Batch Blast Extractor: an automated blastx parser application

MotivationBLAST programs are very efficient in finding similarities for sequences. However for large datasets such as ESTs, manual extraction of the information from the batch BLAST output is needed. This can be time consuming, insufficient, and inaccurate. Therefore implementation of a parser application would be extremely useful in extracting information from BLAST outputs. ResultsWe have developed a java application, Batch Blast Extractor, with a user friendly graphical interface to extract information from BLAST output. The application generates a tab delimited text file that can be easily imported into any statistical package such as Excel or SPSS for further analysis. For each BLAST hit, the program obtains and saves the essential features from the BLAST output file that would allow further analysis. The program was written in Java and therefore is OS independent. It works on both Windows and Linux OS with java 1.4 and higher. It is freely available from: http://mcbc.usm.edu/BatchBlastExtractor

Density-density propagator for one-dimensional interacting spinless fermions with non-linear dispersion and calculation of the Coulomb drag resistivity

Using bosonization-fermionization transformation we map the Tomonaga-Luttinger model of spinless fermions with non-linear dispersion on the model of fermionic quasiparticles whose interaction is irrelevant in the renormalization group sense. Such mapping allows us to set up an expansion for the density-density propagator of the original Tomonaga-Luttinger Hamiltonian in orders of the (irrelevant) quasiparticle interaction. The lowest order term in such an expansion is proportional to the propagator for free fermions. The next term is also evaluated. The propagator found is used for calculation of the Coulomb drug resistivity $r$ in a system of two capacitively coupled one-dimensional conductors. It is shown that $r$ is proportional to $T^2$ for both free and interacting fermions. The marginal repulsive in-chain interaction acts to reduce $r$ as compared to the non-interacting result. The correction to $r$ due to the quasiparticle interaction is found as well. It scales as $T^4$ at low temperature.Comment: 5 pages, 1 eps figure; the new version of the e-print corrects an error, which exists in the original submission; fortunately, all important conclusions of the study remain vali

RiboaptDB: A Comprehensive Database of Ribozymes and Aptamers

BACKGROUND: Catalytic RNA molecules are called ribozymes. The aptamers are DNA or RNA molecules that have been selected from vast populations of random sequences, through a combinatorial approach known as SELEX. The selected oligo-nucleotide sequences (~200 bp in length) have the ability to recognize a broad range of specific ligands by forming binding pockets. These novel aptamer sequences can bind to nucleic acids, proteins or small organic and inorganic chemical compounds and have many potential uses in medicine and technology. RESULTS: The comprehensive sequence information on aptamers and ribozymes that have been generated by in vitro selection methods are included in this RiboaptDB database. Such types of unnatural data generated by in vitro methods are not available in the public 'natural' sequence databases such as GenBank and EMBL. The amount of sequence data generated by in vitro selection experiments has been accumulating exponentially. There are 370 artificial ribozyme sequences and 3842 aptamer sequences in the total 4212 sequences from 423 citations in this RiboaptDB. We included general search feature, and individual feature wise search, user submission form for new data through online and also local BLAST search. CONCLUSION: This database, besides serving as a storehouse of sequences that may have diagnostic or therapeutic utility in medicine, provides valuable information for computational and theoretical biologists. The RiboaptDB is extremely useful for garnering information about in vitro selection experiments as a whole and for better understanding the distribution of functional nucleic acids in sequence space. The database is updated regularly and is publicly available at

The Origins of Ashkenaz, Ashkenazic Jews, and Yiddish

Recently, the geographical origins of Ashkenazic Jews (AJs) and their native language Yiddish were investigated by applying the Geographic Population Structure (GPS) to a cohort of exclusively Yiddish-speaking and multilingual AJs. GPS localized most AJs along major ancient trade routes in northeastern Turkey adjacent to primeval villages with names that resemble the word "Ashkenaz." These findings were compatible with the hypothesis of an Irano-Turko-Slavic origin for AJs and a Slavic origin for Yiddish and at odds with the Rhineland hypothesis advocating a Levantine origin for AJs and German origins for Yiddish. We discuss how these findings advance three ongoing debates concerning (1) the historical meaning of the term "Ashkenaz;" (2) the genetic structure of AJs and their geographical origins as inferred from multiple studies employing both modern and ancient DNA and original ancient DNA analyses; and (3) the development of Yiddish. We provide additional validation to the non-Levantine origin of AJs using ancient DNA from the Near East and the Levant. Due to the rising popularity of geo-localization tools to address questions of origin, we briefly discuss the advantages and limitations of popular tools with focus on the GPS approach. Our results reinforce the non-Levantine origins of AJs

Damping of zero sound in Luttinger liquids

We calculate the damping gamma_q of collective density oscillations (zero sound) in a one-dimensional Fermi gas with dimensionless forward scattering interaction F and quadratic energy dispersion k^2 / 2 m at zero temperature. For wave-vectors | q| /k_F small compared with F we find to leading order gamma_q = v_F^{-1} m^{-2} Y (F) | q |^3, where v_F is the Fermi velocity, k_F is the Fermi wave-vector, and Y (F) is proportional to F^3 for small F. We also show that zero-sound damping leads to a finite maximum proportional to |k - k_F |^{-2 + 2 eta} of the charge peak in the single-particle spectral function, where eta is the anomalous dimension. Our prediction agrees with photoemission data for the blue bronze K_{0.3}MoO_3.Comment: final version as published; with more technical details; we have added a discussion of recent work which appeared after our initial cond-mat posting; 13 pages, 5 figure

Microarray Analysis Uncovers a Role for Tip60 in Nervous System Function and General Metabolism

Background: Tip60 is a key histone acetyltransferase (HAT) enzyme that plays a central role in diverse biological processes critical for general cell function; however, the chromatin-mediated cell-type specific developmental pathways that are dependent exclusively upon the HAT activity of Tip60 remain to be explored. Methods and Findings: Here, we investigate the role of Tip60 HAT activity in transcriptional control during multicellular development in vivo by examining genome-wide changes in gene expression in a Drosophila model system specifically depleted for endogenous dTip60 HAT function. Conclusions: We show that amino acid residue E431 in the catalytic HAT domain of dTip60 is critical for the acetylation of endogenous histone H4 in our fly model in vivo, and demonstrate that dTip60 HAT activity is essential for multicellular development. Moreover, our results uncover a novel role for Tip60 HAT activity in controlling neuronal specific gene expression profiles essential for nervous system function as well as a central regulatory role for Tip60 HAT function in general metabolism

Transcriptomic analysis of RDX and TNT interactive sublethal effects in the earthworm Eisenia fetida

<p>Abstract</p> <p>Background</p> <p>Explosive compounds such as TNT and RDX are recalcitrant contaminants often found co-existing in the environment. In order to understand the joint effects of TNT and RDX on earthworms, an important ecological and bioindicator species at the molecular level, we sampled worms (<it>Eisenia fetida</it>) exposed singly or jointly to TNT (50 mg/kg soil) and RDX (30 mg/kg soil) for 28 days and profiled gene expression in an interwoven loop designed microarray experiment using a 4k-cDNA array. Lethality, growth and reproductive endpoints were measured.</p> <p>Results</p> <p>Sublethal doses of TNT and RDX had no significant effects on the survival and growth of earthworms, but significantly reduced cocoon and juvenile counts. The mixture exhibited more pronounced reproductive toxicity than each single compound, suggesting an additive interaction between the two compounds. In comparison with the controls, we identified 321 differentially expressed transcripts in TNT treated worms, 32 in RDX treated worms, and only 6 in mixture treated worms. Of the 329 unique differentially expressed transcripts, 294 were affected only by TNT, 24 were common to both TNT and RDX treatments, and 3 were common to all treatments. The reduced effects on gene expression in the mixture exposure suggest that RDX might interact in an antagonistic manner with TNT at the gene expression level. The disagreement between gene expression and reproduction results may be attributed to sampling time, absence of known reproduction-related genes, and lack of functional information for many differentially expressed transcripts. A gene potentially related to reproduction (echinonectin) was significantly depressed in TNT or RDX exposed worms and may be linked to reduced fecundity.</p> <p>Conclusions</p> <p>Sublethal doses of TNT and RDX affected many biological pathways from innate immune response to oogenesis, leading to reduced reproduction without affecting survival and growth. A complex interaction between mixtures of RDX and TNT was observed at the gene expression level that requires further study of the dynamics of gene expression and reproductive activities in <it>E. fetida</it>. These efforts will be essential to gain an understanding of the additive reproductive toxicity between RDX and TNT.</p

Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida

<p>Abstract</p> <p>Background</p> <p><it>Eisenia fetida</it>, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test organism in terrestrial ecotoxicology. In order to understand its gene expression response to environmental contaminants, we cloned 4032 cDNAs or expressed sequence tags (ESTs) from two <it>E. fetida </it>libraries enriched with genes responsive to ten ordnance related compounds using suppressive subtractive hybridization-PCR.</p> <p>Results</p> <p>A total of 3144 good quality ESTs (GenBank dbEST accession number <ext-link ext-link-type="gen" ext-link-id="EH669363">EH669363</ext-link>–<ext-link ext-link-type="gen" ext-link-id="EH672369">EH672369</ext-link> and <ext-link ext-link-type="gen" ext-link-id="EL515444">EL515444</ext-link>–<ext-link ext-link-type="gen" ext-link-id="EL515580">EL515580</ext-link>) were obtained from the raw clone sequences after cleaning. Clustering analysis yielded 2231 unique sequences including 448 contigs (from 1361 ESTs) and 1783 singletons. Comparative genomic analysis showed that 743 or 33% of the unique sequences shared high similarity with existing genes in the GenBank nr database. Provisional function annotation assigned 830 Gene Ontology terms to 517 unique sequences based on their homology with the annotated genomes of four model organisms <it>Drosophila melanogaster</it>, <it>Mus musculus</it>, <it>Saccharomyces cerevisiae</it>, and <it>Caenorhabditis elegans</it>. Seven percent of the unique sequences were further mapped to 99 Kyoto Encyclopedia of Genes and Genomes pathways based on their matching Enzyme Commission numbers. All the information is stored and retrievable at a highly performed, web-based and user-friendly relational database called EST model database or ESTMD version 2.</p> <p>Conclusion</p> <p>The ESTMD containing the sequence and annotation information of 4032 <it>E. fetida </it>ESTs is publicly accessible at <url>http://mcbc.usm.edu/estmd/</url>.</p