Tag: MISeq

Post-Doctoral in Genomics and Bioinformatics (8991) job with Mohammed VI Polytechnic University

Mohammed VI Polytechnic University is an institution dedicated to research and innovation in Africa and aims to position itself among world-renowned universities in its fields The University is engaged in economic and human development and puts research and innovation at the forefront of African development. A mechanism that enables it…

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NifH database for taxonomic assignment in qiime2 – General Discussion

JThurston (Josh Thurston) January 19, 2024, 8:05pm 1 Hi all! I’m currently working through a Qiime2 pipeline analysing Illumina miseq paired-end amplicon data. I’ve successfully analysed bacterial (16s) amplicons from importing, filtering through to taxonomic assignment. However, I also have amplicon data for a functional gene (nifH; nitrogenase for N2…

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Endogenous Coriobacteriaceae enriched by a high-fat diet promotes colorectal tumorigenesis through the CPT1A-ERK axis

Bacteria Strain Cori.ST1911 was isolated from fresh stool of 20-week-old C57/BL6J mice fed a HFD at the Animal Center of the West China Hospital of Sichuan University. Briefly, faecal particles were ground with a glass grinding rod and suspended in sterile phosphate-buffered saline (PBS). After gradient dilution, the suspension was…

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Domestic pigs are susceptible to experimental infection with non-human primate-derived Reston virus without the need for adaptation

Ethics and animal welfare statement All infectious work with RESTV, including sample inactivation, was performed in the Containment Level 4 laboratory (CL4) in accordance with the policies and protocols outlined by the Canadian Science Centre for Human and Animal Health Institutional Biosafety Committee. All animal work was performed in strict…

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Building the taxonomic profile of the Riniaie Marwah hot spring of Kishtwar in Jammu and Kashmir: the first high-throughput sequencing-based metagenome study

Background and objectives: Rinaie Marwah hot spring Kishtwar (RMHSK) is one of the geothermal springs located at 33°51’51″N 75°32’07″E with an elevation of 2134 meters above sea level in Jammu and Kashmir, India. We aimed to study the microbial diversity of this geothermal spring using metagenomics. Materials and methods: In…

Continue Reading Building the taxonomic profile of the Riniaie Marwah hot spring of Kishtwar in Jammu and Kashmir: the first high-throughput sequencing-based metagenome study

How to whole genome assemble when I have three references

How to whole genome assemble when I have three references 0 Hello, I am new to bioinformatics and am having trouble with an assembly. I have illumina miseq short pair-ended reads from an organism that has multiple yeast chromosomes and a single bacterial chromosome with portions of a plasmid inside….

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Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the national academy of sciences 2011, 108(Supplement 1):4516-4522.

1The Nelson Mandela African Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania 2BecA-ILRI Hub International Livestock Research Institute, P. O. Box 30709, Nairobi, Kenya 3Departments of Biochemistry and Molecular Biology, W238A Millennium Science Complex University Park, PA 16802, Penn State University, USA 4Huck Institutes of Life Sciences, Department…

Continue Reading Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the national academy of sciences 2011, 108(Supplement 1):4516-4522.

Pair ended short reads assemble to multiple references with a plasmid also inside

Pair ended short reads assemble to multiple references with a plasmid also inside 0 Hello, I am new to bioinformatics and am having trouble doing an assembly and alignment. First I will describe my sample data, I have Illumina MiSeq data of pair ended reads on a yeast organism. This…

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Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain

Mouse brain tissues All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee under protocol number 18-00006. Adult (P56) C57BL/6J male mice were purchased from the Jackson Laboratory at 7 weeks of age and maintained in the Salk animal barrier facility on 12-h dark–light…

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A laboratory ice machine as a cold oligotrophic artificial microbial niche for biodiscovery

Flemming, H.-C. & Wuertz, S. Bacteria and archaea on earth and their abundance in biofilms. Nat. Rev. Microbiol. 17, 247–260 (2019). Article  CAS  PubMed  Google Scholar  Flemming, H.-C., Neu, T. R. & Wozniak, D. J. The EPS matrix: The “house of biofilm cells”. J. Bacteriol. 189, 7945–7947 (2007). Article  CAS …

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How does sequencing depth affect the identification of bacteria, fungi and viruses?

What are some latest advances in clinical metagenomic diagnostics for pathogen detection using shirt and long read sequencing?5 answersClinical metagenomic diagnostics for pathogen detection using short and long read sequencing have seen several recent advances. Traditional pathogenic diagnosis methods have limitations such as low positivity rates and inability to identify…

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Resin acids play key roles in shaping microbial communities during degradation of spruce bark

Bark preparation Spruce bark was obtained from the Iggesund pulp and paper mill (Iggesund, Holmen AB, Sweden), from a bark pile resulting from stripping of spruce logs at the mill after harvest, with the average age of trees at harvest being ~70 years. The bark was left to dry at…

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A Step Forward In Vaccine Technology: Exploring The Effects Of N1-methylpseudouridine In MRNA Translation

In a recent study published in Nature, a group of researchers explored how the incorporation of N1-methylpseudouridine (1-methylΨ) into messenger ribonucleic acids (mRNAs) affects ribosomal frameshifting and the overall fidelity of mRNA translation. Study: N1-methylpseudouridylation of mRNA causes +1 ribosomal frameshifting. Image Credit: MattL_Images/Shutterstock.com Background  Therapeutic in vitro-transcribed (IVT) mRNAs,…

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mothur

mothur is an open source software package for bioinformatics data processing.[8] The package is frequently used in the analysis of DNA from uncultured microbes. mothur is capable of processing data generated from several DNA sequencing methods including 454 pyrosequencing, Illumina HiSeq and MiSeq, Sanger, PacBio, and IonTorrent.[9] The first release…

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Applications of NGS Technology in Forensic DNA Analysis

Caratti S, Turrina S, Ferrian M et al (August 2015) MiSeq FGx sequencing system: a new platform for forensic genetics. Forensic Sci Int Genet Suppl Ser 5:e98–e100. doi.org/10.1016/j.fsigss.2015.09.040 Elkins KM, Garloff AT, Zeller CB (2023) Additional predictions for forensic DNA phenotyping of externally visible characteristics using the ForenSeq and Imagen…

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Characterization of 16S rRNA of the gut microbiome in long-tailed macaque (Macaca fascicularis) with spontaneous type 2 diabetes mellitus

Ahmad A, Yang W, Chen G, Shafiq M, Javed S, Zaidi SSA, Shahid R, Liu C, Bokhari H. 2019. Analysis of gut microbiota of obese individuals with type 2 diabetes and healthy individuals. PLoS One. 14(12):1–15. doi:10.1371/ journal.pone.0226372. Arora A, Behl T, Sehgal A, Singh S, Sharma N, Bhatia S,…

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Strong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP

ISCA fabrication VeroGray polymer was used to create 3D-printed moulds on an Objet30 3D printer (Stratasys), using previously described protocols32. Each ISCA consisted of 25 wells arranged in a 5 × 5 array. Each 110 µL well possessed a 800-μm-diameter port that connected the inside of the well with the surrounding seawater and…

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Using metagenome assembly and binning to identify and mitigate contamination in a genome

Hi everyone, This may be a silly question, but I am interested if using metagenome assembly and binning is a valid method of determining if a sample contains a mixture of species. Similarly, can metagenomics be used to identify and remove contamination from a single genome? For some background, I…

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Lightcast Skills Library | mothur

BGSC5E91BB7A0035EA0A mothur is an open source software package for bioinformatics data processing. The package is frequently used in the analysis of DNA from uncultured microbes. mothur is capable of processing data generated from several DNA sequencing methods including 454 pyrosequencing, Illumina HiSeq and MiSeq, Sanger, PacBio, and IonTorrent. The first…

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Errors in cluster.split – Commands in mothur

Hello I get the following error:[ERROR]: M03557_132_000000000-KYB35_1_ is not in your count table. Please correct./******************************************/[ERROR]: Could not open stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.singletons.temp mothur >[ERROR]: You are missing ([ERROR]: Invalid. when running cluster.split. I didn’t encounter any error when I did the MiSeq SOP tutorial. Please let me know if you need any other…

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Beginner questions: Working step for organism identification

Kanapol November 30, 2023, 9:57am 1 Hello everyone, I am the beginner for this area of study, and I have no one to ask these simple questions. I want to identify organism using NGS sequencing. I read from tutorial and I known that I have to make contigs and filter…

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Obesity-resistant shrews can aid weight loss in mice

Globally, the prevalence of obesity has increased, which has had severe detrimental effects on physical health in recent years. Several hypotheses explain the causes of obesity. The change in people’s eating habits is one significant reason, with high-fat diets (HFD) being of particular concern. Research has indicated that the gut…

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Genetic predisposition to early breast cancer

image:    Figure 2: The spectrum of pathogenic variants in the early-onset breast cancer cohort. view more  Credit: 2023 Zhunussova et al. “Our study may reveal previously uncharacterized population-specific variants that may increase the risk of BC in the Kazakh population.” BUFFALO, NY- November 22, 2023 – A new research…

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Genomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencing

In this study, we sequenced and characterized 49 SARS-CoV-2 samples from Uganda, collected between April 2020 and July 2021, using MinION Nanopore sequencing. Overall, the ARTIC protocol used was able to generate the required libraries for successful sequencing on the long-read sequencer. MinION Oxford Nanopore technology enabled the identification of…

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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

Installing mothur error – mothur

makeg++ -O3 -std=c++11 -pthread -DVERSION=“”1.48.0″” -DRELEASE_DATE=“”5/20/22″” -DUSE_READLINE -I. -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -c -o source/calculators/accuracy.o source/calculators/accuracy.cppIn file included from source/datastructures/sabundvector.hpp:4,from source/calculators/calculator.h:5,from source/calculators/accuracy.hpp:12,from source/calculators/accuracy.cpp:9:source/datastructures/datavector.hpp:4:10: fatal error: mothurout.h: No such file or directory4 |…

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Saponin treatment for eukaryotic DNA depletion alters the microbial DNA profiles by reducing the abundance of Gram-negative bacteria in metagenomics analyses

INTRODUCTION Microbiome research, especially the detection of microorganisms by molecular techniques, has become a fundamental tool for investigating host-associated bacteria, such as those harbored by veterinary or human clinical samples[1,2]. Next-generation sequencing (NGS) approaches now enable the identification of slow-growing, non-cultivable, or non-viable bacteria contained in clinical specimens without relying…

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Head of Bioinformatics Job in Greater London, Career, Permanent Jobs in Bactobio

We are looking for an exceptional microbial bioinformatician to join our leadership team at Bactobio as Head of Bioinformatics. Company Bactobio is a London-based biotechnology company founded in 2020. We use breakthrough technologies in synthetic biology, next-generation sequencing, and machine learning to cultivate the 99% previously unculturable microbes. These…

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Recovery of microbial DNA by agar-containing solution from extremely low-biomass specimens including skin

Ethical considerations This study complies with relevant institutional, national, and international guidelines and legislation. The Ethics Committee at the RIKEN Center for Integrative Medical Sciences (H30-4) approved this study, and written informed consent was obtained from all volunteers who provided specimens. Sampling solutions The AgST solution was prepared as follows:…

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Analysis of microbial composition and sharing in low-biomass human milk samples: a comparison of DNA isolation and sequencing techniques

Victora CG, Bahl R, Barros AJD, França GVA, Horton S, Krasevec J, et al. Breastfeeding in the 21st century: Epidemiology, mechanisms, and lifelong effect. Lancet. 2016;387:475–90. Article  PubMed  Google Scholar  Bardanzellu F, Fanos V, Strigini FAL, Artini PG, Peroni DG. Human breast milk: Exploring the linking ring among emerging components….

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The MiSeq’s Cameras And The Economics of DNA Sequencers

I’m fascinated by how much scientific instrumentation costs. Why for example does a MiSeq cost so much more than a high end digital camera? What does it say about our society, that we’ve decided to cost optimize cameras and mobile phones but not DNA sequencers? Cheap DNA sequencers seem like…

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Dataset for metagenomic analysis of bacterial community grown in sediments contaminated with pulp paper mill waste pollutants

Published: 6 November 2023| Version 2 | DOI: 10.17632/gpmwyfhbp3.2 Contributors: Vineet Kumar, Pradeep Verma Description Pulp and paper mills (PPMs) generate complex and recalcitrant chlorolignin pollutants in their waste stream, posing a significant environmental and health threat. To understand how microbial communities can help in the clean-up of chlorolignin waste…

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MiSeq Sequencer

  Broad Applications Base The MiSeq System facilitates your research with a wide range of sequencing applications. It is capable of automated paired-end reads and up to 15 Gb per run, delivering over 600 bases of sequence data per read. The library prep kits that it uses are optimized for…

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Leveraging Bioinformatic Algorithms to Improve the Genomic and Metagenomic Analyses of Bacterial Pathogens

Leveraging Bioinformatic Algorithms to Improve the Genomic and Metagenomic Analyses of Bacterial Pathogens Contact: Zhao (Jack) Chen, MS, PhD zhchen29@umd.edu Overview Advances in next-generation sequencing have revolutionized genomics and metagenomics of bacterial pathogens by increasing throughput exponentially over first-generation Sanger sequencing. Short reads with a low error rate of…

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Illumina MiSeq Gene Sequencer | LabX.com

Listing SKU:  DIS-50372-362788 Seller:  Surplus Solutions, LLC Warranty:  No Listing Date:  1st November, 2023 Last Updated:  1st November, 2023 Surplus Solutions, LLC Surplus Solutions is the global provider of new and used surplus industrial machinery and equipment. Surplus Solutions is dedicated to servicing the following industries: Biotech Lab PharmaceuticalContract Packaging…

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Aegis Writes a New Chapter on Pathogen Surveillance

A US lab broadens its surveillance efforts to be able to respond to emerging pathogens and envision a future of improved public health NORTHAMPTON, MA / ACCESSWIRE / November 2, 2023 / Illumina Originally published on Illumina News Center Before SARS-CoV-2, Aegis Sciences Corporation was a small, well-established lab with…

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Influence of 16S rRNA target region on the outcome of microbiome studies in soil and saliva samples

Abstract Next generation sequencing methods are widely used in evaluating the structure and functioning of microbial communities, especially those centered on 16S rRNA subunit. Since Illumina Miseq, the most used sequencing platform, does not allow the full sequencing of 16S rRNA gene, this study aims to evaluate whether the choice…

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The metagenomic and metabolomic profile of the gut microbes in Chinese full-term and late preterm infants treated with Clostridium butyricum

Ethics approval and consent to participate The study was approved by the Human Research Ethics Committees of the Children’s Hospital of Soochow University (Reference 2020CS017). All specimens were collected according to the guidelines set by the Children’s Hospital of Soochow University. All authors confirm that all methods were performed in…

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Illumina sequencing | Cornell Institute of Biotechnology

Description Internal price (Cornell and Cornell affiliates) External price MiSeq V2 kit, 50 bp (12-15 M/fc, 0.6-0.75 Gbp/run) $992 $1,627 MiSeq V2 kit, 300 bp (12-15 M/fc, 3.6-4.5 Gbp/run) $1,263 $2,071 MiSeq V2 kit, 500 bp (12-15 M/fc, 7.2-9 Gbp/run) $1,422 $2,333 MiSeq V3 kit, 150 bp (22-25 M/fc, 3.3-3.75…

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MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing | Genome Biology

Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhang C-Z, Wala J, Mermel CH. Pan-cancer patterns of somatic copy number alteration. Nat Genet. 2013;45:1134–40. Article  CAS  PubMed  PubMed Central  Google Scholar  Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı…

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Sequencing and Genotyping / Technological Facilities / Facilities / CRI – Fondazione E. Mach

Instruments MISEQ ILLUMINA NGS sequencing platform that allows to generate up to 25 million reads from 25 to 300 nucleotides in paired end mode (PE 2X300)  MinION ONT Portable real time device for DNA and RNA sequencing by nanopore technology 3730xl GENETIC ANALYZER Capillary electrophoresis platform for high throughput genetic…

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Higher abundance of Campylobacter in the oral microbiome of Japanese patients with moyamoya disease

A flow diagram of the study is shown in Fig. 3. Figure 3 Flow diagram of the study. Ethical approval and consent to participant This study was approved by the Institutional Review Board of the Nagoya University Graduate School of Medicine (approval number 2022-0084; approval date, June 3, 2022). Written informed…

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Illumina MiSeq Silver Package Maintenance

This is a Combined Synopsis/Solicitation for commercial items prepared in accordance with the format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotes are being requested and a written solicitation will not be issued. Solicitation number 12405B24Q0010 is issued as…

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Bid on On-site System Health Checks for Illumina Miseq and Nextseq Sequencing Instruments (IFB) in Texas Department of State Health Services Laboratory 1100 W. 49 th St., Austin

On-site System Health Checks for Illumina Miseq and Nextseq Sequencing Instruments (IFB) Login for complete opportunity report. Added/Updated: 10/25/23 Solicitation Title: On-site System Health Checks for Illumina Miseq and Nextseq Sequencing Instruments (IFB) Scope: To establish contract(s) for on-site system health checks for illumina miseq and nextseq sequencing instruments.  …

Continue Reading Bid on On-site System Health Checks for Illumina Miseq and Nextseq Sequencing Instruments (IFB) in Texas Department of State Health Services Laboratory 1100 W. 49 th St., Austin

How-to: NGS Quality Control

Thanks to the introduction of high-throughput next generation sequencing (NGS) methods, generating nucleic acid sequencing data has never been easier. Now, DNA and RNA samples can be sequenced within hours, creating millions of DNA fragments (known as reads), which can then be aligned to a reference genome.  Quality control is…

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Get.oturep using abundance method – mothur

Hi all, I am following the MiSeq SOP and ran the get.oturep command:get.oturep(list=final.tx.list, count=stability.contigs.good.count_table, method=abundance)The list file I used is phylotype based.For the output generated, can I assume that the order of sequences follows the same order of # of phylotypes so that I can align them with the taxonomy…

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Compute In The MiSeq and Ion Torrent PGM

Compute in the MiSeq and Ion Torrent PGM I thought it would be fun to quickly compare the compute in the Ion Torrent PGM and MiSeq. On the surface these are very similar instruments, both released around 2010. And both generating in the range of “a few million reads”. But…

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J066–Illumina MiSeq Warranty Coverage – Deadline October 26,2023, US Federal USA , US Federal US Federal

– RFP Status –ActiveExpiredAll – Response Submission Type –AllDigital RFP SubmissionPhysical RFP SubmissionBoth (Physical or Digital) – Select Country –USACanadaIndiaAfghanistanAlbaniaAlgeriaAndorraAngolaAntigua and BarbudaArgentinaArmeniaAustraliaAustriaAzerbaijanBahamasBahrainBangladeshBarbadosBelarusBelgiumBelizeBeninBhutanBoliviaBosnia and HerzegovinaBotswanaBrazilBrunei BulgariaBurkina FasoBurundiCabo VerdeCambodiaCameroonCentral African RepublicChadChileChinaColombiaComorosCongo, Democratic Republic of Congo, Republic of theCosta RicaCote d’IvoireCroatiaCubaCyprus Czech RepublicDenmarkDjiboutiDominicaDominican RepublicEcuadorEgyptEl SalvadorEquatorial GuineaEritreaEstoniaEthiopiaFijiFinlandFranceGabonGambiaGeorgiaGermanyGhanaGreeceGrenadaGuatemalaGuineaGuinea-BissauGuyanaHaitiHondurasHungaryIcelandIndonesiaIranIraqIrelandIsraelItalyJamaicaJapanJordanKazakhstanKenyaKiribatiKosovoKuwaitKyrgyzstanLaosLatviaLebanonLesothoLiberiaLibya LiechtensteinLithuaniaLuxembourgMacedoniaMadagascarMalawiMalaysiaMaldivesMaliMaltaMarshall IslandsMauritaniaMauritiusMexicoMicronesiaMoldovaMonacoMongoliaMontenegroMoroccoMozambiqueMyanmar (Burma)NamibiaNauruNepalNetherlandsNew ZealandNicaraguaNigerNigeriaNorth KoreaNorwayOmanPakistanPalauPalestinePanamaPapua New GuineaParaguayPeruPhilippinesPolandPortugalQatarRomaniaRussiaRwandaSamoaSan…

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Custom Software Solution for Forensic mtDNAnalysis of MiSeq Data

Abstract The use of a next-generation sequencing (NGS) approach for mitochondrial (mt) DNA analysis in forensic casework is imminent. A feature of the NGS approach is the ability to detect and report mtDNA heteroplasmy, which will significantly enhance the discrimination potential of the testing method. The current article addresses the…

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Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing

Phuangkum, P., Lair, R. C. & Angkawanith, T. Elephant Care Manual for Mahouts and Camp Managers (FAO Regional Office for Asia and the Pacific, 2005). Google Scholar  Sukumar, R. The Asian Elephant: Ecology and Management (Cambridge University Press, 1992). Google Scholar  Bansiddhi, P., Brown, J. L., Thitaram, C., Punyapornwithaya, V….

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Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing

Population and clinical samples The province of Alberta has a population of approximately 4.4 million. During July 19 to December 31, 2022 (the period of this study), molecular testing for SARS-CoV-2 was performed for individuals at risk for severe illness who would benefit from early treatment with antivirals, healthcare workers,…

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Plants | Free Full-Text | Guidelines for Performing CRISPR/Cas9 Genome Editing for Gene Validation and Trait Improvement in Crops

2.2. Design of Guide RNAs The purpose of this step is to design and select sgRNAs that will create the desirable edits in the target areas of the genome with high efficiency. Currently, there are many online software tools (online software without the need to be installed) for the design…

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Microbiome Sequencing Market Update 2023 : to Reach USD 3.4 Billion Revenue by 2031, Claims Report

The microbiome sequencing market size was valued for $859.42 million in 2021 and is estimated to reach $3,417.09 million by 2031, exhibiting a CAGR of 14.8% from 2022 to 2031. Understanding the Microbiome Before delving into the technological advancements, it’s essential to understand what the microbiome is. The microbiome refers…

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OmicsSuite: Tailored Pipeline for Multi-Omics Big Data Analysis

Abstract: With the advancements in high-throughput sequencing technologies such as Illumina, PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry, large volumes of biological data in multiple formats can now be obtained through multi-omics analysis. Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems, however it is challenging…

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Broad Genome Sequencing of Environmental and Clinical Strains and Genotyping

doi: 10.1007/978-1-0716-3473-8_12. Affiliations Expand Affiliations 1 Faculty of Medicine and Surgery, “Kore” University of Enna, Enna, Italy. alfonso.esposito@unikore.it. 2 Computational Biology Unit, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy. Item in Clipboard Alfonso Esposito et al. Methods Mol Biol. 2024. Show details Display options Display options Format AbstractPubMedPMID…

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Diabetic Foot Ulcer and the Bacterial Colony of the Skin

Introduction Diabetes is a growing public health problem with increasing prevalence and mortality that threatens the health of people globally.1 In 2021, the global prevalence of diabetes in adults aged 20 to 79 years was estimated at 537 million, mainly caused by type 2 diabetes, and the number is expected…

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Targeted knockout of a conserved plant mitochondrial gene by genome editing

Plant material and growth conditions Nicotiana tabacum cultivar Petit Havana was used for all experiments. The TALEN design and the TALEN-expressing line Nt-JF1006-30 were described previously19. For plant growth under sterile conditions, surface-sterilized seeds were germinated on Murashige and Skoog (MS) medium52 consisting of premixed MS salts and modified vitamins…

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Assistant Professor in Forensic Sciences job with NORTHUMBRIA UNIVERSITY

ABOUT THE ROLE Working within the Department of Applied Sciences, this role involves both teaching and research. The successful candidate will be part of a multidisciplinary team that teaches undergraduate and postgraduate forensic science students, on programmes accredited by the Chartered Society of Forensic Sciences. This post will involve designing,…

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INVADEseq to identify cell-adherent or invasive bacteria and the associated host transcriptome at single-cell-level resolution

Anderson, N. M. & Simon, M. C. The tumor microenvironment. Curr. Biol. 30, R921–R925 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Kostic, A. D. et al. Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe 14, 207–215 (2013). Article  CAS  PubMed  PubMed Central  Google Scholar …

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Broken String Biosciences strengthens senior leadership team to accelerate product development and commercialization

Broken String Biosciences (“Broken String”), a genomics company building a technology platform to drive the development of cell and gene therapies that are safer by design, today announced the expansion of its senior leadership team with the appointments of Vincent Smith, Ph.D., as Chief Technology Officer and Jessica Rich as…

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PTEN-induced kinase 1 gene single-nucleotide variants as biomarkers in adjuvant chemotherapy for colorectal cancer: a retrospective study | BMC Gastroenterology

Tissue samples A total of 84 analytic samples from surgical or biopsy specimens were collected from 84 patients who underwent radical surgery for CRC at Saitama Medical University International Medical Center between January and December 2016. One case was excluded because the specimen was too small; therefore, we used a…

Continue Reading PTEN-induced kinase 1 gene single-nucleotide variants as biomarkers in adjuvant chemotherapy for colorectal cancer: a retrospective study | BMC Gastroenterology

Selection and enrichment of microbial species with an increased lignocellulolytic phenotype from a native soil microbiome by activity-based probing

Soil incubation and cell extraction Approximately 3 kg of unmanaged marginal soil (pH 8) was collected from the Pacific Northwest National Laboratory field site in Prosser, Washington (46° 15′ 04″ N and 119° 43′ 43″ W) [23], homogenized, sieved (4 mm mesh size), and stored at 4 °C until further processing. Probe specific…

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Cost-effective DNA methylation profiling by FML-seq

The FML-seq method The protocol for FML-seq comprises only three steps (Fig 1A). First, genomic DNA (gDNA) is digested by a methylation-dependent restriction endonuclease that cuts at a certain distance from the 5-methylcytosine or 5-hydroxymethylcytosine in its motif and leaves a short overhang (10). Second, a master mix is added…

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The Genomic Renaissance: Recent Whole Exome Sequencing Market Changes

(MENAFN– EIN Presswire) Whole Exome Sequencing Market Size Exome sequencing is a technique for sequencing all of the exome and protein-coding genes in a genome. PORTLAND, OREGON, UNITED STATES, September 28, 2023 /EINPresswire/ — Allied Market Research added new research on Whole Exome Sequencing Market – Opportunity Analysis and Industry…

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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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Cancer Biopsy Market’s Soaring Trajectory: US$ 131.4 Billion Forecasted by 2033, CAGR of 18%

In a recently published analysis report, Future Market Insights reveals that the global Cancer Biopsy Market achieved remarkable sales of US$ 22.2 Billion in 2022. Anticipating an impressive 18% Compound Annual Growth Rate (CAGR), the market’s projected growth from 2023 to 2033 is set to surpass historical trends. Notably, the…

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Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast

Rubin, S., Parr, T., Da Costa, L. & Friston, K. Future climates: Markov blankets and active inference in the biosphere. J. R. Soc. Interface 17, 20200503 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Cantonati, M. et al. Characteristics, main impacts, and stewardship of natural and artificial freshwater environments: Consequences…

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Genome-Based Prediction of Bacterial Antibiotic Resistance

Abdelbary M, Basset P, Blanc D et al (2017) In: Tibayrenc M (ed) Genetics and evolution of infectious diseases: the evolution and dynamics of methicillin-resistant Staphylococcus aureus, 2nd edn. Elsevier, pp 553–572. ISBN: 9780127999425 CrossRef  Google Scholar  Allard MW, Stevens EL, Brown EW (2019) All for one and one for…

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mRNA vaccine quality analysis using RNA sequencing

Design and synthesis of reference plasmid A reference construct was first designed, with the intention of optimising the production of RNA therapeutics for pre-clinical research. The coding sequence of eGFP30 was selected as a reporter in the coding region, as its protein product can be assayed simply through Flow cytometry…

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Effects of a postbiotic SLFC non scalp microbiome

Introduction Sensitive scalp is a skin syndrome caused by the hyper-reactivity to environmental stimuli, which might cause inflammatory symptoms and abnormal sensory reactions of the scalp including pruritus, prickling, tightness, pain, and burning, but without visible signs of inflammation.1 Various circumstances, such as the atmospheric environment, heat, pollution, hair care…

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A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil

Field sample collection Topsoil samples (0–15 cm, roughly 0.5 m3) from replicate field plots were collected from the Hopland Research and Extension Center (HREC) in Northern California, which is unceded land of the Shóqowa and Hopland People, on August 28th, 2018 after experiencing mean annual precipitation during the rainy season, see our…

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Lecturer in Forensic Sciences job with NORTHUMBRIA UNIVERSITY

ABOUT THE ROLE Working as part of multi-disciplinary teams, you will be responsible for contributing to an exceptional student experience through the delivery of teaching, research, knowledge exchange and business and enterprise engagement activity. Colleagues appointed into our Lecturer grade are usually early career academics who are supported through their…

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DNA sequencing of Caenorhabditis elegans recombinant inbred lines containing a human alpha-synuclein trans-gene

DNA sequencing of Caenorhabditis elegans recombinant inbred lines containing a human alpha-synuclein trans-gene Record number 618962 Title DNA sequencing of Caenorhabditis elegans recombinant inbred lines containing a human alpha-synuclein trans-gene Author(s) Sterken, Mark; Ruitenbeek, Stefan van de; Huang, Yuqing Source Wageningen University & Research centre Department(s) EPSLaboratory of Nematology Publication…

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Longitudinal genomic surveillance of carriage and transmission of Clostridioides difficile in an intensive care unit

Guh, A. Y. et al. Trends in U.S. Burden of Clostridioides difficile infection and outcomes. N. Engl. J. Med. 382, 1320–1330 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Antibiotic Resistance Threats in the United States (Centers for Disease Control and Prevention, 2019); doi.org/10.15620/cdc:82532 Evans, C. T. & Safdar, N….

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Post-Doctoral Associate in the Division of Science (Biology), Dr. Shady Amin job with NEW YORK UNIVERSITY ABU DHABI

Description The Marine Microbiomics Lab at New York University Abu Dhabi seeks to appoint a Postdoctoral Associate starting January 15, 2024 to work on diatom ecophysiology under the supervision of Professor Shady Amin. We are looking for applicants with strong culturing or field work experience, and with bioinformatics and/or computational biology familiarity…

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Pitt UPMC Center for Advanced Research Genomics

Health Sciences Sequencing Core All PITT/UPMC prices below are effective March 1, 2023. Sample Preparation Unit Price RNA/DNA extraction tissue Sample $32 RNA/DNA extraction biofluid (PaxGene, blood) or FFPE Sample $47 Quality checks Unit Price Agilent TapeStation DNA or RNA Sample $9 Qubit Fluorometric Quantification Sample $5 RNA Library preparation…

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Ovation Ultralow Methyl-Seq Library Systems and Miseq sequencing

Cancer research has been transformed through numerous molecular techniques, with RNA sequencing (RNA-seq) playing a crucial role in understanding the complexity of the disease. Maša Ivin, Ph.D., Scientific Writer at Lexogen, and Yvonne Goepel Ph.D., Product Manager at Lexogen, remarked that “The high-throughput nature of RNA-seq allows for rapid profiling…

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Whole genomes from bacteria collected at diagnostic units around the world 2020

Preparation of partners to collect samples Partners registered for participation by contributing isolates or DNA samples to the study. Material was sent to partners according to their registered participation format. This included material for sample collection, metadata registration, DNA extraction and sample shipment to Denmark. Specific protocols were provided, according…

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Viruses | Free Full-Text | Optimizing the Conditions for Whole-Genome Sequencing of Avian Reoviruses

1. Introduction Avian orthoreoviruses (avian reoviruses, ARVs) are a persistent challenge to poultry producers in the United States and globally. Infection with ARVs has been associated with a variety of symptoms and syndromes in commercial poultry, including tenosynovitis/viral arthritis, enteric symptoms such as watery diarrhea, respiratory symptoms, myocarditis, viral hepatitis,…

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Comparative evaluation of 16S rRNA metagenomic sequencing in the diagnosis and understanding of bacterial endophthalmitis

Introduction Endophthalmitis is a severe infection in the eye that can occur as a consequence of intraocular surgery, intraocular injections, trauma, the presence of a central venous catheter and systemic infectious diseases such as sepsis, abscesses or urinary tract infection.1 2 Acute bacterial endophthalmitis represents a significant ocular pathology that…

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Error: Alpha rarefaction curve after merging the data of two different runs – Technical Support

Hi!I am facing a problem in alpha rarefaction curve plotting. In this study my samples were sequenced in two different runs “under same conditions” using Illumina Platform- MiSeq. For that reason I have merged the data from both the runs using same filtering parameters and following DADA2. Till “phylogeny align-to-tree-mafft-fasttree”…

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Illumina MISEQ SY-410-1003 – France

Listing description Illumina MISEQ SY-410-1003 Last maintenance October 2022 done by Illumina Price is negotiable Illumina’s MiSeq uses sequencing by synthesis (SBS) technology: cluster generation+ sequencing+ data analysis in a very short time. Key features: – Automation: Miseq includes a buffer bottle, flow cell and reagent cartridge, enabling both cluster…

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DNA Sequencing Equipment market research report provides critical insights that can help shape business development by providing a CAGR of 7.3% from 2023 to 2030

This “DNA Sequencing Equipment Market” highlights key external drivers that affect the industry and assesses the current performance and revenue growth of the industry. This report helps to collect industry information for target audiences before commencing any advertising campaign. The DNA Sequencing Equipment market is expected to grow annually by…

Continue Reading DNA Sequencing Equipment market research report provides critical insights that can help shape business development by providing a CAGR of 7.3% from 2023 to 2030

An analysis of the demand for the Automated DNA Sequencers market, key suppliers, and significant geographic regions from 2023 to 2030, with a projected CAGR of 4.7%, is presented in this report.

This market research report shows the present level and the future prospects of the “Automated DNA Sequencers Market” from 2023 to 2030. This entire report is of 147 pages. The Automated DNA Sequencers market is expected to grow annually by 4.7% (CAGR 2023 – 2030). Automated DNA Sequencers Market Outlook…

Continue Reading An analysis of the demand for the Automated DNA Sequencers market, key suppliers, and significant geographic regions from 2023 to 2030, with a projected CAGR of 4.7%, is presented in this report.

Applications of High-Throughput DNA Sequencing to Single-Domain Antibody Discovery and Engineering

doi: 10.1007/978-1-0716-3381-6_26. Affiliations Expand Affiliations 1 Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada. 2 Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada. kevin.henry@nrc-cnrc.gc.ca. 3 Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada. kevin.henry@nrc-cnrc.gc.ca. Item in Clipboard Michael…

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Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation

Location and sample collection Samples were taken from 10 composting piles (between May and August 2020) at a food waste (FW) composting facility (Zhejiang, China; 30°52′51.50″N; 119°46′12.87″E). A consistent pre-treatment method was used for each pile. Specifically, about 8 tons of FW was collected every 3 days and subsequently crushed into…

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Functional conservation of microbial communities determines composition predictability in anaerobic digestion

Lin Q, De Vrieze J, Li C, Li J, Li J, Yao M, et al. Temperature regulates deterministic processes and the succession of microbial interactions in anaerobic digestion process. Water Res. 2017;123:134–43. Article  CAS  PubMed  Google Scholar  Coban O, De Deyn GB, van der Ploeg M. Soil microbiota as game-changers…

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Molecular detection and characterization of SARS-CoV-2 in cats and dogs of positive owners during the first COVID-19 wave in Brazil

Study design This was an observational study conducted between October 2020 and June 2021 in five large metropolitan areas in Brazil, belonging to four of the five different Brazilian geographical regions (Recife, Belo Horizonte, São Paulo, Campo Grande and Curitiba). Dogs and cats whose owners tested positive for SARS-CoV-2 by…

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Effects of host species on microbiota composition in Phlebotomus and Lutzomyia sand flies | Parasites & Vectors

Maroli M, Feliciangeli MD, Bichaud L, Charrel RN, Gradoni L. Phlebotomine sandflies and the spreading of leishmaniases and other diseases of public health concern. Med Vet Entomol. 2013;27:123–47. CAS  PubMed  Google Scholar  Akhoundi M, Kuhls K, Cannet A, Votypka J, Marty P, Delaunay P, et al. Historical overview of the…

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Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection

Bacterial strains and growth conditions for eBW1 B. subtilis 168 and E. coli (MG1655) were streaked out from a frozen glycerol stock onto an LB plate and grown overnight at 37 °C. Following a night of growth, a single colony was picked and inoculated into 5 ml of LB broth and grown…

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Challenging interpretation of germline TP53 variants based on the experience of a national comprehensive cancer centre

Subjects TP53 gene was investigated in 880 consecutive oncology patients referred for molecular genetic testing at our national centres (Department of Laboratory Medicine, Semmelweis University and Department of Molecular Genetics, National Institute of Oncology) between 2021 and 2022. This cohort consisted of patients with potential hereditary tumour predisposition. Their genetic…

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Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data

Publicly available mock community sequencing datasets 136 mock community sequencing samples were collected in total from four publicly available sequencing datasets and analyzed in our evaluation. 69 samples are from Lluch et al.33; 33 samples are from Kozich et al.34; 29 samples are from Fouhy et al.35; and 5 samples…

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A highly efficient scheme for library preparation from single-stranded DNA

Vector construction The gene encoding VTopoI (GenBank: L13447.1) was synthesized by Eurofins Genomics Inc (Tokyo, Japan), with codon optimization for Escherichia coli K-12, exclusion of internal BamHI and EcoRI sites, and their inclusion at the 5′- and 3′-ends of the DNA, respectively (Supplementary Sequences). The BamHI-EcoRI fragment of the gene…

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Cannot upload files to qiime2 – Technical Support

Siyu_Song (Siyu Song) August 22, 2023, 8:19pm 1 Hi everyone, I am new to qiime and I am struggling so much on how to upload my sequences to qiime2. So I have generated a manifest file as below, and I tried to import my sequence with the code: qiime tools…

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Microorganisms | Free Full-Text | Genome-Wide and 16S rRNA Sequencing-Based Analysis on the Health Effects of Lacticaseibacillus paracasei XLK401 on Chicks

1. Introduction Since 2006, the European Union has prohibited the use of antibiotics in animal feed to boost growth [1]. This ban has resulted in a significant rise in disease outbreaks in broiler farming [2]. Therefore, there is an urgent need to find effective antibiotic alternatives for use in the…

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Transnetyx Acquires Sequencing, Genotypic Services Firm Laragen

NEW YORK — Transnetyx said on Tuesday that it has acquired sequencing and genotyping services firm Laragen. Financial terms of the transaction were not disclosed. Based in Culver City, California, Laragen offers a range of services to academic and industry customers including Sanger sequencing, mouse genotyping, Illumina MiSeq sequencing, cell…

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Mitochondrial impairment and synaptic dysfunction are associated with neurological defects in iPSCs-derived cortical neurons of MERRF patients | Journal of Biomedical Science

Cell culture of MERRF iPSCs The 6 lines of human iPSCs used in this study were generated from the skin fibroblasts established from 3 patients harboring the MERRF syndrome-specific m.8344A > G mutation. Among them, two patients are the members of a Taiwanese MERRF family, a 15-year-old girl (M1-iPSCs) and her 13-year-old…

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Potential pathogenicity of Non-O1, Non-O139 V. cholerae

Introduction Vibrio cholerae is a Gram-negative bacterium that can be classified into different serotypes based on the O surface antigen, with O1 and O139 being responsible for causing cholera in humans. Cholera is a highly infectious and severe diarrheal disease that is prevalent worldwide, particularly in Africa, South Asia, and…

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Diatom DNA library preparation for Illumina Miseq Sequencing using the rbcL marker gene

Bruder, K., & Medlin, L. K. (2007). Molecular assessment of phylogenetic relationships in selected species/genera in the naviculoid diatoms (Bacillariophyta). I. The genus Placoneis. Nova Hedwigia, 85(3), 331–352. doi.org/10.1127/0029-5035/2007/0085-0331 Keck, F., Vasselon, V., Rimet, F., Bouchez, A., & Kahlert, M. (2018). Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of…

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NGS Firms Pursue Slice of Low-Throughput Market

NEW YORK – Sequencing technology firms not named Illumina are reaching down to grab a chunk of the low-throughput end of the market, offering new instruments and reagents that are changing calculations about how to spend research dollars. Earlier this month, MGI Tech — which also does business as Complete…

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