Tag: CRyPTIC

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….

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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…

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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 …

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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….

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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…

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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…

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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 …

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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…

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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…

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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…

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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…

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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…

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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.,…

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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)….

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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…

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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…

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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…

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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,…

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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…

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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…

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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…

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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….

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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…

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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 …

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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…

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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…

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