759 research outputs found
Genome landscapes and bacteriophage codon usage
Across all kingdoms of biological life, protein-coding genes exhibit unequal
usage of synonmous codons. Although alternative theories abound, translational
selection has been accepted as an important mechanism that shapes the patterns
of codon usage in prokaryotes and simple eukaryotes. Here we analyze patterns
of codon usage across 74 diverse bacteriophages that infect E. coli, P.
aeruginosa and L. lactis as their primary host. We introduce the concept of a
`genome landscape,' which helps reveal non-trivial, long-range patterns in
codon usage across a genome. We develop a series of randomization tests that
allow us to interrogate the significance of one aspect of codon usage, such a
GC content, while controlling for another aspect, such as adaptation to
host-preferred codons. We find that 33 phage genomes exhibit highly non-random
patterns in their GC3-content, use of host-preferred codons, or both. We show
that the head and tail proteins of these phages exhibit significant bias
towards host-preferred codons, relative to the non-structural phage proteins.
Our results support the hypothesis of translational selection on viral genes
for host-preferred codons, over a broad range of bacteriophages.Comment: 9 Color Figures, 5 Tables, 53 Reference
Conserved Usage of Alternative 5′ Untranslated Exons of the GATA4 Gene
BACKGROUND:GATA4 is an essential transcription factor required for the development and function of multiple organs. Despite this important role, our knowledge of how the GATA4 gene is regulated remains limited. To better understand this regulation, we characterized the 5' region of the mouse, rat, and human GATA4 genes. METHODOLOGY/PRINCIPAL FINDINGS:Using 5' RACE, we identified novel transcription start sites in all three species. GATA4 is expressed as multiple transcripts with varying 5' ends encoded by alternative untranslated first exons. Two of these non-coding first exons are conserved between species: exon 1a located 3.5 kb upstream of the GATA4 ATG site in exon 2, and a second first exon (exon 1b) located 28 kb further upstream. Expression of both mRNA variants was found in all GATA4-expressing organs but with a preference for the exon 1a-containing transcript. The exception was the testis where exon 1a- and 1b-containing transcripts were similarly expressed. In some tissues such as the intestine, alternative transcript expression appears to be regionally regulated. Polysome analysis suggests that both mRNA variants contribute to GATA4 protein synthesis. CONCLUSIONS/SIGNIFICANCE:Taken together, our results indicate that the GATA4 gene closely resembles the other GATA family members in terms of gene structure where alternative first exon usage appears to be an important mechanism for regulating its tissue- and cell-specific expression
Small representations of finite classical groups
Finite group theorists have established many formulas that express
interesting properties of a finite group in terms of sums of characters of the
group. An obstacle to applying these formulas is lack of control over the
dimensions of representations of the group. In particular, the representations
of small dimensions tend to contribute the largest terms to these sums, so a
systematic knowledge of these small representations could lead to proofs of
important conjectures which are currently out of reach. Despite the
classification by Lusztig of the irreducible representations of finite groups
of Lie type, it seems that this aspect remains obscure. In this note we develop
a language which seems to be adequate for the description of the "small"
representations of finite classical groups and puts in the forefront the notion
of rank of a representation. We describe a method, the "eta correspondence", to
construct small representations, and we conjecture that our construction is
exhaustive. We also give a strong estimate on the dimension of small
representations in terms of their rank. For the sake of clarity, in this note
we describe in detail only the case of the finite symplectic groups.Comment: 18 pages, 9 figures, accepted for publications in the proceedings of
the conference on the occasion of Roger Howe's 70th birthday (1-5 June 2015,
Yale University, New Haven, CT
Using synthetic biological parts and microbioreactors to explore the protein expression characteristics of Escherichia coli
Synthetic
biology has developed numerous parts for the precise
control of protein expression. However, relatively little is known
about the burden these place on a host, or their reliability under
varying environmental conditions. To address this, we made use of
synthetic transcriptional and translational elements to create a combinatorial
library of constructs that modulated expression strength of a green
fluorescent protein. Combining this library with a microbioreactor
platform, we were able to perform a detailed large-scale assessment
of transient expression and growth characteristics of two <i>Escherichia coli</i> strains across several temperatures. This
revealed significant differences in the robustness of both strains
to differing types of protein expression, and a complex response of
transcriptional and translational elements to differing temperatures.
This study supports the development of reliable synthetic biological
systems capable of working across different hosts and environmental
contexts. Plasmids developed during this work have been made publicly
available to act as a reference set for future research
RNA Unwinding by NS3 Helicase: A Statistical Approach
The study of double-stranded RNA unwinding by helicases is a problem of basic scientific interest. One such example is provided by studies on the hepatitis C virus (HCV) NS3 helicase using single molecule mechanical experiments. HCV currently infects nearly 3% of the world population and NS3 is a protein essential for viral genome replication. The objective of this study is to model the RNA unwinding mechanism based on previously published data and study its characteristics and their dependence on force, ATP and NS3 protein concentration. In this work, RNA unwinding by NS3 helicase is hypothesized to occur in a series of discrete steps and the steps themselves occurring in accordance with an underlying point process. A point process driven change point model is employed to model the RNA unwinding mechanism. The results are in large agreement with findings in previous studies. A gamma distribution based renewal process was found to model well the point process that drives the unwinding mechanism. The analysis suggests that the periods of constant extension observed during NS3 activity can indeed be classified into pauses and subpauses and that each depend on the ATP concentration. The step size is independent of external factors and seems to have a median value of 11.37 base pairs. The steps themselves are composed of a number of substeps with an average of about 4 substeps per step and an average substep size of about 3.7 base pairs. An interesting finding pertains to the stepping velocity. Our analysis indicates that stepping velocity may be of two kinds- a low and a high velocity
Eisenstein series for infinite-dimensional U-duality groups
We consider Eisenstein series appearing as coefficients of curvature
corrections in the low-energy expansion of type II string theory four-graviton
scattering amplitudes. We define these Eisenstein series over all groups in the
E_n series of string duality groups, and in particular for the
infinite-dimensional Kac-Moody groups E9, E10 and E11. We show that,
remarkably, the so-called constant term of Kac-Moody-Eisenstein series contains
only a finite number of terms for particular choices of a parameter appearing
in the definition of the series. This resonates with the idea that the constant
term of the Eisenstein series encodes perturbative string corrections in
BPS-protected sectors allowing only a finite number of corrections. We underpin
our findings with an extensive discussion of physical degeneration limits in
D<3 space-time dimensions.Comment: 69 pages. v2: Added references and small additions, to be published
in JHE
Pattern Comparator Trigger (PACT) for the muon system of the CMS experiment
The general scheme for the fast, pipelined first level trigger on high pt muons in the CMS detector at LHC is presented. The prototype PACT system was tested in the high momentum muon beams in the RD5 experiment during 1993/94 runs. The obtained efficiency curves are shown
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