Target prediction and a statistical sampling algorithm for RNA-RNA interaction

It has been proven that the accessibility of the target sites has a critical influence for miRNA and siRNA. In this paper, we present a program, rip2.0, not only the energetically most favorable targets site based on the hybrid-probability, but also a statistical sampling structure to illustrate the statistical characterization and representation of the Boltzmann ensemble of RNA-RNA interaction structures. The outputs are retrieved via backtracing an improved dynamic programming solution for the partition function based on the approach of Huang et al. (Bioinformatics). The $O(N^6)$ time and $O(N^4)$ space algorithm is implemented in C (available from \url{http://www.combinatorics.cn/cbpc/rip2.html})Comment: 7 pages, 10 figure

A Genetically Encoded AND Gate for Cell-Targeted Metabolic Labeling of Proteins

We describe a genetic AND gate for cell-targeted metabolic labeling and proteomic analysis in complex cellular systems. The centerpiece of the AND gate is a bisected methionyl-tRNA synthetase (MetRS) that charges the Met surrogate azidonorleucine (Anl) to tRNAMet. Cellular protein labeling occurs only upon activation of two different promoters that drive expression of the N- and C-terminal fragments of the bisected MetRS. Anl-labeled proteins can be tagged with fluorescent dyes or affinity reagents via either copper-catalyzed or strain-promoted azide–alkyne cycloaddition. Protein labeling is apparent within 5 min after addition of Anl to bacterial cells in which the AND gate has been activated. This method allows spatial and temporal control of proteomic labeling and identification of proteins made in specific cellular subpopulations. The approach is demonstrated by selective labeling of proteins in bacterial cells immobilized in the center of a laminar-flow microfluidic channel, where they are exposed to overlapping, opposed gradients of inducers of the N- and C-terminal MetRS fragments. The observed labeling profile is predicted accurately from the strengths of the individual input signals

CDD: a Conserved Domain Database for the functional annotation of proteins

NCBI’s Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships. Manually curated models are organized hierarchically if they describe domain families that are clearly related by common descent. As CDD also imports domain family models from a variety of external sources, it is a partially redundant collection. To simplify protein annotation, redundant models and models describing homologous families are clustered into superfamilies. By default, domain footprints are annotated with the corresponding superfamily designation, on top of which specific annotation may indicate high-confidence assignment of family membership. Pre-computed domain annotation is available for proteins in the Entrez/Protein dataset, and a novel interface, Batch CD-Search, allows the computation and download of annotation for large sets of protein queries. CDD can be accessed via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

CDD: specific functional annotation with the Conserved Domain Database

NCBI's Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. The collection can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml, and is also part of NCBI's Entrez query and retrieval system, cross-linked to numerous other resources. CDD provides annotation of domain footprints and conserved functional sites on protein sequences. Precalculated domain annotation can be retrieved for protein sequences tracked in NCBI's Entrez system, and CDD's collection of models can be queried with novel protein sequences via the CD-Search service at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. Starting with the latest version of CDD, v2.14, information from redundant and homologous domain models is summarized at a superfamily level, and domain annotation on proteins is flagged as either ‘specific’ (identifying molecular function with high confidence) or as ‘non-specific’ (identifying superfamily membership only)

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another

Blood Culture Contamination in Children’s Medical Center of Tehran from April to July 2004

Background: Blood culture is the criterion standard for identifying children with bacteremia. However, elevated false-positive rates are common and are associated with substantial health care costs. The aims of this prospective study were to: 1) determine the rate of blood culture contamination 2) determine variety and frequency of contaminant bacteria 3) compare the duration of hospital stay and antibiotic administration in patients with true bacteremia vs those have false positive blood culture. Materials and Methods: Cross-sectional study conducted April through July 2004 among patients aged 14 years or younger who were admitted at Doctor Garib Children Medical Center of Tehran and had a blood culture obtained as part of their care. Bacterial isolates were identified to species level and medical records were reviewed in all cases with a positive blood culture. A number of clinical and laboratory criteria were used to deciding whether a blood isolate is a pathogen or a contaminant. These include the identify of the micro-organism itself, clinical features such as fever and leukocytosis; the proportion of blood culture sets positive as a function of the number of sets obtained and to have an indwelling vascular catheter or prosthetic device. Results: During the study period, 2877 sets of blood culture were evaluated and the rates of positive blood cultures associated with significant bacteremia and contamination were 1.04% and 5.4% respectively. Among the positive blood cultures, over the 84% of isolates were due to contamination and only 15.95% of isolated strains associated with true infection. The frequency of isolated bacteria with respect to true infection and contamination are as following: S. Aureus (infect: 9.0%, contam: 0.0%), S. Epidemidis (infec: 0.0%, contam: 13.3%), Micrococcus sp. (infec: 0.0%, contam: 4.3%), pseudomonas and related species other than P. aeruginosa (infec: 2.1%, contam: 60.6%), viridans group of streptococci (infec: 1.1%, contam: 2.1%), E.coli (infec: 1.06%, contam: 0.0%), Klebsiella pneumoniae (infec: 0.53%, contam: 0.0%), Enterobacter cloacae (infec: 0.53%, contam: 0.0%), and Acinetobacter baumannii (infec: 0.25%, contam: 0.53%). The mean of hospital stay for patients with true bacteremia, 14.83 days, was not significantly higher than that for patients with false-positive blood cultures (10.08 days). 43 patients had administrated one to three antibiotics after false-positive blood cultures. Conclusion: The findings indicate that blood culture contamination rate in studied hospital is higher than standard levels, and very high rate of contamination with environmental pseudomonas species shows an unusuall epidemic condition. The findings also suggests high resource utilization and prolong patients stay due to pseudobacteremia