Homology Scores Research Articles

The relationship between neuropathic pain and serum endocan, ET-1, IL-1, IL-6, IL-8, MCP-1, TNF-α, VEGF-A levels in fibromyalgia patients and molecular docking results

Purpose: The most important clinical finding of fibromyalgia syndrome (FMS) is pain. Its etiology has not been fully elucidated. This study was planned to determine the relationship between endocan, ET-1, IL-1, IL-6, IL-8, MCP-1, TNF-a, VEGF-A levels and pain/neuropathic pain in FMS patients.
 Materials and Methods: Forty-four FMS patients who met the inclusion criteria and 44 age-matched premenopausal healthy controls were recruited. The fibromyalgia group was evaluated in terms of Visual Analog Scale, Beck Depression Scale, Beck Anxiety Scale, Fibromyalgia Impact Questionnaire and LANSS Pain Scale. Serum endocan, ET-1, IL-1, IL-6, IL-8, MCP-1, TNF-α, and VEGF-A values were determined by the ELISA method. Protein-protein interaction was evaluated by molecular docking analysis. Bioinformatics analysis was performed using the STRING v 11.5 protein interaction tool.
 Results: Endocan, ET-1, IL-1, IL-6, IL-8, MCP-1, TNF-α, and VEGF-A were significantly higher in FMS patients than the control group. 24 of 44 patients had neuropathic pain. No correlation was found between pain/neuropathic pain and serum markers levels. High interaction and homology scores of the proteins were defined.
 Conclusion: The pain/neuropathic pain relationship of these markers could not be determined, but the calculated binding energies and activities of the proteins provided important clues for future studies.

Twenty-year follow-up of an outbreak of hepatitis C in a small rural town of Argentina: The O'Brien Project

Introduction and objectivesIn 1999, a population-based survey showed a 5.6 % (102/1832) prevalence of HCV infection in O'Brien, a small rural town of Argentina. The aim of this study was to assess the impact of screening, clinical evaluation and antiviral therapy on elimination of HCV after 20 years of follow-up. Patients and methodsHCV+ subjects (n=102) underwent clinical, biochemical and histological evaluation to assess the presence and severity of liver disease. Antiviral therapy included pegylated interferon + ribavirin in 2005 and direct antiviral agents from 2017. ResultsAll viremic subjects (n=84) had genotype 1b with 90%-97.5% sequence homology scores, suggesting the existence of a common source of infection (use of unsafe injections administered by the same health professional). Liver biopsy (n=55) showed chronic hepatitis in all patients. The prevalence of cirrhosis was 28% overall (29/102) and 34.5% among viremic patients. Sustained virological response (SVR) was obtained in 20/34 (59%) patients treated with interferon. From 2005 to 2017, when oral antivirals became available 37/50 untreated patients died. Median age of this group in 2005 was 67 years. Six interferon non-responders and five naive subjects received direct antiviral agents and all developed SVR. Only 1/31 patient (3.2%) with SVR died and none developed decompensated cirrhosis or HCC. In 2019, a new population-based study showed that the prevalence of HCV in O'Brien decreased 20-fold, from 5.6% to 0.28% (3/1070). ConclusionsDespite the high mortality rate precluding timely access to direct antiviral agents, the O'Brien Project is a good example of HCV micro-elimination studies

Computational Approach to the Systematic Prediction of Glycolytic Abilities: Looking Into Human Microbiota.

Glycoside hydrolases are responsible for the enzymatic deconstruction of complex carbohydrates. Most of the families are known to conserve the catalytic machinery and molecular mechanisms. This work introduces a new method to predict glycolytic abilities in sequenced genomes and thus, gain a better understanding of how to target specific carbohydrates and identify potentially interesting sources of specialised enzymes. Genome sequences are aligned to those of organisms with expertly curated glycolytic abilities. Clustering of homology scores helps identify organisms that share common abilities and the most promising organisms regarding specific glycolytic abilities. The method has been applied to members of the bacterial families Ruminococcaceae (39 genera), Eubacteriaceae (11 genera) and Lachnospiraceae (59 genera), which hold major representatives of the human gut microbiota. The method predicted the potential presence of glycoside hydrolases in 1701 species of these genera. Here, the validity and practical usefulness of the method is discussed based on the predictions obtained for members of the genus Ruminococcus. Results were consistent with existing literature and offer useful, complementary insights to comparative genomics and physiological testing. The implementation of the Gleukos web portal (http://sing-group.org/gleukos) offers a public service to those interested in targeting microbial carbohydrate metabolism for biotechnological and health applications.

Antigenic site of nucleoprotein gene from Indonesian rabies virus isolates.

Background and Aim:Several molecular studies on rabies virus (RABV) have been conducted in Indonesia, but it does not give clear information about molecular characteristics of previous RABV isolate in Indonesia. This study was conducted to know the characteristic of circulating RABV to determine a suitable method to control the spreading of RABV in Indonesia.Materials and Methods:Samples of infected RABV from dog brain were collected from Sumatera, Kalimantan, Sulawesi, and Bali Islands. All samples were examined based on nucleoprotein encoding gene to determine the molecular characteristics based on homology and phylogenetic tree compared to Pasteur Virus and RABV that came from another country within Asia (Indonesia, China, Thailand, India, and Korea). The collected samples were processed by one-step reverse transcriptase-polymerase chain reaction using nucleoprotein encoding gene followed by sequencing. The amino acid of its antigenic site of isolated RABV was also analyzed.Results:The results showed that isolated RABV has 84-85% similarity compared to Pasteur. According to phylogenetic construction, isolated samples do not share the same lineage toward Pasteur. The homology scores of isolated samples compared to RABV within Asia such as Indonesia, China, Thailand, India, and Korea were 98-99%, 92-93%, 88-89%, 86-88%, and 85-88%, respectively. According to antigenic site analysis compared to Pasteur, it was found that there were amino acid mutations within antigenic Site IV of nucleoprotein. Amino acid mutation from isoleucine to valine occurred in amino acid number 240 of 6 Kalimantan, 7 Kalimantan, and 8 Kalimantan. Amino acid mutation from alanine to aspartate and asparagine to threonine occurred within the same antigenic site in amino acid number 246 and 273 of C4 isolate from Sulawesi.Conclusion:According to homology and phylogenetic tree analyses, isolated RABV remained different compared to RABV within Asia and Pasteur. The amino acid mutation occurred in antigenic site of nucleoprotein encoding gene.

Homology and linkage in crossover for linear genomes of variable length.

The use of variable-length genomes in evolutionary computation has applications in optimisation when the size of the search space is unknown, and provides a unique environment to study the evolutionary dynamics of genome structure. Here, we revisit crossover for linear genomes of variable length, identifying two crucial attributes of successful recombination algorithms: the ability to retain homologous structure, and to reshuffle variant information. We introduce direct measures of these properties—homology score and linkage score—and use them to review existing crossover algorithms, as well as two novel ones. In addition, we measure the performance of these crossover methods on three different benchmark problems, and find that variable-length genomes out-perform fixed-length variants in all three cases. Our homology and linkage scores successfully explain the difference in performance between different crossover methods, providing a simple and insightful framework for crossover in a variable-length setting.

Global graph matching using diffusion maps

We present a new algorithm, global positioning graph matching (GPGM), to perform global network alignments between pairs of undirected graphs by minimizing a dissimilarity score over matched vertices. We define structural dissimilarities based on a random walk over each graph to provide a robust me asure of the global graph topology using a nonlinear manifold learning algorithm known as diffusion maps. Measures of vertex-vertex dissimilarity are straightforwardly incorporated in a convex combination. We have tested our approach in pairwise alignments of protein-protein interaction networks of Xenopus laevis (frog), Rattus norvegicus (rat), Caenorhabditis elegans (worm), Mus musculus (mouse), and Drosophila melanogaster (fly). When vertex-vertex dissimilarities are incorporated using homology scores between protein sequences, the performance of GPGM is comparable to that of the IsoRank algorithm (Singh et al. Proc. Natl. Acad. Sci. USA 105 35 12763 (2008)). When homology information is not included, GPGM discovers superior alignments, making it well suited to graph matching applications where vertex labels are unknown or undefined.

Manual classification strategies in the ECOD database.

ECOD (Evolutionary Classification Of protein Domains) is a comprehensive and up-to-date protein structure classification database. The majority of new structures released from the PDB (Protein Data Bank) each week already have close homologs in the ECOD hierarchy and thus can be reliably partitioned into domains and classified by software without manual intervention. However, those proteins that lack confidently detectable homologs require careful analysis by experts. Although many bioinformatics resources rely on expert curation to some degree, specific examples of how this curation occurs and in what cases it is necessary are not always described. Here, we illustrate the manual classification strategy in ECOD by example, focusing on two major issues in protein classification: domain partitioning and the relationship between homology and similarity scores. Most examples show recently released and manually classified PDB structures. We discuss multi-domain proteins, discordance between sequence and structural similarities, difficulties with assessing homology with scores, and integral membrane proteins homologous to soluble proteins. By timely assimilation of newly available structures into its hierarchy, ECOD strives to provide a most accurate and updated view of the protein structure world as a result of combined computational and expert-driven analysis.

Homology cluster differential expression analysis for interspecies mRNA-Seq experiments.

There is an increasing demand for exploration of the transcriptomes of multiple species with extraordinary traits such as the naked-mole rat (NMR). The NMR is remarkable because of its longevity and resistance to developing cancer. It is of scientific interest to understand the molecular mechanisms that impart these traits, and RNA-sequencing experiments with comparator species can correlate transcriptome dynamics with these phenotypes. Comparing transcriptome differences requires a homology mapping of each transcript in one species to transcript(s) within the other. Such mappings are necessary, especially if one species does not have well-annotated genome available. Current approaches for this type of analysis typically identify the best match for each transcript, but the best match analysis ignores the inherent risks of mismatch when there are multiple candidate transcripts with similar homology scores. We present a method that treats the set of homologs from a novel species as a cluster corresponding to a single gene in the reference species, and we compare the cluster-based approach to a conventional best-match analysis in both simulated data and a case study with NMR and mouse tissues. We demonstrate that the cluster-based approach has superior power to detect differential expression.

PRADA: pipeline for RNA sequencing data analysis

Technological advances in high-throughput sequencing necessitate improved computational tools for processing and analyzing large-scale datasets in a systematic automated manner. For that purpose, we have developed PRADA (Pipeline for RNA-Sequencing Data Analysis), a flexible, modular and highly scalable software platform that provides many different types of information available by multifaceted analysis starting from raw paired-end RNA-seq data: gene expression levels, quality metrics, detection of unsupervised and supervised fusion transcripts, detection of intragenic fusion variants, homology scores and fusion frame classification. PRADA uses a dual-mapping strategy that increases sensitivity and refines the analytical endpoints. PRADA has been used extensively and successfully in the glioblastoma and renal clear cell projects of The Cancer Genome Atlas program. http://sourceforge.net/projects/prada/ gadgetz@broadinstitute.org or rverhaak@mdanderson.org Supplementary data are available at Bioinformatics online.

Assessment of allelic variation in the ccrAB locus in methicillin-resistant Staphylococcus aureus clones

To evaluate the allelic variability of ccrA and ccrB among methicillin-resistant Staphylococcus aureus (MRSA) strains belonging to different genetic lineages and carrying different SCCmec types. Internal fragments from both genes were obtained by PCR amplification with pairs of degenerate primers and the nucleotide sequence was determined for both strands. Nucleotide sequences were aligned and the phylogenetic trees were reconstructed. The homology scores obtained confirmed the very close relationships among ccrAB alleles associated with each SCCmec type, which further validate this locus as a good target for SCCmec typing strategies. Using this strategy, particularly for the ccrB gene, SCCmec types with the same ccrAB allotype, as detected by PCR, could be discriminated and some strains with non-typeable ccrAB loci were resolved. We propose that sequencing an internal fragment of ccrB is a strategy for SCCmec typing that may be easily incorporated into other sequence-based MRSA typing strategies, such as multi-locus sequence typing and spa typing.

The Sinorhizobium meliloti ABC transporter Cho is highly specific for choline and expressed in bacteroids from Medicago sativa nodules.

In Sinorhizobium meliloti, choline is the direct precursor of phosphatidylcholine, a major lipid membrane component in the Rhizobiaceae family, and glycine betaine, an important osmoprotectant. Moreover, choline is an efficient energy source which supports growth. Using a PCR strategy, we identified three chromosomal genes (choXWV) which encode components of an ABC transporter: ChoX (binding protein), ChoW (permease), and ChoV (ATPase). Whereas the best homology scores were obtained with components of betaine ProU-like systems, Cho is not involved in betaine transport. Site-directed mutagenesis of choX strongly reduced (60 to 75%) the choline uptake activity, and purification of ChoX, together with analysis of the ligand-binding specificity, showed that ChoX binds choline with a high affinity (KD, 2.7 microM) and acetylcholine with a low affinity (KD, 145 microM) but binds none of the betaines. Uptake competition experiments also revealed that ectoine, various betaines, and choline derivatives were not effective competitors for Cho-mediated choline transport. Thus, Cho is a highly specific high-affinity choline transporter. Choline transport activity and ChoX expression were induced by choline but not by salt stress. Western blotting experiments with antibodies raised against ChoX demonstrated the presence of ChoX in bacteroids isolated from nitrogen-fixing nodules obtained from Medicago sativa roots. The choX mutation did not have an effect on growth under standard conditions, and neither Nod nor Fix phenotypes were impaired in the mutant, suggesting that the remaining choline uptake system(s) still present in the mutant strain can compensate for the lack of Cho transporter.

Identification and class assignment proteins expressed during mouse oocyte development using proteomics strategy

Identification and class assignment proteins expressed during mouse oocyte development using proteomics strategy

A novel neutral amino acid transporter from the hyperthermophilic archaeon Thermococcus sp. KS-1.

A novel gene encoding a small neutral amino acid transporter was cloned from the genome of the hyperthermophilic archaeon Thermococcus sp. KS-1 by functional cloning using Escherichia coli strain AK430, which is defective in transporting glycine and D-alanine. The cloned gene, snatA, encoded a protein of 216 amino acid residues, SnatA, and was predicted to be a membrane protein with six membrane-spanning segments. E. coli AK430 cells transformed with snatA transported glycine with an apparent K(t) value of 24 micro M, which was one order of magnitude higher than that of other known glycine/alanine transporters, including cycA of E. coli and acp of thermophilic bacterium PS3. Competition studies revealed that SnatA transported various L-type neutral amino acids, but its substrate specificity was different from that of CycA or ACP. The glycine transport was inhibited by a protonophore, FCCP, or valinomycin plus nigericin, indicating that the process is dependent on an electrochemical potential of H(+). Homology searches revealed no homology with any transporters known to date. However, several hypothetical genes in prokaryote cells enrolled in the gene bank showed significantly high homology scores, indicating that snatA and its homologues form a family of prokaryotes. To our knowledge, this is the first report on the cloning of a gene of an amino acid transporter from a hyperthermophilic archaeon.

A Region of Vitamin K-dependent Protein S That Binds to C4b Binding Protein (C4BP) Identified Using Bacteriophage Peptide Display Libraries

Vitamin K-dependent protein S, a blood coagulation inhibitor, interacts with the C4b-binding protein (C4BP) in human plasma with high affinity (KD = 0.1 nM). Identification of a portion of protein S that binds to C4BP has been approached using random libraries of 6- and 15-mer peptides displayed on bacteriophage surfaces. Bacteriophage binding to the beta-chain of C4BP were selected in several rounds of affinity purification with intervening amplification in E. coli. Homology searches of the affinity purified peptide sequences against protein S led to the identification of four regions in protein S that were similar to several of the selected peptides. These regions were synthesized as linear peptides and tested in inhibition experiments. Only one distinct peak (around position 450) was observed when the homology scores versus human protein S sequence were averaged over all affinity purified peptides. A synthetic peptide comprising residues 439-460 in human protein S was found to inhibit protein S binding to C4BP. The same result was found with two overlapping peptides (residues 447-468 and 435-468, respectively) in a second set of synthetic peptides. Direct binding of the peptides to C4BP was inferred from titrations monitored by recording the near UV circular dichroism spectra or the polarization of tryptophan fluorescence. The results suggest that residues 447-460 constitute a portion of protein S that is important for the interaction with C4BP. These findings may have implications for patients suffering from thrombosis, due to the lack of free protein S, by directing the design of drugs that disrupt protein S binding to C4BP.

Phytochrome of the green alga Mougeotia: cDNA sequence, autoregulation and phylogenetic position.

A cDNA clone encoding phytochrome (apoprotein) of the zygnematophycean green alga Mougeotia scalaris has been isolated and sequenced. The clone consisted of 3372 bp, encoded 1124 amino acids, and showed strainspecific nucleotide exchanges for M. scalaris, originating from different habitats. No indication was found of multiple phytochrome genes in Mougeotia. The 5' non-coding region of the Mougeotia PHY cDNA harbours a striking stem-loop structure. Homologies with higher-plant phytochromes were 52-53% for PHYA and 57-59% for PHYB. Highest homology scores were found with lower-plant phytochromes, for example 67% for Selaginella (Lycopodiopsida), 64% for Physcomitrella (Bryopsida) and 73% for Mesotaenium (Zygnematophyceae). In an unrooted phylogenetic tree, the position of Mougeotia PHY appeared most distant to all other known PHYs. The amino acids Gly-Val in the chromophore-binding domain (-Arg-Gly-Val-His-Gly-Cys-) were characteristic of the zygnematophycean PHYs known to date. There was no indication of a transmembrane region in Mougeotia phytochrome in particular, but a carboxyl-terminal 16-mer three-fold repeat in both, Mougeotia and Mesotaenium PHYs may represent a microtubule-binding domain. Unexpected for a non-angiosperm phytochrome, its expression was autoregulated in Mougeotia in a red/far-red reversible manner: under Pr conditions, phytochrome mRNA levels were tenfold higher than under Pfr conditions.

Molecular cloning of a P-type Ca(2+)-ATPase from the halotolerant alga Dunaliella bioculata.

We have determined the complete primary structure of a putative P-type Ca(2+)-ATPase from the unicellular, halotolerant alga Dunaliella bioculata. The protein (DBCA1) with a calculated molecular mass of 114 kDa and eight to ten putative transmembrane segments contains all amino acid motifs specific to the family of P-type ATPases. Highest homology scores were obtained by comparison with (sarco)endoplasmic reticulum-type plant and animal Ca(2+)-ATPases (54% identity, 70% similarity). In addition, all amino acids shown to be essential for Ca2+ transport in animal sarcoplasmic reticulum Ca(2+)-ATPases are preserved in DBCA1. Significantly lower homologies were found with animal plasma membrane Ca(2+)-ATPases (33% identity, 55% similarity), and the carboxyterminus of DBCA1 gave no indications of possible calmodulin-binding sites, characteristic of those enzymes. It is assumed that DBCA1 is a representative of the endomembrane class of Ca(2+)-ATPases. In Northern blot experiments with polyadenylated RNA, a 3.7-kb transcript was detected at levels which were very low compared with those of the plasma membrane H(+)-ATPase from D. bioculata (DBPMA1; Wolf et al., 1995, Plant Mol Biol 28: 657-666). Southern blot analyses suggest the existence of additional Ca(2+)-ATPase genes in the haploid genome of D. bioculata.

Characterization of cDNA encoding for phosphoglucose isomerase of rice (Oryza safivaL.)

Two types of genes (Pgi-a and Pgi-b) encoding phosphoglucose isomerase (PGI; EC 5.3.1.9) were cloned from cDNA libraries of rice cultured cells (Oryza sativa L.). Pgi-a and Pgi-b consisted of 2132 and 2030 nucleotides, respectively. The homology between these genes was 93.0% at nucleotide level. The homology scores between these genes in protein coding region and 3' non-coding region were 95.6% and 79.4%, respectively. PGI proteins encoded by Pgi-a and Pgi-b consisted of 567 and 568 amino acid, respectively, sharing 95.8% homology at amino acid sequences. Of 11 PGI genes from other plant species and organisms whose amino acid sequences had been determined, a dicotyledonous plant Clarkia lewisii PGI showed the highest homology (about 80%) with rice PGIs. GC contents at the third position of rice PGI genes were about 40%. In order to confirm the enzyme activity of the protein encoded by the rice cDNA, Pgi-a was subcloned into an expression vector, pBluescript II SKp, which was introduced into Escherichia coli. The transformant had an additional PGI activity from Pgi-a.

Stalling of Escherichia coli RNA Polymerase in the +6 to +12 Region in Vivo is Associated with Tight Binding to Consensus Promoter Elements

Three synthetic promoters, PS1, PS2 and PS3, which differ in their core promoter elements, were studied in vivo and in vitro. Whereas an increased homology score correlates with higher rates of RNA polymerase binding, it does not correlate with activity in vivo. Permanganate probing in vivo reveals that PS1, which exhibits the lowest homology score, is rate-limited during the early phase of promoter-RNA polymerase interactions. By contrast, PS2 and PS3, with higher homology scores, are limited at a late step involving an open DNA region spanning from +6 to +12, indicating a stalling of RNA polymerase. These complexes disappear upon treatment of cells with rifampicin and are replaced by open complexes covering the start site. Because initiated complexes are selectively insensitive to rifampicin action, this confirms that RNA polymerase stalled at +6 to +12 has initiated RNA synthesis. Kinetic studies indicate that the enzyme is released slowly from this position and that this slow release appears to be responsible for the low promoter activity. For PS3, which exhibits the highest homology score and which binds RNA polymerase most efficiently, the release of the stalled complex is particularly slow. PS3 is found to be the weakest of the three promoters in vivo. These results support models in which promoter activity can be determined by various rate limiting steps, including those following the formation of open complexes and even the initiation of RNA synthesis.

Identification of novel sequences in the repertoire of hypervariable TRE17 genes from immortalized nonmalignant and malignant human keratinocytes

The TRE17 oncogene, originally cloned from transfected DNA of Ewing's sarcoma cells, maps to chromosome 17q and is expressed in a wide variety of human cancer cells. We recently detected the variants of this gene by using the polymerase chain reaction (PCR) and sequencing from the first exon to the third intron. Based on sequence homology scores, the variants could be grouped into three families, denoted α, β, and γ. Here, we used human keratinocytes from healthy skin which had been spontaneously immortalized and then rendered malignant by serum privation in vitro. Both immortalized and malignant cells expressed TRE17 sequences to the same extent, and, according to the restriction site analysis of cloned PCR products, both contained common and rare TRE17 variants in similar proportions. These variants, one of each from both cell types, were then sequenced and compared with those from the previous study. In the phylogenetic tree, they clustered with α and γ at the most distant tree positions. The overall fraction of conserved sites in the whole TRE17 repertoire was 80%. An unexpected feature of the observed variability was that intronic sites were significantly better conserved than exonic sites. Members of TRE17γ detected in immortalized and malignant keratinocytes differed one from another, and both differed from the TRE17γ already identified in Ewing's sarcoma. No TRE17γ has been found so far in healthy tissues, thus leaving open the possibility of its origin from TRE17β by somatic changes during tumor progression.

The amino acid sequence of hemoglobin III from the symbiont-harboring clamLucina pectinata

The cytoplasmic hemoglobin III from the gill of the symbiont-harboring clam Lucina pectinata consists of 152 amino acid residues, has a calculated Mm of 18,068, including heme, and has N-acetyl-serine as the N-terminal residue. Based on the alignment of its sequence with other vertebrate and nonvertebrate globins, it retains the invariant residues Phe45 at position CD1 and His98 at the proximal position F8, as well as the highly conserved Trp16 and Pro39 at positions A12 and C2, respectively. The most likely candidate for the distal residue at position E7 is Gln66. Lucina hemoglobin III shares 95 identical residues with hemoglobin II (J. D. Hockenhull-Johnson et al., J. Prot. Chem. 10, 609-622, 1991), including Tyr at position B10, which has been shown to be capable of entering the distal heme cavity and placing its hydroxyl group within a 2.8 A of the water molecule occupying the distal ligand position, by modeling the hemoglobin II sequence using the crystal structure of sperm whale metmyoglobin. The amino acid sequences of the two Lucina globins are compared in detail with the known sequences of mollusc globins, including seven cytoplasmic and 11 intracellular globins. Relative to 75% homology between the two Lucina globins (counting identical and conserved residues), both sequences have percent homology scores ranging from 36-49% when compared to the two groups of mollusc globins. The highest homology appears to exist between the Lucina globins and the cytoplasmic hemoglobin of Busycon canaliculatum.