Taking U out, with two nucleases?

BACKGROUND: REX1 and REX2 are protein components of the RNA editing complex (the editosome) and function as exouridylylases. The exact roles of REX1 and REX2 in the editosome are unclear and the consequences of the presence of two related proteins are not fully understood. Here, a variety of computational studies were performed to enhance understanding of the structure and function of REX proteins in Trypanosoma and Leishmania species. RESULTS: Sequence analysis and homology modeling of the Endonuclease/Exonuclease/Phosphatase (EEP) domain at the C-terminus of REX1 and REX2 highlights a common active site shared by all EEP domains. Phylogenetic analysis indicates that REX proteins contain a distinct subfamily of EEP domains. Inspection of three-dimensional models of the EEP domain in Trypanosoma brucei REX1 and REX2, and Leishmania major REX1 suggests variations of previously characterized key residues likely to be important in catalysis and determining substrate specificity. CONCLUSION: We have identified features of the REX EEP domain that distinguish it from other family members and hence subfamily specific determinants of catalysis and substrate binding. The results provide specific guidance for experimental investigations about the role(s) of REX proteins in RNA editing

Environmental friendly method for the extraction of cellulose from Triflolium resopinatum and its characterization

The leaves of Triflolium resopinatum were collected from the mountains of Malakand division, Khyber Pukhtoonkhwa, Pakistan and was grinded into smaller particles and converted into powder. The ground biomass was treated with different solvents in the Soxhlet apparatus for the removal of soluble extractive like pectin, cutin and wax substances. For bond breaking the alkaline substance was kept in the autoclave. Ethylene diamine tetra-acetate (EDTA) and hydrogen peroxide (H2O2) were used for the removal of most polar substances like pectin, cutin, waxes and other extractives. Furthermore, raw cellulose was purified through acetic acid and nitric acid. Double distilled water was used for the neutralization of pH.The analysis of purified cellulose was carried out through different procedures such as X-ray Diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA) and scanning electron microscopy (SEM). The extracted cellulose has high degree of purity and crystallinity (72%) and thermal stability indicating that the process for the extraction of cellulose is quite adequate.               KEY WORDS: Triflolium resopinatum, Cellulose, FTIR, XRD, TGA, SEM Bull. Chem. Soc. Ethiop. 2019, 33(1), 61-68DOI: https://dx.doi.org/10.4314/bcse.v33i1.

A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data

<p>Abstract</p> <p>Background</p> <p>A genetic network can be represented as a directed graph in which a node corresponds to a gene and a directed edge specifies the direction of influence of one gene on another. The reconstruction of such networks from transcript profiling data remains an important yet challenging endeavor. A transcript profile specifies the abundances of many genes in a biological sample of interest. Prevailing strategies for learning the structure of a genetic network from high-dimensional transcript profiling data assume sparsity and linearity. Many methods consider relatively small directed graphs, inferring graphs with up to a few hundred nodes. This work examines large undirected graphs representations of genetic networks, graphs with many thousands of nodes where an undirected edge between two nodes does not indicate the direction of influence, and the problem of estimating the structure of such a sparse linear genetic network (SLGN) from transcript profiling data.</p> <p>Results</p> <p>The structure learning task is cast as a sparse linear regression problem which is then posed as a LASSO (<it>l</it>₁-constrained fitting) problem and solved finally by formulating a Linear Program (LP). A bound on the Generalization Error of this approach is given in terms of the Leave-One-Out Error. The accuracy and utility of LP-SLGNs is assessed quantitatively and qualitatively using simulated and real data. The Dialogue for Reverse Engineering Assessments and Methods (DREAM) initiative provides gold standard data sets and evaluation metrics that enable and facilitate the comparison of algorithms for deducing the structure of networks. The structures of LP-SLGNs estimated from the I<smcaps>N</smcaps>S<smcaps>ILICO</smcaps>1, I<smcaps>N</smcaps>S<smcaps>ILICO</smcaps>2 and I<smcaps>N</smcaps>S<smcaps>ILICO</smcaps>3 simulated DREAM2 data sets are comparable to those proposed by the first and/or second ranked teams in the DREAM2 competition. The structures of LP-SLGNs estimated from two published <it>Saccharomyces cerevisae </it>cell cycle transcript profiling data sets capture known regulatory associations. In each <it>S. cerevisiae </it>LP-SLGN, the number of nodes with a particular degree follows an approximate power law suggesting that its degree distributions is similar to that observed in real-world networks. Inspection of these LP-SLGNs suggests biological hypotheses amenable to experimental verification.</p> <p>Conclusion</p> <p>A statistically robust and computationally efficient LP-based method for estimating the topology of a large sparse undirected graph from high-dimensional data yields representations of genetic networks that are biologically plausible and useful abstractions of the structures of real genetic networks. Analysis of the statistical and topological properties of learned LP-SLGNs may have practical value; for example, genes with high random walk betweenness, a measure of the centrality of a node in a graph, are good candidates for intervention studies and hence integrated computational – experimental investigations designed to infer more realistic and sophisticated probabilistic directed graphical model representations of genetic networks. The LP-based solutions of the sparse linear regression problem described here may provide a method for learning the structure of transcription factor networks from transcript profiling and transcription factor binding motif data.</p

Bears in Pakistan: Distribution, Population Biology and Human Conflicts

We conducted questionnaire based interviews (n = 1873) of respondents coming from 258 localities about bear tracts in northern parts of Pakistan in 2012-2014 to study Himalyan brown (U. arctos isalbellinus) and Himalayan black (U. t. laniger) bears. Brown bears were more frequent in northern latitudes (northern Chitral, Ghizer, Gilgit and Skardu), while black bears were widely distributed in southern latitudes (Battagram). Both brown and black bears are present in central latitudes (Astor, Diamir, Kohistan and Mansehra). We identified 34 populations of brown bears; a large population in the Deosai Plateau and small to very small populations in other localities. We identified 9 isolated meta-populations sharing common gene pools; 7 (Bomborat, Gias, Chowgram, Laspur-Malkov, Koshi-Palas, Phunder-Yasin, Khunjerab) very small with serious inbreeding and threat of extinction, while Deosai and Diamir-Astor populations were large but were expected to have a high level inbreeding. Black bears were present in 45 localities; larger populations in three localities of Battagram (Nagram, Rahing and Shamli). We identified 6 meta-populations of black bears; Kohistan-Batagram-Mansehra, Diamir-Astor and south Chitral meta-populations were large; but 3 other populations (Thack, Hisper-Minipin and Chasma) were small/very small, possibly having high inbreeding. Bears raid standing maize crops (regular and severe in 2 localities and irregular and severe in 6) and fruit (apricot, grape, mulberry and walnut). Average annual bears depredation of 54 cattle, 188 goat/sheep, 4 yaks, and 9 horses/donkeys/mules were reported, inflicting an economic loss of Pak Rs. 2,840,000 (US$ 28,400) to the livestock farming community. Respondents reported 4 incidences of bear attack (1 killed, 3 injured) and 2 cases of cub poaching during 2013

Food Limitation as a Potentially Emerging Contributor to the Asian Vulture Crisis

It was believed that the reason for decline in Asian vulture population is the drug, Diclofenac sodium (DFS), used in livestock. Even after declaring the DFS use banned by the government, apparent decrease in the population of vultures was reported. Alternate hypothesis was suggested that food limitation may be a cause of Asian vulture crisis in Pakistan. Very recent shifts in livestock utilization observed in Pakistan may present a significant barrier to vulture recovery. Increased livestock utilization is translated to fewer carcasses. Since 2005, no livestock carcasses were found in 1650 km transect in the habitat of vultures. Carcasses recorded 13 in 1999 gradually declined to almost zero in 2005 and onwards, which suggests DFS may not be the only cause of Asian Vulture Crisi

On Individual, Sex and Age Differentiation of Indian House Crow (\u3cem\u3eCorvus splendens\u3c/em\u3e) Call: A Preliminary Study in Potohar, Pakistan

Considering importance of acoustics studies in population biology, 500 calls of the Indian House Crow (Corvus splendens) were recorded in morning - mid-afternoon hours (January-February, 2009) from 23 sites of urban areas of Potahar (Punjab, Pakistan). Calls were recorded using Sony CFS 1030 S sound records (sampling rate = 48 KHz) and edited using Sound Analysis Pro (Version 1.02). software using FFT method rate 50%, data window 9.27 ms, advanced window 1.36 ms. Through editing of calls, we selected 60 (37 ♂♂, 17 ♀♀, 6 Juvenile ♂♂) good quality spectrograms for detailed analysis. Spectrograms were characterized by rapid frequency modulations using 6 (call pitch, mean pitch goodness, mean frequency of the calls, frequency of modulations, mean amplitude modulation, mean wiener entropy) acoustic parameters. Significance of difference was analysed using Multivariate and Discriminate Function Analysis. Calls could be assigned to correct individual in 10.8% males, 21.0% females, and 42.9% juveniles, which was significantly higher than percentage of correct classification per chance. Calls could be attributes to correct sex in 88.5% and to correct age group in 80.6% of cases