Tag: orf

Antimicrobial potential of Streptomyces coeruleofuscus SCJ isolated from microbiologically unexplored garden soil in Northwest Morocco

Zaman, S. B. et al. A review on antibiotic resistance: Alarm bells are ringing. Cureus doi.org/10.7759/cureus.1403 (2017). Article  PubMed  PubMed Central  Google Scholar  Peterson, E. & Kaur, P. Antibiotic resistance mechanisms in bacteria: Relationships between resistance determinants of antibiotic producers, environmental bacteria, and clinical pathogens. Front. Microbiol. 9, 2928 (2018)….

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Crispr Library Download

CRISPR guide RNA libraries have been iteratively improved to provide increasingly efficient reagents, although their large size is a barrier for many applications. We design an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9) by mining existing large-scale gene loss-of-function datasets, resulting in a greater than 42% reduction in size compared…

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Trying to understand STAR fastqLog.final.out File

Trying to understand STAR fastqLog.final.out File 0 Hello, I am analyzing ribo-seq data and am trying to understand if my interpretation of star’s log file is correct. I do not have extensive bioinformatics/computational experience, so it’s been a bit difficult trying to understand how to proceed (the guides online are…

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Molecular characterization of a tetra segmented ssDNA virus infecting Botrytis cinerea worldwide | Virology Journal

Analysis of the multisegmented nature of BcssDV1 genome B. cinerea field isolates were previously obtained from infected grapes of vineyards of Italy and Spain and their mycovirome was determined [8]. A new ssDNA virus (BcssDV1, Genbank accession no. MN625247) was discovered and characterized. The sequence previously characterized of BcssDV1 (from…

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Frontiers Publishing Partnerships | Construction of recombinant adenovirus-5 vector to prevent replication-competent adenovirus occurrence

Introduction In recent years, recombinant adenoviral vectors have been used in different fields of biomedical sciences such as in vitro and in vivo gene transfer, vaccine development, and gene therapy (Russell, 2000; Mitani and Kubo, 2002). Multiple features of recombinant adenoviral vectors such as high packaging capacity for transgene insertion,…

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Evidence of an intracellular creatine-sensing mechanism that modulates creatine biosynthesis via AGAT expression in human HAP1 cells

Cell lines and reagents HAP1 cells used to generate the reporter cells were grown from a frozen stock of HAP1 (C859) passage 6 purchased from Horizon Discovery LTD (Cambridge, UK). Iscove’s media (Ref: 098–150, Wisent) supplemented with 10% Fetal Bovine serum (Multicell) was used to grow HAP1 cells. All cells…

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10 You have a sequence of DNA obtained from GenBank and you are trym .docx – 10 You have a sequence of DNA obtained from GenBank and you are trym

10 You have a sequence of DNA obtained from GenBank and you are trym Sequence (nucleotide positions given on right): GCAGAGAGACTTAATGAGTACCTTATCCCCATATGGCGC ACCTTGTGGAAGAA TATAGCGACAATGGTATATGTCTAGAAGTTCGGAATATAT ATACAATATCATATGTT TTTCACATTGAAAGGGGAGGAGAATCATTAAACAACAA AAACGGCTCC TTACGCCCGATTGCTGACGCTGTTATTTGCGCTCATCTTC TTGCTGCCTCATTT CTGCAGCAGCGGCGGCAAATCTTAATGGGACGCTATGC AA (112) (160) (214) (254) (0.5 point) Which of these two is more likely to be an actual start codon for…

Continue Reading 10 You have a sequence of DNA obtained from GenBank and you are trym .docx – 10 You have a sequence of DNA obtained from GenBank and you are trym

An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes

Background: The corona virus SARS-CoV-2 is the causative agent of recent most global pandemic. Its genome encodes various proteins categorized as non-structural, accessory, and structural proteins. The non-structural proteins, NSP1-16, are located within the ORF1ab. The NSP3, 4, and 6 together are involved in formation of double membrane vesicle (DMV)…

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Script Error using TRAVIS.Core.pl script within TRAVIS transcriptome viral scanner

Script Error using TRAVIS.Core.pl script within TRAVIS transcriptome viral scanner 0 Hi, I’m new to bioinformatics, and I’m trying to run the TRAVIS Transcriptome virus scanner on my sequences. When running the Core script, I see this error message pop up. Is this a script error that I should report…

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An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes | BMC Infectious Diseases

When compared to the genomes of other RNA viruses, coronaviruses have been found to possess largest genome sizes. They are capable of establishing reservoirs in both human and zoonotic populations, enabling their transmission and circulation among a range of animal hosts, including bats, pangolins, civets, cats, mice, pigs, whales, dogs,…

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Biosensors | Free Full-Text | CRISPR/Cas12a-Based Detection Platform for Early and Rapid Diagnosis of Scrub Typhus

1. Introduction Orientia tsutsugamushi (OT) is an obligate intracellular parasite bacteria and the causative agent of scrub typhus (ST), which is associated with acute febrile illness (AFI) [1] and transmitted by mites through an infected chigger bite (in the larval stage). This disease, which was earlier believed to be endemic…

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A naturally occurring polyacetylene isolated from carrots promotes health and delays signatures of aging

Cell culture conditions Unless otherwise stated, cells were cultured with DMEM (Sigma Aldrich; #D6429) and 4.5 g/l glucose, phenol red, 10% FBS, and 1% penicillin/streptomycin with pH 7.4 and were incubated at 37 °C, 5% CO2, and 95% relative humidity. Wild-type HepG2 (#300198), HEK293 (#300192), and MCF-7 (#300273) were derived from CLS…

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Identification of the protein coding capability of coronavirus defective viral genomes by mass spectrometry | Virology Journal

In the current study, nanopore direct RNA sequencing and liquid chromatography-tandem mass spectrometry (LC–MS/MS) analysis were employed to examine whether DVGs can encode proteins in infected cells. With the protein databases generated by nanopore direct RNA sequencing, six DVG-encoded proteins were identified by LC–MS/MS based on the featured fusion peptides…

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CRISPR-created strawberries that stay firmer and fresher longer could revolutionize fruit industry

The cultivated strawberry (Fragaria × ananassa, Duch.) is one of the Rosaceae family renowned for its flavor and health benefits, making it an important agricultural commodity. However, its soft texture leads to a brief shelf life and consequent economic losses. Current breeding aims to enhance firmness without compromising quality, but…

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Complete mitochondrial genome analyses confirm that bat Polychromophilus and ungulate Plasmodium constitute a distinct clade independent of other Plasmodium species

Blood samples, DNA extraction, mitochondrial genome amplification and sequencing Following established procedures, bat blood samples were collected from designated sampling sites in Kanchanaburi, located in western Thailand, during the years 2019 and 202123,33,34. For this study, four bat samples (2 Myotis siligoensis and 2 Hipposideros gentilis) were utilized. These samples…

Continue Reading Complete mitochondrial genome analyses confirm that bat Polychromophilus and ungulate Plasmodium constitute a distinct clade independent of other Plasmodium species

CRISPR/Cas9 editing enhances fruit firmness and extends shelf life

Susceptibility to Botrytis in wild type and FaPG1 edited line #13. Credit: Horticulture Research The cultivated strawberry (Fragaria × ananassa, Duch.) is one of the Rosaceae family renowned for its flavor and health benefits, making it an important agricultural commodity. However, its soft texture leads to a brief shelf life…

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Forecasting the dynamics of a complex microbial community using integrated meta-omics

Characterization of the microbial community From the experimental period between 21 March 2011 and 3 May 2012 (ref. 27), we previously obtained and analysed 51 weekly samples, to which we added 21 samples collected in the month of June during the years 2012–2016. The 72 samples were submitted to the…

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Conceptual question about open reading frames

Conceptual question about open reading frames 0 Many publications state that typical way to classify mRNA vs. lncRNA is based off whether they have an open-reading frame, and that typical open-reading frames must be 300 nucleotides long. If that is the case (or at least typical assumption), why do many…

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Transcriptional and epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens

Developing an epigenetic screening platform in human T cells Staphylococcus aureus Cas9 (SaCas9) has been extensively used for genome editing in vivo as its compact size (3,159 bp) relative to the conventional Streptococcus pyogenes Cas9 (SpCas9) enables packaging into adeno-associated virus26,27,28. However, SaCas9 has not been widely used for targeted gene…

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ACADVL Protein Vector (Human) (pPM-C-HA)

Cat. No. 11144021 Print Name ACADVL Protein Vector (Human) (pPM-C-HA) Unit 500 ng Gene Name ACADVL Gene Full Name acyl-CoA dehydrogenase, very long chain Alias VLCAD, LCACD, ACAD6 Accession Number NM_000018 Species Human Vector Map pPM-C-HA (click blue link to view) System Non-Viral Vector Insert Size 1968 Vector Size 4765…

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Genomic disturbance of vitellogenin 2 (vtg2) leads to vitellin membrane deficiencies and significant mortalities at early stages of embryonic development in zebrafish (Danio rerio)

A large deletion mutation of 2811 bp of gDNA was introduced into zebrafish vtg2 via CRISPR/Cas9 genome editing. A schematic representation of the general strategy for CRISPR target design and application is given in Fig. 1A–C. The introduced deletion involved 1692 bp of the vtg2 transcript, encoding 564 aa of its respective protein, and…

Continue Reading Genomic disturbance of vitellogenin 2 (vtg2) leads to vitellin membrane deficiencies and significant mortalities at early stages of embryonic development in zebrafish (Danio rerio)

Some common deleterious mutations are shared in SARS-CoV-2 genomes from deceased COVID-19 patients across continents

Demographic summary of the retrieved genomes of the SARS-CoV-2 To investigate the spectrum of nucleotide (NT) and amino acid (AA) mutations and their effects  in different variants of the SARS-CoV-2, sequenced from COVID-19 deceased patients, we retrieved 243,270 whole genome sequence (WGS) with high read coverage (> 29,000 bp) from the global initiative…

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Diet-induced rewiring of the Wnt gene regulatory network connects aberrant splicing to fatty liver and liver cancer in DIAMOND mice

DIAMOND mice develop HCC in the context of obesity and insulin resistance To investigate in depth the genome-wide transcriptional and epigenetic changes that occur during development of MAFLD and obesity-related hepatocellular carcinoma (HCC), we performed RNA-sequencing (RNA-seq) and Chromatin ImmunoPrecipitation-sequencing (ChIP-seq) of liver tumours (HCC) and liver control tissue (FL)…

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Gene: MEFV (ENSG00000103313) – Summary – Homo_sapiens

ENST00000219596.1 MEFV-001 3499 781aa ENSP00000219596.1   Gene/transcipt that contains an open reading frame (ORF).Protein coding CCDS10498 O15553 NM_000243.2 The GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).GENCODE basic, ENST00000339854.4 MEFV-010 2959 601aa ENSP00000339639.4   Gene/transcipt that contains an…

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The parapoxvirus Orf virus inhibits dsDNA-mediated type I IFN expression via STING-dependent and STING-independent signalling pathways

The parapoxvirus Orf virus inhibits dsDNA-mediated type I IFN expression via STING-dependent and STING-independent signalling pathways | Microbiology Society 1887 This is a required field Please enter a valid email address Approval was a Success Invalid data An Error Occurred Approval was partially successful, following selected items could…

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GPP Web Portal – Gene Details

Gene: Human LOC642131 (642131) immunoglobulin IGHV1OR15-3-like pseudogene Source: NCBI, updated 2019-09-11 Taxon: Homo sapiens (human) Chromosome: 15 Wildtype Transcripts: NR_135667.1 Additional Resources: NBCI Gene record: LOC642131 (642131) NCBI Gene records for discontinued versions of this gene: LOC102724835 (102724835) sgRNA constructs originally intended to target this gene (CRISPRko, NGG PAM) NOTE:…

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Characteristics, Biogenesis and Functions of CircRNAs

Circular RNA (CircRNA), a single-stranded closed-loop RNA that lacks terminal 5′ caps and 3′ poly (A) tails, is more stable than linear RNA. CircRNA was first discovered in plant-infected viroids and was later observed in eukaryotes, although it was not produced via the back-splicing mechanism. 1. Characteristics Circular RNA (CircRNA),…

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Is it possible to get taxonomy identifiers from diamond output without using –taxonmap during makedb?

Is it possible to get taxonomy identifiers from diamond output without using –taxonmap during makedb? 1 I want to run diamond and also get taxon identifiers for each hit. Is the only way to do this by incorporating it during the makedb step? Is there any other option? The reason…

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Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space

Viromics datasets represent the sequence space of protected extracellular DNA (peDNA) The majority of samples prepared for “viromics” include GTAs and EVs, in addition to virus particles. All three entities are small protein- and/or lipid-containing particles that can enclose cellular DNA [3] or were found to bind cellular DNA on…

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circAtlas

Introduction Welcome to circAtlas 3.0 (a gateway to consistently curated vertebrate circular RNAs). circAtlas 3.0 contains a compendium of 2,674 RNA-seq libraries from 33 normal tissues from human, macaque, mouse, rat, rabbit, cat, dog, pig, sheep and chicken. Main characteristics of circAtlas include: circAtlas uses the standardized nomenclature scheme proposed…

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Immunoglobulin superfamily member 3 is required for the vagal neural crest cell migration and enteric neuronal network organization

Immunohistochemistry The tissue sections were processed using the TSA kit (Perkin Elmer) according to the manufacturer’s instructions. The deparaffinization of fixed tissues were performed by immersing the slides in tissue clear and rehydrated with graded ethanol (100–70%) and water. The heat-induced antigen retrieval was performed using citrate buffer (1.8 mM…

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Functional analysis of differentially expressed circular RNAs in sheep subcutaneous fat | BMC Genomics

Chikwanha, O. C., P. Vahmani, V. Muchenje, M. E. R. Dugan and C. Mapiye (2018). Nutritional enhancement of sheep meat fatty acid profile for human health and wellbeing. Food research international (Ottawa, Ont.) 104: 25–38. doi.org/10.1016/j.foodres.2017.05.005. Khan R, Raza SHA, Schreurs N, Xiaoyu W, Hongbao W, Ullah I, et al….

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Examining the genesis of CRISPR’s molecular scissors

Pervasive distribution of IS200/IS605-like elements in G. stearothermophilus. a, Schematic of a representative IS200/IS605 element. tnpA encodes a Y1-family tyrosine transposase that is responsible for DNA excision and integration; tnpB/iscB encodes RNA-guided nucleases whose biological roles are unknown. b, Bottom, schematic of a non-autonomous IS element encoding TnpB and its…

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Comparative analysis of bioinformatics tools to characterize SARS-CoV-2 subgenomic RNAs

Introduction The coronavirus infectious diseases-2019 worldwide pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently ongoing after being emerged from Wuhan (China) in December 2019 (Ecdc, 2020; Zhu et al, 2020; Spiteri et al, 2020). Up to now, SARS-CoV-2 has infected more than 750 million people and…

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Merging the filename with tsv files for master file

Merging the filename with tsv files for master file 0 Hi all, I have a query. I have a file named as hCoV-19_USA_TN-SPHL-2527_2022_orf.tsv and merged.tsv in the same folder. I want to take the filename for eg, hCoV-19_USA_TN-SPHL-2527_2022 from orf.tsv file and add it to same merged.tsv file which are…

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The leaderless communication peptide (LCP) class of quorum-sensing peptides is broadly distributed among Firmicutes

Leaderless communication peptide (LCP) system is broadly distributed To assess the distribution of SIP-like LCP-based qs systems across bacteria, we employed a large-scale search strategy that includes: (i) search for RopB homologs across a dataset of 129,001 bacterial genomes and 9,421 reference metagenomics-assembled genomes (MAGs), (ii) probing the genomic vicinity…

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Game-changing point-of-care assay could revolutionize Mpox detection worldwide

In a proof-of-concept study published in The Lancet Microbe, researchers from Australia developed a point-of-care assay for the rapid detection of mpox virus (MPXV) in clinical samples based on isothermal amplification along with clustered regularly interspaced short palindromic repeats (CRISPR) CRISPR-associated protein (Cas) technology. The assay was found to be…

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Optimization of Cas12a for multiplexed genome-scale transcriptional activation.

Cas12a CRISPR technology, unlike Cas9, allows for facile multiplexing of guide RNAs from a single transcript, simplifying combinatorial perturbations. While Cas12a has been implemented for multiplexed knockout genetic screens, it has yet to be optimized for CRISPR activation (CRISPRa) screens in human cells. Here, we develop a new Cas12a-based transactivation…

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5. Obtain the sequences given by the following

5. Obtain the sequences given by the following reference numbers (NG_016141.1, NM_176817.5, NG_059281.1, NM_000518.5), go to the following websites and use the settings given to complete the table below (www.ncbi.nlm.nih.gov/, www.ncbi.nlm.nih.gov/orffinder/, web.expasy.org/translate/) * (see directions below) Reference Sequences (NCBI) Name of gene Size of gene Type of nucleotide sequence Reading…

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Circular RNA vaccine in disease prevention and treatment

CircRNAs are a class of single-stranded RNAs with covalently linked head-to-tail topology. In the decades since its initial discovery, their biogenesis, regulation, and function have rapidly disclosed, permitting a better understanding and adoption of them as new tools for medical applications. With the development of biotechnology and molecular medicine, artificial…

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htseq-count reports count values for deleted genes

htseq-count reports count values for deleted genes 0 I am using htseq-count on BAM files from a bacterial species. We are comparing WT strains as well as two strains with genes knocked out. The knockouts have been verified with whole genome sequencing, but do retain the first 15 and last…

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Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater

Lulu Island waste resource recovery ecosystem The Lulu Island WWTP operated by Metro Vancouver in Richmond, British Columbia, Canada (Longitude: −123.14498° or 123° 8’ 42” W, Latitude: 49.11491° or 49° 6’ 54” N) provides primary and secondary treatment of >30 billion liters of mixed-sourced wastewater from ~200,000 residents each year….

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Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland

Growth conditions and identification The growth of the strain W-6 was measured at different temperatures of 4, 10, 15, 20, 25, 30, and 37 °C. It can be seen that strain W-6 could grow at the range from 4 to 30 °C with the optimal growth temperature 15 °C. Then, the growth curve of…

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MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets

MArVD2 is a random forest classifier, implemented in the scikit-learn python package for novel archaeal virus discovery (Fig. 1) [61] where it’s trained and tested with separate datasets of archaeal viruses to best represent its performance in a variety of environments (Fig. 1). Integrating MArVD2 with machine learning introduces several practical and…

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The non-classical major histocompatibility complex II protein SLA-DM is crucial for African swine fever virus replication

Cell lines and viruses Cell lines were received from the cell culture collection for veterinary medicine (CCVM) of the Friedrich-Loeffler-Institut (FLI). The highly passaged wild boar lung cell line (WSL-R-HP, #1346; abbreviated as WSL) was maintained in Ham’s F12 cell culture medium (Ham’s F-12, 5.32 g/L; IMDM, 8.80 g/L; NaHCO3, 2.45 g/L; pH 7.2)…

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KEGG T31084: 3118

Entry 30322             CDS       T31084                                  Name OSD52_2014-06-21_1m_NPL022_spades_contig-30470_-_63_1127_orf-1   KO K00548   5-methyltetrahydrofolate–homocysteine methyltransferase [EC:2.1.1.13] Best hit pga:PGA1_c16040 (best score: 558.14) Taxonomy Alphaproteobacteria [GN:pga]Taxonomy Pathway 00270   Cysteine and methionine metabolism 00450   Selenocompound metabolism 00670   One carbon pool by folate 01100   Metabolic pathways 01110   Biosynthesis of secondary metabolites 01230   Biosynthesis of amino acids AA seq 354 aa…

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Multidrug-resistant Providencia rettgeri strain YQ150713.

Introduction Providencia rettgeri is a Gram-negative opportunistic human pathogenic bacterium that belongs to the Proteae bacteria. It is a pathogen commonly found in the hospitals that mainly cause urinary tract infections, pneumonia, bacteremia, neonatal sepsis, eye infections, meningitis, endocarditis, and diarrhea.1–3 The pathogen Providencia rettgeri demonstrates inherent resistance to numerous…

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Characterization of the pig lower respiratory tract antibiotic resistome

Composition and distribution of ARGs in the pig lower respiratory tract microbiome Using 745 metagenome data of the lower respiratory tract microbiome from 675 experimental pigs across five populations, we constructed a swine respiratory microbial gene catalog containing 10,337,194 non-redundant genes. Of these, 1228 open reading frames (ORFs) were identified…

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ncRNA | Free Full-Text | Investigation into the Role of Long-Non-Coding RNA MIAT in Leukemia

1. Introduction Recent advances in RNA-based approaches and Next Generation Technologies have unveiled the existence of non-coding RNAs (ncRNA), transcripts that lack the ability to code for proteins [1,2]. ncRNAs typically lack an open reading frame (ORF) and are subdivided into housekeeping and regulatory transcripts. Housekeeping ncRNAs are usually 50–500…

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Molecular characterization of emerging chicken and turkey parvovirus variants and novel strains in Guangxi, China

PCR confirmation of Guangxi ChPV and TuPV strains The nonstructural (NS) and VP genes of the positive samples were amplified by PCR using primers targeting the conserved 561-bp NS1 region and 249-bp VP1/VP2 region, respectively. The epidemiological survey results are shown in Table 1. Table 1 shows that the total…

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Transcriptional variation in Babesia gibsoni (Wuhan isolate) between in vivo and in vitro cultures in blood stage | Parasites & Vectors

Morphological observation of continuous in vitro cultured B. gibsoni (Wuhan isolate) Babesia gibsoni was successfully cultured in vitro in 20% serum. After splitting, parasitemia reached 10% ± 1.5% on day 3 (Fig. 1A). Fig. 1 Changes in parasitemia and morphology of in vitro cultured B. gibsoni (Wuhan isolate). A Changes in parasitemia of…

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Annovar and the ‘Otherinfo’ column in VCF inputs

Hi all, I am relatively new to bioinformatics research and am trying to use annovar on a vcf file I inherited from another person. I am running the following line of code: perl /project/annovar/table_annovar.pl \ –vcfinput exome_calls_pass_step2_normalized.vcf \ /project/annovar/humandb/ \ -buildver hg19 \ -out exome_calls_pass_step2_normalized_anno \ -remove \ -protocol refGene,genomicSuperDups,avsnp147,esp6500siv2_all,1000g2015aug_all,exac03,gnomad_exome,gnomad_genome,cadd13,dbnsfp33a,mpc,bravo,…

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Investigating open reading frames in known and novel transcripts using ORFanage

O’Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion and functional annotation. Nucleic Acids Res. 44, D733–D745 (2016). Google Scholar  Frankish, A. et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. 51, D942–D949 (2023). Google Scholar  Pertea,…

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Reference-guided search for open reading frames

An open reading frame (ORF) refers to a continuous DNA (deoxyribonucleic acid) sequence with the potential to encode a protein. Identifying ORFs is like scanning through a long string of letters, trying to determine the precise start and end positions. This task is challenging since a DNA sequence may give…

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ORF Genetics on molecular farming, growth factors, and cultivated meat

Growth factors—signaling proteins used to stimulate cell growth and differentiation in cultivated meat production—come with a hefty price tag, putting pressure on firms to express them more efficiently in everything from fruit flies to microbes. But is it more cost effective to produce them in plants? Founded in Kópavogur, Iceland,…

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Viruses | Free Full-Text | Astragaloside IV Regulates cGAS-STING Signaling Pathway to Alleviate Immunosuppression Caused by PRRSV Infection

Received: 12 June 2023 / Revised: 1 July 2023 / Accepted: 13 July 2023 / Published: 20 July 2023 Round 1 Reviewer 1 Report This manuscript examines the effects of AS-IV treatment of PAMs infected with a strain of PRRSV-2. Specifically, aspects of immune regulation responses are investigated. Specific comments:…

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Effects of Candidatus Liberibacter asiaticus infection on metagenome of Diaphorina citri gut endosymbiont

Psyllid sampling, tissue collection and DNA isolation Adult D. citri newly emerged (five days old) was initially harvested from Citrus Tachibana uninfected CLas in 2020 at Guangxi province, China, and was successively reared on Murraya paniculata at Guangxi Special Crops Research Institute for more than 15 generations. All cages and…

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Characterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution

Isolation of crAss-like phages CrAss-like phages were searched in 12 sewage samples from five wastewater treatment plants using three different qPCR assays, the one designed from ΦCrAss001 genome in this study and two previously described12,19. Depending on the qPCR assay employed and the samples, values in wastewater ranged from 103−106…

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Amphioxus adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U and A-to-I deamination of DNA

Animals and cells Adult amphioxus B. japonicum collected from the sandy bottom of the sea near Qingdao, China, were cultured in aerated seawater at room temperature and fed with single-celled algae once a day. Zebrafish (D. rerio) aged 3 months and adult Japanese scallops (M. yessoensis) were purchased from Nanshan…

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is a bioinformatics certificate worth it

Application criteria may vary depending on the program you wish to be admitted to. Microbiology Course. Hello all, I have a BS in molecular biology, and after working for a bit and dipping my feet in the wet lab, I realize it is not the place I want to be….

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ResR/McdR-regulated protein translation machinery contributes to drug resilience in Mycobacterium tuberculosis

Bacterial strains and culture conditions Escherichia coli strain DH5α (Thermo Fisher) was used for the propagation of plasmids, whereas E. coli BL21 DE3 (Novagen) was used for the expression and purification of ResR/McdR protein. Mtb Erdman was obtained from Dr. Ramandeep Singh at THSTI, India, and Mtb H37Rv mc2 790242…

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Molecular Pharming Market Future Trends and Scope Analysis Report 2023-2030

PRESS RELEASE Published July 10, 2023 InsightAce Analytic Pvt. Ltd. announces the release of a market assessment report on the “Global Molecular Pharming Market Size, Share & Trends Analysis Report By Crop Source (Maize, Barley, Tobacco, Safflower, Rice, Alfalfa), By Technology (Gene Gun, Agroinfiltration, Electroporation, Agrobacterium-Mediated Gene Transfer), By Application (Recombinant…

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Optimizing mRNA for the discovery of transformative medicines

By Dr. Alexander Zehnder, CEO, CureVac The success of mRNA vaccines in COVID-19 propelled the role of this new modality to the forefront of medicine. Not only are new prophylactic mRNA vaccines for various respiratory diseases advancing through clinical development, but mRNA medicines are now being developed in many wide-ranging…

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Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi

Global identification of 3′ ends Initial computational predictions of open reading frames (ORFs) in B. burgdorferi38 overlooked elements such as mRNA boundaries, sRNA genes, and translation initiation from non-canonical start codons. B. burgdorferi transcription start sites (TSSs) and 5′ processed RNA ends were previously detected using 5′RNA-seq37. Here we sought…

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Advanced Slurm | OIST Groups

Were we’ll describe some advanced usage patterns for Slurm. While we call them “advanced”, they’re not very difficult to use, and they solve some common problems that you tend to encounter when you use a cluster. For our introduction to Slurm, see this page. Also, more than a few of…

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KEGG T31096: 24216

Entry 56821             CDS       T31096                                  Name OSD65_2014-06-20_0.1m_NPL022_spades_contig-81008_-_453_821_orf-1   KO K07127   5-hydroxyisourate hydrolase [EC:3.5.2.17] Best hit mis:MICPUN_108340 (best score: 240.736) Taxonomy Green algae [GN:mis]Taxonomy Pathway 00230   Purine metabolism 01100   Metabolic pathways 01120   Microbial metabolism in diverse environments LinkDB All DBs AA seq 122 aa AA seqDB searchMGRSPITTHVLDTTRGRPAKDVPVTLATVSVADGSSWTVSGVTDADGRIADLLPVTHDLQPGVYVITFECEEYFRRTAAAYGVSGFYPKVSIHFEVKADQVKEHYHVPLLLNPYGYSTYRGS NT seq 369 nt NT seq  +upstreamnt  +downstreamntatggggcgatctcccatcaccacgcacgtgctggacacgacccgcggtcgacccgcgaaggatgtccccgtgactctcgccaccgtcagcgtggcggacgggtcctcgtggacggtcagcggcgtgaccgacgcggacgggcgcatcgccgatctcctcccagtcacgcacgacctacagcccggcgtgtacgtcataaccttcgagtgcgaggagtacttccggcgcaccgccgccgcgtacggggtctccgggttctacccaaaggtgtccatccacttcgaggtcaaggcggatcaggtcaaggagcactaccacgtcccactgctcctcaacccctatgggtacagcacgtacagaggcagctga Read more…

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Detection of possible sgRNAs for allexivirus CRPs.

(A) The 5′ RACE PCR products for possible sgRNAs of GarV-B and GarV-D in agarose gels. The black arrowheads indicate the PCR products corresponding to either subgenomic RNAs for CP (sgRNA-CP) or for sgRNA-CRP. Size marker (M): 1 kb DNA marker. (B) Map of the 5′ ends of the PCR…

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Annovar Error

I am trying to annotate a vcf using annovar using the following command perl /annovar/table_annovar.pl chr21.vcf.gz annovar/humandb/ -buildver hg38 -out chr21 -remove -protocol refGene,ensGene,esp6500siv2_aa,esp6500siv2_ea,esp6500siv2_all -operation g,g,r,r,r -nastring . -vcfinput –nopolish I am not getting the output in VCF format, not understanding the error. Error and log NOTICE: Running with system…

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[Detailed Question] How to Normalize of Metagenomics Gene Abundances (with HMMs models)

Hi everyone, Me and my colleagues have been thinking about normalization for quite some time, and we have a hard time finding a consensus both within us, and within the literature, for this reason, this is going to be a long and detailed post. Talking with other researchers we feel…

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Antibiotics | Free Full-Text | Whole Genome Sequencing and Phenotypic Analysis of Antibiotic Resistance in Filifactor alocis Isolates

1. Introduction Filifactor alocis is an obligate anaerobic, non-sporeforming, Gram-positive rod [1,2]. This microorganism was first described in 1985 after being isolated from patients with periodontitis or gingivitis [3]. However, it was not until the early to mid-2000s, with the improvement of molecular identification techniques, when F. alocis was first…

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Molecular Pharming Market Key Players Business Strategies Analysis Report to 2031

PRESS RELEASE Published June 13, 2023 InsightAce Analytic Pvt. Ltd. announces the release of a market assessment report on the “Global Molecular Pharming Market Size, Share & Trends Analysis Report By Crop Source (Maize, Barley, Tobacco, Safflower, Rice, Alfalfa), By Technology (Gene Gun, Agroinfiltration, Electroporation, Agrobacterium-Mediated Gene Transfer), By Application…

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Host-adaptive traits in the plant-colonizing Pseudomonas donghuensis P482 revealed by transcriptomic responses to exudates of tomato and maize

P. donghuensis P482 achieved high populations on the roots of soil-grown tomato and maize, confirming it to be a suitable model for studying bacterial adaptations to different hosts P482 Rif was present on the roots of 18-day-old tomato and maize plants grown in soil from inoculated seeds. Based on arithmetic…

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A graph-based genome and pan-genome variation of the model plant Setaria

Variation and evolution in Setaria We collected genome-wide resequencing data for 630 wild (S. viridis), 829 landrace and 385 modern cultivated accessions from the Setaria genus with an average sequencing depth of ~15×, of which 1,004 were newly generated and 840 were from previous studies16,21 (Supplementary Table 1). After aligning…

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A set of vectors and strains for chromosomal integration in fission yeast

Isolation of amino acid auxotrophic mutants using the CRISPR/Cas9 system To allow pDUAL-type single crossover chromosomal integration, strains having a point mutation in genes preferably encoding proteins functioning in the amino acid or nucleotide biosynthesis pathway are needed. There are several such auxotrophic mutants in fission yeast. However, the mutation…

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Gene prediction software

Tool:Gene prediction software 1 Hi, I need to predict pseudogenes from the assembled genome of a catfish. For this, I need to predict the genes from the genome and make a parent protein set for finding similarity in intergenic regions of the genome. There is possibility of processed pseudogene being…

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Exploring the potential role of defensins in differential vector competence of body and head lice for Bartonella quintana | Parasites & Vectors

Amino acid alignments and phylogenetic analysis of defensins 1 and 2 of body and head lice Defensins 1 and 2 of the body and head lice were aligned using the CLC Main Workbench 8 (Qiagen, Hilden, Germany) (Fig. 1). The open reading frame (ORF) sequences of body louse defensin 1 (BLDef1)…

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Lack of Cas13a inhibition by anti-CRISPR proteins from Leptotrichia prophages

Summary CRISPR systems are prokaryotic adaptive immune systems that use RNA-guided Cas nucleases to recognize and destroy foreign genetic elements. To overcome CRISPR immunity, bacteriophages have evolved diverse families of anti-CRISPR proteins (Acrs). Recently, Lin et al. (2020) described the discovery and characterization of 7 Acr families (AcrVIA1–7) that inhibit…

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Pancreatic cancer microbiome discovery holds treatment hope

iNtRON Biotechnology has announced the identification of prophage and (non-) ORF-jamphage from the microbiome frequently observed in long-term pancreatic cancer survivors.  The company said the ‘significant identification’ was achieved as part of its ongoing PHAGERIARUS development project conducted by the new drug part of the company. The PHAGERIARUS development project…

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Highly lethal genotype I and II recombinant African swine fever viruses detected in pigs

Recombinant ASFVs with mosaic genomes of genotype I and II viruses detected from field samples in China During our surveillance in China, we isolated three ASFVs from pig samples collected in Jiangsu province, Henan province, and Inner Mongolia Autonomous Region, respectively, and designated them Pig/Jiangsu/LG/2021 (JS/LG/21), Pig/Henan/123014/2022 (HeN/123014/22), and Pig/Inner…

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Occurrence and genetic diversity of prophage sequences identified in the genomes of L. casei group bacteria

Occurrence of prophage sequences in L. casei group genomes The first stage of the analysis involved the identification of prophage-like sequences in 439 genomic sequences of bacterial strains belonging to the following 5 species: L. casei (27), L. paracasei (200), L. rhamnosus (204), L. zeae (6) and L. chiayiensis (2)….

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How do you add an ORF that overlaps the two regions where a circular genome is cut in Genbank?

How do you add an ORF that overlaps the two regions where a circular genome is cut in Genbank? 1 Dear Biostars community, I had a question regarding the BankIt (Genbank) submission for circularized genomes. Let’s say I have a circularized genome from 1 to 100000 bp. And I also…

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uridine-derived ribose as an alternative energy source

In a recent study published in Nature Metabolism, researchers attempted to identify new genes and molecular pathways that might supply energy when the availability of glucose or other nutrients is limited. Study: Salvage of ribose from uridine or RNA supports glycolysis in nutrient-limited conditions. Image Credit: Irina Anosova/Shutterstock.com Background In…

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How to pass from DNA to AA fasta

How to pass from DNA to AA fasta 0 Hi, I hope you are well. I am trying to figure out how can I pass a eukaryotic gene that has introns to aa sequence. The only way that I have thought is to transcribe all the gene then translate it…

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$3m boost for Equine herpesvirus vaccine development

Image by Frohe Weihnachten Research into equine herpesvirus (EHV) has received a major boost with funding for two projects from the Grayson-Jockey Club Research Foundation. Equine herpesvirus (EHV-1) and Equid Herpesvirus Myeloencephalopathy (EHM) are highly contagious, affecting horses of every breed and discipline, and they continue to cause significant economic…

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Rising Trends of Molecular Pharming Market will Witness Substantial Growth With in-detailed Competitor Analysis Forecast to 2023-2030

“Stratagem Market Insights offers a 70% discount on Molecular Pharming Market Reports on Single User Access and Unlimited User Access“ The Molecular Pharming Market research study is a professional report with premium insights into the size of the business, current patterns, drivers, risks, potential outcomes, and major segments. The Industry…

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ttc30a gene cDNA ORF clone, Xenopus tropicalis(tropical clawed frog)

The following ttc30a gene cDNA ORF clone sequences were retrieved from the NCBI Reference Sequence Database (RefSeq). These sequences represent the protein coding region of the ttc30a cDNA ORF which is encoded by the open reading frame (ORF) sequence. ORF sequences can be delivered in our standard vector, pcDNA3.1+/C-(K)DYK or…

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TTC30A gene cDNA ORF clone, Macaca mulatta(Rhesus monkey)

The following TTC30A gene cDNA ORF clone sequences were retrieved from the NCBI Reference Sequence Database (RefSeq). These sequences represent the protein coding region of the TTC30A cDNA ORF which is encoded by the open reading frame (ORF) sequence. ORF sequences can be delivered in our standard vector, pcDNA3.1+/C-(K)DYK or…

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Mosquito densovirus significantly reduces the vector susceptibility to dengue virus serotype 2 in Aedes albopictus mosquitoes (Diptera: Culicidae) | Infectious Diseases of Poverty

Identification of MDV presence using open access sequencing data Metagenomic next-generation sequencing (NGS) data for field mosquitoes in China were searched from the NCBI SRA database (www.ncbi.nlm.nih.gov/sra) and CNGB Sequence Archive database (db.cngb.org/cnsa/) using the keywords “mosquito OR Anopheles OR Aedes OR Culex”. Followed by removing the datasets with less…

Continue Reading Mosquito densovirus significantly reduces the vector susceptibility to dengue virus serotype 2 in Aedes albopictus mosquitoes (Diptera: Culicidae) | Infectious Diseases of Poverty

Introduction to Computational Evolutionary Biology

R is a very flexible programming language, and it allows developers to create their own data structures (called classes) for their packages. Over the years, some packages have become so popular that the classes they use to store data are now used the “standard” representations for particular types of data….

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Hybrids of RNA viruses and viroid-like elements replicate in fungi

Ribozyme search of the Sequence Read Archive Observing that ribozymes are sufficiently short to be captured on a short sequence read (less than 100 nt), we reasoned it will be possible to screen large volumes of sequencing data to identify libraries potentially containing ribozyme agents. To this end we adapted…

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The association of prokaryotic antiviral systems and symbiotic phage communities in drinking water microbiomes

The abundance and composition of prokaryotes carrying antiviral system in DWDS microbiome Prokaryotes have evolved various defense systems to prevent virus infection and prophage activation [8]. DefenseFinder revealed various prokaryotic antiviral systems harbored by the drinking water microbiome [9], and PCoA analysis showed that prokaryotic antiviral systems clustered separately in…

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IJMS | Free Full-Text | A Split-Marker System for CRISPR-Cas9 Genome Editing in Methylotrophic Yeasts

1. Introduction The discovery of prokaryotic adaptive defense systems, which consist of the clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated (cas) genes [1,2,3], has led to the development of efficient tools for genome editing in different organisms. Type II CRISPR-Cas systems include the Cas9 protein, which forms an…

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Midwest PRRSV L1C variant heads east

In 2020, porcine reproductive and respiratory syndrome virus Lineage 1C variant RFLP 1-4-4 emerged in Minnesota and quickly spread across neighboring states, causing severe losses in the swine industry (Kikuti et al. 2021; Trevisan et al. 2021). Known as a highly virulent variant with severe clinical outcomes in pigs, this…

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Using the 27-primates UCSC Multiz Alignment

Using the 27-primates UCSC Multiz Alignment 0 Hello, I am attempting to use the 27-primates UCSC multiz alignment data so that I can find an orthogonal sequence (across different mammals) to a human reference sequence (whether an ORF, a transcript, etc). I downloaded all the data in the maf folders…

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A ferritin-based COVID-19 nanoparticle vaccine that elicits robust, durable, broad-spectrum neutralizing antisera in non-human primates

IgG plasmids Antibody sequences and Fc-tagged ACE2 were cloned into the CMV/R plasmid backbone for expression under a CMV promoter. The antibodies with variable HC/LC were cloned between the CMV promoter and the bGH poly(A) signal sequence of the CMV/R plasmid to facilitate improved protein expression. The variable region was…

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Optimization of Cas12a for multiplexed genome-scale transcriptional activation

Abstract Cas12a CRISPR technology, unlike Cas9, allows for multiplexing guide RNAs from a single transcript, simplifying combinatorial perturbations. While Cas12a has been implemented for multiplexed knockout genetic screens, it has yet to be optimized for CRISPR activation (CRISPRa) screens in human cells. Here we develop a new Cas12a-based transactivation domain…

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Clarification on conceptual question regarding ORF-calling

Clarification on conceptual question regarding ORF-calling 1 Hello, I have a conceptual question that I think I may have the answer to, but would appreciate feedback. There are many ORF-calling tools out there, and many of them take in a fasta file as input (such as orfipy). My question is:…

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tool that reports *every* ORF, including from nested starts?

tool that reports *every* ORF, including from nested starts? 2 (I am defining ORF as, between an ATG start and a downstream stop codon) Given a situation like this: showing a ~1kb region, forward strand, 3 frame prediction of starts (green) and stops (red), for the frame 3 span between…

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Associate toxin-antitoxin with CRISPR-Cas to kill multidrug-resistant pathogens

Search for creTA elements associating with I-F CRISPR-Cas Previously identified creTA genes all surround the cas6 gene of a type I or III CRISPR-Cas19. Yet, within the I-F CRISPR-Cas loci of Acinetobacter species, we did not find any creTA-like elements by searching the sequences surrounding csy4 (a subtype-specific cas6 gene)….

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Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms

Novel Roseobacter strains isolated from marine biofilms We isolated and cultured bacterial strains from biofilms on natural rocks immersed in coastal waters. After preliminary analyses of 16S rRNA gene sequences generated by Sanger sequencing, more than 500 non-redundant strains were identified, including 54 distant strains affiliated with Roseobacter (hereafter referred…

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