Molecular biology: Coordination of sequence data

Nature ◽  
1985 ◽  
Vol 314 (6009) ◽  
pp. 318-319 ◽  
Author(s):  
Arthur M. Lesk
Keyword(s):  
Molecular Biology ◽  
Sequence Data

scholarly journals Protocols for Northern Analysis of Exosome Substrates and Other Noncoding RNAs

2019 ◽  
pp. 83-103
Author(s):  
Cristina Cruz ◽  
Jonathan Houseley
Keyword(s):  
Molecular Biology ◽  
Sequence Data ◽  
Noncoding Rnas ◽  
Northern Blotting ◽  
Northern Analysis ◽  
Standard Laboratory ◽  
Agarose Gels ◽  
The Past ◽  
Technical Advances ◽  
Biology Lab

AbstractOver the past decade a plethora of noncoding RNAs (ncRNAs) have been identified, initiating an explosion in RNA research. Although RNA sequencing methods provide unsurpassed insights into ncRNA distribution and expression, detailed information on structure and processing are harder to extract from sequence data. In contrast, northern blotting methods provide uniquely detailed insights into complex RNA populations but are rarely employed outside specialist RNA research groups. Such techniques are generally considered difficult for nonspecialists, which is unfortunate as substantial technical advances in the past few decades have solved the major challenges. Here we present simple, reproducible and highly robust protocols for separating glyoxylated RNA on agarose gels and heat denatured RNA on polyacrylamide–urea gels using standard laboratory electrophoresis equipment. We also provide reliable transfer and hybridization protocols that do not require optimization for most applications. Together, these should allow any molecular biology lab to elucidate the structure and processing of ncRNAs of interest.

scholarly journals The European Nucleotide Archive in 2019

2019 ◽  
Author(s):  
Clara Amid ◽  
Blaise T F Alako ◽  
Vishnukumar Balavenkataraman Kadhirvelu ◽  
Tony Burdett ◽  
Josephine Burgin ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Molecular Biology ◽  
Scientific Community ◽  
Sequence Data ◽  
European Bioinformatics Institute ◽  
Data Types ◽  
Nucleotide Sequence Data ◽  
European Nucleotide Archive ◽  
Access Services ◽  
Insight Into

Abstract The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena) at the European Molecular Biology Laboratory’s European Bioinformatics Institute provides open and freely available data deposition and access services across the spectrum of nucleotide sequence data types. Making the world’s public sequencing datasets available to the scientific community, the ENA represents a globally comprehensive nucleotide sequence resource. Here, we outline ENA services and content in 2019 and provide an insight into selected key areas of development in this period.

scholarly journals Generating DNA sequence data with limited resources for molecular biology: Lessons from a barcoding project in Indonesia

2018 ◽  
Vol 6 (7) ◽  
pp. e01167 ◽  
Author(s):  
Gillian H. Dean ◽  
Rani Asmarayani ◽  
Marlina Ardiyani ◽  
Yessi Santika ◽  
Teguh Triono ◽  
...  
Keyword(s):  
Molecular Biology ◽  
Dna Sequence ◽  
Sequence Data ◽  
Limited Resources ◽  
Dna Sequence Data

scholarly journals TESTING FOR EVOLUTIONARY RELATIONSHIP: AN APPLICATION OF MATHEMATICS IN MOLECULAR BIOLOGY

COSMOS ◽  
2005 ◽  
Vol 01 (01) ◽  
pp. 29-45
Author(s):  
A. D. BARBOUR
Keyword(s):  
Molecular Biology ◽  
Theoretical Analysis ◽  
Sequence Data ◽  
Evolutionary Relationship ◽  
Biological Applications ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Mathematical Problems

The paper illustrates some mathematical problems that are motivated by molecular biological applications and the techniques that are used to address them. The context is that of detecting evolutionary relationship on the basis of molecular sequence data and of measuring its strength. The Stein–Chen method is shown to play a central role in the theoretical analysis of many of the procedures used in practice.

scholarly journals A window into lysogeny: Revealing temperate phage biology with transcriptomics

2019 ◽  
Author(s):  
Siân V. Owen ◽  
Rocío Canals ◽  
Nicolas Wenner ◽  
Disa L. Hammarlöf ◽  
Carsten Kröger ◽  
...  
Keyword(s):  
Molecular Biology ◽  
Sequence Data ◽  
Temperate Phage ◽  
Phage Resistance ◽  
Bacterial Cells ◽  
Rna Seq ◽  
Bacterial Genomes ◽  
Transcriptomic Data ◽  
Dna Sequence Data ◽  
Bacterial Rna

ABSTRACTIntegrated phage elements, known as prophages, are a pervasive feature of bacterial genomes. Prophages can enhance the fitness of their bacterial hosts by conferring beneficial functions, such as virulence, stress tolerance or phage resistance, which are encoded by accessory loci. Whilst the majority of phage-encoded genes are repressed during lysogeny, accessory loci are often highly expressed. However, novel prophage accessory loci are challenging to identify based on DNA sequence data alone. Here, we use bacterial RNA-seq data to examine the transcriptional landscapes of five Salmonella prophages. We show that transcriptomic data can be used to heuristically enrich for prophage features that are highly expressed within bacterial cells and often represent functionally-important accessory loci. Using this approach we identify a novel anti-sense RNA species in prophage BTP1, STnc6030, which mediates superinfection exclusion of phage BTP1 and immunity to closely-related phages. Bacterial transcriptomic datasets are a powerful tool to explore the molecular biology of temperate phages.

Application of evidence from molecular biology to the biogeography of angiosperms

1991 ◽  
Vol 4 (1) ◽  
pp. 111 ◽  
Author(s):  
PG Martin ◽  
JM Dowd
Keyword(s):  
New Zealand ◽  
Molecular Biology ◽  
Nucleic Acids ◽  
Sequence Data ◽  
Upper Jurassic ◽  
Geophysical Information ◽  
The Mean ◽  
Break Up

Previously published sequence data from species, whose ancestors are thought to have been separated during the break-up of Gondwanaland, yield mean number of inferred nucleotide differences (i.n.d.) for two comparisons, Africa versus Australia and New Zealand versus Australia. In the geophysical literature, the dating of these separations appears to be uncontroversial, viz. 130 Ma and 80 Ma respectively. The mean rates for the two comparisons are one i.n.d. in 11.7 Ma and 11.9 Ma. The similarity of these estimates encouraged us to deduce the dates of other events for which we present new data. The deepest division detected within the angiosperms corresponds to 244 Ma (Triassic). This is compared with recent equivalent datings. The division between representatives of northern primitive families (Magnoliaceae, Calycanthaceae) and southern primitive families (Winteraceae, Idiospermataceae) corresponds to 162 Ma (Upper Jurassic). This is discussed briefly in relation to geophysical information. Although there is considerable scope for error in this approach, it is considered to be worth pursuing in the light of the imminence of more and longer sequences from nucleic acids and of the interest and difficulty of such biogeographical problems.

Biochemical Evolution and the History of Life

1988 ◽  
Vol 1 ◽  
pp. 138-145
Author(s):  
W. Ford Doolittle
Keyword(s):  
Molecular Biology ◽  
Data Base ◽  
Sequence Data ◽  
Darwinian Evolution ◽  
Phylogenetic Distance ◽  
Homologous Proteins ◽  
Random Mutation ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
History Of

Molecular biology has contributed to the construction of the neoDarwinian synthesis, as it is articulated in the 1980's, in two ways. First, it has provided a nearly complete understanding of the processes of DNA replication and expression, and mutation. We know in detail how genotypes are passed on and how random mutation can provide the variation which must be present in populations if natural selection is to “cause” evolution. (We do not yet understand in detail how genotype determines phenotype in any complex multicellular organism, but there is probably no barrier other than complexity in our way.) Second, molecular biology has provided us with a data base from which to draw conclusions about phylogenetic relationships between species, or between genes, and a powerful way of approaching that data base. Zuckerkandl and Pauling's (1965) contention – that comparisons of amino acid or nucleotide sequences of homologous proteins or nucleic acids from contemporary species should allow measurements of phylogenetic distance – has been amply confirmed. Earlier chapters in this volume provide some details about methods and their application to major groups of organisms. Here I would like to discuss what molecular sequence data, and phylogenetic conclusions drawn from them, might have to say about the very earliest stages of Darwinian evolution, before there were cells.

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