GRASP: Guided Reference-based Assembly of Short Peptides

Protein sequences predicted from metagenomic datasets are annotated by identifying their homologs via sequence comparisons with reference or curated proteins. However, a majority of metagenomic protein sequences are partial-length, arising as a result of identifying genes on sequencing reads or on assembled nucleotide contigs, which themselves are often very fragmented. The fragmented nature of metagenomic protein predictions adversely impacts homology detection and, therefore, the quality of the overall annotation of the dataset. Here we present a novel algorithm called GRASP that accurately identifies the homologs of a given reference protein sequence from a database consisting of partial-length metagenomic proteins. Our homology detection strategy is guided by the reference sequence, and involves the simultaneous search and assembly of overlapping database sequences. GRASP was compared to three commonly used protein sequence search programs (BLASTP, PSI-BLAST and FASTM). Our evaluations using several simulated and real datasets show that GRASP has a significantly higher sensitivity than these programs while maintaining a very high specificity. GRASP can be a very useful program for detecting and quantifying taxonomic and protein family abundances in metagenomic datasets. GRASP is implemented in GNU C++, and is freely available at http://sourceforge.net/projects/grasp-release.     

Modeling nonlinear errors in surface electromyography due to baseline noise: A new methodology

The surface electromyographic (EMG) signal is often contaminated by some degree of baseline noise. It is customary for scientists to subtract baseline noise from the measured EMG signal prior to further analyses based on the assumption that baseline noise adds linearly to the observed EMG signal. The stochastic nature of both the baseline and EMG signal, however, may invalidate this assumption. Alternately, “true” EMG signals may be either minimally or nonlinearly affected by baseline noise. This information is particularly relevant at low contraction intensities when signal-to-noise ratios (SNR) may be lowest. Thus, the purpose of this simulation study was to investigate the influence of varying levels of baseline noise (approximately 2–40% maximum EMG amplitude) on mean EMG burst amplitude and to assess the best means to account for signal noise. The simulations indicated baseline noise had minimal effects on mean EMG activity for maximum contractions, but increased nonlinearly with increasing noise levels and decreasing signal amplitudes. Thus, the simple baseline noise subtraction resulted in substantial error when estimating mean activity during low intensity EMG bursts. Conversely, correcting EMG signal as a nonlinear function of both baseline and measured signal amplitude provided highly accurate estimates of EMG amplitude. This novel nonlinear error modeling approach has potential implications for EMG signal processing, particularly when assessing co-activation of antagonist muscles or small amplitude contractions where the SNR can be low.     

Microtubule assembly dynamics: an attractive target for anticancer drugs

Microtubules, composed of alphabeta tubulin dimers, are dynamic polymers of eukaryotic cells. They play important roles in various cellular functions including mitosis. Microtubules exhibit differential dynamic behaviors during different phases of the cell cycle. Inhibition of the microtubule assembly dynamics causes cell cycle arrest leading to apoptosis; thus, qualifying them as important drug targets for treating several diseases including cancer, neuronal, fungal, and parasitic diseases. Although several microtubule-targeted drugs are successfully being used in cancer chemotherapy, the development of resistance against these drugs and their inherent toxicities warrant the development of new agents with improved efficacy. Several antimicrotubule agents are currently being evaluated for their possible uses in cancer chemotherapy. Benomyl, griseofulvin, and sulfonamides have been used as antifungal and antibacterial drugs. Recent reports have shown that these drugs have potent antitumor potential. These agents are shown to inhibit proliferation of different types of tumor cells and induce apoptosis by targeting microtubule assembly dynamics. However, unlike vincas and taxanes, which inhibit cancer cell proliferation in nanomolar concentration range, these agents act in micromolar range and are considered to have limited toxicities. Here, we suggest that these drugs may have a significant use in cancer chemotherapy when used in combination with other anticancer drugs.     

Antiapoptotic activity of 30 kDa lipoproteins family from fat body tissue of silkworm,Bombyx mori

The family of 30 kDa lipoproteins (LP1–5) is abundant in silkworm pupa fat body (FB) and hemolymph. One of its members, the 29 kDa protein decreased in concentration from peripheral (PP) FB tissue but was sustained in perivisceral (PV) FB tissue at the time of apoptosis. This study investigated the correlation of the 30 kDa proteins with FB apoptosis. Two protein fractions were purified, a 29 and a 30/31 kDa protein fraction, and they were used to test for activity against actinomycin D‐induced apoptosis in the FB tissues. Concentrations as little as 50 μg/mL of the 29 kDa protein fraction efficiently inhibited apoptosis. Less antiapoptotic activity was detected for the higher MW fraction; DNA fragmentation was observed in FB tissue treated with 50 μg/mL of the 30/31 kDa fraction. The viability of the cells in the 29 kDa protein‐supplemented culture was 40% higher than in the 31 kDa protein‐supplemented culture. However, the 30 kDa lipoproteins were not able to prevent scheduled FB degeneration during silkworm metamorphosis. Thus, it is hypothesized that the antiapoptotic 29 kDa protein needs to be proteolytically degraded by a regulatory mechanism to allow programmed cell death of FB tissue.     

Phyto-synthesis of silver nanoparticles using <Emphasis Type="Italic">Alternanthera tenella</Emphasis> leaf extract: an effective inhibitor for the migration of human breast adenocarcinoma (MCF-7) cells

In this study, phyto-synthesis of silver nanoparticles (AgNPs) was achieved using an aqueous leaf extract of Alternanthera tenella. The phytochemical screening results revealed that flavonoids are responsible for the AgNPs formation. The AgNPs were characterised using UV–visible spectrophotometer, field emission scanning microscopy/energy dispersive X-ray, transmission electron microscopy, fourier transform infrared spectroscopy (FT-IR), and X-ray diffraction. The average size of the nanoparticles was found to be ≈48 nm. The EDX results show that strong signals were observed for the silver atoms. The strong band appearing at 1601–1595 cm^?1 correspond to C–C stretching vibration from dienes in FT-IR spectrum indicating the formation of AgNPs. Human breast adenocarcinoma (MCF-7) cells treated with various concentrations of AgNPs showed a dose-dependent increase in cell inhibition. The IC₅₀ value of the AgNPs was calculated to be 42.5 μg mL^?1. The AgNPs showed a significant reduction in the migration of MCF-7 cells.     

Phosphorylation of pyrimidine L-deoxynucleoside analog diphosphates. Kinetics of phosphorylation and dephosphorylation of nucleoside analog diphosphates and triphosphates by 3-phosphoglycerate kinase

Anticancer and antiviral D- and L-nucleoside analogs are phosphorylated stepwise in the cells to the pharmacologically active triphosphate metabolites. We recently reported that in the last step, L-deoxynucleoside analog diphosphates are phosphorylated by 3-phosphoglycerate kinase (PGK). To explain the preference of PGK for L- over D-deoxynucleoside analog diphosphates, the kinetics of their phosphorylation were compared with the dephosphorylation of the respective triphosphates using recombinant human PGK. The results attributed favorable phosphorylation of L-deoxynucleoside analog diphosphates by PGK to differences in k(cat), which were consequences of varied orientations of the sugar and diphosphates in the catalytic site of PGK. The amino acids involved in the catalytic reaction of PGK (including Glu(344), Lys(220), and Asn(337)) were therefore mutated. The impact of mutations on the phosphorylation of L- and D-deoxynucleoside analog diphosphates was different from those on dephosphorylation of the respective triphosphates. This suggested that the interactions of the nucleoside analogs with amino acids during the transition state are different in the phosphorylation and dephosphorylation reactions. Thus, reversible action of the enzyme may not involve the same configuration of the active site. Furthermore, the amino acid determinants of the action of PGK for L-deoxynucleotides were not the same as for the D-deoxynucleotides. This study also suggests the potential impact of nucleoside analog diphosphates and triphosphates on the multiple cellular functions of PGK, which may contribute to the action of the analogs.     

Kinetics of maize leaf elongation IV. Effects of (+)- and (-)-abscisic acid

Abscisic acid (ABA) is involved in many of the responses of plants to environmental stress. This study focuses on the inhibitory effect of ABA on leaf expansion. In addition, the effects of (+)-ABA, the natural form of ABA, were compared to the effects of (-)-ABA. Leaf elongation rates (LER) were measured for the 3rd leaf of maize plants. ABA concentrations were measured by RIA for total ABA and an ELISA specific for (+)-ABA. ABA was added to the hydroponic solution and changes in the LER were measured over time. ABA could inhibit LER within 30 min ad reached steady-state LER within 4 h. Internal ABA concentrations in the growing zone of the leaf also reached steady-state concentrations after 4 h. This effect of ABA was reversible, because LER was fully restored upon removal of externally applied ABA, and internal concentrations of ABA in the growing zone returned to normal levels, whereas ABA concentrations remained elevated in mature tissue. Thus, steady-state LER was highly correlated with the steady-state internal ABA concentration of the growing zone. ABA inhibited leaf expansion by increasing the apparent cell wall yield threshold; no other growth parameters were affected. The (-)-enantiomer of ABA had much less effect on LER than (+)-ABA when compared upon an external concentration basis. Internal ABA concentrations rationalized the response, showing that (-)-ABA accumulation was very low, most likely due to low uptake rates. From this analysis, it was determined that LER was equally sensitive to internal concentrations of (+)- or (-)-ABA.