Tag: rRNA

Pipeline for species-resolved full-length16S rRNA amplicon nanopore sequencing analysis of low-complexity bacterial microbiota

Abstract 16S rRNA amplicon sequencing is a fundamental tool for characterizing prokaryotic microbial communities. While short-read 16S rRNA sequencing is a proven standard for examining complex microbiomes, it cannot achieve taxonomic classification beyond genus level. Third-generation sequencing technologies, particularly nanopore sequencing, have allowed for full-length 16S rRNA gene sequencing enabling…

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Metagenomic Sequencing Market worth $4.5 billion in 2028

PRESS RELEASE Published December 5, 2023 “The European market is the second-largest metagenomic sequencing market globally, mainly due to factors such as increasing number of research projects, especially in the field of soil microbiome metagenomics, in the region.” Browse 226 market data Tables and 44 Figures spread through 266 Pages…

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Functional conservation of specialized ribosomes bearing genome-encoded variant rRNAs in Vibrio species

Fig 1. rrnI-dependent expression of HspA in V. vulnificus MO6-24/O strains. (A) Schematic representation of the allele-specific RT-PCR analysis analyzing the relative amounts of I-rRNA or G-rRNA. (B) The number of I-rRNA or G-rRNA amplicons and other rRNAs amplified from the cDNA of the MO6 WT, MO6+rrnG, and MO6+rrnI strains…

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PROTEIN-RNA INTERACTIONS AND THEIR CONTRIBUTION TO RIBOSOME ASSEMBLY AND FUNCTION

Protein-RNA interactions play a crucial role in the assembly and function of the ribosome, the cellular machinery responsible for protein synthesis. These interactions involve a complex interplay between ribosomal proteins and various RNA molecules, including ribosomal RNA (rRNA) and messenger RNA (mRNA). Understanding the structural features of these interactions provides…

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Exploration of S-ECC microbiota through a novel developed nutrient enriched microbiological medium, high through-put 16S rRNA sequencing and culturomics.rar

Abstract Introduction: Severe early childhood caries (S-ECC) is a widespread disease that harms children physically and mentally. Microorganisms are regarded as the dominant etiology of caries, however, S-ECC microbiome remains largely unknown, near 1/4 of them remained uncultivated. To explore S-ECC microbiota, a new bacterial medium, nutrient-enriched microbiological medium (NEMM)…

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Kinnex – PacBio

Kinnex full-length RNA kit Kinnex single-cell RNA kit Kinnex 16S rRNA kit Kit advantage Full-length isoform discovery with flexible sample multiplexing Cell type-specific isoform isoform discovery with the highest accuracy Full-length 16S rRNA for species identification Total throughput 15M (Sequel II)40M (Revio) 30M (Sequel II)80M (Revio) 25M (Sequel II)60M (Revio)…

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Optimizing PCR using mtDNA Universal Primers for Detecting Indigenous Domestic Animal Species from Pakistan

Abstract The prevalence of specific animal meat consumption is integral to human nutrition but is jeopardized by the widespread issue of meat adulteration, posing threats to both the industry and consumer health. Escalating demand has led to fraudulent practices, necessitating reliable techniques for authentic source identification, aligning with ethical and…

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Diversity of ribosomes at the level of rRNA variation associated with human health and disease

Abstract With hundreds of copies of ribosomal DNA (rDNA) it is unknown whether they possess sequence variations that ultimately form different types of ribosomes. Here, we developed an algorithm for variant-calling between paralog genes (termed RGA) and compared rDNA variations with rRNA variations from long-read sequencing of translating ribosomes (RIBO-RT)….

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A tool to assess the mock community samples in 16S rRNA gene-based microbiota profiling studies

doi: 10.20517/mrr.2022.18. eCollection 2023. Affiliations Expand Affiliations 1 Center for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, Netherlands. 2 Department of Medical Microbiology and Infection Prevention, Virology and Immunology Research Group, University Medical Center Groningen, Hanzeplein 1, Groningen 9713…

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Comparing 16S rRNA (culture) sequences with metagenome

Comparing 16S rRNA (culture) sequences with metagenome 0 I have 8 metagenome from a sample and also other team extracted several bacteria from the same sample and did 16S rRNA sequencing for them. Approximately 400 and isolation is still progressing. Now, I wanted to match the 16S rRNA data to…

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01 | Ribo-off rRNA depletion kit (Plant) Anawa

The Ribo-off rRNA depletion kit (Plant) is designed to deplete rRNA (including 5S, 18S and 25S rRNA) from total RNA of plant roots, seeds and leaves and to obtain mRNA and other non-coding RNA. This kit is suitable for removing rRNA from 1 μg – 5μg of plant total RNA….

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Combining vertebrate mitochondrial 12S rRNA gene sequencing and shotgun metagenomic sequencing to investigate the diet of the leopard cat (Prionailurus bengalensis) in Korea

Fig 2. Vertebrate mitochondrial 12S rRNA gene sequencing results. Relative abundance of the top 20 genera identified from fecal samples (n = 22) by vertebrate mitochondrial 12S rRNA gene sequencing is shown. The ambiguous reads that were not identified at the genus level and the reads that were assigned to…

Continue Reading Combining vertebrate mitochondrial 12S rRNA gene sequencing and shotgun metagenomic sequencing to investigate the diet of the leopard cat (Prionailurus bengalensis) in Korea

Lower-limb ulcers in participants with leprosy sequelae

Introduction Leprosy is a disabling infectious disease that predominantly occurs in the skin and peripheral nerves and is transmitted by contact with pathogenic bacteria through the respiratory tract and broken skin. Leprosy is attributed to infection with Mycobacterium leprae (M. leprae)1 and the more recently discovered Mycobacterium lepromatosis.2 In addition,…

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Lane, D. J. (1991). 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons, New York.

1Industrial Waste Water Research Laboratory Division of Applied & Environmental Microbiology Enviro Technology Limited Gujarat, India Journal of Applied & Environmental Microbiology. 2014, Vol. 2 No. 4, 176-184DOI: 10.12691/jaem-2-4-11Copyright © 2014 Science and Education Publishing Cite this paper:M. Shah. An Application of Sequencing Batch Reactors in the Identification of Microbial…

Continue Reading Lane, D. J. (1991). 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons, New York.

16s rRNA & 18s rRNA.docx – 16S rRNA and 18s rRNA Ribosomal RNA rRNA are important structural components pertaining to ribosomes they are useful in

16S rRNAand18s rRNA Ribosomal RNA (rRNA) are important structural components pertaining to ribosomes; they are useful in recognizing portions of mRNAs and tRNAs, but the main takeaway is they are heavily involved in the mechanism of protein synthesis. 16s rRNA and 18s rRNA are major subunits of the ribosome, although…

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Are there any primers that are specifically designed for the molecular identification of Fusarium species?

Which region of the rRNA is used for synethsizing primers for species identification?5 answersThe region of the rRNA used for synthesizing primers for species identification is the mitochondrial 12S rRNA gene. This gene segment is commonly targeted in PCR-based methods for species identification and taxonomic classification. It has been used…

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Organ-specific characteristics govern the relationship between histone code dynamics and transcriptional reprogramming during nitrogen response in tomato

A supply of nitrate triggers organ-specific changes of histone modifications at specific gene loci To investigate the organ specificity of dynamic histone modifications in response to N changes, we treated 3-week-old tomato seedlings (Solanum lycopersicum, cultivar M82) with four days of N starvation, followed by N-supply (2.8 mM NO3−; +N) or…

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Solved You are given a list of seven 16S rRNA gene sequences

You are given a list of seven 16S rRNA gene sequences (below) from unknown organisms. Based on the instructions below go to Genbank and identify them. Then Google or go to the original publication that describe the organism to find out what each is famous for (for example “fixes nitrogen”,…

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117187006 – Listeria monocytogenes rRNA

SNOMED code 117187006 name Listeria monocytogenes rRNA status active date introduced 2002-01-31 fully specified name(s) Ribosomal ribonucleic acid of Listeria monocytogenes (substance) synonyms Listeria monocytogenes rRNA Ribosomal ribonucleic acid of Listeria monocytogenes parents Microorganism rRNA   118251005 hierarchies a selection of possible paths SNOMED CT Concept   138875005  Substance  …

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Chapter 6 GGHH 2023 – notes – Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes

Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes Define an eQTL Summarise the methodology of RNAseq Understand the reason for expressing RNAseq outcomes as transcripts per million (TPM) Explain why patterns of H3K4me3 and H3K27ac can be used as markers of transcriptionally active genes Incorporate this data into a…

Continue Reading Chapter 6 GGHH 2023 – notes – Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes

Which region of the rRNA is used for synethsizing primers for species identification?

Why rRNA gene is used for species identification?5 answersThe rRNA gene is used for species identification because it provides a reliable and fast method for determining the species of an organism. The gene can be sequenced and compared to known reference sequences to match and classify the species. The use…

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Molecular typing of Leptospira spp. based on putative O-antigen polymerase gene (wzy), the benefit over 16S rRNA gene sequence

Molecular typing of Leptospira spp. based on putative O-antigen polymerase gene (wzy), the benefit over 16S rRNA gene sequence – Fingerprint — UK Health Security Agency Sort by Weight Alphabetically Medicine & Life Sciences O-antigen polymerase 100% Leptospira 70% Molecular Typing 66% rRNA Genes 53% 16S Ribosomal RNA 52% Serogroup…

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Roles of rRNA N-methyladenosine modification in the function of ribosomes

Review doi: 10.1002/cbf.3891. Online ahead of print. Affiliations Expand Affiliations 1 Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, China. 2 Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China. Item in Clipboard Review…

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Comparative 16S rRNA gene surveys of granular sludge from three upflow anaerobic bioreactors treating purified terephthalic acid (PTA) wastewater.

The microbial communities from three upflow anaerobic bioreactors treating purified terephthalic acid (PTA) wastewater were characterized with 16S ribosomal RNA gene sequencing surveys. Universal bacterial and archaeal primers were used to compare the bioreactor communities to each other. A total of 1,733 bacterial sequences and 383 archaeal sequences were characterized….

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Ribo-Zero Plus Microbiome rRNA Depletion Kit

Description Depletion of abundant transcripts from host and bacterial rRNA for metatranscriptomics research. Single-tube depletion of abundant transcripts from multiple species or transcripts Input Quantity Minimum 25 ng of total RNA, 50 ng recommended for optimal performance 1-1000 ng total RNA for standard-quality RNA samples….

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What is the advantage of having multiple copies of the 16S rRNA gene in bacteria?

Is the 16S rRNA gene the only sporulating gene in human microbiome?5 answersThe 16S rRNA gene is not the only sporulating gene in the human microbiome. The abstracts do not mention anything about the presence or absence of sporulating genes in the human microbiome. How long is the 16s rRNA…

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Dahanukar Lecture 6 bio107 – Necessary components:! !1. mRNA (with RBS, AUG and termination codon)!

Necessary components:! !1. mRNA (with RBS, AUG and termination codon)! !2. different tRNAs! !3. initiation factors! !4. elongation factors! !5. termination (release) factors! !6. amino acids! !7. 20 aminoacyl-tRNA synthetases! !8. GTP, ATP for energy requiring steps! !9. large and small ribosomal subunits! Translation (Recap)! Ribosome binding site! (Shine-Dalgarno in…

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Human microbiota dysbiosis after SARS-CoV-2 infection have the potential to predict disease prognosis | BMC Infectious Diseases

Wu Z, McGoogan JM. Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72314 Cases From the Chinese Center for Disease Control and Prevention. JAMA. 2020;323(13):1239–42. Article  CAS  PubMed  Google Scholar  Kesheh MM, Hosseini P, Soltani S, Zandi M. An…

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Two-dimensional RFLP analyses reveal megabase-sized clusters of rRNA gene variants in Arabidopsis thaliana, suggesting local spreading of variants as the mode for gene homogenization during concerted evolution.

@article{Copenhaver1996TwodimensionalRA, title={Two-dimensional RFLP analyses reveal megabase-sized clusters of rRNA gene variants in Arabidopsis thaliana, suggesting local spreading of variants as the mode for gene homogenization during concerted evolution.}, author={Gregory P. Copenhaver and Craig S. Pikaard}, journal={The Plant journal : for cell and molecular biology}, year={1996}, volume={9 2}, pages={ 273-82 },…

Continue Reading Two-dimensional RFLP analyses reveal megabase-sized clusters of rRNA gene variants in Arabidopsis thaliana, suggesting local spreading of variants as the mode for gene homogenization during concerted evolution.

Metagenome Dataset of Maize Rhizosphere for Saline Soil from Mau Region of Uttar Pradesh by Alok Kumar Singh, Alok Kumar Srivastava, Mala Trivedi :: SSRN

Abstract In India, after rice and wheat, maize (Zea mays L.) is most significant food crop. Like others, maize is also influenced by the rhizospheric region’s microbial communities, which are incredibly diverse and unquestionably play a key role in the nutrient cycle and growth productivity. Maize rhizospheric soil samples were…

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Why rRNA is used for identification?

Why is strain identification for labeling accuracy of probiotic products important?5 answersStrain identification for labeling accuracy of probiotic products is important because probiotic health benefits are strain-specific. Different strains of probiotics have different effects on human health, and therefore it is crucial to include the correct strains in probiotic products…

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RHEX-RNAseq – a tagmentation-based, rRNA blocked, random hexamer primed RNAseq method for generating stranded RNAseq libraries directly from very low numbers of lysed cells.

Gustafsson C, Hauenstein J, Frengen N, Krstic A, Luc S, Månsson R BMC Genomics 24 (1) 205 [2023-04-17; online 2023-04-17] RNA sequencing has become the mainstay for studies of gene expression. Still, analysis of rare cells with random hexamer priming – to allow analysis of a broader range of transcripts…

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Tandemly arranged variant 5S ribosomal RNA genes in the yeast Saccharomyces cerevisiae.

Tandemly arranged variant 5S ribosomal RNA genes in the yeast Saccharomyces cerevisiae. Publication ,  Journal Article McMahon, ME; Stamenkovich, D; Petes, TD Published in: Nucleic Acids Res Most of the ribosomal RNA genes of the yeast Saccharomyces cerevisiae are about 9 kilobases (kb) in size and encode both the 35S rRNA…

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MUSCLE Protein Alignment of Distantly Related Proteins

MUSCLE Protein Alignment of Distantly Related Proteins 0 Hello everyone, I am trying to infer phylogenetic relationships between a set of approximately 60 proteins. They are all putative antibacterial proteins, but their sequences (and predicted functions) are different. Within this set, there are multiple subgroups: for example, there are tRNases…

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QUESTION 5Match the following statements with the

QUESTION 5 Match the following statements with the three major types of RNA molecules: Ribosomal RNA (rRNA) Transfer RNA (tRNA) Messenger RNA (mRNA) Carries genetic information for protein synthesis ✓ Carries an amino acid at its 3‘–end for protein synthesis ✓ Is synthesized by RNA polymerase I in eukaryotes Is…

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Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel.

Suarez C, Hackl T, Wilen BM, Persson F, Hagelia P, Jetten MSM, Dalcin Martins P FEMS Microbiol. Lett. 370 (-) – [2023-01-17; online 2023-06-09] The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion…

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Proteomics and metabolomics analyses of Streptococcus agalactiae isolates from human and animal sources

Shen, C.-H. Molecular diagnosis of infectious diseases in Diagnostic Molecular Biology Ch. 15, 387–411 (Academic Press, C 2019). Katholm, J., Bennedsgaard, T. W., Koskinen, M. T. & Rattenborg, E. Quality of bulk tank milk samples from Danish dairy herds based on real-time polymerase chain reaction identification of mastitis pathogens. J….

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Whole genome sequencing provides evidence for Bacillus velezensis SH-1471 as a beneficial rhizosphere bacterium in plants

Inhibition effect of strain SH-1471 on plant pathogenic fungi The results of the plate confrontation experiment showed that B. velezensis SH-1471 had good inhibitory effects on various pathogenic microorganisms (Fig. 1). Specifically, our experiment showed that its inhibition rates on Sclerotinia scrotiorum, Phoma mateuciicola, and Fusarium oxysporum were 93.5%, 90.3%, and…

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Sequence-Based Classification and Identification | SpringerLink

Adékambi T, Drancourt M, Raoult D (2009) The rpoB gene as a tool for clinical microbiologists. Trends Microbiol 17:37–45 CrossRef  PubMed  Google Scholar  Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 CrossRef  CAS  PubMed  Google Scholar  Arahal DR,…

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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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High-throughput identification and quantification of bacterial cells in the microbiota based on 16S rRNA sequencing with single-base accuracy using BarBIQ

Zmora, N., Suez, J. & Elinav, E. You are what you eat: diet, health and the gut microbiota. Nat. Rev. Gastroenterol. Hepatol. 16, 35–56 (2019). Article  CAS  PubMed  Google Scholar  Lamont, R. J., Koo, H. & Hajishengallis, G. The oral microbiota: dynamic communities and host interactions. Nat. Rev. Microbiol. 16,…

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Enhanced specificity of Bacillus metataxonomics using a tuf-targeted amplicon sequencing approach

Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol. 2020;70:5607–12. Article  PubMed  PubMed Central  Google Scholar  Saxena AK, Kumar M, Chakdar H, Anuroopa N, Bagyaraj DJ. Bacillus species in soil…

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Metagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface

Sampling sites and depths Metagenomes were produced from sediment samples at drilling sites U1545B to U1549B that follow a northwest-to-southeast transect across the northwestern flanking region of Guaymas Basin (Fig. 1A) and include an off-axis hydrothermal system, the Ringvent site (Fig. 1B). The samples were selected to coordinate with depths used for…

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Solved In regards to bacterial DNA and sequencing, answer

Transcribed image text: In regards to bacterial DNA and sequencing, answer the following Statements as True or False: About 95% of DNA is identical among different species of bacteria. Looking at the different sequences will identify specific species. After sequencing, we use the BLAST computer database to identify the bacterial…

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Phylogenetic chronometer biomolecules chronicles both long and short evolutionary distance accurately

Advent of molecular phylogeny chronometer usher in a new era where evolutionary relationships between different species could be described by sequence divergence and differences at the DNA and protein level. Currently, 16S rRNA is the de facto gold standard for molecular phylogeny of microbial species, which presents particular challenges for…

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Match the following statements with the three major

Match the following statements with the three major types of RNA molecules: Ribosomal RNA (TRNA) Transfer RNA (TRNA) Messenger RNA (mRNA) Carries genetic information for protein synthesis Carries an amino acid at its 3‘–end for protein synthesis A. mRNA and tRNA and rRNA B.TRNA Is synthesized by RNA polymerasel in…

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Solved at At least three types of RNA are required for

at At least three types of RNA are required for protein synthesis. Compare and contrast mRNA, rRNA, and tRNA by moving the descriptions of their structure and function to the appropriate categories. Some phrases may describe all three types of RNA. mRNA rRNA tRNA mRNA, rRNA, and tRNA Answer Bank…

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Solved 1 0.4 points eBook References Diagnosing Infections

1 0.4 points eBook References Diagnosing Infections Drag and drop the labels into the correct empty boxes to complete the concept map. confirmatory data breakthrough methods PCR, rRNA analysis, sequencing Immunologic methods genotypic methods MALDI-TOF biochemical analysis phenotypic methods ELISA and Western blotting presumptive data indirect testing methods direct testing…

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Future of Global Metagenomic Sequencing Service Market During

Global Leading Market Research Publisher QYResearch announces the release of its latest report “Global Metagenomic Sequencing Service Market Report, History and Forecast 2018-2029, Breakdown Data by Manufacturers, Key Regions, Types and Application”. Based on current situation and impact historical analysis (2018-2022) and forecast calculations (2023-2029), this report provides a comprehensive…

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Depletion of tRNA CCA-adding enzyme in Mycobacterium tuberculosis leads to polyadenylation of transcripts and precursor tRNAs

Rv3907c is the CCA-adding enzyme in Mycobacterium It remains unclear whether the rv3907c gene product, originally annotated as poly(A) polymerase, is in fact the CCA-adding enzyme in Mtb. Rv3907c is composed of three domains, an N-terminal class II polymerase β superfamily domain, a central RNA-binding domain and a C-terminal HD…

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The Efg1-Bud22 dimer associates with the U14 snoRNP contacting the 5′ rRNA domain of an early 90S pre-ribosomal particle

doi: 10.1093/nar/gkad1109. Online ahead of print. Affiliations Expand Affiliation 1 Biochemie-Zentrum der Universität Heidelberg (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany. Item in Clipboard Olga Beine-Golovchuk et al. Nucleic Acids Res. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1093/nar/gkad1109. Online ahead of print. Affiliation 1 Biochemie-Zentrum der Universität…

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Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster | Microbiome

Diversity of the RCA cluster and genome characteristics The phylogenomic analysis yielded three major clades within the RCA cluster (Fig. 1) Genomes of the three clades were relatively distinct with appr. < 70% average nucleotide identity (ANI), resulting in the proposal of three genera, the known genus Planktomarina, and two new genera without…

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Solved Ribosomes are composed of rRNA and proteins. In

Ribosomes are composed of rRNA and proteins. In prokaryotes the small ribosomal subunit contains a 16S rRNA and the large ribosomal subunit contains a 23S rRNA. Match the following roles in translation to the rRNA subunit that may interact at that point? Question: a. Located at the anticodon of the…

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“DNA Methylation, Chromatin Structure and Expression of Maize Ribosomal” by Eldon Ralph Jupe

Document Type Dissertation Degree Name Doctor of Philosophy (PhD) First Advisor Elizabeth A. Zimmer Abstract The restriction endonuclease HpaII was utilized to examine ribosomal RNA gene (rDNA) methylation in maize and teosinte leaf DNA. Much of the rDNA was inaccessible to HpaII cleavage indicating that these repeat units were completely…

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Development and evaluation of specific polymerase chain reaction assays for detecting Theileria equi genotypes | Parasites & Vectors

Knowles DP, Kappmeyer LS, Stiller D, Hennager SG, Perryman LE. Antibody to a recombinant merozoite protein epitope identifies horses infected with Babesia equi. J Clin Microbiol. 1992;30:3122–6. CAS  PubMed  PubMed Central  Google Scholar  Ueti MW, Palmer GH, Kappmeyer LS, Statdfield M, Scoles GA, Knowles DP. Ability of the vector tick…

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Multi-omics analyses from a single sample: prior metabolite extraction does not alter the 16S rRNA-based characterization of prokaryotic community in a diversity of sample types

doi: 10.1093/femsle/fnad125. Online ahead of print. Affiliations Expand Affiliations 1 UMR7245 Molécules de Communication et Adaptation des Micro-organismes, Muséum National d’Histoire Naturelle, CNRS, Paris, France. 2 UMR7618 iEES-Paris, Sorbonne Université, Paris, France. 3 Université de Pau et des Pays de l’Adour, E2S-UPPA, CNRS, IPREM, Pau, France. Item in Clipboard Sébastien…

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Implications for future eDNA projects

Environmental DNA metabarcoding (eDNA) is a rapidly emerging field in which high-throughput sequencing is used to catalogue the biodiversity of ecosystems through the amplification of DNA extracted from environmental samples (water, air, faeces and soil). Although eDNA has strong links to DNA barcoding, the molecular marker most often used to…

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Decline of DNA damage response along with myogenic differentiation

Introduction Proper functioning of all living organisms depends on the faithful maintenance and transmission of genomic information stored in the molecule of DNA. However, DNA integrity is continuously challenged by a variety of endogenous and exogenous agents causing DNA lesions which have a critical impact on cellular activities and homeostasis….

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Solved describe the steps that are involved in protein

describe the steps that are involved in protein synthesis (Translation). Be sure to include the following terms in your discussion: Transcription, Translation, mRNA, tRNA, rRNA, ribosome (30S and 50S subunits), cytoplasm, nucleus, s tart codon, stop codon, anti codon, amino acids, proteins, A site, P site, polypeptide bond, and, polypeptide….

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Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost

Tarnocai C, Canadell JG, Schuur EA, Kuhry P, Mazhitova G, Zimov S. Soil organic carbon pools in the northern circumpolar permafrost region. Global Biogeochem Cycles. 2009;23:1–11. Article  Google Scholar  Hugelius G, Strauss J, Zubrzycki S, Harden JW, Schuur EA, Ping CL, et al. Estimated stocks of circumpolar permafrost carbon with…

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Solved splicing. rRNA processing occurs in the 22.tRNAs

Transcribed image text: splicing. rRNA processing occurs in the 22.tRNAs contain modified bases. For example, the structure shown at right is abbreviated 23. tRNAs do require splicing. Such splicing replaces the 3′ tRNA end with Also the loop is shortened by splicing. 24. Another modified base is shown at right…

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How does the use of semiconductor chips in DNA sequencing technology compare to other methods?

what types of research are GFPs used for? 5 answers How does mitochondrial DNA variation in forensic science help to identify an individual? 5 answers What are the future research directions for semiconductor chip-based sequencing? 5 answers What are the advantages and disadvantages of different short read mapping algorithms? 5…

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ASM1645882v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::03/19/2023 23:53:55 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.4 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA Genes (total)::2,406 CDSs (total)::2,346 Genes (coding)::2,318 CDSs (with protein)::2,318 Genes (RNA)::60 rRNAs::4, 4, 4 (5S, 16S, 23S) complete rRNAs::4, 4, 4…

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Fermentation | Free Full-Text | Whole-Genome Sequencing of Lactiplantibacillus plantarum YY-112 and Investigation of Its Immune-Modulating Abilities In Vivo

Author Contributions Conceptualization, Y.Y. and Y.G.; Data curation, M.L. and W.Z.; Formal analysis, M.L., W.Z., W.T. and J.L.; Funding acquisition, Y.Y. and Y.G.; Investigation, J.X., Y.Y. and Y.G.; Methodology, M.L., J.L. and Y.Y.; Project administration, Y.Y.; Resources, J.X., Y.Y. and Y.G.; Software, M.L., W.Z. and W.T.; Supervision, J.X., Y.Y. and…

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2023.pdf – 2023/2024 EXAM GUIDE HISTOLOGY NBME rRNA is synthesized here – CORRECT ANSWER-nucleolus intercellular junction type in the intestines –

~differentiation~ spermatozoa direct signal transduction event that follows binding of growth factor to its receptor – CORRECT ANSWER-exocytosis of constitutively secreted protein a patient overdoses on barbiturates.. what part of the cell will have an abundance – CORRECT ANSWER-SER (liver) during the final stage of secretory glycoprotein formation, before exocytosis,…

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Solved d) The mRNA would be 5’AUGGCCGGUUAUUAAGCA-3′ and the

Transcribed image text: d) The mRNA would be 5’AUGGCCGGUUAUUAAGCA-3′ and the protein will be MACY. 8. The RNA world hypothesis proposes that the first complex molecule was RNA and it preceded protein formation. Which major function of the ribosomal RNA supports the hypothesis? a) rRNA has catalytic properties in the…

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What factors can introduce bias to 16S rRNA gene sequencing?

What are the advantages and disadvantages of using conformal prediction in Bayesian optimization? 5 answers What are the latest findings in Bayesian deep learning? 3 answers What is the evidence for the effectiveness of the vivaire procedure? 4 answers is attention layers hard to train ? 5 answers How do…

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Improving Species Level-taxonomic Assignment from 16S rRNA Sequencing Technologies

Affiliations Expand Affiliations 1 Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, Barcelona, Catalonia, Spain. 2 ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain. 3 Department of Clinical Sciences, Faculty of Medicine and Health Sciences and Universitat de Barcelona Institute…

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Solved c) Only DNA will result in the production of

Transcribed image text: c) Only DNA will result in the production of defective proteins. The DNA mutation, if not corrected, is permanent. Production of defective protein ceases when the DNA strand deteriorates. d) Only mRNA will result in the production of defective proteins. The mRNA mutation will only affect proteins…

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What PCR-related factors can introduce bias to 16S rRNA gene sequencing?

Are Beta blockers effective for atrial fibrillation? 5 answers Cancer Res. 2008 May 1;68(9):3505-15. Estrogen receptor regulation of carbonic anhydrase XII through a distal enhancer in breast cancer. 5 answers What is the relationship between auxin, flavonol, and rhamnose? 5 answers Is lower trapezius tendon transfer better than superior capsule…

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A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics

Título:  Autor:  Haro-Moreno, José M.; Cabello-Yeves, Pedro J.; Garcillán-Barcia, M. Pilar; Zakharenko, Alexandra; Zemskaya, Tamara I.; Rodriguez-Valera, Francisco Palabras clave:  Ca. PatescibacteriaLake BaikalLong-read metagenomics16S rRNA Fecha de publicación:  2023 Editor:  Springer Nature Citación:  Environmental Microbiome 18: 12 (2023) Resumen:  [Background]: Lake Baikal, the world’s deepest freshwater lake, contains important numbers…

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Clinical, genetic and structural delineation of RPL13-related spondyloepimetaphyseal dysplasia suggest extra-ribosomal functions of eL13

Clinical and radiographic findings The most common features were mild to moderate short stature, delayed carpal bone ossification and epimetaphyseal dysplasia in the lower limbs. Height ranged from −5,8 to −1,2 SDS. A summary of the clinical observations can be found in Table 1 and Fig. 2, while the radiological…

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Metagenomic Sequencing Market Forecasted 17.6% Growth Rate,

The Metagenomic Sequencing Market witnessed a significant global revenue of US$ 1.2 Billion in 2022. It is projected to experience a remarkable growth rate of 17.6% from 2023 to 2033, ultimately reaching a valuation of US$ 7.1 Billion by the conclusion of the forecast period. The Metagenomic Sequencing Market has…

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MBG 3040 NOTES.docx – MBG 3040 NOTES First Quiz Thursday September 21. Lecture 1 Enhancers regulate inducible responses. Basal transcription elements

MBG 3040 NOTES First Quiz Thursday September 21. Lecture 1 Enhancers regulate inducible responses. Basal transcription elements regulate basal promoter strength. Prokaryotes have only 1 RNA polymerase while Eukaryotes have 3 different RNA polymerases. Eukaryotes need more transcription factors than Prokaryotes. RNA pol 1 = found in nucleolus. Accounts for…

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16 rRNA & 18 rRNA.docx – Ribosomal RNA 16S &18S 16S rRNA and 18S rRNA Both belong to the ribosomal RNA category. Substances under the ribosomal RNA

Ribosomal RNA 16S &18S 16S rRNA, and 18S rRNA Both belong to the ribosomal RNA category. Substances under the ribosomal RNA category convert genetic code into proteins. There’s two different subunits that are under the prokaryotic ribosome, one being a small subunit of 30S and the other being a large…

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Why use 16S rRNA used for bacteria?

How does polymer concentration affect semisolid extrusion formulation printing pressure? 5 answers How can lipid particles for RNA delivery be prepared by self-assembly? 3 answers How do the Lewis acid active sites in MOFs affect the catalytic activity? 5 answers What are some effective storytelling techniques that can be used…

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Why use 16S rRNA used for bacteria, metagenomics, cultured?

What are the effects of aggregate gradation on performance of asphalt concrete? 5 answers Does the particle size of heavy metals affect the removal efficiency? 5 answers What is the Bligh and Dy method? 5 answers Does the particulate size of heavy metals affect the removal efficiency of a water…

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A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei,Nature Communications

Trypanosomes are protozoan parasites that cycle between insect and mammalian hosts and are the causative agent of sleeping sickness. Here, we describe the changes of pseudouridine (Ψ) modification on rRNA in the two life stages of the parasite using four different genome-wide approaches. CRISPR-Cas9 knock-outs of all four snoRNAs guiding…

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Cataloging bacterial diversity within tumor samples

It is said in Spanish, “si no existe, créalo” or “if it does not exist, create it.” This is exactly what sometimes occurs at the Fred Hutch. When we do not have the tools to test a hypothesis, we must be creative! A great example is a collaboration between Dr. Susan Bullman,…

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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…

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Unexpected separation of RNA-seq samples on PCA plot

Unexpected separation of RNA-seq samples on PCA plot 0 Hello Biostars, I have been dealing with an interesting issue regarding 9 RNA-seq green algae samples. These samples come from three conditions, each having 3 biological replicates. To remove rRNA from the samples, rRNA was depleted with varying success in order…

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Exploring Subglacial Environments: Insights from Blood Falls

Subglacial environments on Earth serve as valuable analogs for the study of Ocean World targets within our solar system. These unique ecosystems, filled with microbial life, present a challenge for scientists due to the thick glacial ice that hampers access. However, recent research conducted at Blood Falls, Antarctica, has shed…

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Solved location within ribosome where it performs

Transcribed image text: location within ribosome where it performs dehydration reaction to connect two amino acids together and breaks bond holding one amino acid to its tRNA catalytic rRNA within ribosome that breaks a bond and synthesizes a bond sequence of three RNA nucleotides in a tRNA molecule hydrogen bonds…

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Solved Using excel:The four samples that were analyzed are

Using excel: The four samples that were analyzed are described in the table below as well as in the “Measurements” table in the Excel file. First, calculate the copy number/mLwater for each of the replicates in the spreadsheet Then, report the average copy number/mL of E. coli 16S rRNA genes…

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Ethnic disparity in diagnosing asymptomatic bacterial vaginosis using machine learning

Dataset The dataset was originally reported by Ravel et al.16. The study was registered at clinicaltrials.gov under ID NCT00576797. The protocol was approved by the institutional review boards at Emory University School of Medicine, Grady Memorial Hospital, and the University of Maryland School of Medicine. Written informed consent was obtained…

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Metaproteogenomic analysis of saliva samples from Parkinson’s disease patients with cognitive impairment

Characteristics of participants and analyses A total of 115 individuals (43 PDD, 45 PD-MCI) and 27 HC were included in this study. Both 16 S rRNA gene amplicon sequencing based microbiome analysis and metaproteomics profiling were performed for all salivary samples collected from the participants (Fig. 1). Fig. 1: Experimental overview….

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Simultaneous analysis of seven 16S rRNA hypervariable gene regions increases efficiency in marine bacterial diversity detection

doi: 10.1111/1462-2920.16530. Online ahead of print. Affiliations Expand Affiliations 1 Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany. 2 Marine Ecosystems Functioning, AZTI, Marine Research, Basque Research and Technology Alliance, Pasia, Gipuzkoa, Spain. 3 Molecular Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany. 4 SeqIT, Laboratory for Molecular Diagnostics and…

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Part 2 Nuclear Bodies Lect Notes – Part 2 Nuclear Bodies Lecture Notes: The 45 S pre-rRNA is the

Part 2 Nuclear Bodies Lecture Notes: The 45 S pre-rRNA is the primary transcript of rRNA genes in higher eukaryotes. ● The pre-rRNA is processed through a series of cleavages, which is the same for all eukaryotes. ● The pre-rRNA also undergoes significant base modification during processing, including the addition…

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New therapeutic strategy to reduce neuronal death in amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that affects neurons in the brain and spinal cord causing loss of muscle control. A study by the University of Barcelona has designed a potential therapeutic strategy to tackle this pathology that has no treatment to date. It is a molecular trap…

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18S rRNA WAINVILLE’S 7. Short essay. This entire

18S rRNA WAINVILLE’S 7. Short essay. This entire question is worth 10 points. For this question, use the following diagram of the ITS1 DNA barcode, used in identifying fungi. ITS1 primer ITS1 region Section: 5.8s ITS2 region 28s rRNA ITS 2 is that they ITS4 primer efly explain how DNA…

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Metagenomics Sequencing Market Sets New Record, Projected

Metagenomics Sequencing Market Metagenomics comprises studies that use sequencing technologies and bioinformatics tools to obtain useful insights on the diversities in the microbial community and the interaction of the microbes in a community. Metagenomic technologies have enabled improved understanding of the microbial ecology and the role of microbiology in the…

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Guidelines for performing ribosome profiling in plants including structural analysis of rRNA fragments

Abstract Ribosome profiling (or Ribo-seq) is a technique that provides genome-wide information on the translational landscape (translatome). Across different plant studies, variable methodological setups have been described which raises questions about the general comparability of data that were generated from diverging methodologies. Furthermore, a common problem when performing Ribo-seq are…

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Novel Therapy Strategy Limits Neuron Death in ALS

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that affects neurons in the brain and spinal cord causing loss of muscle control. A study by the University of Barcelona has designed a potential therapeutic strategy to tackle this pathology that has no treatment to date. It is a molecular trap…

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Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2’-fucosyllactose utilization can be facilitated by coexisting species

Stewart, C. J. et al. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature 562, 583–588 (2018). Article  CAS  ADS  PubMed  PubMed Central  Google Scholar  Tamburini, S., Shen, N., Wu, H. C. & Clemente, J. C. The microbiome in early life: implications for health outcomes….

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Global perspective of environmental distribution and diversity of Perkinsea (Alveolata) explored by a meta-analysis of eDNA surveys

Phylogenetic classification of environmental Perkinsea sequences Using a phylogenetic approach, we investigated the diversity and community structure of Perkinsea ASV sequences retrieved from the published EukBank dataset37. We first conducted a phylogenetic analysis using a reference tree derived from an alignment of 1790 characters, which included representative alveolate groups and…

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Transgenerational epigenetic effects imposed by neonicotinoid thiacloprid exposure

This study is aimed at revealing the transgenerational effects of thia. We chose the developmental window from embryonic days 6.5 to E15.5 because of its importance in germ cell program establishment. The mice breeding was described in the Materials and Methods section “Mouse treatment and dissection.” The design of the…

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Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient

Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA. 103, 626–631 (2006). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Gao, C. & Guo, L. Progress on microbial species diversity, community assembly and functional traits. Biodivers. Sci. 30, 22429 (2022)….

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A streamlined pipeline based on HmmUFOtu for microbial community profiling using 16S rRNA amplicon sequencing

Microbial community profiling using 16S rRNA amplicon sequencing allows for taxonomic characterization of diverse microorganisms. While amplicon sequence variant (ASV) methods are increasingly favored for their fine-grained resolution of sequence variants, they often discard substantial portions of sequencing reads during quality control, particularly in datasets with large number samples. We…

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Gardnerella Vaginalis rRNA PCR Swab Test

What are the other Names for this Test? (Equivalent Terms) G. Vaginalis rRNA Vaginal Swab Test What is Gardnerella Vaginalis rRNA PCR Swab Test? (Background Information) Gardnerella vaginalis, or G. vaginalis, is a bacterium most commonly associated with bacterial vaginosis or inflammation of the vaginal tract The vagina normally contains…

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Evaluation of the fresh beef bacterial community through processing retail display conditions using 16S rRNA gene amplification sequencing

Microorganisms are ubiquitous and provide challenges in the food production system. Beyond monitoring for pathogens or food safety hazards, there is a need for understanding and controlling spoilage organisms, and indicators of potential spoilage especially with products that have a more limited shelf-life, such as fresh meat. Arguably, just as…

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