485 research outputs found
RepSeq-A database of amino acid repeats present in lower eukaryotic pathogens
BACKGROUND Amino acid repeat-containing proteins have a broad range of functions and their identification is of relevance to many experimental biologists. In human-infective protozoan parasites (such as the Kinetoplastid and Plasmodium species), they are implicated in immune evasion and have been shown to influence virulence and pathogenicity. RepSeq http://repseq.gugbe.com is a new database of amino acid repeat-containing proteins found in lower eukaryotic pathogens. The RepSeq database is accessed via a web-based application which also provides links to related online tools and databases for further analyses. RESULTS The RepSeq algorithm typically identifies more than 98% of repeat-containing proteins and is capable of identifying both perfect and mismatch repeats. The proportion of proteins that contain repeat elements varies greatly between different families and even species (3 - 35% of the total protein content). The most common motif type is the Sequence Repeat Region (SRR) - a repeated motif containing multiple different amino acid types. Proteins containing Single Amino Acid Repeats (SAARs) and Di-Peptide Repeats (DPRs) typically account for 0.5 - 1.0% of the total protein number. Notable exceptions are P. falciparum and D. discoideum, in which 33.67% and 34.28% respectively of the predicted proteomes consist of repeat-containing proteins. These numbers are due to large insertions of low complexity single and multi-codon repeat regions. CONCLUSION The RepSeq database provides a repository for repeat-containing proteins found in parasitic protozoa. The database allows for both individual and cross-species proteome analyses and also allows users to upload sequences of interest for analysis by the RepSeq algorithm. Identification of repeat-containing proteins provides researchers with a defined subset of proteins which can be analysed by expression profiling and functional characterisation, thereby facilitating study of pathogenicity and virulence factors in the parasitic protozoa. While primarily designed for kinetoplastid work, the RepSeq algorithm and database retain full functionality when used to analyse other species
Multi-user video streaming using unequal error protection network coding in wireless networks
In this paper, we investigate a multi-user video streaming system applying unequal error protection (UEP) network coding (NC) for simultaneous real-time exchange of scalable video streams among multiple users. We focus on a simple wireless scenario where users exchange encoded data packets over a common central network node (e.g., a base station or an access point) that aims to capture the fundamental system behaviour. Our goal is to present analytical tools that provide both the decoding probability analysis and the expected delay guarantees for different importance layers of scalable video streams. Using the proposed tools, we offer a simple framework for design and analysis of UEP NC based multi-user video streaming systems and provide examples of system design for video conferencing scenario in broadband wireless cellular networks
Fluctuations and Instabilities of Ferromagnetic Domain Wall pairs in an External Magnetic Field
Soliton excitations and their stability in anisotropic quasi-1D ferromagnets
are analyzed analytically. In the presence of an external magnetic field, the
lowest lying topological excitations are shown to be either soliton-soliton or
soliton-antisoliton pairs. In ferromagnetic samples of macro- or mesoscopic
size, these configurations correspond to twisted or untwisted pairs of Bloch
walls. It is shown that the fluctuations around these configurations are
governed by the same set of operators. The soliton-antisoliton pair has exactly
one unstable mode and thus represents a critical nucleus for thermally
activated magnetization reversal in effectively one-dimensional systems. The
soliton-soliton pair is stable for small external fields but becomes unstable
for large magnetic fields. From the detailed expression of this instability
threshold and an analysis of nonlocal demagnetizing effects it is shown that
the relative chirality of domain walls can be detected experimentally in thin
ferromagnetic films. The static properties of the present model are equivalent
to those of a nonlinear sigma-model with anisotropies. In the limit of large
hard-axis anisotropy the model reduces to a double sine-Gordon model.Comment: 15 pages RevTex 3.0 (twocolumn), 9 figures available on request, to
appear in Phys Rev B, Dec (1994
UHMWPE/SBA-15 nanocomposites synthesized by in situ polymerization
Different nanocomposites have been attained by in situ polymerization based on ultra-high molecular
weight polyethylene (UHMWPE) and mesoporous SBA-15, this silica being used for immobilization of the
FI catalyst bis [N-(3-tert-butylsalicylidene)-2,3,4,5,6-pentafluoroanilinato] titanium (IV) dichloride and as
filler as well. Two distinct approaches have been selected for supporting the FI catalyst on the SBA-15
prior polymerization. A study on polymerization activity of this catalyst has been performed under
homogenous conditions and upon heterogenization. A study of the effect of presence of mesoporous
particles and of the immobilization method is also carried out. Moreover, the thermal characterization,
phase transitions and mechanical response of some pristine UHMWPEs and UHMWPE/SBA-15 materials
have been carried out. Relationships with variations on molar mass, impregnation method of catalyst and
final SBA-15 content have been established
A Simple & Convenient Solid Phase Synthesis of Bacterial Origin Octapeptide Sequence, Glu-Asp-Gly-Asn-Lys-Pro-Gly-Lys-OH
The repeating octapeptide sequence, Glu-Asp-Gly-Asn-Lys-Pro-Gly-Lys-OH derived from the glycoprotein found in Staphylococcus aureus cell wall is assembled by simple solid phase peptide synthesis methodology using a base labile linker
Opportunistic routing in wireless mesh networks
Opportunistic Routing (OR) has been proposed as a way to increase the performance of wireless networks by exploiting its broadcast nature. In OR, instead of pre-selecting a single specific node to be the next-hop as a forwarder for a packet, multiple nodes can potentially be selected as the next-hop forwarder. Thus the source can use multiple potential paths to deliver the packets to the destination. More specially, when the current node transmits a packet, all the candidates that receive the packet successfully will coordinate with each other to determine which one would actually forward the packet according to some criteria, while the other nodes will simply discard the packet. In this chapter, we survey the state of the art in OR, then focus on the candidates selection algorithms and carry out a comparative performance evaluation of the most relevant proposals appeared in the literature.Peer ReviewedPostprint (author’s final draft
DNA repair systems and the pathogenesis of Mycobacterium tuberculosis: varying activities at different stages of infection
Mycobacteria, including most of all MTB (Mycobacterium tuberculosis), cause pathogenic infections in humans and, during the infectious process, are exposed to a range of environmental insults, including the host's immune response. From the moment MTB is exhaled by infected individuals, through an active and latent phase in the body of the new host, until the time they reach the reactivation stage, MTB is exposed to many types of DNA-damaging agents. Like all cellular organisms, MTB has efficient DNA repair systems, and these are believed to play essential roles in mycobacterial pathogenesis. As different stages of infection have great variation in the conditions in which mycobacteria reside, it is possible that different repair systems are essential for progression to specific phases of infection. MTB possesses homologues of DNA repair systems that are found widely in other species of bacteria, such as nucleotide excision repair, base excision repair and repair by homologous recombination. MTB also possesses a system for non-homologous end-joining of DNA breaks, which appears to be widespread in prokaryotes, although its presence is sporadic within different species within a genus. However, MTB does not possess homologues of the typical mismatch repair system that is found in most bacteria. Recent studies have demonstrated that DNA repair genes are expressed differentially at each stage of infection. In the present review, we focus on different DNA repair systems from mycobacteria and identify questions that remain in our understanding of how these systems have an impact upon the infection processes of these important pathogens
Formation of regulatory modules by local sequence duplication
Turnover of regulatory sequence and function is an important part of
molecular evolution. But what are the modes of sequence evolution leading to
rapid formation and loss of regulatory sites? Here, we show that a large
fraction of neighboring transcription factor binding sites in the fly genome
have formed from a common sequence origin by local duplications. This mode of
evolution is found to produce regulatory information: duplications can seed new
sites in the neighborhood of existing sites. Duplicate seeds evolve
subsequently by point mutations, often towards binding a different factor than
their ancestral neighbor sites. These results are based on a statistical
analysis of 346 cis-regulatory modules in the Drosophila melanogaster genome,
and a comparison set of intergenic regulatory sequence in Saccharomyces
cerevisiae. In fly regulatory modules, pairs of binding sites show
significantly enhanced sequence similarity up to distances of about 50 bp. We
analyze these data in terms of an evolutionary model with two distinct modes of
site formation: (i) evolution from independent sequence origin and (ii)
divergent evolution following duplication of a common ancestor sequence. Our
results suggest that pervasive formation of binding sites by local sequence
duplications distinguishes the complex regulatory architecture of higher
eukaryotes from the simpler architecture of unicellular organisms
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