Bioinformatics analysis of SARS coronavirus genome polymorphism

BACKGROUND: We have compared 38 isolates of the SARS-CoV complete genome. The main goal was twofold: first, to analyze and compare nucleotide sequences and to identify positions of single nucleotide polymorphism (SNP), insertions and deletions, and second, to group them according to sequence similarity, eventually pointing to phylogeny of SARS-CoV isolates. The comparison is based on genome polymorphism such as insertions or deletions and the number and positions of SNPs. RESULTS: The nucleotide structure of all 38 isolates is presented. Based on insertions and deletions and dissimilarity due to SNPs, the dataset of all the isolates has been qualitatively classified into three groups each having their own subgroups. These are the A-group with "regular" isolates (no insertions / deletions except for 5' and 3' ends), the B-group of isolates with "long insertions", and the C-group of isolates with "many individual" insertions and deletions. The isolate with the smallest average number of SNPs, compared to other isolates, has been identified (TWH). The density distribution of SNPs, insertions and deletions for each group or subgroup, as well as cumulatively for all the isolates is also presented, along with the gene map for TWH. Since individual SNPs may have occurred at random, positions corresponding to multiple SNPs (occurring in two or more isolates) are identified and presented. This result revises some previous results of a similar type. Amino acid changes caused by multiple SNPs are also identified (for the annotated sequences, as well as presupposed amino acid changes for non-annotated ones). Exact SNP positions for the isolates in each group or subgroup are presented. Finally, a phylogenetic tree for the SARS-CoV isolates has been produced using the CLUSTALW program, showing high compatibility with former qualitative classification. CONCLUSIONS: The comparative study of SARS-CoV isolates provides essential information for genome polymorphism, indication of strain differences and variants evolution. It may help with the development of effective treatment

The mechanism of the NH4 ion oscillatory transport across the excitable cell membrane

This paper presents results on typical oscillations of the membrane potential induced by the excitation of the cell membrane by different concentrations of the NH4Cl solution. The existence of four classes of oscillations of the membrane potential and several different single and local impulses rhythmically occurring were determined. It is known that the oscillatory processes of the membrane potential are in direct dependence on oscillatory transport processes of NH4 and Cl ions across the excitable cell membrane. A hypothesis on a possible mechanism of oscillatory transport processes of NH4 and Cl ions across the excitable cell membrane is also presented

Bioinformatics analysis of disordered proteins in prokaryotes

<p>Abstract</p> <p>Background</p> <p>A significant number of proteins have been shown to be intrinsically disordered, meaning that they lack a fixed 3 D structure or contain regions that do not posses a well defined 3 D structure. It has also been proven that a protein's disorder content is related to its function. We have performed an exhaustive analysis and comparison of the disorder content of proteins from prokaryotic organisms (i.e., superkingdoms Archaea and Bacteria) with respect to functional categories they belong to, i.e., Clusters of Orthologous Groups of proteins (COGs) and groups of COGs-Cellular processes (Cp), Information storage and processing (Isp), Metabolism (Me) and Poorly characterized (Pc).</p> <p>We also analyzed the disorder content of proteins with respect to various genomic, metabolic and ecological characteristics of the organism they belong to. We used correlations and association rule mining in order to identify the most confident associations between specific modalities of the characteristics considered and disorder content.</p> <p>Results</p> <p>Bacteria are shown to have a somewhat higher level of protein disorder than archaea, except for proteins in the Me functional group. It is demonstrated that the Isp and Cp functional groups in particular (L-repair function and N-cell motility and secretion COGs of proteins in specific) possess the highest disorder content, while Me proteins, in general, posses the lowest. Disorder fractions have been confirmed to have the lowest level for the so-called order-promoting amino acids and the highest level for the so-called disorder promoters.</p> <p>For each pair of organism characteristics, specific modalities are identified with the maximum disorder proteins in the corresponding organisms, e.g., high genome size-high GC content organisms, facultative anaerobic-low GC content organisms, aerobic-high genome size organisms, etc. Maximum disorder in archaea is observed for high GC content-low genome size organisms, high GC content-facultative anaerobic or aquatic or mesophilic organisms, etc. Maximum disorder in bacteria is observed for high GC content-high genome size organisms, high genome size-aerobic organisms, etc.</p> <p>Some of the most reliable association rules mined establish relationships between high GC content and high protein disorder, medium GC content and both medium and low protein disorder, anaerobic organisms and medium protein disorder, Gammaproteobacteria and low protein disorder, etc. A web site <it>Prokaryote Disorder Database </it>has been designed and implemented at the address <url>http://bioinfo.matf.bg.ac.rs/disorder</url>, which contains complete results of the analysis of protein disorder performed for 296 prokaryotic completely sequenced genomes.</p> <p>Conclusions</p> <p>Exhaustive disorder analysis has been performed by functional classes of proteins, for a larger dataset of prokaryotic organisms than previously done. Results obtained are well correlated to those previously published, with some extension in the range of disorder level and clear distinction between functional classes of proteins. Wide correlation and association analysis between protein disorder and genomic and ecological characteristics has been performed for the first time. The results obtained give insight into multi-relationships among the characteristics and protein disorder. Such analysis provides for better understanding of the evolutionary process and may be useful for taxon determination. The main drawback of the approach is the fact that the disorder considered has been predicted and not experimentally established.</p

Statistička zavisnost sekundarne strukture proteina od frekvencije digrama aminokiselina

The statistical dependence of protein secondary structure on amino acid bigram frequencies was studied. Proteins in the PDBSELECT subset of the Protein Data Bank database were investigated. Protein secondary structures were determined using DSSP software. The conditional probabilities of protein secondary structures were calculated and presented. The results on bigrams show the frequencies of all the possible bigrams in all secondary structure types. These results elucidate some factors important for the prediction of the secondary structures of proteins based on the amino acid sequence. © 2017, CI and CEQ. All rights reserved.U radu je opisana statistička zavisnost sekundarne strukture proteina od bigrama aminokiselina. Istraživanje je urađeno na proteinima koji se nalaze u podskupu PDBSELECT baze podataka o proteinima Protein Data Bank (PDB). Sekundarne strukture proteina su određene primenom programa DSSP. Izračunate su i prikazane uslovne verovatnoće pojavljivanja različitih sekundarnih struktura. Rezultati za bigrame su prikazani za sve tipove sekundarnih struktura. Rezultati ukazuju na faktore koji su značajni za predviđanje sekundarne strukture proteina koje je zasnovano na redosledu aminokiselina u proteinu

Variable mechanisms of action of lithium during generating of membrane potential oscilations across the excitable membrane of the Nitela cell

This study presents results on variable mechanisms of lithium transport processes during generating of membrane potential oscillations across the very excitable membrane of the Nittela cell. Generating of several classes of oscillations, single and local impulses of the membrane potential, were presented in dependence on effects of a high LiCl concentration (10 mM), with which the cell membrane is very excited. Results on membrane potential oscillations are presented, and then some of oscillogram parameters were displayed. The assertion is that oscillations of the membrane potential are caused by total oscillatory transport processes: Li+, K+, Na+ and Cl-across the very excitable cell membrane. The paper presents the hypothesis on mechanisms of oscillatory transport processes of ions (Li, Na, K and Cl) expressed over different classes of oscillations, single and local impulses of the membrane potential across the excitable membrane of the Nittela cell

Detecting the phase transition in thylakoid membrane of maize inbred lines by means of delayed fluorescence

In this paper the changes on growth, photosynthesis and water relations were tested by non-invasive fluorescence method. The applications of this method allow to determine some functional properties of prestigious maize inbred lines with erect top leaves. So the temperature dependency of delayed fluorescence intensity maximum of ZPPL 16 is observed at higher temperatures than for ZPPZ 62. This fact correlates with low values of phase transition of activation energy Ea in thylakoid membrane and accompanied by a decrease of the angle and area of the leaf, as well as with the content and the rate of water release from the seed. It seems reasonable to assume that, DF can be applied in breeding and maize hybrid seed production for the estimation of prestigious maize inbred lines and their resistance adaptability to increased and high temperatures, as well as, to drought

Дослідження методами інфрачервоної спектроскопії валентних і деформаційних коливань хімічних зв'язків у функціональних групах органічних сполук, що містяться в зернах інбредних ліній кукурудзи

The infrared spectroscopy was applied on kernels of the following maize inbred lines with significant traits: ZPPL 186, ZPPL 225 and M1-3-3 Sdms, with the aim to determine structural properties of organic compounds and their unstable state. The set hypothesis was that it was necessary to observe the existence of numerous and different spectral bands, not studied so far, occurring in various patterns (bands of low intensity, single or grouped) and to explain the nature and the dynamics of their formation. Such spectral bands were observed in the wave number range of 400—2925 cm—1 and are caused by the different types of vibration movements (valence and deformation vibrations) of organic compounds: alkenes, aromatic compounds, alcohols, ethers, carboxylic acids, esters, amines, amides, alkanes, nitro compounds, ketones, aldehydes, alkynes, nitriles and phenols. In this way, it is possible to establish not only the structure of organic compounds of kernels of observed maize inbred lines, but also it is possible to point out to their unstable, conformational and functional properties. The importance of intensity, shape and kinetics of spectral bands, expressing unstable processes in biological systems and bioactive organic molecules, has been studied and emphasised for the first time.В работе рассмотрено применение метода инфракрасной спектроскопии зерен элитных инбредных линий кукурузы ZPPL 186, ZPPL 225 и M1-3-3 Sdms с целью определения структурных характеристик органических соединений и их неустойчивого состояния. Выдвинута гипотеза о необходимости изучения различных многочисленных спектральных полос, неисследованных до сих пор, появляющихся в различных формах (полосы низкой интенсивности, одиночные или сгруппированные), объяснения природы и динамики их образования. Такие спектральные полосы наблюдались в диапазоне волн 400—2925 см—1, они вызваны различными типами колебаний (валентных и деформационных) органических соединений: алкенов, ароматических соединений, спиртов, простых эфиров, карбоновых кислот, сложных эфиров, аминов, амидов, алканов, нитросоединений, кетонов, альдегидов, алкинов, нитрилов и фенолов. Таким образом, можно установить не только структуру органических соединений зерен наблюдаемых инбредных линий кукурузы, но также указать их неустойчивые, конформационные и функциональные свойства. В работе впервые акцентирована важность изучения формы, кинетики и интенсивности спектральных полос, выражающих неустойчивые процессы в биологических системах и биоактивных органических молекулах.У роботі розглянуто застосування методу інфрачервоної спектроскопії зерен елітних інбредних ліній кукурудзи ZPPL 186, ZPPL 225 і M1-3-3 Sdms з метою визначення структурних характеристик органічних сполук та їх нестійкого стану. Висунуто гіпотезу про необхідність вивчення різних численних спектральних смуг, недосліджених досі, що з'являються в різних формах (смуги низької інтенсивності, поодинокі або згруповані), пояснення природи і динаміки їх утворення. Такі спектральні смуги спостерігали в діапазоні хвиль 400—2925 см-1, вони спричинені різними типами коливань (валентних і деформаційних) органічних сполук: алкенів,ароматичних сполук, спиртів, простих ефірів, карбонових кислот, складних ефірів, амінів, амідів, алканів, нітросполук, кетонів, альдегідів, алкінів, нітрилів і фенолів. Отже, можна встановити не тільки структуру органічних сполук зерен досліджуваних інбредних ліній кукурудзи, а й вказати їх нестійкі, конформаційні та функціональні властивості. У роботі вперше акцентована важливість вивчення форми, кінетики та інтенсивності спектральних смуг, що виражають нестійкі процеси в біологічних системах і біоактивних органічних молекулах

Towards a database for genotype-phenotype association research: mining data from encyclopaedia

To associate phenotypic characteristics of an organism to molecules encoded by its genome, there is a need for well-structured genotype and phenotype data. We use a novel method for extracting data on phenotype and genotype characteristics of microorganisms from text. As a resource, we use an encyclopedia of microorganisms, which holds phenotypic and genotypic data and create a structured, flexible data resource, which can be exported to a range of database formats, containing genotype and phenotype data for 2412 species and 873 genera of microbes. This data source has great potential as a resource for future biological research on genotype-phenotype associations. In this paper, we focus on describing the structure and content of the resulting database and on evaluating the method used for extracting the data. We conclude that the resulting database can be used as a reliable complementary resource for research into genotype-phenotype association

Structural disorder of plasmid-encoded proteins in Bacteria and Archaea

Abstract Background In the last decade and a half it has been firmly established that a large number of proteins do not adopt a well-defined (ordered) structure under physiological conditions. Such intrinsically disordered proteins (IDPs) and intrinsically disordered (protein) regions (IDRs) are involved in essential cell processes through two basic mechanisms: the entropic chain mechanism which is responsible for rapid fluctuations among many alternative conformations, and molecular recognition via short recognition elements that bind to other molecules. IDPs possess a high adaptive potential and there is special interest in investigating their involvement in organism evolution. Results We analyzed 2554 Bacterial and 139 Archaeal proteomes, with a total of 8,455,194 proteins for disorder content and its implications for adaptation of organisms, using three disorder predictors and three measures. Along with other findings, we revealed that for all three predictors and all three measures (1) Bacteria exhibit significantly more disorder than Archaea; (2) plasmid-encoded proteins contain considerably more IDRs than proteins encoded on chromosomes (or whole genomes) in both prokaryote superkingdoms; (3) plasmid proteins are significantly more disordered than chromosomal proteins only in the group of proteins with no COG category assigned; (4) antitoxin proteins in comparison to other proteins, are the most disordered (almost double) in both Bacterial and Archaeal proteomes; (5) plasmidal proteins are more disordered than chromosomal proteins in Bacterial antitoxins and toxin-unclassified proteins, but have almost the same disorder content in toxin proteins. Conclusion Our results suggest that while disorder content depends on genome and proteome characteristics, it is more influenced by functional engagements than by gene location (on chromosome or plasmid)

Statistical Dependence of Protein Secondary Structure on Amino Acid Bigrams

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