DOI: 10.1101/2023.05.17.541127 Researchers at the University of Basel have developed a new approach for a vaccine against COVID-19. This vaccine is based on a modified coronavirus that can enter body cells and trigger an effective immune response but cannot multiply in…
A preliminary study of the use of MinION sequencing to specifically detect Shiga toxin-producing Escherichia coli in culture swipes containing multiple serovars of this species
Tarr, P. I., Gordon, C. A. & Chandler, W. L. Shiga toxin-producing Escherichia coli and haemolytic uremic syndrome. Lancet 365, 1073–1086 (2006). Google Scholar Koudelka, G. B., Arnold, J. W. & Chkraborty, D. Evolution of STEC virulence: Insights from the antipredator activities of shiga toxing-producing E. coli. Int. J. Med….
Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels
Dubilier N, Bergin C, Lott C. Symbiotic diversity in marine animals: the art of harnessing chemosynthesis. Nat Rev Microbiol. 2008;6:725–40. Article CAS PubMed Google Scholar Sogin EM, Kleiner M, Borowski C, Gruber-Vodicka HR, Dubilier N. Life in the dark: phylogenetic and physiological diversity of chemosynthetic symbioses. Annu Rev Microbiol. 2021;75:695–718….
Postdoctoral Associate- Cellular Heterogeneity and Circuit Organization of Brains job with Baylor College of Medicine (BCM)
Summary The Jiang laboratory in the Departments of Neuroscience at Baylor College of Medicine is seeking applicants for postdoc associate positions. The specific goal of the postdoc fellows for these positions is to use a multi-disciplinary approach, including single-cell transcriptomics, Patch-seq, multi-patch clamp recording, machine learning, and complicated genetic tools…
Nobel Laureate Jennifer Doudna Opens Presidential Symposium
LOS ANGELES — That the honor of opening the Presidential Symposium of the American Society of Gene and Cell Therapy (ASGCT) conference should fall to 2020 Nobel laureate Jennifer Doudna, PhD, the CRISPR genome editing pioneer, was no surprise. But the topic of Doudna’s presentation—new research in the arena of…
Ancient gene linkages support ctenophores as sister to other animals
Ryan, J. F. et al. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342, 1242592 (2013). Article PubMed PubMed Central Google Scholar Halanych, K. M. The ctenophore lineage is older than sponges? That cannot be right! Or can it? J. Exp. Biol. 218,…
Apoptotic gene loss in Cnidaria is associated with transition to parasitism
Elmore, S. Apoptosis: A review of programmed cell death. Toxicol. Pathol. 35, 495–516 (2007). Article CAS PubMed PubMed Central Google Scholar Shi, Y. Caspase activation, inhibition, and reactivation: A mechanistic view. Protein Sci. 13, 1979–1987 (2004). Article CAS PubMed PubMed Central Google Scholar Alberts, B., Johnson, A. & Lewis, J….
Hallmarks of cardiovascular ageing | Nature Reviews Cardiology
Bergmann, O. et al. Evidence for cardiomyocyte renewal in humans. Science 324, 98–102 (2009). Article CAS PubMed PubMed Central Google Scholar Senyo, S. E. et al. Mammalian heart renewal by pre-existing cardiomyocytes. Nature 493, 433–436 (2013). Article CAS PubMed Google Scholar Bergmann, O. et al. Dynamics of cell generation and…
Novel ‘CLEVER’ method accelerates engineering and genetic study of SARS-CoV-2 and its variants
A recent study posted to the bioRxiv*preprint server described rapid mutagenesis and rescue of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants without cloning, using a novel reverse genetics strategy. Study: Rapid cloning-free mutagenesis of new SARS-CoV-2 variants using a novel reverse genetics platform. Image Credit: kentoh/Shutterstock.com *Important notice: bioRxiv publishes preliminary…
Introduction to R for Microbiome Data
Abubucker, Sahar, Nicola Segata, Johannes Goll, Alyxandria M. Schubert, Jacques Izard, Brandi L. Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat, Owen White, Scott T. Kelley, Barbara Methé, Patrick D. Schloss, Dirk Gevers, Makedonka Mitreva, and Curtis Huttenhower. 2012. Metabolic reconstruction for metagenomic data and its application to the…
A global phylogeny of butterflies reveals their evolutionary history, ancestral hosts and biogeographic origins
Chazot, N. et al. Priors and posteriors in Bayesian timing of divergence analyses: the age of butterflies revisited. Syst. Biol. 68, 797–813 (2019). Article PubMed PubMed Central Google Scholar Allio, R. et al. Whole genome shotgun phylogenomics resolves the pattern and timing of swallowtail butterfly evolution. Syst. Biol. 69, 38–60…
Predictive network analysis identifies JMJD6 and other potential key drivers in Alzheimer’s disease
Cerejeira, J., Lagarto, L. & Mukaetova-Ladinska, E. B. Behavioral and psychological symptoms of dementia. Front. Neurol. 3, 73 (2012). Article CAS PubMed PubMed Central Google Scholar Murphy, M. P. & LeVine, H. III Alzheimer’s disease and the amyloid-beta peptide. J. Alzheimers Dis. 19, 311–323 (2010). Article PubMed PubMed Central Google…
Cost-effective Whole Exome Sequencing discovers pathogenic variant causing Neurofibromatosis type 1 in a family from Jammu and Kashmir, India
Cawthon, R. M. et al. A major segment of the neurofibromatosis type 1 gene: cDNA sequence, genomic structure, and point mutations. Cell 62, 193–201 (1990). Article CAS PubMed Google Scholar Buske, A. et al. Recurrent NF1 gene mutation in a patient with oligosymptomatic neurofibromatosis type 1 (NF1). Am. J. Med….
Bantu people came from Congo, genetic data shows
This is a relatively well-known story. About 4,000 years ago, a band of Bantu speakers left West Africa and moved to colonise half of Africa. They pushed through the Congo rainforest spreading to southern and eastern Africa. Some eventually settled in what is modern-day Kenya. They migrated further from Kenya…
The Biostar Herald for Thursday, May 11, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
Identification of a genomic DNA sequence that quantitatively modulates KLF1 transcription factor expression in differentiating human hematopoietic cells
Laurenti, E. & Gottgens, B. From haematopoietic stem cells to complex differentiation landscapes. Nature (London) 553, 418–426 (2018). ADS CAS PubMed Google Scholar Miller, I. J. & Bieker, J. J. A novel, erythroid cell-specific murine transcription factor that binds to the CACCC element and is related to the Krüppel family…
Pan genome based assembly
Pan genome based assembly 1 Hi, I have some queries related to Pangenome. I have 8 genome assemblies of single eukaryotic species, could I make a pan-genome from this? Should I follow the Denovo approach method? Resequencing data is not available. ngs assembly Pangenome denovo • 69 views bioinfo –…
Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments
Dekker, J. & Mirny, L. The 3D genome as moderator of chromosomal communication. Cell 164, 1110–1121 (2016). Article CAS PubMed PubMed Central Google Scholar Oudelaar, A. M. et al. The relationship between genome structure and function. Nat. Rev. Genet. 22, 154–168 (2021). Article CAS PubMed Google Scholar Lieberman-Aiden, E. et…
How will generative AI disrupt data science in drug discovery?
Brown, T. B. et al. In Adv. Neural Inf. Process. Syst. 33 (eds Larochelle, H. et al.) 1877–1901 (Curran Associates, 2020). Open AI. Preprint at arXiv doi.org/10.48550/arXiv.2303.08774 (2023). Nguyen, N. & Nadi, S. In Proc. 19th Intl Conf. Mining Software Repositories 1–5 (Association for Computing Machinery, 2022); doi.org/10.1145/3524842.3528470 Nan, Y….
Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae)
Liu, J. et al. Integrating a comprehensive DNA barcode reference library with a global map of yews (Taxus L.) for forensic identification. Mol. Ecol. Resour. 18, 1115–1131 (2018). Article CAS Google Scholar Parveen, I., Singh, H. K., Raghuvanshi, S., Pradhan, U. C. & Babbar, S. B. DNA barcoding of endangered…
Twist Bioscience Reports Fiscal Second Quarter 2023 Financial Results
– Record revenue of $60.2M in 2QFY23; up 25% over $48.1M in 2QFY22 – – Orders increased to $64.2M in 2QFY23; up 17% over 2QFY22 – – Decisive Actions to Accelerate Path to Profitability – SOUTH SAN FRANCISCO, Calif., May 05, 2023–(BUSINESS WIRE)–Twist Bioscience Corporation (NASDAQ: TWST), a company enabling…
Resurrecting the alternative splicing landscape of archaic hominins using machine learning
Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222 (2012). Article CAS PubMed PubMed Central Google Scholar Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014). Article PubMed Google Scholar Prüfer, K. et…
Researchers use generative AI to design novel proteins
Model overview. Credit: Nature Computational Science (2023). DOI: 10.1038/s43588-023-00440-3 Researchers at the University of Toronto have developed an artificial intelligence system that can create proteins not found in nature using generative diffusion, the same technology behind popular image-creation platforms such as DALL-E and Midjourney. The system will help advance the…
Protocols to Study Host-Pathosystems | SpringerLink
Alkooranee JT, Liu S, Aledan TR, Yin Y, Li M (2015) First report of powdery mildew caused by erysiphe cruciferarum on brassica napus in China. Plant Dis 99(11):1651 CrossRef Google Scholar Al-Lami HFD, You MP, Barbetti MJ (2019a) Incidence, pathogenicity and diversity of Alternaria spp. associated with alternaria leaf spot…
Biochemical and genotyping analyses of camels (Camelus dromedaries) trypanosomiasis in North Africa
Igbokwe, I. O. Evolving anti-disease strategies from biochemical pathogenesis of African trypanosomiasis. Adv. Cytol. Pathol. 3(2), 33–39 (2018). Google Scholar Njiru, Z. K., Constantine, C. C., Gitonga, P. K., Thompson, R. C. & Reid, S. A. Genetic variability of Trypanosoma evansi isolates detected by inter-simple sequence repeat anchored-PCR and microsatellite….
The Biostar Herald for Monday, May 01, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
Applications of single-cell RNA sequencing in drug discovery and development
DiMasi, J. A., Grabowski, H. G. & Hansen, R. W. Innovation in the pharmaceutical industry: new estimates of R&D costs. J. Health Econ. 47, 20–33 (2016). Article PubMed Google Scholar Wouters, O. J., McKee, M. & Luyten, J. Estimated research and development investment needed to bring a new medicine to…
Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes
Sagan, L. On the origin of mitosing cells. J. Theor. Biol. 14, 225 (1967). Article ADS CAS Google Scholar McBride, H. M., Neuspiel, M. & Wasiak, S. Mitochondria: More than just a powerhouse. Curr. Biol. 16, R551–R560 (2006). Article CAS PubMed Google Scholar Dietrich, M. O., Liu, Z.-W. & Horvath,…
Why it’s worth making computational methods easy to use
Jean Fan is an assistant professor at Johns Hopkins University in Baltimore, Maryland.Credit: Mayling Chen Art isn’t complete until it’s shared, the saying goes. If that’s true, is a computational method complete if others cannot use it? When I was a student, I was often eager to apply new computational…
The genome-wide mutational consequences of DNA hypomethylation
Goldberg, A. D., Allis, C. D. & Bernstein, E. Epigenetics: A landscape takes shape. Cell 128, 635–638 (2007). Article PubMed Google Scholar Mohn, F. & Schübeler, D. Genetics and epigenetics: Stability and plasticity during cellular differentiation. Trends Genet. 25, 129–136 (2009). Article PubMed Google Scholar Takahashi, K. et al. Induction…
Two transects reveal remarkable variation in gene flow on opposite ends of a European toad hybrid zone
Abbott R, Albach D, Ansell S, Arntzen JW, Baird SJE, Bierne N, Zinner D (2013) Hybridization and speciation. J Evolut Biol 26:229–246. doi.org/10.1111/j.1420-9101.2012.02599.x Article CAS Google Scholar Arntzen JW (2019) An amphibian species pushed out of Britain by a moving hybrid zone. Mol Ecol 28:5145–5154 Article PubMed PubMed Central Google…
Molecular Glue ‘Shreds’ Cas9 and Enables a New Form of CRISPR Control
Groundbreaking clinical trials that could result in powerful new CRISPR treatments against HIV, genetic blindness, and other conditions are now underway, but some concerns around safety remain. One worry is that if CRISPR is put directly into patients’ bodies, they could have severe immune reactions to Cas9, the enzyme with…
The Biostar Herald for Monday, April 24, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
The therapeutic potential of neurofibromin signaling pathways and binding partners
Bergqvist, C. et al. Neurofibromatosis 1 French national guidelines based on an extensive literature review since 1966. Orphanet J. Rare Dis. 15, 1–23 (2020). Article Google Scholar Martin, G. A. et al. The GAP-related domain of the neurofibromatosis type 1 gene product interacts with ras p21. Cell 63, 843–849 (1990)….
TREM2 Protects the Brain From Herpes. The Virus Fights Back.
20 Apr 2023 Retroviruses lurking in the human genome aren’t the only potential troublemakers in neurodegenerative diseases (see Part 5 of this series). Herpes simplex virus type 1 (HSV-1) integrates into the genome of trigeminal ganglia nerves, can lie dormant for decades, and flare up as cold sores throughout a person’s…
Mirusviruses link herpesviruses to giant viruses
Vincent, F., Sheyn, U., Porat, Z., Schatz, D. & Vardi, A. Visualizing active viral infection reveals diverse cell fates in synchronized algal bloom demise. Proc. Natl Acad. Sci. USA 118, e2021586118 (2021). Article CAS PubMed PubMed Central Google Scholar Suttle, C. A. Marine viruses — major players in the global…
Association of 410L, 1016I and 1534C kdr mutations with pyrethroid resistance in Aedes aegypti from Ouagadougou, Burkina Faso, and development of a one-step multiplex PCR method for the simultaneous detection of 1534C and 1016I kdr mutations | Parasites & Vectors
Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, et al. The global distribution and burden of dengue. Nature. 2013;496:504–7. doi.org/10.1038/nature12060. Article CAS PubMed PubMed Central Google Scholar WHO. WHO | Dengue Fever – Burkina Faso. World Health Organization 2017 www.who.int/emergencies/disease-outbreak-news/item/6-november-2017-dengue-burkina-faso-en; 2017. Tarnagda Z, Cissé A, Bicaba…
Application of CRISPR/Cas9-mediated gene editing for abiotic stress management in crop plants
1 Introduction Abiotic stresses such as drought, heat, cold, salt, pesticides, metals and metalloids deteriorate agro-ecological conditions and hence, negatively impact upon agricultural production. The abiotic stress impairs with regular growth and development of plant plants, thus limiting their yield and quality of produce (Boyer, 1982; Pandey et al., 2017). Plants…
Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding
FAO. Faostat: FAO Statistical Databases. (Food & Agriculture Organization of the United Nations (FAO), 2000). The war in Ukraine is exposing gaps in the world’s food-systems research. Nature 604, 217–218 (2022). Chapman, M. A., He, Y. & Zhou, M. Beyond a reference genome: pangenomes and population genomics of underutilized and…
The Biostar Herald for Monday, April 17, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
Biogeographic patterns of biosynthetic potential and specialized metabolites in marine sediments
Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL, et al. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol. 2006;4:102–12. Article CAS PubMed Google Scholar Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JBH. Beyond biogeographic patterns: processes shaping the microbial landscape. Nat Rev Microbiol. 2012;10:497–506….
Can New Technology Detect Cancer Sooner?
Credit : BlackJack3D / iStock / Getty Images Plus Decades ago, the oncology community took on the crucial challenge of detecting cancer at the earliest possible stage. Overall, survival rates improve dramatically for cancers detected before metastasis. For example, the U.S. Centers for Disease Control and Prevention (CDC) notes that…
Mitochondrial Inheritance Following Nuclear Transfer: From Cloned Animals to Patients with Mitochondrial Disease
Rojansky R, Cha M-Y, Chan DC (2016) Elimination of paternal mitochondria in mouse embryos occurs through autophagic degradation dependent on PARKIN and MUL1. eLife 5:e17896. doi.org/10.7554/eLife.17896 CrossRef CAS PubMed PubMed Central Google Scholar Wei W, Pagnamenta AT, Gleadall N et al (2020) Nuclear-mitochondrial DNA segments resemble paternally inherited mitochondrial DNA…
An ancient metalloenzyme evolves through metal preference modulation
Jayaraman, V., Toledo-Patino, S., Noda-Garcia, L. & Laurino, P. Mechanisms of protein evolution. Protein Sci. 31, e4362 (2022). Article CAS PubMed Google Scholar Huang, R. et al. Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates. Proc. Natl Acad. Sci. USA 109, 2966–2971 (2012). Article CAS PubMed PubMed Central …
Expanding known viral diversity in the healthy infant gut
Moeller, A. H. et al. Cospeciation of gut microbiota with hominids. Science 353, 380–382 (2016). Article CAS PubMed PubMed Central Google Scholar Milani, C. et al. The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol. Mol. Biol. Rev. 81, e00036-17…
That’s What Makes Fungi ‘So Interesting’
When the topic of fungi arises, the majority of people would likely think about the mushrooms they gather in the autumn, or possibly the yeast they use in baking or wine-making. Some might even recollect the rotten bread or cucumbers they stumbled upon in their refrigerator last week. For ages,…
Do all fungi matter? Yes, new study argues
Maps showing the collection localities for the (A) Sanger sequences and (B) metabarcoding sequences that came with geo-coordinates (36,559 Sanger collection localities and 3,688 metabarcoding collection localities). Credit: MycoKeys (2023). DOI: 10.3897/mycokeys.96.102669 Mention fungi, and most people will probably think of the mushrooms they pick in fall, or maybe the…
The Biostar Herald for Monday, April 10, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, Pavel, and was edited by…
Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno
Philippi M, Kitzinger K, Berg JS, Tschitschko B, Kidane AT, Littmann S, et al. Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue. Nat Commun. 2021;12:4774. Article CAS PubMed PubMed Central Google Scholar Xiong Y, Guilbaud R, Peacock CL, Cox RP, Canfield DE, Krom MD,…
Experimental characterization of de novo proteins and their unevolved random-sequence counterparts
Schmitz, J. F. & Bornberg-Bauer, E. Fact or fiction: updates on how protein-coding genes might emerge de novo from previously non-coding DNA. F1000Research 6, 57 (2017). Article PubMed PubMed Central Google Scholar Vakirlis, N. et al. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat. Commun. 11,…
Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species
Giovannoni, J. J. Genetic regulation of fruit development and ripening. Plant Cell 16, S170–S180 (2004). CAS PubMed PubMed Central Google Scholar Tieman, D. et al. A chemical genetic roadmap to improved tomato flavor. Science 355, 391–394 (2017). CAS PubMed Google Scholar Peralta, I. E., Spooner, D. M. & Knapp, S….
Channel activity of SARS-CoV-2 viroporin ORF3a inhibited by adamantanes and phenolic plant metabolites
Gorbalenya, A. E. et al. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat. Microbiol. 5(4), 536–544. doi.org/10.1038/s41564-020-0695-z (2020). Article CAS Google Scholar Wang, Y., Grunewald, M. & Perlman, S. coronaviruses: an updated overview of their replication and pathogenesis. In Coronaviruses: Methods and Protocols (eds…
The Biostar Herald for Monday, April 03, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
Base Editing Shows Promise vs. SMA
David R. Liu, PhD, a professor at Harvard University, the Broad Institute of MIT and Harvard, and the Howard Hughes Medical Institute A research team led by gene editing pioneer David R. Liu, PhD, reports the application of base editing technology to develop a one-time treatment for spinal muscular atrophy…
No evidence for a common blood microbiome based on a population study of 9,770 healthy humans
Singer, M. et al. The third international consensus definitions for sepsis and septic shock (Sepsis-3). JAMA 315, 801–810 (2016). Article CAS PubMed PubMed Central Google Scholar Brecher, M. E. & Hay, S. N. Bacterial contamination of blood components. Clin. Microbiol. Rev. 18, 195–204 (2005). Article PubMed PubMed Central Google Scholar …
COVID-19 activates endogenous retroviruses within our genome
*Important notice: bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, which is otherwise known as the coronavirus disease 2019 (COVID-19), continues to pose significant…
Long-read sequencing: the key to a more complete cancer transcriptome
Uncover the mysteries of RNA dysregulation in cancer Our understanding of the complex biology of cancers is currently limited by the sequencing technology that we have available. For example, a study previously published in Science Advances showed that short-read based RNA-seq approaches only capture a faction of RNA isoforms that…
Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome
Bradley, B. A. et al. Cheatgrass (Bromus tectorum) distribution in the intermountain western United States and its relationship to fire frequency, seasonality, and ignitions. Biol. Invasions 20, 1493–1506 (2018). Article Google Scholar Balch, J. K., Bradley, B. A., D’Antonio, C. M. & Gomez-Dans, J. Introduced annual grass increases regional fire…
Identification and gene expression analysis of serine proteases and their homologs in the Asian corn borer Ostrinia furnacalis
Ross, J., Jiang, H., Kanost, M. R. & Wang, Y. Serine proteases and their homologs in the Drosophila melanogaster genome: An initial analysis of sequence conservation and phylogenetic relationships. Gene 304, 117–131 (2003). Article CAS PubMed Google Scholar Rawlings, N. D. & Barrett, A. J. Evolutionary families of peptidases. Biochem….
Normative Modeling of Brain Morphometry Across the Lifespan Using CentileBrain: Algorithm Benchmarking and Model Optimization,bioRxiv – Bioinformatics
Background Normative modeling is a statistical approach to quantify the degree to which a particular individual-level measure deviates from the pattern observed in a normative reference population. When applied to human brain morphometric measures it has the potential to inform about the significance of normative deviations for health and disease….
Development of QSAR Models to Identify Mycobacterium tuberculosis enoyl-ACP-reductase Enzyme Inhibitors,bioRxiv – Bioinformatics
Development of QSAR Models to Identify Mycobacterium tuberculosis enoyl-ACP-reductase Enzyme Inhibitors bioRxiv – Bioinformatics Pub Date : 2023-03-19 , DOI: 10.1101/2023.03.13.532463 Aureo Andre Karolczak, Luis Fernando Saraiva Macedo Timmers,…
Accelerating Minimap2 for Accurate Long Read Alignment on GPUs
doi: 10.26502/jbb.2642-91280067. Epub 2023 Jan 20. Affiliations Expand Affiliations 1 Department of Computer Science and Engineering, University of Michigan Ann Arbor, MI 48109, USA. 2 NVIDIA Corporation, Santa Clara, CA 95051, USA. Free PMC article Item in Clipboard Harisankar Sadasivan et al. J Biotechnol Biomed. 2023. Free PMC article Show details…
Detection of biallelic loss of DNA repair genes in formalin-fixed, paraffin-embedded tumor samples using a novel tumor-only sequencing panel
Brown JS O’Carrigan B Jackson SP Yap TA Targeting DNA Repair in Cancer: Beyond PARP Inhibitors. Cancer Discov. 2017; 7: 20-37 Farmer H McCabe N Lord CJ Tutt AN Johnson DA Richardson TB Santarosa M Dillon KJ Hickson I Knights C Martin NM Jackson SP Smith GC Ashworth A Targeting…
Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data
Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014). Article PubMed PubMed Central Google Scholar Weyrich, L. S. et al. Laboratory contamination over time during low-biomass sample analysis. Mol. Ecol. Resour. 19, 982–996 (2019). Article CAS PubMed PubMed Central …
Researchers Aim to Boost Liquid Biopsy cfDNA Yields Using Novel Priming Agents
NEW YORK – Lipid nanoparticles that inhibit cellular uptake of cell-free DNA (cfDNA) and engineered antibodies that protect cfDNA from degradation are showing early success in boosting liquid biopsy cfDNA yields, which could eventually lead to improved cancer diagnostic and prognostic assays. Investigators from the Broad Institute and the Koch…
Biology:Circular RNA databases and resources
In molecular biology, Circular RNAs (circRNAs) refer to a class of circular RNA molecules found across all kingdoms of life.[1][2][3] Studies in 2013 have suggested that circRNAs play important regulatory roles in miRNA activity. Researchers found that CDR1as circRNA acts as a miR-7 super-sponge that contains about 70 target sites…
The Biostar Herald for Monday, March 13, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
Cracking the code of cellular protein-protein interactions: Alphafold and whole-cell crosslinking to the rescue
doi: 10.15252/msb.202311587. Online ahead of print. Affiliations Expand Affiliations 1 Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany. 2 Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany. 3 Biozentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany. 4 Institute of Chemical Biology, National…
Accurate prediction by AlphaFold2 for ligand binding in a reductive dehalogenase and implications for PFAS (per- and polyfluoroalkyl substance) biodegradation
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021). Article ADS CAS PubMed PubMed Central Google Scholar Baek, M. et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science 373, 871–876 (2021). Article ADS CAS PubMed PubMed Central Google…
Mock community as an in situ positive control for amplicon sequencing of microbiotas from the same ecosystem
Proctor, L. Priorities for the next 10 years of human microbiome research. Nature 569(7758), 623–625 (2019). Article ADS CAS PubMed Google Scholar Bahl, M. I., Bergström, A. & Licht, T. R. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis….
Genome Editing Tool Looks Beyond CRISPR and Prime
Omar Abudayyeh, PhD, McGovern fellow at MIT’s McGovern Institute for Brain Research A recently patented genome editing tool called PASTE holds genuine promise for expanding the universe of treatable genetic diseases. The approach combines elements of CRISPR and prime editing with a pair of enzymes designed to enable the integration…
Chromosomal instability as central hallmark of Breast Cancer
Introduction In recent years, CIN has gained great importance due to its implications for both, the diagnosis and prognosis of cancer. Recent studies have suggested that both CIN and clonal heterogeneity, influence cancer progression, aggressiveness, prognosis, and response to therapy.1–4 The above because both, CIN and clonal heterogeneity, lead to…
Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection
Bergwerk, M. et al. Covid-19 breakthrough infections in vaccinated health care workers. N. Engl. J. Med. 385, 1474–1484 (2021). Article CAS PubMed Google Scholar V’Kovski, P., Kratzel, A., Steiner, S., Stalder, H. & Thiel, V. Coronavirus biology and replication: implications for SARS-CoV-2. Nat. Rev. Microbiol. 19, 155–170 (2021). Article PubMed …
A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes
Inagaki, F., Takai, K., Kobayashi, H., Nealson, K. H. & Horikoshi, K. Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing e-proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough. Int. J. Syst. Evol. Microbiol. 53, 1801–1805 (2003). Article CAS PubMed Google Scholar Timmer-Ten Hoor, A. A new type of…
Finally, Scientists Sequence Single Cells with Long-Read Technology
Traditional sequencing is often likened to making a smoothie: researchers blend a bunch of cells, obtain an average sequence, and draw conclusions on the ingredients that comprise the slush. More recently, scientists have gained the ability to perform single-cell sequencing, which can reveal rare variations between cells and the evolution…
The molecular pathology of schizophrenia: an overview of existing knowledge and new directions for future research
Jones HB. Pathology. In: Wexler P. (eds). Information resources in toxicology (Fourth Edition). Academic Press: San Diego, 2009, pp 357–63. Griesinger W. Die Pathologie und therapie der psychischen krankheiten. (Krabbe:Stuttgart, 1861). Kraepelin E. Psychiatrie: ein Lehrbuch für Studierende und Aerzte. (Verlag von Johann Ambrosius Barth:Leipzig, 1899). Jauhar S, Johnstone M,…
Alzheimer’s Gene MS4A4A Governs the State of Microglia
03 Mar 2023 Of the dozens of loci genome-wide association studies have linked to Alzheimer’s, most are mysterious to scientists. How do they contribute to disease? Much work focuses on changes in expression of individual genes, but as reported in a preprint posted to medRxiv on February 8, scientists led…
Sequencing 101: long-read sequencing – PacBio
Long-read sequencing technologies such as PacBio HiFi sequencing are quickly becoming the new gold standard in genomics research. This article provides an introductory look at what long-read sequencing is, and explores topics including advantages, applications, and more. Background Deciphering the essence of what makes living things work has been a…
BridgePRS
BridgePRS 1 Hi there, I am reading the new method of PRS – BridgePRS (www.biorxiv.org/content/10.1101/2023.02.17.528938v1), this is a very interesting paper regarding the transferability of PRS. I am trying to study about the methods (my statistics and mathematics background is quite weak), but one thing I don’t understand is that…
Fixation Before Dissociation Using a Deep Eutectic Solvent Preserves In Vivo States and Phospho-Signalling in Single-Cell Sequencing Presented
Researchers at the University of Alabama at Birmingham have demonstrated a novel way of fixing cells and preserving their biomolecules prior to single cell dissociation without the need for harsh enzymatic/mechanical approaches. Single-cell RNA sequencing has the opportunity to deconstruct cellular networks but was previously limited by the loss of…
Interpersonal variability of the human gut virome confounds disease signal detection in IBD
Willing, B. P. et al. A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 139, 1844–1854 (2010). Article PubMed Google Scholar Morgan, X. C. et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 13, R79 (2012)….
Network analysis of 16S rRNA sequences suggests microbial keystone taxa contribute to marine N2O cycling
Fuhrman, J. A. Microbial community structure and its functional implications. Nature 459, 193–199 (2009). Article CAS PubMed Google Scholar Graham, E. B. et al. Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes? Front. Microbiol. 7, 214 (2016). Article PubMed PubMed Central Google Scholar …