Nucleotide Sequence Data Research Articles

Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters.

Interactions occur between two or more organisms affecting each other. Interactions are decisive for the ecology of the organisms. Without direct experimental evidence the analysis of interactions is difficult. Correlation analyses that are based on co-occurrences are often used to approximate interaction. Here, we present a new mathematical model to estimate the interaction strengths between taxa, based on changes in their relative abundances across environmental gradients.

How the Aridification of Australia Structured the Biogeography and Influenced the Diversification of a Large Lineage of Australian Cicadas.

Over the last 30 million years, Australia's landscape has undergone dramatic cooling and drying due to the establishment of the Antarctic Circumpolar Current and change in global CO$_{2}$ levels. Studies have shown that many Australian organisms went extinct during these major cooling events, while others experienced adaptive radiations and increases in diversification rates as a result of exploiting new niches in the arid zone. Despite the many studies on diversification and biogeography in Australia, few have been continent-wide and none have focused on a group of organisms adapted to feeding on plants. We studied 162 species of cicadas in the Australian Pauropsalta complex, a large generic lineage within the tribe Cicadettini. We asked whether there were changes in the diversification rate of Pauropsalta over time and if so: 1) which clades were associated with the rate change? 2) did timing of rate shifts correspond to known periods of dramatic historical climate change, 3) did increases in diversification rate along select lineages correspond to adaptive radiations with movement into the arid zone? To address these questions, we estimated a molecular phylogeny of the Pauropsalta complex using ${\sim}$5300 bp of nucleotide sequence data distributed among five loci (one mtDNA locus and four nDNA loci). We found that this large group of cicadas did not diversify at a constant rate as they spread through Australia; instead the signature of decreasing diversification rate changed roughly around the time of the expansion of the east Antarctic ice sheets ${\sim}$16 Ma and the glaciation of the northern hemisphere ${\sim}$3 Ma. Unlike other Australian taxa, the Pauropsalta complex did not explosively radiate in response to an early invasion of the arid zone. Instead multiple groups invaded the arid zone and experienced rates of diversification similar to mesic-distributed taxa. We found evidence for relictual groups, located in pre-Mesozoic habitat, that have not diversified and continue to reside on mesic hosts in isolated "habitat islands". Future work should focus on groups of similar ages with similar distribution patterns to determine whether this tempo and pattern of diversification and biogeography is consistent with evidence from other phytophagous insects.

DNA barcoding of flat oyster species reveals the presence of Ostrea stentina Payraudeau, 1826 (Bivalvia: Ostreidae) in Japan

BackgroundDNA barcoding is an effective method of accurately identifying morphologically similar oyster species. However, for some of Japan’s Ostrea species there are no molecular data in the international DNA databases.MethodsWe sequenced the mitochondrial large subunit ribosomal DNA (LSrDNA) and cytochrome c oxidase subunit I (COI) gene of five known and two unidentified Ostrea species. Phylogenetic comparison with known Ostrea species permitted accurate species identification by DNA barcoding.ResultsThe molecular data, which were deposited in an international DNA database, allowed for a clear distinction among native Ostrea species in Japan. Moreover, the nucleotide sequence data confirmed that O. stentina (Atsuhime-gaki) inhabits Kemi and Ibusuki, Japan.ConclusionsThis is the first record of O. stentina in Japan. These results provided for accurate species identification by DNA barcoding of the taxonomically problematic species O. futamiensis, O. fluctigera, O. setoensis and O. stentina in Japan.

Evaluation of MC1R high-throughput nucleotide sequencing data generated by the 1000 Genomes Project.

The advent of next-generation sequencing allows simultaneous processing of several genomic regions/individuals, increasing the availability and accuracy of whole-genome data. However, these new approaches may present some errors and bias due to alignment, genotype calling, and imputation methods. Despite these flaws, data obtained by next-generation sequencing can be valuable for population and evolutionary studies of specific genes, such as genes related to how pigmentation evolved among populations, one of the main topics in human evolutionary biology. Melanocortin-1 receptor (MC1R) is one of the most studied genes involved in pigmentation variation. As MC1R has already been suggested to affect melanogenesis and increase risk of developing melanoma, it constitutes one of the best models to understand how natural selection acts on pigmentation. Here we employed a locally developed pipeline to obtain genotype and haplotype data for MC1R from the raw sequencing data provided by the 1000 Genomes FTP site. We also compared such genotype data to Phase 3 VCF to evaluate its quality and discover any polymorphic sites that may have been overlooked. In conclusion, either the VCF file or one of the presently described pipelines could be used to obtain reliable and accurate genotype calling from the 1000 Genomes Phase 3 data.

Identification and characterization of GmPDIL7, a soybean ER membrane-bound protein disulfide isomerase family protein.

The nucleotide sequence data for the GmPDIL7 cDNA are available in the DNA Data Bank of Japan (DDBJ) databases under the accession numbers LC158001. Protein disulfide isomerase: EC 5.3.4.1.

A phylogeny of the treehopper subfamily Heteronotinae reveals convergent pronotal traits (Hemiptera: Auchenorrhyncha: Membracidae)

AbstractEven within an insect family famous for its morphological diversity, the treehopper subfamily Heteronotinae is a microcosm of pronotal variation, displaying remarkably dissimilar thoracic ornamentations among its ten included genera. Presented here is a reconstruction of heteronotine relationships based on DNA nucleotide sequence data from five nuclear and two mitochondrial genes from a comprehensive sample of ingroup taxa (including exemplars of all genera except for the monotypic Dysyncritus Fowler, 1895). Concordant phylogenetic estimates support the monophyly of Heteronotinae sensu stricto (i.e. excluding Darnoides Fairmaire, 1846), as well as the monophyly of the included genera Heteronotus Laporte, 1832, Nassunia Stål, 1862, Omolon Walker, 1862, Rhexia Stål, 1867, and Smiliorachis Fairmaire, 1846. Conversely, Anchistrotus Buckton, 1902, Allodrilus Evangelista, 2014 and Iria Stål, 1867 were not recovered as monophyletic, although topology comparison tests failed to reject the nonmonophyly of the latter two genera, nor Heteronotinae, as currently circumscribed. These results are interpreted in the context of available morphological evidence, which generally supports these findings. Also addressed here is the evolution of selected pronotal features representing major aspects of heteronotine morphology. Bayesian stochastic mapping of pronotal traits estimated multiple character state transitions, suggesting repeated acquisition of pronotal features, most of which have evolved independently within the diverse genus Heteronotus. These convergences may provide insight into the role of the pronotum in heteronotine groups that appear to serve different adaptive strategies, such as mimicry, crypsis and defence against predators. Furthermore, our results show a substantial diversity in need of formal description, including possible new genera, and several unique sexually dimorphic syndromes that may constitute a species complex within Heteronotus delineatus Walker, 1858. Nomenclatural changes are proposed for Nassunia nigromacula (Funkhouser, 1940) new combination and Smiliorachis inornata Stål, 1862 combination reinstated, which were found to be misplaced at the generic and subfamily levels according to our analyses.

Mutations in TP53 Gene Is Independent Prognostic Factor for High Grade B-Cell Lymphoma

Background.TP53 mutations were described to have a negative impact on prognosis of patients with B-chronic lymphoid leukemia and diffuse large cell lymphoma. However, a role of TP53 mutations in high-grade B-cell lymphomas (HGL) is not well defined in context of other genetic aberrations.Materials and methods. 23 patients (7 males and 16 females) had diagnosis of HGL were treated in National Research Center for hematology, Moscow, Russia. Median age was 49 years old (30-76). 5 patients had HGL with c-MYC (MYC-R) and BCL2 genes rearrangements and 2 - HGB with MYC-R and BCL6 rearrangements. 17 (74%) patients had MYC-R, 11/23 (48%) had double expresser lymphoma (MYC≥40%, BCL2≥50%) (DE). Median of observation time was 29,1 months (6,3-99,8). 19 (82%) of patients had IPI score 3-5 points. 16 patients underwent LM-B-04 with rituximab (Table 1), 5 - R-(DA)-EPOCH, 2 - R-CHOP-21. In 5 cases autologous stem cell transplantation was performed. Sanger sequencing was performed to identify mutations in exons 5-8 of TP53 gene using DNA extracted from formalin fixed paraffin embedded tissue («Extra-DNA» kit, «Genetechnology» LLC). Primers to TP53 gene were synthesized based on nucleotide sequences data available online on website ncbi.com by «Evrogene». To evaluate an influence of such factors as TP53 mutation (TP53mut), MYC-R, DHL, DE, gender, therapy on overall survival (OS) and time to progression (TTP) were performed multivariate dispersion analysis and Cox regression analysis (STATISTICA 10).Results: 8 (35%) cases with TP53mut were identified: c.535C>T 45,6% p.H179Y, c.524G>C 15,6% p.R175P, c.743G>A 75,6% p.R247Q, c.487T>A 25,2% p.Y163N, c.824G>A 75% p.C275Y, c.713G>A 87,7% p.C238Y, c.745A>G 31,9% p.R249G, c.639A>G 41,8% p.R213R. 7/8 of them harbored MYC-R, 2/8 had DHL. In univariate (Picture 1, 2) and multivariate analysis pts harboring TP53mut had worse OS (median OS was 6,2 (0,7-9,5) vs 25,5 (0,7-99,8) months, p=0,004) and shorter TTP (median TTP 3,5 (0,7-9,5) vs 23,1 (0,7-99,8) months, p=0,027) than patients without TP53mut. DHL status had also an adverse effect on OS with lower significance than in pts with TP53mut (p=0,022). Adverse effect of TP53mut trends to play a role in combination with c-MYC gene rearrangement, thus5 pts TP53mut/MYC-R had shorter TTP than 5 DHL pts (3,4 (1,1-9,5) vs 7,3 (0,6-67,1) months, p=0,07).Conclusion: High-grade lymphoma has a more powerful and independent prognostic factor than double-hit status - TP53 mutation that contribute inferior prognosis. This factor shouldn't be underestimated in routine diagnostics because of its frequency and requirement of a different therapeutic approach. [Display omitted] [Display omitted] [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

A settled sub-family for the orphan tree: The phylogenetic position of the endemic Colombian genus Orphanodendron in the Leguminosae

Orphanodendron is a taxonomically and geographically isolated South American genus of two species. When first described by Barneby and Grimes in 1990, the genus was placed in Leguminosae subfamily Caesalpinioideae, but that placement was doubted and the name Orphanodendron (Gr. orphanos, orphan + dendron, tree) was chosen to reflect the uncertain subfamilial relationship of the genus. In this study, nucleotide sequence data from five Orphanodendron specimens were added to 662 other, previously sampled, Leguminosae taxa representing all three currently recognized subfamilies (Caesalpinioideae, Mimosoideae and Papilionoideae) in a matK maximum parsimony analysis that resolved Orphanodendron as a member of the genistoid s.l. clade of subfamily Papilionoideae. Two additional Bayesian phylogenetic analyses with reduced taxon sampling of plastid (matK combined with trnL-F) and nuclear (ITS) loci strongly support the monophyly of Orphanodendron and unambiguously establish Orphanodendron as a member of the genistoid sensu lato clade. Although our plastid phylogenetic analysis finds relatively low support for a sister-group relationship with the African genus Camoensia, the nuclear-encoded ITS resolves Orphanodendron as sister to the Bowdichia clade with strong support and Camoensia as sister to other core genistoids. The phylogenetic resolution of Orphanodendron as a member of the genistoid s.l. legumes based on nuclear and plastid sequences will undoubtedly advance future evolutionary investigations of this Colombian endemic tropical tree genus.

DNA Data Bank of Japan.

The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987). We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), in collaboration with the US National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EBI). The DDBJ Center also services Japanese Genotype-phenotype Archive (JGA), with the National Bioscience Database Center to collect human-subjected data from Japanese researchers. Here, we report our database activities for INSDC and JGA over the past year, and introduce retrieval and analytical services running on our supercomputer system and their recent modifications. Furthermore, with the Database Center for Life Science, the DDBJ Center improves semantic web technologies to integrate and to share biological data, for providing the RDF version of the sequence data.

Regulatory Analysis of Effects of Hepatitis C Virus NS5A Polymorphisms on Efficacy of Elbasvir and Grazoprevir

Elbasvir (an NS5A inhibitor) and grazoprevir (an NS3/4A protease inhibitor) are direct-acting antiviral agents recently approved in the United States for treatment of chronic hepatitis C virus (HCV) genotype 1 and 4 infections, as a fixed-dose combination. Trials of elbasvir and grazoprevir, with or without ribavirin, demonstrated high rates of sustained virologic response 12 weeks after treatment ended (SVR12). However, 12 weeks of treatment with elbasvir and grazoprevir failed in a small proportion of patients with HCV genotype 1 infection. We summarize findings from independent US Food and Drug Administration analyses of drug resistance data from trials of elbasvir and grazoprevir, with and without ribavirin. We independently analyzed HCV drug resistance and HCV RNA measurement results that were submitted to the US Food and Drug Administration to support the regulatory approval of elbasvir and grazoprevir. These data were reported from selected phase 2 and 3 clinical trials of elbasvir and grazoprevir, with and without ribavirin. Genotypic resistance analyses were conducted using Sanger population nucleotide sequencing data derived from blood samples from study patients. In 56 of 506 (11%) patients with HCV genotype 1a infection who received elbasvir and grazoprevir for 12 weeks, baseline HCV genetic variants encoding amino acid polymorphisms in NS5A (M28, Q30, L31, or Y93) reduced treatment efficacy; rates of SVR12 were 70% and 98% for patients with or without NS5A polymorphisms, respectively (P < .0001). Most patients with treatment failure acquired resistance-associated substitutions in NS3 and/or NS5A. Based on data from a small number of patients (n= 6), an intensified 16-week regimen of elbasvir and grazoprevir plus ribavirin could increase efficacy in patients with HCV genotype 1a infection with NS5A polymorphisms. Among patients with HCV genotype 4a or 4d infections with NS5A polymorphisms, all 26 who received the elbasvir and grazoprevir regimens recommended in prescribing information achieved an SVR12. The combination of elbasvir and grazoprevir, with or without ribavirin is safe and effective for patients with HCV genotype 1 or 4 infections. In patients with HCV genotype 1a infection, polymorphisms in NS5A at baseline (before treatment) can affect the efficacy of this direct-acting antiviral regimen, and pretreatment resistance analyses can optimize treatment selection.

VSEARCH: a versatile open source tool for metagenomics.

BackgroundVSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use.MethodsWhen searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads.ResultsVSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e., format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging. VSEARCH is slower than USEARCH when performing clustering and chimera detection, but significantly faster when performing paired-end reads merging and dereplication. VSEARCH is available at https://github.com/torognes/vsearch under either the BSD 2-clause license or the GNU General Public License version 3.0.DiscussionVSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH. A free and open-source versatile tool for sequence analysis is now available to the metagenomics community.

Analysis of Genetic Variation in Brevipalpus yothersi (Acari: Tenuipalpidae) Populations from Four Species of Citrus Host Plants.

We studied species diversity and genetic variation among populations of Brevipalpus mites from four species of citrus host plants. We sampled mites on orange, lime, grapefruit and mandarin trees from orchards at six localities distributed in the five most important citrus producing states in Mexico. Genetic variation among citrus host plants and localities were assessed by analysis of nucleotide sequence data from fragments of the mitochondrial cytochrome oxidase subunit I (COI). Both Brevipalpus yothersi and B. californicus were found at these sites, and B. yothersi was the most abundant species found on all citrus species and in all localities sampled. B. californicus was found mainly on orange and mandarin and only in two of the states sampled. AMOVA and haplotype network analyses revealed no correlation between B. yothersi genetic population structure and geographical origin or citrus host plant species. Considering that a previous study reported greater genetic diversity in B. yothersi populations from Brazil than we observed in Mexico, we discuss the possibility that the Mexican populations may have originated in the southern region of America.

&lt;p align="left"&gt;Taxonomy and phylogeny of cercosporoid fungi (Mycosphaerellaceae) from China 1

Cercosporoid fungi include a large number of mostly plant pathogenic fungi with a wide geographic distribution, being usually associated with leaf spots on a broad range of plant hosts. Here we initiate a series of studies on Chinese cercosporoid fungi, focussing on the identification of some common, rare and new plant diseases caused by these leaf-spotting ascomycetes. The aim of the series is to resolve the taxonomy and DNA phylogeny of this important group of phytopathogens in China. In this study, nine isolates of cercosporoid fungi were collected from five host species. Partial nucleotide sequence data of four gene loci (ITS, LSU, TUB and tef1-α rDNA) were generated for all isolates. Based on morphological characters in vivo and in vitro and phylogenetic data, a new species, Pseudocercospora pauciseptata (on living leaves of Pyracantha fortuneana), is introduced including a detailed description, illustration and comparison with similar species. In addition, Passalora circumscissa, Pseudocercospora cercidis-chinensis, P. lindericola, and P. prunicola are described, illustrated and phylogenetically characterized. Cerasus pseudocerasus represents a new host record for Passalora circumscissa in China, while Lindera reflexa is a new host for P. lindericola.

Bioinformatic Identification of Rare Codon Clusters (RCCs) in HBV Genome and Evaluation of RCCs in Proteins Structure of Hepatitis B Virus.

BackgroundHepatitis B virus (HBV) as an infectious disease that has nine genotypes (A - I) and a ‘putative’ genotype J.ObjectivesThe aim of this study was to identify the rare codon clusters (RCC) in the HBV genome and to evaluate these RCCs in the HBV proteins structure.MethodsFor detection of protein family accession numbers (Pfam) in HBV proteins, the UniProt database and Pfam search tool were used. Protein family accession numbers is a comprehensive and accurate collection of protein domains and families. It contains annotation of each family in the form of textual descriptions, links to other resources and literature references. Genome projects have used Pfam extensively for large-scale functional annotation of genomic data; Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). The Pfam search tools are databases that identify Pfam of proteins. These Pfam IDs were analyzed in Sherlocc program and the location of RCCs in HBV genome and proteins were detected and reported as translated EMBL nucleotide sequence data library (TrEMBL) entries. The TrEMBL is a computer-annotated supplement of SWISS-PROT that contains all the translations of European molecular biology laboratory (EMBL) nucleotide sequence entries not yet integrated in SWISS-PROT. Furthermore, the structures of TrEMBL entries proteins were studied in the PDB database and 3D structures of the HBV proteins and locations of RCCs were visualized and studied using Swiss PDB Viewer software®.ResultsThe Pfam search tool found nine protein families in three frames. Results of Pfams studies in the Sherlocc program showed that this program has not identified RCCs in the external core antigen (PF08290) and truncated HBeAg gene (PF08290) of HBV. By contrast, the RCCs were identified in gene of hepatitis core antigen (PF00906 and the residues 224 - 234 and 251 - 255), large envelope protein S (PF00695 and the residues 53-56 and 70 - 84), X protein (PF00739 and the residues 10 - 24, 29 - 83, 95 - 99. 122 - 129, 139 - 143), DNA polymerase (viral) N-terminal domain (PF00242 and the residues 59 - 62, 214 - 217, 407 - 413) and protein P (Pf00336 and the residues 225 - 228). In HBV genome, seven RCCs were identified in the gene area of hepatitis core antigen, large envelope protein S and DNA polymerase, while protein structures of TrEMBL entries sequences found in Sherlocc program outputs were not complete.ConclusionsBased on the location of detected RCCs in the structure of HBV proteins, it was found that these RCCs may have a critical role in correct folding of HBV proteins and can be considered as drug targets. The results of this study provide new and deep perspectives about structure of HBV proteins for further researches and designing new drugs for treatment of HBV.

Pathogen metadata platform: software for accessing and analyzing pathogen strain information.

BackgroundPathogen metadata includes information about where and when a pathogen was collected and the type of environment it came from. Along with genomic nucleotide sequence data, this metadata is growing rapidly and becoming a valuable resource not only for research but for biosurveillance and public health. However, current freely available tools for analyzing this data are geared towards bioinformaticians and/or do not provide summaries and visualizations needed to readily interpret results.ResultsWe designed a platform to easily access and summarize data about pathogen samples. The software includes a PostgreSQL database that captures metadata useful for disease outbreak investigations, and scripts for downloading and parsing data from NCBI BioSample and BioProject into the database. The software provides a user interface to query metadata and obtain standardized results in an exportable, tab-delimited format. To visually summarize results, the user interface provides a 2D histogram for user-selected metadata types and mapping of geolocated entries. The software is built on the LabKey data platform, an open-source data management platform, which enables developers to add functionalities. We demonstrate the use of the software in querying for a pathogen serovar and for genome sequence identifiers.ConclusionsThis software enables users to create a local database for pathogen metadata, populate it with data from NCBI, easily query the data, and obtain visual summaries. Some of the components, such as the database, are modular and can be incorporated into other data platforms. The source code is freely available for download at https://github.com/wchangmitre/bioattribution.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1231-2) contains supplementary material, which is available to authorized users.

Empirical Bayes Estimation of Coalescence Times from Nucleotide Sequence Data.

We demonstrate the advantages of using information at many unlinked loci to better calibrate estimates of the time to the most recent common ancestor (TMRCA) at a given locus. To this end, we apply a simple empirical Bayes method to estimate the TMRCA. This method is both asymptotically optimal, in the sense that the estimator converges to the true value when the number of unlinked loci for which we have information is large, and has the advantage of not making any assumptions about demographic history. The algorithm works as follows: we first split the sample at each locus into inferred left and right clades to obtain many estimates of the TMRCA, which we can average to obtain an initial estimate of the TMRCA. We then use nucleotide sequence data from other unlinked loci to form an empirical distribution that we can use to improve this initial estimate.

Quantitative monitoring of HCMV DNAlactia in human milk by real time PCR assay: Implementation of internal control contributes to standardization and quality control

For cytomegalovirus screening of breastfeeding mothers of preterm infants under risk, we present a rapid, quantitative real-time PCR protocol using the hybridization format of the viral gB target region. For quantification, we used an external gB fragment cloned into a vector system. For standardization, we created an internal control-plasmid by site-directed mutagenesis with an exchange of 9 nucleotides. Spiked with internal control, patient wildtype amplicons could be discriminated from internal controls by hybridization probes using two-channel fluorescence detection. Potential bias of formerly reported false nucleotide sequence data of gB-hybridization probes was excluded. Using this approach, we could demonstrate excellent analytical performance and high reproducibility of HCMV detection during lactation. This assay shows very good correlation with a commercial quantitative HCMV DNA PCR and may help to identify rapidly HCMV shedding mothers of very low birth weight preterm infants to prevent HCMV transmission. On the other hand, negative DNA amplification results allow feeding of milk samples of seropositive mothers to their preterm infants under risk (<30 weeks of gestational age, <1000g birth weight) during the onset and late stage of HCMV shedding during lactation.

Comparison of the activation peptide regions of protease-activated receptors (PAR) in members of the Family Felidae.

There is limited information regarding the nucleotides encoding or the predicted amino acid composition of protease-activated receptors (PAR) in cats. The purpose of the study was to determine the nucleotide sequence and predicted amino acid composition of the activation peptide regions of protease-activated receptors PAR1, PAR3, and PAR4 in Felidae family members. Genomic DNA isolated from whole blood samples collected from 10 domestic cats and 45 big cats representing 11 species was subjected to PCR using primers flanking the coding regions for the activation peptides of PAR1, PAR3, and PAR4. PCR products were isolated from agarose gels and submitted for sequencing. Nucleotide sequence data was used to predict the amino acid composition of the activation peptide and flanking regions of the 3 receptors. Predicted amino acid sequences were compared between Felidae members and to human beings. Variations in the predicted amino acid composition of the activation peptides and flanking regions of the various PAR were observed when comparing Felidae family members to each other and to human beings. While the activation peptide regions of the various PAR tend to be conserved, there are differences that may impact the ability of some agonists to mediate biased signaling events documented to occur in human platelets.

UTILIZATION OF cpDNA SEQUENCES TO IDENTIFY 15 MANGO ACCESSIONS

Information about genetic relationship and genetic diversity are an inevitable need in mango breeding program. Base substitution value, genetic distance and grouping of 15 mango accessions based on accessions in chloroplast DNA (cpDNA) among 15 mango accessions were assessed. The samples were originated from Mango Germplasm, Cukur Gondang Research Station of Indonesian Tropical Fruits Research Institute, Pasuruan, East Java. Sequencing of Chloroplast DNA was used to obtain nucleotide sequence data. Paired specific primer rpl20 F - rps12 R and atp F - rbcL R were used for amplification of non-coding area of mango DNA chloroplast and sequencing processes as well. All data were analyzed using Software MEGA 6. The result showed that total numbers and nucleotide base sequences varied among all accessions. All accessions were grouped in five different clusters that might be used as source of parental breeding.

Characterization and pathogenicity of a novel mammalian orthoreovirus from wild short-nosed fruit bats

Mammalian orthoreoviruses (MRVs) have a wide range of geographic distribution and have been isolated from humans and various animals. This study describes the isolation, molecular characterization and analysis of pathogenicity of MRV variant B/03 from wild short-nosed fruit bats. Negative stain electron microscopy illustrated that the B/03 strain is a non-enveloped icosahedral virus with a diameter of 70nm. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) migration patterns showed that the B/03 viral genome contains 10 segments in a 3:3:4 arrangement. The isolate belongs to MRV serotype 1 based on S1 gene nucleotide sequence data. BALB/c mice experimentally infected with B/03 virus by intranasal inoculation developed severe respiratory distress with tissue damage and inflammation. Lastly, B/03 virus has an increased transmission risk between bats and humans or animals.