Tag: CRyPTIC

Diving into PyTorch: A Beginner’s Tale of Contribution | by Weinheimergracia | Dec, 2023

Hey there, fellow code wranglers and AI enthusiasts! I’m Cami, your friendly neighborhood tech explorer, and I’m about to take you on a wild ride through my latest adventure: contributing to PyTorch without being an expert in it. Yes, you read that right! My Unexpected Journey into PyTorch So, I…

Continue Reading Diving into PyTorch: A Beginner’s Tale of Contribution | by Weinheimergracia | Dec, 2023

Assessment of genetic diversity, population structure and wolf-dog hybridisation in the Eastern Romanian Carpathian wolf population

Kershaw, F. et al. The Coalition for Conservation Genetics: Working across organizations to build capacity and achieve change in policy and practice. Conserv. Sci. Pract. 4, e12635 (2022). Article  Google Scholar  Waits, L. P. & Paetkau, D. Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations…

Continue Reading Assessment of genetic diversity, population structure and wolf-dog hybridisation in the Eastern Romanian Carpathian wolf population

Sequencing 101: Structural variation – PacBio

Over the last 50 years, many monumental achievements in genetics and biology have unfolded before our eyes. From the invention of DNA sequencing technologies to the completion of the human genome project and the emergence of genomic medicine, we have made many intellectual and technological leaps in our understanding of…

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‘Shark dust’ helps researchers ID threatened species in Indonesia fish trade

Researchers have developed a new tool to identify a wide range of threatened and protected sharks being processed at fish factories in Indonesia. The method relies on DNA analysis of “shark dust,” the tiny fragments of skin and cartilage swept from the floors of fish-processing plants and export warehouses. From…

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Potent latency reversal by Tat RNA-containing nanoparticle enables multi-omic analysis of the HIV-1 reservoir

Participants and blood collection A total of n = 23 HIV-1 seropositive individuals on stably suppressive ART were included in this study (Supplementary Table 1). Participants were recruited at Ghent University Hospital. 2/23 individuals are female, 21/23 are male; the limited representation of female individuals in our study is a direct reflection of…

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Helen Flanagan shows off her figure in a white mini skirt and black fur-trim top as she poses for sizzling snaps (and her engagement ring is STILL on)

Helen Flanagan looked stunning as she posed for a slew of racy Instagram pictures on Sunday. The former Coronation Street star, 33, displayed her toned physique in sizzling mirror selfies, which also clearly showed her engagement ring from ex-fiancé Scott Sinclair. Helen and the Bristol Rovers footballer split in July 2022 after 13…

Continue Reading Helen Flanagan shows off her figure in a white mini skirt and black fur-trim top as she poses for sizzling snaps (and her engagement ring is STILL on)

Chromosome-level genome assembly of the Stoliczka’s Asian trident bat (Aselliscus stoliczkanus)

Dobson, G. E. On a new genus and species of Rhinolophidae, with description of a new species of Vesperus, and notes on some other species of insectivorous bats from Persia. J. Asiat. Soc. Bengal. 40, 455–461 (1871). Google Scholar  Bates, P., Bumrungsri, S., Francis, C., Csorba, G. & Furey, N….

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r – Problem with significance test using stat_signif() coupled with a ggplot2 boxplot

I am attempting to produce a boxplot with the results of a significance text, ideally with Student’s test and/or a Wilcoxon’s test comparing two groups of concentrations between two different auto-analysers. If I run the following code (Note the code does not include the input statements for the datafiles but…

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‘Dust’ DNA Metabarcoding Revolutionizes Shark Trade Monitoring

GAMBIER ISLANDS, FRENCH POLYNESIA – FEBRUARY 2018: A white tip reef shark (Triaenodon obesus) swims … [+] above the reef on February 16, 2018, Gambier Islands, French Polynesia, South Pacific. Here, in French Polynesia, Triaenodon obesus is called Mamaru. (Photo by Alexis Rosenfeld/Getty Images) Getty Images In recent years, the…

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Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles

Rignot, E., Jacobs, S., Mouginot, J. & Scheuchl, B. Ice-shelf melting around antarctica. Science (80-) 341, 266–270 (2013). Article  ADS  CAS  Google Scholar  Wadham, J. L. et al. Ice sheets matter for the global carbon cycle. Nat. Commun. 10, 1–17 (2019). Google Scholar  Adusumilli, S., Fricker, H. A., Medley, B.,…

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High-throughput sequencing of Diatoms using V4 region of 18S rRNA gene in Bayug Island, Iligan City, Philippines

Almarez DN, Almarez FJS, Baulete EM. 2014. Bayug Island Aquasilvi Program: An Eco-Governance Strategy for Climate Change Adaptation and Mitigation. J Govern Dev 10(2): 35-54. DOI: 10.32890/jgd. Alongi DM. 2014. Carbon cycling and storage in mangrove forests. Ann Rev Mar Sci 6: 195-219. DOI: 10.1146/annurev-marine-010213-135020. Balint M, Pfenninger M, Grossart…

Continue Reading High-throughput sequencing of Diatoms using V4 region of 18S rRNA gene in Bayug Island, Iligan City, Philippines

Analysis of geometric morphometrics and molecular phylogeny for Anopheles species in the Republic of Korea

World Health Organization (WHO). WHO malaria report. 2022 www.who.int/publications/i/item/9789240064898 (2022). Savi, M. K. An overview of malaria transmission mechanisms, control, and modeling. Med. Sci. 11, 3 (2023). Google Scholar  Bahk, Y. Y. et al. Epidemiological characteristics of re-emerging vivax malaria in the Republic of Korea (1993–2017). Korean J. Parasitol. 56,…

Continue Reading Analysis of geometric morphometrics and molecular phylogeny for Anopheles species in the Republic of Korea

Origin and evolution of the triploid cultivated banana genome

Rouard, M. et al. Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana). Genome Biol. Evol. 10, 3129–3140 (2018). CAS  PubMed  PubMed Central  Google Scholar  Langhe, E. D., Vrydaghs, L., Maret, P. D., Perrier, X. & Denham, T. Why bananas matter: an introduction to the history…

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JoF | Free Full-Text | Reference-Based Restriction-Site-Associated DNA Sequencing Data Are Useful for Species Delineation in a Recently Diverged Asexually Reproducing Species Complex (Parmeliaceae, Ascomycota)

3.4. Taxonomy Parmelina clandestina Barcenas-Peña, Divakar, A. Crespo, Nuñez-Zapata, Lumbsch & Grewe sp. nov. (Figure 4a). Diagnosis: Thallus foliose pale-gray, maculate, usually pruinose, isidia cylindrical, white medulla, lower surface black, apothecia and pycnidia infrequent. Upper cortex K+ (yellow); medulla K-, C+ (red), KC+ (red), P-. Contains atranorin and lecanoric acid….

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NN intro no animation.pdf – Neural Network Announcements Kaggle competition will be released today Task: sentiment analysis r0: Bromwell High is a

Announcements Kaggle competition will be released today Task: sentiment analysis r0: Bromwell High is a cartoon comedy. It ran at the same time as some other programs about school life, such as “Teachers”. My 35 years in the teaching profession lead me to believe that Bromwell High’s satire is much…

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How can mitochondrial DNA be used to study the evolution of different species?

How does the mitochondria evolve?5 answersMitochondria evolved through an endosymbiotic relationship between an alphaproteobacterial endosymbiont and a host cell, leading to the integration of the endosymbiont into the host and the eventual loss of independence to become a mitochondrion. This process involved the transfer of genes from the endosymbiont to…

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Golden mole that ‘swims’ through sand rediscovered in South Africa, last seen in 1936 – Mothership.SG

This beach in South Africa might look barren to the naked eye. Photo by JP Le Roux via Re:wild But beneath the dunes hides the De Winton’s golden mole, a strange-looking creature that was last seen in 1936, and feared extinct by scientists. The species, however, is lost to science…

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Targeting the epigenome to reinvigorate T cells for cancer immunotherapy | Military Medical Research

Tsui C, Kretschmer L, Rapelius S, Gabriel SS, Chisanga D, Knöpper K, et al. MYB orchestrates T cell exhaustion and response to checkpoint inhibition. Nature. 2022;609(7926):354–60. Article  CAS  PubMed  PubMed Central  Google Scholar  Zhu L, Zhou X, Gu M, Kim J, Li Y, Ko CJ, et al. Dapl1 controls NFATc2…

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RNA Pol II Assembly Affects ncRNA Expression[v1]

Preprint Article Version 1 This version is not peer-reviewed Version 1 : Received: 30 November 2023 / Approved: 1 December 2023 / Online: 1 December 2023 (10:10:30 CET) Garrido-Godino, A.I.; Gupta, I.; Pelechano, V.; Navarro, F. RNA Pol II Assembly Affects ncRNA Expression. Preprints 2023, 2023120065. doi.org/10.20944/preprints202312.0065.v1 Garrido-Godino, A.I.; Gupta,…

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Ancient diversity in host-parasite interaction genes in a model parasitic nematode

Van Valen, L. A new evolutionary law. Evol. Theory 1, 1–30 (1973). Google Scholar  Woolhouse, M. E. J., Webster, J. P., Domingo, E., Charlesworth, B. & Levin, B. R. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat. Genet. 32, 569–577 (2002). Article  CAS  PubMed  Google…

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Genome mining reveals novel biosynthetic gene clusters in entomopathogenic bacteria

Katz, L. & Baltz, R. H. Natural product discovery: Past, present, and future. J. Ind. Microbiol. Biotechnol. 43, 155–176 (2016). Article  CAS  PubMed  Google Scholar  Newman, D. J. & Cragg, G. M. Natural products as sources of new drugs from 1981 to 2014. J. Nat. Prod. 79, 629–661 (2016). Article …

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MD Anderson Research Highlights for November 15, 2023

Newswise — HOUSTON ― The University of Texas MD Anderson Cancer Center’s Research Highlights showcases the latest breakthroughs in cancer care, research and prevention. These advances are made possible through seamless collaboration between MD Anderson’s world-leading clinicians and scientists, bringing discoveries from the lab to the clinic and back. Recent…

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cryptic error with pod5 subset tool

I’m running into a error that I haven’t managed to debug so far. The job runs for a few seconds, and then stops writing files. The errors are not always exactly the same, nor they are happening at the same point of the subsetting process. Here is a representative example,…

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Myeloid/Lymphoid Neoplasms with ETV6::PDGFRB Fusion Gene

Introduction The ETV6::PDGFRB fusion gene is commonly associated with myeloid neoplasms with monocytosis (such as CMML), and with eosinophilia.1 The PDGFRB gene, located on 5q33, encodes PDGFRβ, a type III tyrosine kinase comprising an extracellular domain consisting of five immunoglobulin (Ig)-like domains, a single-transmembrane helix domain, a juxtamembrance domain, and…

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Two sympatric lineages of Australian Cnestus solidus share Ambrosiella symbionts but not Wolbachia

Andersen HF, Jordal BH, Kambestad M, Kirkendall LR (2012) Improbable but true: the invasive inbreeding ambrosia beetle Xylosandrus morigerus has generalist genotypes. Ecol Evol 2:247–257 Article  PubMed  PubMed Central  Google Scholar  Arif S, Gerth M, Hone‐Millard WG, Nunes MDS, Dapporto L, Shreeve TG (2021) Evidence for multiple colonisations and Wolbachia…

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In silico prospecting of the mtDNA of Macrobrachium amazonicum from transcriptome data | BMC Genomics

Bentes B, Martinelli J, Souza L, Cavalcante D, Almeida M, Isaac V. Spatial distribution of the amazon river prawn Macrobrachium Amazonicum (Heller, 1862) (Decapoda, Caridea, Palaemonidae) in two perennial creeks of an estuary on the northern coast of Brazil (Guajará Bay, Belém, Pará). Brazilian J Biol. 2011;71:925–35. Article  Google Scholar …

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TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons

Padeken, J., Methot, S. P. & Gasser, S. M. Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat. Rev. Mol. Cell Biol. 23, 623–640 (2022). Article  CAS  PubMed  PubMed Central  Google Scholar  Tchasovnikarova, I. A. et al. Epigenetic silencing by the HUSH complex mediates position-effect variegation…

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Molecular diagnosis, phylogenetic analysis, and antifungal susceptibility profiles of Candida species isolated from neutropenic oncological patients | BMC Infectious Diseases

Eissa S, Khedr R, Romeih M, Halaby L, Elanany M, Madney Y. Clinical characteristics and outcome of invasive fungal sinusitis in children with hematological malignancies. Med Mycol. 2022;60(4):myac010. Article  PubMed  Google Scholar  Lin G-L, Chang H-H, Lu C-Y, Chen C-M, Lu M-Y, Lee P-I, Jou S-T, Yang Y-L, Huang L-M,…

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A Menagerie on a Leaf

Butterflies alighted on Christina Lynggaard’s skin, licking her sweat as she, Jan Gogarten, and a small team of researchers swabbed leaves deep in the rainforest in Uganda’s Kibale National Park. The work was an unplanned side project. Gogarten, a molecular ecologist at the University of Greifswald, had hoped to research pathogens…

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DNA Barcoding: A Molecular Toolkit for Species Identification | by Saitama | Nov, 2023

Photo by SilverV 🧬DNA, or deoxyribonucleic acid, is the hereditary material in humans and almost all other organisms. It is a long, thin molecule that carries our genetic code and is coiled up tightly inside the nucleus of every cell in our body. 🧬DNA barcoding is a molecular technology that…

Continue Reading DNA Barcoding: A Molecular Toolkit for Species Identification | by Saitama | Nov, 2023

Multiple parallel origins of parasitic Marine Alveolates

MALV-II and -IV are closely related to the eleftherids, a new group of free-living heterotrophs We isolated and cultured several strains collectively representing two new species of colorless, eukaryovorous flagellates, which we formally name Eleftheros xomoi (strains Colp-37 and Cur-11, isolated from the surface of a coral in the Caribbean…

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Multiple courses for one instructor/grader in one single user server in JupyterHub on Kuberentes

Hi, I’m trying to set up nbgrader with JupyterHub with KubeSpawner. I want to achieve following: – one instructor is able to work with multiple courses in one notebook instance – several graders are able to access relevant formgraders – students are able to subscribe to multiple courses = see assignments…

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Seasonal dynamics of Amblyomma cajennense (Fabricius, 1787) sensu stricto in a degraded area of the Amazon biome, with notes on Rickettsia amblyommatis infection | Parasites & Vectors

Szabó MPJ, Pinter A, Labruna MB. Ecology, biology and distribution of spotted-fever tick vectors in Brazil. Front Cell Infect Microbiol. 2013;3:27. Article  PubMed  PubMed Central  Google Scholar  Luz HR, Costa FB, Benatti HR, Ramos VN, Serpa A, Martins MC, et al. Epidemiology of capybara-associated Brazilian spotted fever. PLoS Neg Trop…

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Unveiling the Magic of OpenAPI DevTools: Your API Exploration Ally

Unveiling the Magic of OpenAPI DevTools: Your API Exploration Ally Introduction In the digital realm, the exploration of APIs (Application Programming Interfaces) is akin to unveiling the magic that powers applications and websites. Among the wizards of this domain, OpenAPI DevTools emerges as a spellbinding ally. Developed by Andrew Walsh,…

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Novel insights in cryptic diversity of snow and glacier ice algae communities combining 18S rRNA gene and ITS2 amplicon sequencing

doi: 10.1093/femsec/fiad134. Online ahead of print. Affiliations Expand Affiliations 1 Paris Lodron University of Salzburg, Department of Ecology & Biodiversity, Hellbrunnerstr. 34, 5020 Salzburg, Austria. 2 University of Applied Sciences Upper Austria, Stelzhamerstr. 23, 4600 Wels, Austria. 3 Charles University, Faculty of Science, Department of Ecology, Viničná 7, 128 44…

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Invasive Californian death caps develop mushrooms unisexually and bisexually

Mushroom collecting Sporocarps were collected from various herbaria and during three expeditions to Point Reyes National Seashore (PRNS), California in 2004, 2014 and 2015, and in 2015 from three sites in Portugal. A total of 86 sporocarps were collected: 67 Californian sporocarps (one early herbarium sample dates to 1993), 11…

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20 | October | 2023

For all that modern washers and dryers do, they don’t let you know when they’re finished. Or they do, but it’s only a short victory song that plays once and can be easy to miss. What most of us need is a gentle reminder that there’s damp laundry festering in…

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Challenges in Variant Calling and Genotyping with Short-Read Data Mapped to a Pangenome Graph: Seeking Guidance

Challenges in Variant Calling and Genotyping with Short-Read Data Mapped to a Pangenome Graph: Seeking Guidance 0 Hello all, We are reaching out since we have some practical questions regarding variant calling and analyses of short-read data mapped to a pangenome graph. We are working on a project aimed to…

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Pair_style hybrid/overlay with lepton? – LAMMPS General Discussion

bulba October 17, 2023, 2:19pm 1 I would like to use pair_style lepton with DPD thermostat, for which I used pair_style hybrid/overlay. Is there a way to “overlay” two styles. Forgive me if it’s a pretty noobish question (in Baldrick’s words, again it’s because…), but I seems to be unable…

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Kaggle hosts a CTF competition organized by the AI Village community with a $50,000 prize pool

TL;DR: Kaggle hosts a CTF competition by AI Village with $50,000 in prizes. 27 hand-crafted machine learning security challenges await participants. The contest aims to foster a hacker mindset and diversity in AI security. The self-paced event began on October 9 and ended on November 9. Prizes range from $8,000…

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Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle

Falkowski P. G., Raven J. A. Aquatic Photosynthesis (Princeton Univ. Press, 2013). Sanchez-Baracaldo, P., Bianchini, G., Wilson, J. D. & Knoll, A. H. Cyanobacteria and biogeochemical cycles through earth history. Trends Microbiol. 30, 143–157 (2022). Article  CAS  PubMed  Google Scholar  Blankenship, R. E. Early evolution of photosynthesis. Plant Physiol. 154,…

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SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses

A total of 325 wastewater samples from sites listed in Table S1 were amplified and sequenced. Of those, 229 (70.5%) samples had > 1 million reads and were included in the mutational analysis and the heatmap visualization. Out of the 325, 183 (56.3%) samples had >50% sequence coverage of the whole…

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Habitat and climate influence hybridization among three genetically distinct Canada jay (Perisoreus canadensis) morphotypes in an avian hybrid zone complex

Adams RV, Burg TM (2015) Gene flow of a forest-dependent bird across a fragmented landscape. PLoS One 10:1–22 Article  Google Scholar  Aguillon S, Rohwer V (2022) Revisiting a classic hybrid zone: movement of the northern flicker hybrid zone in contemporary times. Evolution 76:1082–1090 Article  PubMed  Google Scholar  Aktas C (2020)…

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Genetic analysis challenges the presence of Ixodes inopinatus in Central Europe: development of a multiplex PCR to distinguish I. inopinatus from I. ricinus | Parasites & Vectors

Estrada-Peña A, de la Fuente J. Host distribution does not limit the range of the tick Ixodes ricinus but impacts the circulation of transmitted pathogens. Front Cell Infect Microbiol. 2017;7:1–10. doi.org/10.3389/fcimb.2017.00405. Article  Google Scholar  Al-Khafaji AM, Clegg SR, Pinder AC, Luu L, Hansford KM, Seelig F, et al. Multi-locus sequence…

Continue Reading Genetic analysis challenges the presence of Ixodes inopinatus in Central Europe: development of a multiplex PCR to distinguish I. inopinatus from I. ricinus | Parasites & Vectors

Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer’s disease brains | Cell & Bioscience

Lo MT, Kauppi K, Fan CC, Sanyal N, Reas ET, Sundar VS, Lee WC, Desikan RS, McEvoy LK, Chen CH, Alzheimer’s Disease Genetics, C. Identification of genetic heterogeneity of Alzheimer’s disease across age. Neurobiol Aging. 2019;84(243):e241-243. doi.org/10.1016/j.neurobiolaging.2019.02.022. Article  Google Scholar  Nacmias B, Bagnoli S, Piaceri I, Sorbi S. Genetic heterogeneity…

Continue Reading Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer’s disease brains | Cell & Bioscience

DNA Study Reveals Cryptic New Species of Pangolin

The newly-identified species, Manis mysteria, is the ninth known pangolin species or the fifth Asian one. The Asian mysterious pangolin (Manis mysteria) separated from the Philippine pangolin (shown here) and Malayan pangolin over 5 million years ago. Image credit: Gregg Yan / CC BY-SA 4.0. Pangolins are mammals of the…

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Snakemake alignment script

I have been trying to write a simple alignment pipeline with Snakemake. Unfortunately, I have a hard time understanding the error messages. In the example below, the message ” ‘str’ object has no attribute ‘name’ ” is a bit cryptic. Does it means that the expression {input.r1} is incorrect? import…

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Genetic Code of Rare Kidney Cancer Cracked

Researchers have decoded the genetic makeup of the rare kidney cancer, reninoma, for the first time. Collaborating institutions identified an error in the NOTCH1 cancer gene as the cause. Using advanced genomic techniques, the team believes existing drugs targeting this gene could treat reninoma without surgery. New study reveals drivers…

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the future of mRNA vaccine analysis and quality assurance?

In a recent study published in Nature Communications, researchers proposed a simplified approach for analyzing messenger ribonucleic acid (mRNA) vaccines using long-read sequencing. Study: mRNA vaccine quality analysis using RNA sequencing. Image Credit: Jo Panuwat D/Shutterstock.com Background Messenger RNA vaccines demonstrated safety and efficacy during the COVID-19 pandemic, but extensive…

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Reconstructing the cytokine view for the multi-view prediction of COVID-19 mortality | BMC Infectious Diseases

Li H, Liu SM, Yu XH, Tang SL, Tang CK. Coronavirus disease 2019 (COVID-19): current status and future perspectives. Int J Antimicrob Agents. 2020;55(5):105951. Article  CAS  PubMed  PubMed Central  Google Scholar  . virusncov.com/. Iwendi C, Bashir AK, Peshkar A, Sujatha R, Chatterjee JM, Pasupuleti S, et al. COVID-19 Patient Health…

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Characterization and organelle genome sequencing of Pyropia species from Myanmar

Yang, L. E. et al. Redefining Pyropia (Bangiales, Rhodophyta): Four new genera, resurrection of Porphyrella and description of Calidia pseudolobata sp. Nov. from China. J. Phycol. 56, 862–879 (2020). Article  CAS  PubMed  Google Scholar  Mumford Jr, T. F. Porphyra as Food: Cultivation and Economics in Algae and Human Affairs (ed….

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First isolation of Rickettsia amblyommatis from Amblyomma mixtum in Colombia | Parasites & Vectors

Fang R, Blanton LS, Walker DH. Rickettsiae as emerging infectious agents. Clin Lab Med. 2017;37:383–400. doi.org/10.1016/j.cll.2017.01.009. Article  PubMed  Google Scholar  Verhoeve VI, Fauntleroy TD, Risteen RG, Driscoll TP, Gillespie JJ. Cryptic genes for interbacterial antagonism distinguish Rickettsia species infecting blacklegged ticks from other Rickettsia pathogens. Front Cell Infect Microbiol. 2022;12:880813….

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Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae

Brocks, J. J. et al. The rise of algae in Cryogenian oceans and the emergence of animals. Nature 548, 578–581 (2017). Article  ADS  CAS  PubMed  Google Scholar  Leliaert, F. Green algae: Chlorophyta and Streptophyta. In Encyclopedia of microbiology 457–468 (Academic Press, 2019). Zhang, Z. et al. Origin and evolution of…

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Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes

Orr, H. A. The genetic theory of adaptation: A brief history. Nat. Rev. Genet. 6, 119–127 (2005). Article  CAS  PubMed  Google Scholar  Dillon, M. E. & Lozier, J. D. Adaptation to the abiotic environment in insects: the influence of variability on ecophysiology and evolutionary genomics. Curr. Opin. Insect Sci. 36,…

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Genomic exploration of canine evolution: Insights from the Dog10K Project

In the profound tapestry of human existence, a remarkable and often cherished dimension is our companionship with canines. Embedded within this intricate narrative are the genetic underpinnings that have sculpted the myriad dog breeds we now adore. A consortium of global scientists, spearheaded by Dr. Jeff Kidd of the University…

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Global determinants of insect mitochondrial genetic diversity

Jenkins, C. N., Pimm, S. L. & Joppa, L. N. Global patterns of terrestrial vertebrate diversity and conservation. Proc. Natl Acad. Sci. USA 110, E2602–E2610 (2013). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Jarzyna, M. A., Quintero, I. & Jetz, W. Global functional and phylogenetic structure of avian assemblages…

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Interrogating the viral dark matter of the rumen ecosystem with a global virome database

Gregory, A. C. et al. Marine DNA viral macro-and microdiversity from pole to pole. Cell 177, 1109–1123.e1114 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  Roux, S. et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537, 689–693 (2016). Article  CAS  PubMed  Google Scholar  Camarillo-Guerrero, L….

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The Male Y Chromosome Has Finally Been Completely Sequenced

Image by Getty / Futurism The human Y chromosome, the determinant of male sex, has finally been completely sequenced. What it unveils could prove crucial to understanding the Y chromosome’s puzzling origins, and — pertinently — how it affects male fertility. You can thank two teams of researchers for the breakthrough,…

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Occurrence of Thelazia callipaeda and its vector Phortica variegata in Austria and South Tyrol, Italy, and a global comparison by phylogenetic network analysis | Parasites & Vectors

Miterpáková M, Trbolová A, Hurníková Z, Balicka A, Čabanová V, Valentová D, et al. Thelazia callipaeda in Slovakia—from sporadic cases to endemic areas. Parasitol Int. 2022;87:102495. doi.org/10.1016/j.parint.2021.102495. Article  PubMed  Google Scholar  Gama A, Pires I, Canado M, Coutinho T, Lopes AP, Latrofa MS, et al. First report of Thelazia callipaeda…

Continue Reading Occurrence of Thelazia callipaeda and its vector Phortica variegata in Austria and South Tyrol, Italy, and a global comparison by phylogenetic network analysis | Parasites & Vectors

Maritime mushroom researchers partner with public in summer Mycoblitz

They can be round and white, and grow in circles in grassy fields. They can be purple or bright orange, and grow among moss and tree trunks. They can even sprout overnight, seemingly out of nowhere.  These are just some of the reasons why researchers like Allison Walker are interested in…

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Well-hidden methanogenesis in deep, organic-rich sediments of Guaymas Basin

Magnabosco C, Lin LH, Dong H, Bomberg M, Ghiorse W, Stan-Lotter H, et al. The biomass and biodiversity of the continental subsurface. Nat Geosci. 2018;11:707–17. Article  CAS  Google Scholar  LaRowe DE, Amend JP. Catabolic rates, population sizes and doubling/replacement times of microorganisms in natural settings. Am J Sci. 2015;315:167–203. Article …

Continue Reading Well-hidden methanogenesis in deep, organic-rich sediments of Guaymas Basin

Genome mining shows that retroviruses are pervasively invading vertebrate genomes

Johnson, W. E. Origins and evolutionary consequences of ancient endogenous retroviruses. Nat. Rev. Microbiol 17, 355–370 (2019). Article  CAS  PubMed  Google Scholar  Stoye, J. P. Studies of endogenous retroviruses reveal a continuing evolutionary saga. Nat. Rev. Microbiol 10, 395–406 (2012). Article  CAS  PubMed  Google Scholar  Zheng, J., Wei, Y. &…

Continue Reading Genome mining shows that retroviruses are pervasively invading vertebrate genomes

A cryptic microdeletion del(12)(p11.21p11.23) within an unbalanced translocation t(7;12)(q21.13;q23.1) implicates new candidate loci for intellectual disability and Kallmann syndrome

To date, there have been reports of three balanced translocations and one microdeletion involving 12q24 associated with hypogonadism or KS1,2,3,4. In a case reported in 1983, all three brothers of Vietnamese Chinese origin were found to have severe primary hypogonadism with a karyotype of 46,XY,t(1;12)(p32;q24)3. Another case, published in 1990,…

Continue Reading A cryptic microdeletion del(12)(p11.21p11.23) within an unbalanced translocation t(7;12)(q21.13;q23.1) implicates new candidate loci for intellectual disability and Kallmann syndrome

Dissecting human population variation in single-cell responses to SARS-CoV-2

Sample collection The individuals of self-reported African (AFB) and European (EUB) descent studied are part of the EVOIMMUNOPOP cohort18. In brief, 390 healthy male donors (188 AFB and 202 EUB) were recruited between 2012 and 2013 in Ghent (Belgium), thus, before the COVID-19 pandemic. Blood was obtained from the healthy…

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From bites to barcodes: uncovering the hidden diversity of black flies (Diptera: Simuliidae) in Vietnam | Parasites & Vectors

The overall efficacy of identification of nominal species was 71% for the 234 COI barcodes of black flies, based on “Best Match” and “Best Close Match” methods. Ambiguous and incorrect identifications were observed for closely related species and members of species complexes, particularly in the S. asakoae, S. feuerborni, S….

Continue Reading From bites to barcodes: uncovering the hidden diversity of black flies (Diptera: Simuliidae) in Vietnam | Parasites & Vectors

Creating a teleost fish traceability program based on genetic data from the Pacific coast of Panama

24 July 2023 Carlos Ramos-Delgado, Ph.D. A total of 34 species from 14 families were identified at the species level from 164 sequences This research provides important information and molecular tools for accurate identification of marine fish species in Panama and their traceability along the supply chain by providing species-specific…

Continue Reading Creating a teleost fish traceability program based on genetic data from the Pacific coast of Panama

DNA barcoding of black flies (Diptera: Simuliidae) in Indonesia | Parasites & Vectors

Adler PH, Takaoka H, Sofian-Azirun M, Chen CD, Suana IW. Evolutionary and biogeographic history of the black fly Simulium wayani (Diptera: Simuliidae) on the island of Timor. Acta Trop. 2019;193:1–6. Article  PubMed  Google Scholar  Adler PH, McCreadie JW. Black flies (Simuliidae). In: Adler PH, McCreadie JW, editors. Medical and veterinary…

Continue Reading DNA barcoding of black flies (Diptera: Simuliidae) in Indonesia | Parasites & Vectors

Increased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil

Mourad, O., Makhani, L. & Chen, L. H. Chikungunya: an emerging public health concern. Curr. Infect. Dis. Rep. 24, 217–228 (2022). Article  PubMed  PubMed Central  Google Scholar  Chala, B. & Hamde, F. Emerging and re-emerging vector-borne infectious diseases and the challenges for control: a review. Front. Public Health 9, 715759…

Continue Reading Increased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil

Organization of the human intestine at single-cell resolution

Tissue collection and processing This study complies with all relevant ethical regulations and was approved by the Washington University Institutional Review Board and the Stanford University Institutional Review Board. Human bowel tissues were procured from deceased organ donors. Written informed consent was obtained from the next-of-kin for all donor participants….

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Best Large Language Models (LLMs)

Unveiling one of the best large language models, OpenAI’s ChatGPT, has provoked a competitive surge in the AI field. A diverse tapestry of participants, ranging from imposing corporate giants to ambitious startups, and extending to the altruistic open-source community, is deeply engrossed in the exciting endeavor to innovate the most…

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Integrating full and partial genome sequences to decipher the global spread of canine rabies virus

RABV sequence and metadata acquisition and composition All 25,787 available sequences for the five genes of the RABV genome were downloaded from the NCBI Virus database5. After quality control, the RABV data set was reduced to 14,752 sequences that spanned 121 countries and were extracted from 192 different host species…

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Cryptosporidium mortiferum n. sp. (Apicomplexa: Cryptosporidiidae), the species causing lethal cryptosporidiosis in Eurasian red squirrels (Sciurus vulgaris) | Parasites & Vectors

Nader JL, Mathers TC, Ward BJ, Pachebat JA, Swain MT, Robinson G, et al. Evolutionary genomics of anthroponosis in Cryptosporidium. Nat Microbiol. 2019;4:826–36. Article  CAS  PubMed  Google Scholar  Tyzzer EE. An extracellular coccidium, Cryptosporidium muris (gen. et sp. nov.) of the gastric glands of the common mouse. J Med Res….

Continue Reading Cryptosporidium mortiferum n. sp. (Apicomplexa: Cryptosporidiidae), the species causing lethal cryptosporidiosis in Eurasian red squirrels (Sciurus vulgaris) | Parasites & Vectors

Mcr-dependent methanogenesis in Archaeoglobaceae enriched from a terrestrial hot spring

Pavlov AA, Brown LL, Kasting JF. UV shielding of NH3 and O2 by organic hazes in the Archean atmosphere. J Geophys Res Atmos. 2001;106:23267–87. Article  CAS  Google Scholar  Zahnle KJ. Earth’s earliest atmosphere. Elements. 2006;2:217–22. Article  CAS  Google Scholar  Arias P, Bellouin N, Coppola E, Jones R, Krinner G, Marotzke…

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Transcription and FACT facilitate the restoration of replication-coupled chromatin assembly defects

Struhl, K. & Segal, E. Determinants of nucleosome positioning. Nat. Struct. Mol. Biol. 20, 267–273 (2013). Article  CAS  PubMed  PubMed Central  Google Scholar  Chereji, R. V. & Clark, D. J. Major determinants of nucleosome positioning. Biophys. J. 114, 2279–2289 (2018). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Morgan, M….

Continue Reading Transcription and FACT facilitate the restoration of replication-coupled chromatin assembly defects

A framework for individualized splice-switching oligonucleotide therapy

Patients The WGS and clinical data of 235 patients with A-T were provided by the Global A-T Family Data Platform of ATCP. Our access to the data was approved by the Data Access Committee of ATCP. Selected patients with A-T enrolled at the Manton Center for Orphan Disease Research under…

Continue Reading A framework for individualized splice-switching oligonucleotide therapy

Metagenomic surveillance for bacterial tick-borne pathogens using nanopore adaptive sampling

Albertsen, M. Long-read metagenomics paves the way toward a complete microbial tree of life. Nat. Methods 20, 30–31 (2023). Article  CAS  PubMed  Google Scholar  van Dijk, E. L., Auger, H., Jaszczyszyn, Y. & Thermes, C. T. years of next-generation sequencing technology. Trends Genet. 30, 418–426 (2014). Article  PubMed  Google Scholar …

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Role of invasive carnivores (Procyon lotor and Nyctereutes procyonoides) in epidemiology of vector-borne pathogens: molecular survey from the Czech Republic | Parasites & Vectors

Braks M, Medlock JM, Hubalek Z, Hjertqvist M, Perrin Y, Lancelot R, et al. Vector-borne disease intelligence: strategies to deal with disease burden and threats. Front Public Heal. 2014. doi.org/10.3389/fpubh.2014.00280. Article  Google Scholar  Faburay B. The case for a “one health” approach to combating vector-borne diseases. African J Disabil. 2015;5:1–4….

Continue Reading Role of invasive carnivores (Procyon lotor and Nyctereutes procyonoides) in epidemiology of vector-borne pathogens: molecular survey from the Czech Republic | Parasites & Vectors

Intragenomic rDNA variation – the product of concerted evolution, mutation, or something in between?

Adams KL, Wendel JF (2005) Polyploidy and genome evolution in plants. Curr Opin Plant Biol 8(2):135–141 Article  CAS  PubMed  Google Scholar  Ambrose CD, Crease TJ (2011) Evolution of the nuclear ribosomal DNA intergenic spacer in four species of the Daphnia pulex complex. BMC Genet 12:13 Article  CAS  PubMed  PubMed Central …

Continue Reading Intragenomic rDNA variation – the product of concerted evolution, mutation, or something in between?

Protocol for coarse grained simulation of protein ligand system using GROMACS

Coarse-grained (CG) simulations are a powerful tool for studying the behavior of biomolecular systems. They are becoming increasingly important tools for drug discovery, as they can be used to study a wide variety of systems over long timescales. CG simulations are faster than all-atom MD simulations, which allows researchers to…

Continue Reading Protocol for coarse grained simulation of protein ligand system using GROMACS

SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat and LRIF1 promoter yet display different modes of action

Somatic loss of LRIF1 or SMCHD1 in control myocytes leads to insufficient DUX4 derepression We have previously shown that SMCHD1 and LRIF1L aid in transcriptional repression of the D4Z4 repeat as short-term depletion of either LRIF1L or SMCHD1 in muscle cells having a D4Z4 repeat of <20 units on a…

Continue Reading SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat and LRIF1 promoter yet display different modes of action

An extended mtDNA phylogeography for the alpine newt illuminates the provenance of introduced populations

Abstract Many herpetofauna species have been introduced outside of their native range. MtDNA barcoding is regularly used to determine the provenance of such populations. The alpine newt has been introduced across the Netherlands, the United Kingdom and Ireland. However, geographical mtDNA structure across the natural range of the alpine newt…

Continue Reading An extended mtDNA phylogeography for the alpine newt illuminates the provenance of introduced populations

Reappraising the evolutionary history of the largest known gecko, the presumably extinct Hoplodactylus delcourti, via high-throughput sequencing of archival DNA

Uetz, P., Slavenko, A., Meiri, S. & Heinicke, M. P. Gecko diversity: A history of global discovery. Israel J. Ecol. Evol. 66, 117–125 (2020). Article  Google Scholar  Grismer, L. L. et al. Phylogenetic partitioning of the third-largest vertebrate genus in the world, Cyrtodactylus Gray, 1827 (Reptilia; Squamata; Gekkonidae) and its…

Continue Reading Reappraising the evolutionary history of the largest known gecko, the presumably extinct Hoplodactylus delcourti, via high-throughput sequencing of archival DNA

Amplicon sequencing allows differential quantification of closely related parasite species: an example from rodent Coccidia (Eimeria) | Parasites & Vectors

Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, et al. Best practices for analysing microbiomes. Nat Rev Microbiol. 2018;16:410–22. doi.org/10.1038/s41579-018-0029-9. Article  CAS  PubMed  Google Scholar  Blaxter M. Counting angels with DNA. Nature. 2003;421:122–3. doi.org/10.1038/421122a. Article  CAS  PubMed  Google Scholar  Cordier T, Alonso-Sáez L, Apothéloz-Perret-Gentil L, Aylagas…

Continue Reading Amplicon sequencing allows differential quantification of closely related parasite species: an example from rodent Coccidia (Eimeria) | Parasites & Vectors

Complete genomes and comparative analyses of Streptomyces phages that influence secondary metabolism and sporulation

Cheng, K. et al. Population genetic analysis of Streptomyces albidoflavus reveals habitat barriers to homologous recombination in the diversification of streptomycetes. Appl. Environ. Microbiol. 81, 966–975 (2015). Article  ADS  PubMed  PubMed Central  Google Scholar  Bentley, S. D. et al. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature…

Continue Reading Complete genomes and comparative analyses of Streptomyces phages that influence secondary metabolism and sporulation

Favorite Splice Site Prediction/Evaluation Tools

Favorite Splice Site Prediction/Evaluation Tools 5 Does anyone have a favorite splice site prediction / evaluation tool? (This would be for evaluating variants in the human genome). I am familiar with the Human Splicing Finder, but am looking to try others. Open-source would be ideal, and if possible something that…

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Applications of long-read sequencing to Mendelian genetics | Genome Medicine

Kingsmore SF, Cakici JA, Clark MM, Gaughran M, Feddock M, Batalov S, et al. A randomized, controlled trial of the analytic and diagnostic performance of singleton and trio, rapid genome and exome sequencing in ill infants. Am J Hum Genet. 2019;105(4):719–33. Article  CAS  PubMed  PubMed Central  Google Scholar  Costain G,…

Continue Reading Applications of long-read sequencing to Mendelian genetics | Genome Medicine

Role of RNA splicing mutation

Introduction Non-Hodgkin lymphoma is a heterogeneous group of cancers that starts during immune system differentiation.1 Recent reports show that more than 100 different lymphoma types have been identified.2 These lymphomas originate from cells of the immune system such as B cells, T cells, and dendritic cells. B-cell lymphomas are another…

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‘Secretive’ creature found slithering in mountains at night is undiscovered species

Researchers recently spotted two “metallic” creatures rustling in the underbrush in the mountains of China. The creatures, found in a forest in the southern province of Hunan, appeared to be a familiar kind of snake, according to a study published on June 13 in the journal ZooKeys. Based on its…

Continue Reading ‘Secretive’ creature found slithering in mountains at night is undiscovered species

‘Metallic’ new creature found slithering in Chinese mountains

A new “secretive” species of snake was discovered in the mountains of Hunan, China, according to a new study. Photo from Wentao Liu, UnSplash Researchers recently spotted two “metallic” creatures rustling in the underbrush in the mountains of China. The creatures, found in a forest in the southern province of…

Continue Reading ‘Metallic’ new creature found slithering in Chinese mountains

Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data

Adamack AT, Gruber B (2014) PopGenReport: simplifying basic population genetic analyses in R. Methods Ecol Evol 5:384–387. doi.org/10.1111/2041-210x.12158 Article  Google Scholar  Aguirre-Liguori JA, Ramírez-Barahona S, Gaut BS (2021) The evolutionary genomics of species’ responses to climate change. Nat Ecol Evol 5:1350–60. doi.org/10.1038/s41559-021-01526-9 Article  PubMed  Google Scholar  Ahrens CW, Rymer PD,…

Continue Reading Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data

Phage diversity in cell-free DNA identifies bacterial pathogens in human sepsis cases

Executive Board, 140. Improving the Prevention, Diagnosis and Clinical Management of Sepsis (The Secretariat, 2017). Grabuschnig, S. et al. Putative origins of cell-free DNA in humans: a review of active and passive nucleic acid release mechanisms. Int. J. Mol. Sci. 21, 1–24 (2020). Article  Google Scholar  Kowarsky, M. et al….

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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…

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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…

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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 …

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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…

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