Tag: CRyPTIC

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…

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…

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;…

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,…

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…

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 …

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 …

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…

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…

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…

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 …

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…

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…

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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…

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;…

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…

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…

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…

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)….

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…

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…

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),…

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…

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,…

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…

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…

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,…

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…

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…

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…

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,…

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…

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…

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…

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…

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…

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….

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 …

‘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%…

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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…

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…

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…

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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…

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]…

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 …

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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…

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…

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]….

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…

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]….

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…

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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…

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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….

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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…

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…

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…

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…

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…

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[*] 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…

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…

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…

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…

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,…

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…

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…

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…

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….

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…

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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…

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…