|
Healthcare Headlines |
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
Notice: Only variable references should be returned by reference in /var/www/vhosts/pmandr.com/httpdocs/includes/domit/xml_domit_nodemaps.php on line 166
|
Genome Biology - Latest Articles
|
-
Goodbye, Columbus
{no abstract}.
-
We are what we eat: how the diet of infants affects their gut microbiome
Simultaneous analysis of the gut microbiome and host gene expression in infants reveals the impact of diet (breastfeeding versus formula) on host-microbiome interactions.See research article http://www.genomebiology.com/2012/13/4/r32
-
Genetic architecture of body size in mammals
Much of the heritability for human stature is caused by mutations of small-to-medium effect. This is because detrimental pleiotropy restricts large-effect mutations to very low frequencies.
-
Economies of scale
{no abstract}
-
A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response
Background:
Gut microbiota and the host exist in a mutualistic relationship, with the functional composition of the microbiota strongly affecting the health and well-being of the host. Thus, it is important to develop a synthetic approach to study the host transcriptome and the microbiome simultaneously. Early microbial colonization in infants is critically important for directing neonatal intestinal and immune development, and is especially attractive for studying the development of human-commensal interactions. Here we report the results from a simultaneous study of the gut microbiome and host epithelial transcriptome of three month old exclusively breast- and formula-fed infants.
Results:
Variation in both host mRNA expression and the microbiome phylogenetic and functional profiles was observed between breast- and formula-fed infants. To examine the interdependent relationship between host epithelial cell gene expression and bacterial metagenomic-based profiles, the host transcriptome and functionally profiled microbiome data were subjected to novel multivariate statistical analyses. Gut microbiota metagenome virulence characteristics concurrently varied with immunity related gene expression in epithelial cells between the formula-fed and the breast-fed infants.
Conclusions:
Our data provide insight into the integrated responses of the host transcriptome and microbiome to dietary substrates in the early neonatal period. We demonstrate that differences in diet can affect, via gut colonization, host expression of genes associated with the innate immune system. Furthermore, the methodology presented in this study can be adapted to assess other host-commensal and host-pathogen interactions using genomic and transcriptomic data, providing a synthetic genomics-based picture of host-commensal relationships.
-
Current challenges in de novo plant genome sequencing and assembly
Genome sequencing is now affordable, but assembling plant genomes de novo remains challenging. We assess the state of the art of assembly and review the best practices for the community.
-
The Arabidopsis clock: time for an about-face?
Three recent studies have altered thinking on the role of TIMING OF CAB EXPRESSION 1 (TOC1), a core element in the plant circadian oscillator.
-
Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel
Background:
With the advent of next generation sequencing it has become possible to detect genomic variation on a large scale. However, predicting which genomic variants are damaging to gene function remains a challenge, as knowledge of the effects of genomic variation on gene expression is still limited. Recombinant inbred panels are powerful tools to study the cis and trans effects of genetic variation on molecular phenotypes such as gene expression.
Results:
We generated a comprehensive inventory of genomic differences between the two founder strains of the rat HXB/BXH recombinant inbred panel: SHR/OlaIpcv and BN-Lx/Cub. We identified 3.2 million single nucleotide variants, 425,924 small insertions and deletions, 907 copy number changes and 1,094 large structural genetic variants. RNA-sequencing analyses on liver tissue of the two strains identified 532 differentially expressed genes and 40 alterations in transcript structure. We identified both coding and non-coding variants that correlate with differential expression and alternative splicing. Furthermore, structural variants, in particular gene duplications, show a strong correlation with transcriptome alterations.
Conclusions:
We show that the panel is a good model for assessing the genetic basis of phenotypic heterogeneity and for providing insights in possible underlying molecular mechanisms. Our results reveal a high diversity and complexity underlying quantitative and qualitative transcriptional differences.
-
Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium
Background:
Recent years have shown a marked increase in the use of next-generation sequencing technologies for quantification of gene expression (RNA sequencing, RNA-Seq). The expression level of a gene is a function both of its rate of transcription and RNA decay, and the influence of mRNA decay rates on gene expression in genome-wide studies of Gram-positive bacteria is under-investigated.
Results:
In this work, we employed RNA-Seq in a genome-wide determination of mRNA half-lives in the Gram-positive bacterium Bacillus cereus. By utilizing a newly developed normalization protocol, RNA-Seq was used successfully to determine global mRNA decay rates at the single nucleotide level. The analysis revealed positional degradation patterns, with mRNAs being degraded from both ends of the molecule, indicating that both 5' to 3' and 3' to 5' directions of RNA decay are present in B. cereus. Other operons showed segmental degradation patterns where specific ORFs within polycistrons were degraded at variable rates, underlining the importance of RNA processing in gene regulation. We determined the half-lives for more than 2700 ORFs in B. cereus ATCC 10987, ranging from less than one minute to more than fifteen minutes, and showed that mRNA decay rate correlates globally with mRNA expression level, GC content, and functional class of the ORF.
Conclusions:
To our knowledge, this study presents the first global analysis of mRNA decay in a bacterium at single nucleotide resolution. We provide a proof of principle for using RNA-Seq in bacterial mRNA decay analysis, revealing RNA processing patterns at the single nucleotide level.
-
RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations.
Visualization and analysis of molecular networks are both central to systems biology. However, there still exists a large technological gap between them, especially when assessing multiple network levels or hierarchies. Here we present RedeR, an R/Bioconductor package combined with a Java core engine for representing modular networks. The functionality of RedeR is demonstrated in two different scenarios: hierarchical and modular organization in gene co-expression networks and nested structures in time-course gene expression subnetworks. Our results demonstrate RedeR as a new framework to deal with the multiple network levels that are inherent to complex biological systems.RedeR is available from http://bioconductor.org/packages/release/bioc/html/RedeR.html
|
|
