here - Genomes Unzipped
... Li et al.[1] sequenced cDNA from lymphoblastoid cell lines derived from 27 individuals whose genomes have been sequenced at low coverage [2], and identified 10,210 sites of mismatches between an individual’s mRNA and DNA sequences (RDD sites, for RNA-DNA difference). RDD sites included all possible ...
... Li et al.[1] sequenced cDNA from lymphoblastoid cell lines derived from 27 individuals whose genomes have been sequenced at low coverage [2], and identified 10,210 sites of mismatches between an individual’s mRNA and DNA sequences (RDD sites, for RNA-DNA difference). RDD sites included all possible ...
Suppl. Material
... Construction of mutants using pJET1.2/blunt cloning vector Insertion mutation was carried out in kdsA and waaG genes of the lipopolysaccharide biosynthesis (LPS) pathway of P.aeruginosa PAO1. Internal fragments of both kdsA and waaG genes were used to construct the recombinant plasmids using CloneJE ...
... Construction of mutants using pJET1.2/blunt cloning vector Insertion mutation was carried out in kdsA and waaG genes of the lipopolysaccharide biosynthesis (LPS) pathway of P.aeruginosa PAO1. Internal fragments of both kdsA and waaG genes were used to construct the recombinant plasmids using CloneJE ...
pure culture
... • Encourages growth of desired microbe • Assume a soil sample contains a few phenoldegrading bacteria and thousands of other bacteria – Inoculate phenol-containing culture medium with the soil and incubate – Transfer 1 ml to another flask of the phenol medium and incubate – Transfer 1 ml to another ...
... • Encourages growth of desired microbe • Assume a soil sample contains a few phenoldegrading bacteria and thousands of other bacteria – Inoculate phenol-containing culture medium with the soil and incubate – Transfer 1 ml to another flask of the phenol medium and incubate – Transfer 1 ml to another ...
Supplementary information
... limma package (6) was used to identify differentially expressed genes between the two groups. The moderated t-test uses an empirical Bayes method to moderate the standard errors of the estimated log-fold changes. This results in more stable inference and improved power, especially for experiments wi ...
... limma package (6) was used to identify differentially expressed genes between the two groups. The moderated t-test uses an empirical Bayes method to moderate the standard errors of the estimated log-fold changes. This results in more stable inference and improved power, especially for experiments wi ...
A general and rapid mutagenesis method using polymerase chain
... flanking primers and one mutant oligo, in conjunction with supercoiled plasmid DNA and a fragment of the target DNA are sufficient to introduce the mutation by two PCR amplifications. Our method permits directing the location of mutations anywhere in the target gene with a very low misincorporation ...
... flanking primers and one mutant oligo, in conjunction with supercoiled plasmid DNA and a fragment of the target DNA are sufficient to introduce the mutation by two PCR amplifications. Our method permits directing the location of mutations anywhere in the target gene with a very low misincorporation ...
Non contiguous-finished genome sequence and description of
... the Nextera Mate Pair sample prep kit (Illumina). The DNAg was quantified by a Qubit assay with the high sensitivity kit (Life technologies, Carlsbad, CA, USA) to 16 ng/μl and dilution was performed to require 1ng of each genome as input to prepare the paired end library. The « tagmentation » st ...
... the Nextera Mate Pair sample prep kit (Illumina). The DNAg was quantified by a Qubit assay with the high sensitivity kit (Life technologies, Carlsbad, CA, USA) to 16 ng/μl and dilution was performed to require 1ng of each genome as input to prepare the paired end library. The « tagmentation » st ...
www.botany.wisc.edu
... The β population consists of 22 nonoverlapping duplicate regions and 13,449 genes (51.6% of the transcriptome) The γ population conists of 7 duplicate regions, some of which overlap with β duplicates, and 5,287 genes (20.3% of the transcriptome) ...
... The β population consists of 22 nonoverlapping duplicate regions and 13,449 genes (51.6% of the transcriptome) The γ population conists of 7 duplicate regions, some of which overlap with β duplicates, and 5,287 genes (20.3% of the transcriptome) ...
Reverse Ecology: From Systems to
... first large-scale dataset of predicted environments. Using various experimentally validated data on microorganisms’ ecologies and environments, it was shown that these computationally determined seed sets accurately describe the organisms’ biochemical surroundings and correlate with various attribut ...
... first large-scale dataset of predicted environments. Using various experimentally validated data on microorganisms’ ecologies and environments, it was shown that these computationally determined seed sets accurately describe the organisms’ biochemical surroundings and correlate with various attribut ...
Analysis of genetic systems using experimental evolution and whole
... environment. Parallel evolution is a hallmark of natural selection: identical or very similar changes reach high frequency or fixation in independent lineages evolving under identical conditions. The use of parallel evolution to infer that adaptation had occurred was first applied to morphological t ...
... environment. Parallel evolution is a hallmark of natural selection: identical or very similar changes reach high frequency or fixation in independent lineages evolving under identical conditions. The use of parallel evolution to infer that adaptation had occurred was first applied to morphological t ...
AronsonDOE group meeting presentation
... • 16S gene is conserved in bacteria, coding for part of the ribosome • Commonly used for molecular‐based OTU iden/fica/on • Used to build phylogene/c trees of microbial communi/es ...
... • 16S gene is conserved in bacteria, coding for part of the ribosome • Commonly used for molecular‐based OTU iden/fica/on • Used to build phylogene/c trees of microbial communi/es ...
Lectre 10
... – Alter the phenotype of an organism – Bioinformatics is the use of computer applications to study genetic data; – Proteomics – proteomics is the study of a cell’s proteins. • determination of all the proteins expressing in the cell ...
... – Alter the phenotype of an organism – Bioinformatics is the use of computer applications to study genetic data; – Proteomics – proteomics is the study of a cell’s proteins. • determination of all the proteins expressing in the cell ...
Functionally Structured Genomes in Lactobacillus kunkeei
... Lactobacillus kunkeei, as inferred from both cultivation experiments and 16 S rRNA surveys (Olofsson and Vasquez 2008; Vasquez et al. 2012; Anderson et al. 2013; Vojvodic et al. 2013). A sampling of 750 bacterial isolates from the honey crop of nine Apis species and three stingless bee species from ...
... Lactobacillus kunkeei, as inferred from both cultivation experiments and 16 S rRNA surveys (Olofsson and Vasquez 2008; Vasquez et al. 2012; Anderson et al. 2013; Vojvodic et al. 2013). A sampling of 750 bacterial isolates from the honey crop of nine Apis species and three stingless bee species from ...
Document
... PCR is quick sensitive and robust and is useful when dealing with small amounts of DNA, or where rapid and high-throughput screening is required. PCR: * The polymerase chain reaction involves many rounds of DNA synthesis. * All DNA synthesis reactions require a template, a primer, a enzyme and a sup ...
... PCR is quick sensitive and robust and is useful when dealing with small amounts of DNA, or where rapid and high-throughput screening is required. PCR: * The polymerase chain reaction involves many rounds of DNA synthesis. * All DNA synthesis reactions require a template, a primer, a enzyme and a sup ...
7.03 Fall 2003 Problem Set #3 Solutions
... never co-transduced with lac2+. This indicates that the distance between lac2- and Tn5 is at least one phage head (105 bp). We know from part (a) that Tn5 and lac1- are within one phage head since their cotransduction frequency was 18%. But since we do not know the relative order of the three marker ...
... never co-transduced with lac2+. This indicates that the distance between lac2- and Tn5 is at least one phage head (105 bp). We know from part (a) that Tn5 and lac1- are within one phage head since their cotransduction frequency was 18%. But since we do not know the relative order of the three marker ...
Genome history in the symbiotic hybrid Euglena gracilis
... Another method for classifying the genes into the above three groups is by the nearest neighbor method. In this approach, the gene is classified into the group of its closest related (i.e., most similar) sequence. We employed the nearest neighbor method by two approaches, first by using only sequenc ...
... Another method for classifying the genes into the above three groups is by the nearest neighbor method. In this approach, the gene is classified into the group of its closest related (i.e., most similar) sequence. We employed the nearest neighbor method by two approaches, first by using only sequenc ...
- CSHL Institutional Repository
... toolkit. GMOD is an open source project initiated in 2002 with the objective of providing generic software so that a small community with limited informatics infrastructure can build a new model organism database. We provide a brief description of the GMOD core components used to build ParameciumDB. ...
... toolkit. GMOD is an open source project initiated in 2002 with the objective of providing generic software so that a small community with limited informatics infrastructure can build a new model organism database. We provide a brief description of the GMOD core components used to build ParameciumDB. ...
Information Sheet on Cornelia de Lange Syndrome Testing
... (7) detected SMC1A mutations in approximately 5% of patients with CdLS (about 9% of those negative for NIPBL mutations). SMC1A has 25 coding exons. Only missense mutations and in-frame deletions have been identified in the SMC1A gene. A small, in-frame deletion of the SMC3 gene [OMIM #606062] gene h ...
... (7) detected SMC1A mutations in approximately 5% of patients with CdLS (about 9% of those negative for NIPBL mutations). SMC1A has 25 coding exons. Only missense mutations and in-frame deletions have been identified in the SMC1A gene. A small, in-frame deletion of the SMC3 gene [OMIM #606062] gene h ...
Gibson Assembly™ – Building a Synthetic Biology Toolset
... In the quest to create the first bacterial cell controlled by a synthetic genome, the J. Craig Venter Institute (JCVI), with support from Synthetic Genomics, Inc. (SGI), developed a variety of powerful new DNA synthesis and assembly methodologies (1–5) to manipulate large, complex DNAs. These method ...
... In the quest to create the first bacterial cell controlled by a synthetic genome, the J. Craig Venter Institute (JCVI), with support from Synthetic Genomics, Inc. (SGI), developed a variety of powerful new DNA synthesis and assembly methodologies (1–5) to manipulate large, complex DNAs. These method ...
Hypothesis for the evolutionary origin of the chloroplast ribosomal
... The amino acid sequence has been aligned with the sequences for L21 r-protein from M. polymorpha (Kochi et al. 1988) and E. coli (Heiland and Wittmann-Liebold 5979) as shown in Fig. 2. The spinach L21 r-protein contains roughly 500 residues common to all three sequences, a region which we term the c ...
... The amino acid sequence has been aligned with the sequences for L21 r-protein from M. polymorpha (Kochi et al. 1988) and E. coli (Heiland and Wittmann-Liebold 5979) as shown in Fig. 2. The spinach L21 r-protein contains roughly 500 residues common to all three sequences, a region which we term the c ...
Whole-transcriptome RNAseq analysis from minute amount of total
... system, TruSeqTM RNA sample preparation, which employs polyA selection for mRNA enrichment and Invitrogen’s RiboMinusTM kit which depletes rRNA. We considered the following criteria in evaluating the RNA-seq methods, some of which are described in literature (10): library complexity, the number of u ...
... system, TruSeqTM RNA sample preparation, which employs polyA selection for mRNA enrichment and Invitrogen’s RiboMinusTM kit which depletes rRNA. We considered the following criteria in evaluating the RNA-seq methods, some of which are described in literature (10): library complexity, the number of u ...
Chloroplast genes for components of the ATP synthase complex
... DNA. In both species, the genes for these subunits are arranged in two clusters, with the gene for p close to that for E and the gene for a close to that for subunit 111, but in wheat the clusters are 20kbp* apart, whereas in pea they are 50 kbp apart. The genes for fl and E subunits are close to, a ...
... DNA. In both species, the genes for these subunits are arranged in two clusters, with the gene for p close to that for E and the gene for a close to that for subunit 111, but in wheat the clusters are 20kbp* apart, whereas in pea they are 50 kbp apart. The genes for fl and E subunits are close to, a ...
3` Untranslated Regions
... Introns - May contain genes expressed independently of the exons they fall between. Many introns code for small nuclear RNAs (snoRNAs). These accumulate in the nucleolus, and may play a role in ribosome assembly. Thus the introns cut out of pre-mRNA may play a role in producing, or regulating produc ...
... Introns - May contain genes expressed independently of the exons they fall between. Many introns code for small nuclear RNAs (snoRNAs). These accumulate in the nucleolus, and may play a role in ribosome assembly. Thus the introns cut out of pre-mRNA may play a role in producing, or regulating produc ...
Multifractal characterisation of length sequences of coding and
... modelling [25,26]. For DNA sequences, application of the multifractal technique seems rare (we have found only Berthelsen et al. [27]). Recently, Yu et al. [28] considered the multifractal property of the measure representation of a complete genome. In this paper, we pay more attention to the multif ...
... modelling [25,26]. For DNA sequences, application of the multifractal technique seems rare (we have found only Berthelsen et al. [27]). Recently, Yu et al. [28] considered the multifractal property of the measure representation of a complete genome. In this paper, we pay more attention to the multif ...
Metagenomics
Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Recent studies use either ""shotgun"" or PCR directed sequencing to get largely unbiased samples of all genes from all the members of the sampled communities. Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale and detail than before.