Tag: CRyPTIC

eDNA technology could revolutionise biodiversity monitoring

Choki Wangmo  Bhutan could save millions on biodiversity monitoring and assessments if environmental DNA (eDNA) sequencing technology could be used in the country, according to experts.    The technology offers cost-effective biodiversity monitoring, potentially saving millions for government and conservation agencies in environmental assessments. It is a collection of mitochondrial DNA…

Continue Reading eDNA technology could revolutionise biodiversity monitoring

CMT2S therapy VCA-894A granted orphan drug status by FDA

The U.S. Food and Drug Administration (FDA) has granted orphan drug status to Vanda Pharmaceuticals’ VCA-894A for treating Charcot-Marie-Tooth disease type 2S (CMT2S). An orphan drug designation seeks to encourage the development of therapies for rare diseases — those affecting fewer than 200,000 people in the U.S. — through benefits such…

Continue Reading CMT2S therapy VCA-894A granted orphan drug status by FDA

Phylogenomic analysis, cryptic species discovery, and DNA barcoding of the genus Cibotium in China based on plastome data

Introduction Traditional Chinese herbal medicine plays an indispensable role in the treatment of multiple diseases in China and other developing countries (Newman et al., 2008). Apart from the traditional usage, many medicinal plants, such as Artemisia annua L. (artemisinin, Tu, 2016), Huperzia javanica (Sw.) C. Y. Yang (Huperzine A, Zangara, 2003;…

Continue Reading Phylogenomic analysis, cryptic species discovery, and DNA barcoding of the genus Cibotium in China based on plastome data

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,…

Continue Reading Long-read genome sequencing identifies cryptic structural variants in congenital aniridia cases | Human Genomics

Refining the evolutionary tree of the horse Y chromosome

Reporting MSY haplogroups in horse populations around the globe A previously-released fine-scale MSY HT topology23,24 provided the basis for the selection of 16 MSY diagnostic markers for major haplogroups (mjHGs) in modern horse breeds. Genotyping these markers helped to differentiate Przewalski’s horses’, as well as six non-Crown and three Crown…

Continue Reading Refining the evolutionary tree of the horse Y chromosome

Backcrossing to different parents produced two distinct hybrid species

Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinforma 12:246. doi.org/10.1186/1471-2105-12-246 Article  Google Scholar  Anderegg WRL, Flint A, Huang C-Y, Flint L, Berry JA, Davis FW et al. (2015) Tree mortality predicted from drought-induced vascular damage. Nat Geosci 8:367–371 Article  CAS  Google Scholar …

Continue Reading Backcrossing to different parents produced two distinct hybrid species

Natural vectors of Plasmodium knowlesi and other primate, avian and ungulate malaria parasites in Narathiwat Province, Southern Thailand

Coatney, G. R., Collins, W. E., Warren, M. & Contacos, P. G. The Primate Malarias (Original Book Published 1971) [CD-ROM]. Version 1.0 (Centers for Disease Control and Prevention, 2003). Google Scholar  Singh, B. & Daneshvar, C. Human infections and detection of Plasmodium knowlesi. Clin. Microbiol. Rev. 26, 165–184 (2013). Article …

Continue Reading Natural vectors of Plasmodium knowlesi and other primate, avian and ungulate malaria parasites in Narathiwat Province, Southern Thailand

Pooled whole genome sequencing of the endangered Banff Springs Snail, Physella johnsoni, reveals genetic separation to P. gyrina and cryptic micro-geographical genetic structure

Allendorf FW, Hohenlohe PA, Luikart G (2010) Genomics and the future of conservation genetics. Nat Rev Genet 11:697–709. doi.org/10.1038/nrg2844 Article  CAS  PubMed  Google Scholar  Beheregaray LB, Caccone A (2007) Cryptic biodiversity in a changing world. J Biol. doi.org/10.1186/jbiol60 Article  PubMed  PubMed Central  Google Scholar  Bickford D, Lohman DJ, Sodhi NS…

Continue Reading Pooled whole genome sequencing of the endangered Banff Springs Snail, Physella johnsoni, reveals genetic separation to P. gyrina and cryptic micro-geographical genetic structure

Amplifying gene expression with RNA-targeted therapeutics

RNA-targeted NBTs that are currently being used to upregulate gene expression address both transcriptional and translational mechanisms and can be roughly divided into two groups: (1) NBTs that increase mRNA abundance by enhancing transcription or increasing mRNA stability (Fig. 3) and (2) NBTs that optimize translation (Fig. 4). Strategies in the first…

Continue Reading Amplifying gene expression with RNA-targeted therapeutics

Genetic determination of regional connectivity in modelling the spread of COVID-19 outbreak for more efficient mitigation strategies

As of October 2021, two years since the start of the pandemic, coronavirus disease 2019 (COVID-19)-related deaths have surpassed 4,800,000 worldwide and 700,000 in the United States. Due to the severity of the pandemic combined with the advent of sequencing technologies, the amount of sequencing data within such a short…

Continue Reading Genetic determination of regional connectivity in modelling the spread of COVID-19 outbreak for more efficient mitigation strategies

Bioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation

Borzi, A. Le communicazioni intracellulari delle nostochinee. Malpighia – Rassegna mensuale di botanica 1 (1886–1887). Simon, R. D. Cyanophycin granules from the blue-green alga anabaena cylindrica: A reserve material consisting of copolymers of aspartic acid and arginine. Proc. Natl. Acad. Sci. U. S. A. 68, 265–267 (1971). Article  ADS  CAS …

Continue Reading Bioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation

Reduced within-population quantitative genetic variation is associated with climate harshness in maritime pine

Aase K, Jensen H, Muff S (2022) Genomic estimation of quantitative genetic parameters in wild admixed populations. Meth Ecol Evol 13:1014–1026 Article  Google Scholar  Aitken SN, Bemmels JB (2015) Time to get moving: Assisted gene flow of forest trees. Evol Appl 9:271–290 Article  PubMed  PubMed Central  Google Scholar  Alberto F…

Continue Reading Reduced within-population quantitative genetic variation is associated with climate harshness in maritime pine

How DNA Sequencing Can Help Tackle the Plight of the Bumblebee

A UK science firm is hoping to help the UK’s beleaguered bee population by using DNA technology to unravel the mystery of the insects’ behaviour – and potentially discover new species. SureScreen Scientifics, based in Morley, is believed to be the first commercial firm in the UK to use DNA…

Continue Reading How DNA Sequencing Can Help Tackle the Plight of the Bumblebee

A rapid diagnosis and treatment of Ornithonyssus bacoti infection

Beck W (2008) Occurrence of a house-infesting tropical rat mite (Ornithonyssus bacoti) on murides and human beings. Travel Med Infect Dis 6:245–249 Article  CAS  PubMed  Google Scholar  Beck W, Pfister K (2006) Mites as a cause of zoonoses in human beings. Wien Klin Wochenschr 118:27–32 Article  PubMed  Google Scholar  Ben-David…

Continue Reading A rapid diagnosis and treatment of Ornithonyssus bacoti infection

DNA Sequencing Revolutionizes UK Scientists’ Efforts To Protect Bumblebees

In the face of the UK’s declining bee population, a UK science firm, SureScreen Scientifics, is pioneering the use of DNA technology to unlock the secrets of bee behavior and potentially discover new species. Situated in Morley, SureScreen Scientifics has become the first commercial firm in the UK to employ…

Continue Reading DNA Sequencing Revolutionizes UK Scientists’ Efforts To Protect Bumblebees

Site-specific gene knock-in and bacterial phytase gene expression in Chlamydomonas reinhardtii via Cas9 RNP-mediated HDR

Introduction Microalgae encompass a large number of organisms with both prokaryotic and eukaryotic nature, making them an archetypal platform for recombinant technology (Malla et al., 2021). The nutraceutical significance of microalgae is characterized by their rich natural biomolecules and high amount of protein, vitamins, and lipid substances (Potvin and Zhang, 2010;…

Continue Reading Site-specific gene knock-in and bacterial phytase gene expression in Chlamydomonas reinhardtii via Cas9 RNP-mediated HDR

A Comparative Phylogeographic Analysis of Mitochondrial DNA Variability in Four Fish Species (Salmonidae and Cyprinidae) in the Northwest Pacific

Bol’shakov, S.G., Some features of biology, growth, and age of Far Eastern redfins—Pacific redfin Tribolodon brandti and big-scaled redfin Tribolodon hakonensis—in southern Primorskii krai, Izv. Tikhookean. Nauchno-Issled. Inst. Rybn. Khoz. Okeanogr., 2013, pp. 141–158. Google Scholar  Brykov, V.A., Polyakova, N.E., and Semina, A.V., Comparative analysis of mitochondrial DNA variability in four…

Continue Reading A Comparative Phylogeographic Analysis of Mitochondrial DNA Variability in Four Fish Species (Salmonidae and Cyprinidae) in the Northwest Pacific

Obtention of the binomial transformed count table with edgeR

Hello! When performing differential expression analysis with RNA-Seq data using DeSeq2, and after data normalisation, there is the option to extract a count table with the transformed abundance levels using the variance stabilisation transformation (vst) method. Line of code vst counts extraction: vst_dds <- vst(res) The DeSeq2 manual itself indicates…

Continue Reading Obtention of the binomial transformed count table with edgeR

‘Guardians of the Galaxy Vol. 3’ movie review: trilogy capper the best MCU film since Phase 3

Rocket Raccoon gets his due in Guardians of the Galaxy Vol. 3, a bombastic intergalactic adventure that maintains the same level of top-tier quality as its predecessors, and might even be the best entry in the trilogy. Bolstered by some wild filmmaking diversions that reference sci-fi classics from David Cronenberg…

Continue Reading ‘Guardians of the Galaxy Vol. 3’ movie review: trilogy capper the best MCU film since Phase 3

A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean

Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: the unseen majority. Proc. Natl Acad. Sci. USA 95, 6578–6583 (1998). Article  CAS  PubMed  PubMed Central  Google Scholar  Herndl, G. J. & Reinthaler, T. Microbial control of the dark end of the biological pump. Nat. Geosci. 6, 718–724 (2013)….

Continue Reading A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean

Study identifies an unknown SARS-CoV-2 lineage on three mink farms in Poland

In a recent study published in the Eurosurveillance Journal, researchers detected a cryptic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage on mink farms in Poland. Study: Cryptic SARS-CoV-2 lineage identified on two mink farms as a possible result of long-term undetected circulation in an unknown animal reservoir, Poland, November 2022…

Continue Reading Study identifies an unknown SARS-CoV-2 lineage on three mink farms in Poland

r – What is the best practice for ggplot graphs from multiple datasets using weights?

Closed. This question is opinion-based. It is not currently accepting answers. Want to improve this question? Update the question so it can be answered with facts and citations by editing this post. I think my title is a bit cryptic, so I’ll explain. I worked…

Continue Reading r – What is the best practice for ggplot graphs from multiple datasets using weights?

Estrogen associates with female predominance in Xp11.2 translocation renal cell carcinoma

Lopez-Beltran, A. et al. 2004 WHO classification of the renal tumors of the adults. Eur. Urol. 49(5), 798–805 (2006). Article  PubMed  Google Scholar  Moch, H. et al. The 2016 WHO classification of tumours of the urinary system and male genital organs-Part A: Renal, penile, and testicular tumours. Eur. Urol. 70(1),…

Continue Reading Estrogen associates with female predominance in Xp11.2 translocation renal cell carcinoma

Characterizing the Wolbachia infection in field-collected Culicidae mosquitoes from Hainan Province, China | Parasites & Vectors

Hilgenboecker K, Hammerstein P, Schlattmann P, Telschow A, Werren JH. How many species are infected with Wolbachia?–a statistical analysis of current data. FEMS Microbiol Lett. 2008;281:215–20. CAS  PubMed  Google Scholar  Duron O, Bouchon D, Boutin S, Bellamy L, Zhou L, Engelstadter J, et al. The diversity of reproductive parasites among…

Continue Reading Characterizing the Wolbachia infection in field-collected Culicidae mosquitoes from Hainan Province, China | Parasites & Vectors

Genome-resolved metagenomics revealed metal-resistance, geochemical cycles in a Himalayan hot spring

Agency for Toxic Substances and Disease Registry (ATSDR) (2002) Toxicological profile for copper. Atlanta, GA: Centers for Disease Control Ahemad M (2012) Implications of bacterial resistance against heavy metals in bioremediation: A review. IIOAB J 3:39–46 CAS  Google Scholar  Alcamán-Arias ME, Pedrós-Alió C, Tamames J, Fernández C, Pérez-Pantoja D, Vásquez M,…

Continue Reading Genome-resolved metagenomics revealed metal-resistance, geochemical cycles in a Himalayan hot spring

From past to present: opportunities and trends in the molecular detection and diagnosis of Strongyloides stercoralis | Parasites & Vectors

Bisoffi Z, Buonfrate D, Montresor A, Requena-Méndez A, Muñoz J, Krolewiecki AJ, et al. Strongyloides stercoralis: a plea for action. PLoS Negl Trop Dis. 2013;7:5. Google Scholar  Schär F, Trostdorf U, Giardina F, Khieu V, Muth S, Marti H, et al. Strongyloides stercoralis: global distribution and risk factors. PLoS Negl…

Continue Reading From past to present: opportunities and trends in the molecular detection and diagnosis of Strongyloides stercoralis | Parasites & Vectors

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…

Continue Reading Expanding known viral diversity in the healthy infant gut

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,…

Continue Reading Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno

Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting

Handa IT, Aerts R, Berendse F, Berg MP, Bruder A, Butenschoen O, et al. Consequences of biodiversity loss for litter decomposition across biomes. Nature. 2014;509:218–21. Article  CAS  PubMed  Google Scholar  Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, et al. Minimum information about an uncultivated virus…

Continue Reading Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting

“Cryptic Transcription”: How Aging Cells Express Fragments of Genes

Senescent cells, those that persist in the body despite having halted cell division, undergo a process called cryptic transcription, whereby they produce RNA transcripts from short sequences nested within individual genes. It is unclear what, if any, functions these transcripts have, and the mechanism behind their expression has long eluded…

Continue Reading “Cryptic Transcription”: How Aging Cells Express Fragments of Genes

Deep genomic characterization highlights complexities and prognostic markers of pediatric acute myeloid leukemia

FG spectrum in pediatric AML patients A combinatorial approach, including conventional and next-generation sequencing (NGS)-based assays, was employed to profile the FG landscape (see Methods). FG analysis was feasible for 138 patients (94% of the entire cohort, Supplementary Data 1) from whom suitable testing materials were available. The most common FGs…

Continue Reading Deep genomic characterization highlights complexities and prognostic markers of pediatric acute myeloid leukemia

CRISPR-resolved virus-host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflicts

Suttle, C. A. Environmental microbiology: Viral diversity on the global stage. Nat. Microbiol. 1, 16205 (2016). Article  CAS  PubMed  Google Scholar  Schulz, F. et al. Giant virus diversity and host interactions through global metagenomics. Nature 578, 432–436 (2020). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Dutilh, B. E., Reyes,…

Continue Reading CRISPR-resolved virus-host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflicts

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…

Continue Reading Base Editing Shows Promise vs. SMA

Reactivated Promoters in Transposable Elements Help Form Unique Tumor Antigens

NEW YORK ­­­­­­­­­­­­– Transposable element (TE) promoters that get reactivated in cancer cells can lead to chimeric transcripts involving parts of protein-coding genes, resulting in cancer-specific cell surface antigens, a new study has found. The findings point to potential new treatment strategies, including immunotherapy and a pan-cancer vaccine. TEs, also…

Continue Reading Reactivated Promoters in Transposable Elements Help Form Unique Tumor Antigens

The Right PMS Partner + Open APIs Can Elevate a Hotels’ Operational Success

Consumers the world over are seeking greater flexibility and control over their travel experiences, and hoteliers love to provide these elements to them whenever possible. Technology is increasingly able to provide the bespoke experiences hoteliers envision delivering, often thanks to new integrations which build on and fill out their existing…

Continue Reading The Right PMS Partner + Open APIs Can Elevate a Hotels’ Operational Success

Accelerating Cryptic Pocket Discovery Using AlphaFold

Cryptic pockets, or pockets absent in ligand-free, experimentally determined structures, hold great potential as drug targets. However, cryptic pocket openings are often beyond the reach of conventional biomolecular simulations because certain cryptic pocket openings involve slow motions. Here, we investigate whether AlphaFold can be used to accelerate cryptic pocket discovery…

Continue Reading Accelerating Cryptic Pocket Discovery Using AlphaFold

Genetic association analysis of 77,539 genomes reveals rare disease etiologies

Motivation for developing a sparse RDB Computational approaches for discovering the etiologies of rare diseases typically depend on the analysis of a heterogeneous set of files, each of which can be very large and follow a distinct convention. Genotypes, for example, are ordinarily stored in VCFs containing data for one…

Continue Reading Genetic association analysis of 77,539 genomes reveals rare disease etiologies

Stunning Diversity of Comb Jellies Revealed Through Genetic Probes

Researchers from the Monterey Bay Aquarium Research Institute (MBARI) have used genetics to study the comb jellies, or ctenophores, and have discovered new diversity within the species. Comb jellies—known to scientists as ctenophores (pronounced “teen-oh-fours”)—mesmerize with their beauty, but these captivating creatures remain poorly studied due to their delicate nature….

Continue Reading Stunning Diversity of Comb Jellies Revealed Through Genetic Probes

Extensive prevalence and significant genetic differentiation of Blastocystis in high- and low-altitude populations of wild rhesus macaques in China | Parasites & Vectors

Andersen LO, Stensvold CR. Blastocystis in health and disease: are we moving from a clinical to a public health perspective? J Clin Microbiol. 2016;54:524–8. Article  CAS  PubMed  PubMed Central  Google Scholar  Hublin JSY, Maloney JG, Santin M. Blastocystis in domesticated and wild mammals and birds. Res Vet Sci. 2021;135:260–82. Article …

Continue Reading Extensive prevalence and significant genetic differentiation of Blastocystis in high- and low-altitude populations of wild rhesus macaques in China | Parasites & Vectors

The era of cryptic exons: implications for ALS-FTD | Molecular Neurodegeneration

‘TDP-43 proteinopathy’ refers to human diseases pathologically defined by cellular nuclear-to-cytoplasmic mislocalisation and aggregation of TAR DNA-binding protein-43 (TDP-43), an RNA-binding protein with a crucial role in RNA metabolism and splicing. TDP-43 proteinopathy encompasses a wide spectrum of progressive neurodegenerative diseases and phenotypes. It is a key feature in ~ 97%…

Continue Reading The era of cryptic exons: implications for ALS-FTD | Molecular Neurodegeneration

Genomic diversity of non-diarrheagenic fecal Escherichia coli from children in sub-Saharan Africa and south Asia and their relatedness to diarrheagenic E. coli

Kaper, J. B., Nataro, J. P. & Mobley, H. L. Pathogenic Escherichia coli. Nat. Rev. Microbiol. 2, 123–140 (2004). Article  CAS  PubMed  Google Scholar  Nataro, J. P. & Kaper, J. B. Diarrheagenic Escherichia coli. Clin. Microbiol. Rev. 11, 142–201 (1998). Article  CAS  PubMed  PubMed Central  Google Scholar  Croxen, M. A….

Continue Reading Genomic diversity of non-diarrheagenic fecal Escherichia coli from children in sub-Saharan Africa and south Asia and their relatedness to diarrheagenic E. coli

What Is DNA Barcoding? | Denver Botanic Gardens

Being able to explore the diversity of our world is one of the privileges of being part of the Research & Conservation Department at Denver Botanic Gardens. One of the challenges we face is in addressing how we explore this diversity. For fungi, recognizing diversity was practiced much in the…

Continue Reading What Is DNA Barcoding? | Denver Botanic Gardens

ncRNA database from previous publications

Here is the database with 3,898 ncRNA that was compared to the set of lncRNA indentified by us. The database was built based on the papers below: Berretta J, Pinskaya M, Morillon A (2008) A cryptic unstable transcript mediates transcriptional trans -silencing of the Ty1 retrotransposon in S. cerevisiae. Genes…

Continue Reading ncRNA database from previous publications

Use of DESeq given unusual experimental data

Use of DESeq given unusual experimental data 0 @glfreynolds-21471 Last seen 13 hours ago United Kingdom Hello, I’ve been using DESeq for some smallRNA-seq I’m working on, but we have some unusual data given what we’re sampling the small RNA-seq data from (sorry to be cryptic, I’m bound by confidentially…

Continue Reading Use of DESeq given unusual experimental data

Alcobiosis, an algal-fungal association on the threshold of lichenisation

Wilkinson, D. At cross purposes. Nature 412, 485 (2001). Article  ADS  CAS  PubMed  Google Scholar  de Bary, H. A. Über Symbiose [On Symbiosis]. Tageblatt für die Versammlung Dtsch. Naturforscher und Aerzte (in Cassel) [Daily J. Conf. Ger. Sci. Phys.] (in Ger. 51, 121–126 (1878). Lücking, R., Leavitt, S. D. &…

Continue Reading Alcobiosis, an algal-fungal association on the threshold of lichenisation

Plastid DNA sequences and oospore characters of some European taxa of Tolypella section Tolypella (Characeae) identify five clusters, including one new cryptic Tolypella taxon from Sardinia, but they do not coincide with current morphological descriptions

1. Introduction Charophytes, extant and fossil members of the order Charales plus the members of the extinct orders Sycidiales and Moellerinales (Schneider et al., 2015) are algae with a complex morphology, which are closely related to modern land plants (Nishiyama et al., 2018). Taxa delineation of charophytes is commonly based on morphological…

Continue Reading Plastid DNA sequences and oospore characters of some European taxa of Tolypella section Tolypella (Characeae) identify five clusters, including one new cryptic Tolypella taxon from Sardinia, but they do not coincide with current morphological descriptions

Taxonomy | Free Full-Text | Deep mtDNA Sequence Divergences and Possible Species Radiation of Whip Spiders (Arachnida, Amblypygi, Phrynidae, Phrynus/Paraphrynus) among Caribbean Oceanic and Cave Islands

1. Introduction The Caribbean archipelago is a recognized biodiversity hotspot due to species richness and especially high, often single island, endemism [1,2,3,4]. Speciation often occurs within the larger islands among habitats or across barriers such as mountain ranges. In the Caribbean, the rich cave systems aptly called habitat ‘islands’ [5,6,7,8,9,10]…

Continue Reading Taxonomy | Free Full-Text | Deep mtDNA Sequence Divergences and Possible Species Radiation of Whip Spiders (Arachnida, Amblypygi, Phrynidae, Phrynus/Paraphrynus) among Caribbean Oceanic and Cave Islands

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 …

Continue Reading Network analysis of 16S rRNA sequences suggests microbial keystone taxa contribute to marine N2O cycling

Diversification of the shell shape and size in Baikal Candonidae ostracods inferred from molecular phylogeny

Claude, J., Paradis, E., Tong, H. & Auffray, J. C. A geometric morphometric assessment of the effects of environment and cladogenesis on the evolution of the turtle shell. Biol. J. Linn. Soc. 79, 485–501 (2003). Article  Google Scholar  Klingenberg, C. P., Duttke, S., Whelan, S. & Kim, M. Developmental plasticity,…

Continue Reading Diversification of the shell shape and size in Baikal Candonidae ostracods inferred from molecular phylogeny

Uncovering the Elusive Origins of the Black Death

The East Smithfield plague pits, which were used for mass burials in 1348 and 1349. Credit: Museum of London Archaeology (MOLA) The researchers analyzed over 600 genome sequences of Yersinia pestis, the bacterium responsible for causing the plague. In an effort to gain deeper insight into the origins and spread…

Continue Reading Uncovering the Elusive Origins of the Black Death

CvkR is a MerR-type transcriptional repressor of class 2 type V-K CRISPR-associated transposase systems

Architecture of cyanobacterial CAST systems Starting from the known CAST components, we searched for conserved genes and genetic elements in their vicinity. These elements included the left and right ends of the transposon, the neighboring tRNA, CRISPR arrays and tracrRNA, the transposase genes (tnsB, tnsC and tniQ), and genes in…

Continue Reading CvkR is a MerR-type transcriptional repressor of class 2 type V-K CRISPR-associated transposase systems

A Trem2R47H mouse model without cryptic splicing drives age- and disease-dependent tissue damage and synaptic loss in response to plaques | Molecular Neurodegeneration

The Trem2 R47H NSS mutation promotes loss of oligodendrocyte gene expression in response to cuprizone treatment. Results of previous studies of mice with the Trem2R47H missense mutation introduced via CRISPR suggested that it acts as a near-complete loss of function, recapitulating phenotypes seen in Trem2 knock-out (KO) mice [34, 36]….

Continue Reading A Trem2R47H mouse model without cryptic splicing drives age- and disease-dependent tissue damage and synaptic loss in response to plaques | Molecular Neurodegeneration

Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks

Croft, M. T., Lawrence, A. D., Raux-Deery, E., Warren, M. J. & Smith, A. G. Algae acquire vitamin B12 through a symbiotic relationship with bacteria. Nature doi.org/10.1038/nature04056 (2005). Article  PubMed  Google Scholar  Kazamia, E. et al. Mutualistic interactions between vitamin B12-dependent algae and heterotrophic bacteria exhibit regulation. Environ. Microbiol. doi.org/10.1111/j.1462-2920.2012.02733.x…

Continue Reading Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks

Water | Free Full-Text | Next-Generation DNA Barcoding for Fish Identification Using High-Throughput Sequencing in Tai Lake, China

1. Introduction It is well recognized that the loss of biodiversity caused by environmental deterioration has adverse ecological consequences [1], for example, nutrient over-enrichment in lakes leads to the simplification of flora and fauna [2]. Biodiversity conservation would be a usual tool for sustaining the health of an ecosystem [3]….

Continue Reading Water | Free Full-Text | Next-Generation DNA Barcoding for Fish Identification Using High-Throughput Sequencing in Tai Lake, China

The Current State of Nanopore Sequencing

Fastest DNA sequencing technique | Guinness World Records. www.guinnessworldrecords.com/world-records/675050-fastest%C2%A0dna-sequencing%C2%A0technique. Accessed 30 May 2022 Gorzynski JE, Goenka SD, Shafin K et al (2022) Ultra-rapid nanopore whole genome genetic diagnosis of dilated cardiomyopathy in an adolescent with cardiogenic shock. Circ Genom Precis Med CIRCGEN121003591. doi.org/10.1161/circgen.121.003591 First DNA Sequencing in Space a Game…

Continue Reading The Current State of Nanopore Sequencing

Species richness of bat flies and their associations with host bats in a subtropical East Asian region | Parasites & Vectors

Scott M, Dobson A. The role of parasites in regulating host abundance. Parasitol Today. 1989;5:176–83. CAS  Google Scholar  Tompkins D, Dobson A, Arneberg P, Begon M, Cattadori I, Greenman J, et al. Parasites and host population dynamics. The ecology of wildlife diseases. 2002; 45–62. Thomas F, Poulin R, Brodeur J….

Continue Reading Species richness of bat flies and their associations with host bats in a subtropical East Asian region | Parasites & Vectors

Inferring genetic structure when there is little: population genetics versus genomics of the threatened bat Miniopterus schreibersii across Europe

Charlesworth, B. & Charlesworth, D. Population genetics from 1966 to 2016. Heredity 118, 2–9 (2017). CAS  Google Scholar  Orsini, L., Vanoverbeke, J., Swillen, I., Mergeay, J. & Meester, L. Drivers of population genetic differentiation in the wild: Isolation by dispersal limitation, isolation by adaptation and isolation by colonization. Mol. Ecol….

Continue Reading Inferring genetic structure when there is little: population genetics versus genomics of the threatened bat Miniopterus schreibersii across Europe

Origins and diversification of animal innate immune responses against viral infections

Harvey, E. & Holmes, E. C. Diversity and evolution of the animal virome. Nat. Rev. Microbiol. 20, 321–334 (2022). Article  CAS  Google Scholar  Flajnik, M. F. & du Pasquier, L. Evolution of innate and adaptive immunity: can we draw a line? Trends Immunol. 25, 640–644 (2004). Article  CAS  Google Scholar …

Continue Reading Origins and diversification of animal innate immune responses against viral infections

Acquisition of antibodies to Plasmodium falciparum and Plasmodium vivax antigens in pregnant women living in a low malaria transmission area of Brazil | Malaria Journal

WHO. World Malaria Report. Geneva: World Health Organization; 2019. Google Scholar  Rogerson SJ, Hviid L, Duffy PE, Leke RF, Taylor DW. Malaria in pregnancy: pathogenesis and immunity. Lancet Infect Dis. 2007;7:105–17. Article  CAS  PubMed  Google Scholar  Salanti A, Dahlback M, Turner L, Nielsen MA, Barfod L, Magistrado P, et al….

Continue Reading Acquisition of antibodies to Plasmodium falciparum and Plasmodium vivax antigens in pregnant women living in a low malaria transmission area of Brazil | Malaria Journal

Cryptic Cython Error Message – ASKSAGE: Sage Q&A Forum

I have been coding a basic algorithm to compute infinite dimensional path integrals in cython cell in sagemath and have received an error message I am completely baffled by. Despite a good amount of effort I can not reproduce this in a short code sequence. I don’t expect anyone to…

Continue Reading Cryptic Cython Error Message – ASKSAGE: Sage Q&A Forum

Remarkably low host specificity in the bat fly Penicillidia fulvida (Diptera: Nycteribiidae) as assessed by mitochondrial COI and nuclear 28S sequence data | Parasites & Vectors

Zachos FE. Species concepts in biology: historical development, theoretical foundations and practical relevance. Berlin: Springer; 2016. Google Scholar  Perkins SL. Species concepts and malaria parasites: detecting a cryptic species of Plasmodium. Proc Biol Sci. 2000;267:2345–50. CAS  PubMed  PubMed Central  Google Scholar  Mayr E. Systematics and the origin of species. New…

Continue Reading Remarkably low host specificity in the bat fly Penicillidia fulvida (Diptera: Nycteribiidae) as assessed by mitochondrial COI and nuclear 28S sequence data | Parasites & Vectors

Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data

Ai H, Fang X, Yang B, Huang Z, Chen H, Mao L et al. (2015) Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat Genet 47:217–225 CAS  PubMed  Article  Google Scholar  Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC…

Continue Reading Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data

Hidden paths to endless forms most wonderful: ecology latently shapes evolution of multicellular development in predatory bacteria

Carroll, S. B. Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom (Quercus, 2005). Dobzhansky, T. & Spassky, B. Genetics of natural populations. XI. Manifestation of genetic variants in Drosophila pseudoobscura in different environments. Genetics 29, 270–290 (1944). CAS  PubMed  PubMed Central …

Continue Reading Hidden paths to endless forms most wonderful: ecology latently shapes evolution of multicellular development in predatory bacteria

The genus Serratia revisited by genomics

Merlino, C. P. Bartolomeo Bizio’s letter to the most eminent priest, Angelo Bellani, concerning the phenomenon of the red-colored polenta [translated from the Italian]. J. Bacteriol. 9, 527–543 (1924). Grimont, P. A. D. & Dulong de Rosnay, H. L. C. Numerical study of 60 strains of Serratia. J. Gen. Microbiol….

Continue Reading The genus Serratia revisited by genomics

Unveiling new perspective of phylogeography, genetic diversity, and population dynamics of Southeast Asian and Pacific chickens

Food and Agriculture Organization. The state of the world’s animal genetic resources for food and agriculture (Rome, 2007). Lawler, A. Dawn of the chicken revealed in Southeast Asia. Science 368, 1411 (2020). ADS  CAS  PubMed  Article  Google Scholar  Sykes, N. A social perspective on the introduction of exotic animals: the…

Continue Reading Unveiling new perspective of phylogeography, genetic diversity, and population dynamics of Southeast Asian and Pacific chickens

Three families of Asgard archaeal viruses identified in metagenome-assembled genomes

Liu, Y. et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 593, 553–557 (2021). CAS  PubMed  Google Scholar  Dombrowski, N., Teske, A. P. & Baker, B. J. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat. Commun. 9, 4999 (2018). PubMed  PubMed…

Continue Reading Three families of Asgard archaeal viruses identified in metagenome-assembled genomes

Phylogenomics and species delimitation of the economically important Black Basses (Micropterus)

Arlinghaus, R. et al. Governing the recreational dimension of global fisheries. Proc. Nat. Acad. Sci. USA 116, 5209–5213 (2019). CAS  PubMed  PubMed Central  Article  Google Scholar  Cowx, I. G. & Gerdeaux, D. The effects of fisheries management practises on freshwater ecosystems. Fish. Manag. Ecol. 11, 145–151 (2004). Article  Google Scholar …

Continue Reading Phylogenomics and species delimitation of the economically important Black Basses (Micropterus)

In vivo hypermutation and continuous evolution

Arnold, F. H. Design by directed evolution. Acc. Chem. Res. 31, 125–131 (1998). Google Scholar  Packer, M. S. & Liu, D. R. Methods for the directed evolution of proteins. Nat. Rev. Genet. 16, 379–394 (2015). Google Scholar  Drake, J. W., Charlesworth, B., Charlesworth, D. & Crow, J. F. Rates of…

Continue Reading In vivo hypermutation and continuous evolution

Genetic and chemotherapeutic influences on germline hypermutation

DNM filtering in 100,000 Genomes Project We analysed DNMs called in 13,949 parent–offspring trios from 12,609 families from the rare disease programme of the 100,000 Genomes Project. The rare disease cohort includes individuals with a wide array of diseases, including neurodevelopmental disorders, cardiovascular disorders, renal and urinary tract disorders, ophthalmological…

Continue Reading Genetic and chemotherapeutic influences on germline hypermutation

Frontiers | Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data

Introduction Incipient species are critical for evolutionary biologists to study speciation, but they also challenge taxonomy due to gene flow or ancestral polymorphism. The former and contrasting population size lead to larger intraspecific than interspecific variations, a phenomenon called the species-definition anomaly zone (Jiao and Yang, 2021). The latter results…

Continue Reading Frontiers | Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data

Genomic sequencing aids the global tuberculosis fight

Total number of isolates for each drug by sensitivity. Each drug is represented by a colored circle weighted by the prevalence of phenotypic resistance to that drug. The center of each circle shows the intersection between values on the x-axis and y-axis. Group 1 = associated with resistance. Group 2…

Continue Reading Genomic sequencing aids the global tuberculosis fight

Mitogenome of a stink worm (Annelida: Travisiidae) includes degenerate group II intron that is also found in five congeneric species

Tan, M. H. et al. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci. Rep. 9, 1–16 (2019). ADS  Google Scholar  Zhang, Y. et al. Phylogeny, evolution and mitochondrial gene order rearrangement in scale worms (Aphroditiformia, Annelida). Mol. Phylogenet. Evol. 125, 220–231 (2018). CAS  PubMed  Google…

Continue Reading Mitogenome of a stink worm (Annelida: Travisiidae) includes degenerate group II intron that is also found in five congeneric species

Human induced pluripotent stem cells improve visual acuity, vascular health — ScienceDaily

Researchers at Indiana University School of Medicine, in collaboration with the University of Alabama at Birmingham and five other institutions, are investigating novel regenerative medicine approaches to better manage vascular health complications from type 2 diabetes that could someday support blood vessel repair in the eye among diabetic patients with…

Continue Reading Human induced pluripotent stem cells improve visual acuity, vascular health — ScienceDaily

The Clam Cyclina sinensis (Gmelin) Phylogeography Study with 28S rRNA Gene and Potential of Nuclear rRNA Genes in Genetic Assessments of Molluscs

Avise, J. C., 2009. Phylogeography: Retrospect and prospect. Journal of Biogeography, 36: 3–15. Article  Google Scholar  Beheregaray, L. B., 2008. Twenty years of phylogeography: The state of the field and the challenges for the Southern Hemisphere. Molecular Ecology, 17: 3754–3774. Google Scholar  Clement, M., Posada, D., and Crandall, K. A.,…

Continue Reading The Clam Cyclina sinensis (Gmelin) Phylogeography Study with 28S rRNA Gene and Potential of Nuclear rRNA Genes in Genetic Assessments of Molluscs

Genomic variation from an extinct species is retained in the extant radiation following speciation reversal

Vamosi, J. C., Magallon, S., Mayrose, I., Otto, S. P. & Sauquet, H. Macroevolutionary patterns of flowering plant speciation and extinction. Annu. Rev. Plant Biol. 69, 685–706 (2018). CAS  PubMed  Google Scholar  Rhymer, J. M. & Simberloff, D. Extinction by hybridization and introgression. Annu. Rev. Ecol. Syst. 27, 83–109 (1996)….

Continue Reading Genomic variation from an extinct species is retained in the extant radiation following speciation reversal

sequence alignment – MarkDuplicatesSpark failing with cryptic error message. MarkDuplicates succeeds

[*] I have been trying to follow the GATK Best Practice Workflow for ‘Data pre-processing for variant discovery’ (gatk.broadinstitute.org/hc/en-us/articles/360035535912). This has all been run on Windows Subsystem for Linux 2 on the Bash shell. I started off with FASTQ files from IGSR (www.internationalgenome.org/data-portal) and performed alignment with Bowtie2 (instead of…

Continue Reading sequence alignment – MarkDuplicatesSpark failing with cryptic error message. MarkDuplicates succeeds

Dryad Data — Phylogenomic analysis reveals dispersal-driven speciation and divergence with gene flow in Lesser Sunda Flying Lizards (Genus Draco)

The Lesser Sunda Archipelago offers exceptional potential as a model system for studying the dynamics of dispersal-driven diversification. The geographic proximity of the islands suggests the possibility for successful dispersal, but this is countered by the permanence of the marine barriers and extreme intervening currents that are expected to hinder…

Continue Reading Dryad Data — Phylogenomic analysis reveals dispersal-driven speciation and divergence with gene flow in Lesser Sunda Flying Lizards (Genus Draco)

Human microRNA inhibits expression of pathogenic gene underlying facioscapulohumeral muscular dystrophy

Fig. 1: miR-675 targets the DUX4 ORF and 3′UTR. a RenLuc-DUX4-FL dual-luciferase reporter and CMV.H19 constructs, and U6.MIR675, H1.MIR675, U6.MIR675-3p, and U6.MIR675-5p miRNAs. RenLuc-DUX4-FL contains DUX4 ORF and 3′UTR sequences fused to Renilla luciferase after the stop codon. Exons 1–3 are indicated (Ex1,2,3). *SD5 indicates silent mutation of a cryptic…

Continue Reading Human microRNA inhibits expression of pathogenic gene underlying facioscapulohumeral muscular dystrophy

Genome-wide analysis reveals associations between climate and regional patterns of adaptive divergence and dispersal in American pikas

Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664 CAS  PubMed  PubMed Central  Article  Google Scholar  Alexander DH, Shringarpure SS, Novembre J, Lange K (2015) Admixture 1.3 software manual. UCLA Hum Genet Softw Distrib, Los Angeles Google Scholar  Angert AL, Bontrager…

Continue Reading Genome-wide analysis reveals associations between climate and regional patterns of adaptive divergence and dispersal in American pikas

Mutational Analysis of Mitochondrial tRNA Genes

Introduction Diabetes is a very complex disease characterized by the presence of chronic hyperglycemia. Clinically, insulin-dependent type 1 and non-insulin-dependent type 2 are the main types of diabetes. Among them, type 2 diabetes mellitus (T2DM, [MIM125853]) is a common endocrine disorder affecting approximately 10% of adult population.1 In most cases,…

Continue Reading Mutational Analysis of Mitochondrial tRNA Genes

The taxonomy of two uncultivated fungal mammalian pathogens is revealed through phylogeny and population genetic analyses

After 90 years of taxonomic uncertainties, using phenotypic, phylogenetic, and population genetics analyses, the two uncultivated fungi causing skin disease in humans and dolphins, long known as Lacazia loboi8, are now placed as separate species within the genus Paracoccidioides. Early studies using phenotypic or phylogenetic data alone erroneously placed these two…

Continue Reading The taxonomy of two uncultivated fungal mammalian pathogens is revealed through phylogeny and population genetic analyses

Oxford Nanopore Stock: The Internet of Living Things

If you took all the stocks in the world and put them in a single basket, about 58% of that combined market cap would be U.S. stocks. If you want to look that number up, just download a fact sheet for the MSCI ACWI IMI Index. All those cryptic acronyms…

Continue Reading Oxford Nanopore Stock: The Internet of Living Things

What is the best QC to do on imputed UK Biobank data?

What is the best QC to do on imputed UK Biobank data? 0 I am receiving imputed data from UK Biobank to conduct a GWAS on. Previously I have carried out GWAS on genotype data, which I have QC’d for missingness per individual and per SNP, sex discrepancy, MAF filter…

Continue Reading What is the best QC to do on imputed UK Biobank data?

Bacterial endosymbionts protect beneficial soil fungus from nematode attack

A healthy soil nourishes plants and animals, purifies water and air, and promotes sustainable agriculture. Characteristic for highly complex and competitive soil ecosystems are the frequent and direct interactions between all soil-dwelling microorganisms, animals, and plants (1, 2), all of which need to be provided with minerals and carbon sources….

Continue Reading Bacterial endosymbionts protect beneficial soil fungus from nematode attack

Transformation of Lactobacillus acidophilus TK8912 by electroporation with pULA105E plasmid

An efficient method for the transformation of Lactobacillus acidophilus TK8912 by electroporation is presented. The plasmid vector pULA105E was constructed by joining a cryptic plasmid, pLA 105, from L. acidophilus TK8912, the Escherichia coli vector pUC19, and the erythromycin resistance gene of the Streptococcus-Escherichia coli shuttle vector pVA838. Plasmid pULA105E…

Continue Reading Transformation of Lactobacillus acidophilus TK8912 by electroporation with pULA105E plasmid

Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs

1. Thompson, J. N. & Pellmyr, O. Evolution of oviposition behavior and host preference in Lepidoptera. Annu. Rev. Entomol. 36, 65–89 (1991). Article  Google Scholar  2. Bowers, M. D. Iridoid glycosides and host-plant specificity in larvae of the buckeye butterfly, Junonia coenia (Nymphalidae). J. Chem. Ecol. 10, 1567–1577 (1984). CAS …

Continue Reading Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs

Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates

Feasibility of genomic skimming on the ONT minION sequencer The term ’genomic skimming’ was first coined by in 2012 by Straub et al. (2012)20 as a way to utilize shallow sequencing of gDNA to obtain relatively deeper coverage of high-copy portions of the genome, including mitogenomes. In combining genomic skimming…

Continue Reading Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates

Biohackers Season 3 Release Date to be Announced by September 2021

Biohackers is a German decent techno-thriller Netflix original series created by Christian Ditter. The main cast includes Luna Wedler, Jessica Schwarz and BennoFürmann. The first two seasons have six episodes of 35-45 minutes each and have made an image imposing with authenticity. It has 6.8/10 as an IMDb rating. The…

Continue Reading Biohackers Season 3 Release Date to be Announced by September 2021