N-gram analysis of 970 microbial organisms reveals presence of biological language models

<p>Abstract</p> <p>Background</p> <p>It has been suggested previously that genome and proteome sequences show characteristics typical of natural-language texts such as "signature-style" word usage indicative of authors or topics, and that the algorithms originally developed for natural language processing may therefore be applied to genome sequences to draw biologically relevant conclusions. Following this approach of 'biological language modeling', statistical n-gram analysis has been applied for comparative analysis of whole proteome sequences of 44 organisms. It has been shown that a few particular amino acid n-grams are found in abundance in one organism but occurring very rarely in other organisms, thereby serving as genome signatures. At that time proteomes of only 44 organisms were available, thereby limiting the generalization of this hypothesis. Today nearly 1,000 genome sequences and corresponding translated sequences are available, making it feasible to test the existence of biological language models over the evolutionary tree.</p> <p>Results</p> <p>We studied whole proteome sequences of 970 microbial organisms using n-gram frequencies and cross-perplexity employing the Biological Language Modeling Toolkit and Patternix Revelio toolkit. Genus-specific signatures were observed even in a simple unigram distribution. By taking statistical n-gram model of one organism as reference and computing cross-perplexity of all other microbial proteomes with it, cross-perplexity was found to be predictive of branch distance of the phylogenetic tree. For example, a 4-gram model from proteome of <it>Shigellae flexneri 2a</it>, which belongs to the <it>Gammaproteobacteria </it>class showed a self-perplexity of 15.34 while the cross-perplexity of other organisms was in the range of 15.59 to 29.5 and was proportional to their branching distance in the evolutionary tree from <it>S. flexneri</it>. The organisms of this genus, which happen to be pathotypes of <it>E.coli</it>, also have the closest perplexity values with <it>E. coli.</it></p> <p>Conclusion</p> <p>Whole proteome sequences of microbial organisms have been shown to contain particular n-gram sequences in abundance in one organism but occurring very rarely in other organisms, thereby serving as proteome signatures. Further it has also been shown that perplexity, a statistical measure of similarity of n-gram composition, can be used to predict evolutionary distance within a genus in the phylogenetic tree.</p

Engineered Anopheles Immunity to Plasmodium Infection

A causative agent of human malaria, Plasmodium falciparum, is transmitted by Anopheles mosquitoes. The malaria parasite is under intensive attack from the mosquito's innate immune system during its sporogonic development. We have used genetic engineering to create immune-enhanced Anopheles stephensi mosquitoes through blood meal-inducible expression of a transgene encoding the IMD pathway-controlled NF-kB Rel2 transcription factor in the midgut and fat-body tissue. Transgenic mosquitoes showed greater resistance to Plasmodium and microbial infection as a result of timely concerted tissue-specific immune attacks involving multiple effectors. The relatively weak impact of this genetic modification on mosquito fitness under laboratory conditions encourages further investigation of this approach for malaria control

Multi-wavelength characterization of the blazar S5 0716+714 during an unprecedented outburst phase

Context. The BL Lac object S5 0716+714, a highly variable blazar, underwent an impressive outburst in January 2015 (Phase A), followed by minor activity in February (Phase B). The MAGIC observations were triggered by the optical flux observed in Phase A, corresponding to the brightest ever reported state of the source in the R-band.Aims.The comprehensive dataset collected is investigated in order to shed light on the mechanism of the broadband emission.Methods. Multi-wavelength light curves have been studied together with the broadband spectral energy distributions (SEDs). The sample includes data from Effelsberg, OVRO, Metsahovi, VLBI, CARMA, IRAM, SMA, Swift-UVOT, KVA, Tuorla, Steward, RINGO3, KANATA, AZT-8+ST7, Perkins, LX-200, Swift-XRT, NuSTAR, Fermi-LAT and MAGIC.Results. The flaring state of Phase A was detected in all the energy bands, providing for the first time a multi-wavelength sample of simultaneous data from the radio band to the very-high-energy (VHE, E> 100 GeV). In the constructed SED, the Swift-XRT +NuSTAR data constrain the transition between the synchrotron and inverse Compton components very accurately, while the second peak is constrained from 0.1 GeV to 600 GeV by Fermi+MAGIC data. The broadband SED cannot be described with a one-zone synchrotron self-Compton model as it severely underestimates the optical flux in order to reproduce the X-ray to y-ray data. Instead we use a two-zone model. The electric vector position angle (EVPA) shows an unprecedented fast rotation. An estimation of the redshift of the source by combined high-energy (HE, 0.1 GeV < E < 100 GeV) and VHE data provides a value of ,z = 0.31 +/- 0.02(stats) +/- 0.05(sys), confirming the literature value.Conclusions. The data show the VHE emission originating in the entrance and exit of a superluminal knot in and out of a recollimation shock in the inner jet. A shock-shock interaction in the jet seems responsible for the observed flares and EVPA swing. This scenario is also consistent with the SED modeling

Multi-wavelength characterization of the blazar S5~0716+714 during an unprecedented outburst phase

The BL Lac object S5~0716+714, a highly variable blazar, underwent an impressive outburst in January 2015 (Phase A), followed by minor activity in February (Phase B). The MAGIC observations were triggered by the optical flux observed in Phase A, corresponding to the brightest ever reported state of the source in the R-band. The comprehensive dataset collected is investigated in order to shed light on the mechanism of the broadband emission. Multi-wavelength light curves have been studied together with the broadband Spectral Energy Distributions (SEDs). The data set collected spans from radio, optical photometry and polarimetry, X-ray, high-energy (HE, 0.1 GeV 100 GeV) with MAGIC. The flaring state of Phase A was detected in all the energy bands, providing for the first time a multi-wavelength sample of simultaneous data from the radio band to the VHE. In the constructed SED the \textit{Swift}-XRT+\textit{NuSTAR} data constrain the transition between the synchrotron and inverse Compton components very accurately, while the second peak is constrained from 0.1~GeV to 600~GeV by \textit{Fermi}+MAGIC data. The broadband SED cannot be described with a one-zone synchrotron self-Compton model as it severely underestimates the optical flux in order to reproduce the X-ray to $\gamma$-ray data. Instead we use a two-zone model. The EVPA shows an unprecedented fast rotation. An estimation of the redshift of the source by combined HE and VHE data provides a value of $z = 0.31 \pm 0.02_{stats} \pm 0.05_{sys}$, confirming the literature value. The data show the VHE emission originating in the entrance and exit of a superluminal knot in and out a recollimation shock in the inner jet. A shock-shock interaction in the jet seems responsible for the observed flares and EVPA swing. This scenario is also consistent with the SED modelling

Influence of N-Acetyl cysteine on selected extrapyramidal movement disorders and oxidative stress induced by haloperidol in rats

Haloperidol (HAL) is a widely used neuroleptic drug for the treatment of acute and chronic psychosis. Its use is limited by its tendency to produce a range of extrapyramidal movement disorders such as, tardive dyskinesia (TD), akathisia, dystonia and parkinsonism. Increased levels of thiobarbituric-acid reactive products have been found inthe cerebrospinal fluid and plasma of patients treated with neuroleptics, especially those with movement disorders. HAL, is metabolized by an oxidase, generates large quantities of oxyradicals and a potent toxic pyridinium-like metabolite and induces oxidative stress. It is proposed to study the effect of n-acetyl cysteine (NAC) on selected  extrapyramidal movement disorders (tardive dykinesia and catalepsy), total antioxidant status and lipid peroxidation induced by HAL. HAL (1 mg/kg/i.p) was injected for 21 days in rats, and NAC at doses of 30, 100 and 300 mg/kg dissolved in normal saline was administered,intra-peritoneally once (30 minutes prior to haloperidol) on the last day of HAL treatment. NAC supplementation significantly decreased haloperidol induced TD and catalepsy dose dependently. However, further work is required to investigate the effect of chronicadministration of NAC in the improvement of TD so as to confirm the usefulness of NAC assupplements for improved control of TD

Thermodynamic insights into the role of aromatic residues in chitooligosaccharide binding to the transglycosylating chitinase-D from Serratia proteamaculans

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High-density lipoproteins: a novel therapeutic target for cardiovascular disease

TS Mohamed Saleem1, PV Sandhya Rani1, K Gauthaman21Department of Pharmacology, Annamacharya College of Pharmacy, New Boyanapalli, Andhrapradesh, India; 2Department of Drug Technology, Faculty of Medical Technology, Derna, LibyaAbstract: Cardiovascular disease has a high rate of mortality in both Western and developing countries. Atherosclerosis and generation of reactive oxygen species through oxidative stress is the major risk factor for cardiovascular disease. Atherothrombosis with low levels of high-density lipoprotein (HDL) and high levels of low-density lipoprotein is a major risk factor for atherosclerosis-induced cardiovascular disease. Lipid-lowering drugs like statins, niacin, fibrates, and some newer agents, ie, the apolipoprotein A-I mimetics and the cholesteryl ester transfer protein inhibitors, not only increase HDL levels but are also effective in reducing key atherogenic lipid components, including triglyceride-rich lipoproteins. The aim of this review is to discuss the accumulating evidence suggesting that HDL possesses a diverse range of biological actions, and that increasing HDL levels by drug treatment may be beneficial in the prevention of cardiovascular disease.Keywords: cardiovascular disease, lipoproteins, statins, apolipoprotein, atherosclerosi

Synthesis and characterization of cuo electrospum nanofiber using poly(vinyl acetate)/Cu(CH3COO)2 annealing method

One dimensional nanofibers of organic and inorganic materials have been used in filters, optoelectronic devices, sensors etc. It is difficult to obtain ultra fine fibers of inorganic materials having lengths in the order of millimeter as they tend to break during formation due to thermal and other mechanical stresses. In this study, we have investigated the mechanism to prevent the defect formation and the breaking of CuO nanofibers by using optimized heat flow rates. CuO nanofibers were obtained by heat treating the poly(vinyl acetate) PVA composite fibers formed by electrospinning. The morphology and structural characteristics of prepared samples were investigated by Scanning electron microscopy, Transmission electron microscopy and X-ray diffraction. It was found that the morphology of the composite and annealed nanofibers could be influenced by the concentration of the polymer content. A lower concentration favors the formation of defects along the fiber and the number of defects reduces when the concentration is increased. © 2013 VBRI press

Thermodynamic insights into the role of aromatic residues in chitooligosaccharide binding to the transglycosylating chitinase-D from Serratia proteamaculans

publishedVersio