dictyBase and the Dicty Stock Center (version 2.0) - a progress report.

After serving the Dictyostelium community for many years, the first version of dictyBase (Chisholm et al., 2006; Fey et al., 2006) was in need of a decisive update. The original dictyBase software was not adaptable to more current demands such as handling the import of large-scale data from recently sequenced genomes, keeping up with changes in the Gene Ontology (GO), or handling the automatic annotation of over 20,000 new strains. Therefore, we have embarked on a complete overhaul of dictyBase. The new infrastructure will allow the introduction of new data, such as more expressive GO annotations and Dictyostelium disease orthologs. A modern user interface aims to streamline usage of the database including orders from the Dicty Stock Center (DSC). New displays will allow novel views including the combination of data in two new tools. With the underlying software infrastructure now in place, dictyBase software engineers and curators are currently adding the user interfaces, new tools and content pages for the evolving version 2.0 of dictyBase. This review highlights the emerging status of the new dictyBase, updated pages and annotations that will soon be available in the new environment, an overview of our annotation procedures, and plans to involve the community in curation efforts.

RNAcentral: a comprehensive database of non-coding RNA sequences.

RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/.

Is lithium essential for epididymal sperm maturation?

A wider biological role of ultratrace element lithium in the mammalian reproduction has been reported, however, presence of lithium in the epididymal luminal fluid (ELF) and its influence on sperm during maturation events in the epididymal regions are still unknown. A pilot study was carried out in Jamunapari buck which revealed that levels of lithium in the ELF diminished gradually and significantly (P<0.01) from caput to cauda epididymis, concomitantly, a distinct increase (P<0.01) in the spermatozoan motility, viability and hypo-osmotic reactive sperm were observed, except spermatozoan motility that was found absent in the caput epididymis. Therefore, we hypothesize that levels of lithium in the epididymal regions is one of the motility initiation and/or regulatory factor for epididymal sperm maturation essential for acquiring fertilizing competence of sperm cells, hence, lithium could also be considered as one of the biomarker of sperm maturation in any species.

dictyBase 2015: Expanding data and annotations in a new software environment.

dictyBase is the model organism database for the social amoeba Dictyostelium discoideum and related species. The primary mission of dictyBase is to provide the biomedical research community with well-integrated high quality data, and tools that enable original research. Data presented at dictyBase is obtained from sequencing centers, groups performing high throughput experiments such as large-scale mutagenesis studies, and RNAseq data, as well as a growing number of manually added functional gene annotations from the published literature, including Gene Ontology, strain, and phenotype annotations. Through the Dicty Stock Center we provide the community with an impressive amount of annotated strains and plasmids. Recently, dictyBase accomplished a major overhaul to adapt an outdated infrastructure to the current technological advances, thus facilitating the implementation of innovative tools and comparative genomics. It also provides new strategies for high quality annotations that enable bench researchers to benefit from the rapidly increasing volume of available data. dictyBase is highly responsive to its users needs, building a successful relationship that capitalizes on the vast efforts of the Dictyostelium research community. dictyBase has become the trusted data resource for Dictyostelium investigators, other investigators or organizations seeking information about Dictyostelium, as well as educators who use this model system.

Cytological Study of Breast Carcinoma Before and After Oncotherapy with Special Reference to Morphometry and Proliferative Activity.

Our study was done to assess the cytological changes due to oncotherapy in breast carcinoma especially on morphometry and proliferative activity. Cytological aspirates were collected from a total of 32 cases of invasive ductal carcinoma both before and after oncotherapy. Morphometry was done on the stained cytological smears to assess the different morphological parameters of cell dimension by using the ocular morphometer and the software AutoCAD 2007. Staining was done with Ki-67 and proliferating cell nuclear antigen (PCNA) as proliferative markers. Different morphological parameters were compared before and after oncotherapy by unpaired Student's t test. Statistically significant differences were found in morphometric parameters, e.g., mean nuclear diameter, mean nuclear area, mean cell diameter, and mean cell area, and in the expression of proliferative markers (Ki-67 and PCNA). Statistical analysis was done by obtaining p values. There are statistically significant differences between morphological parameter of breast carcinoma cells before and after oncotherapy.

One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012.

dictyBase (http://dictybase.org), the model organism database for Dictyostelium discoideum, includes the complete genome sequence and expression data for this organism. Relevant literature is integrated into the database, and gene models and functional annotation are manually curated from experimental results and comparative multigenome analyses. dictyBase has recently expanded to include the genome sequences of three additional Dictyostelids and has added new software tools to facilitate multigenome comparisons. The Dicty Stock Center, a strain and plasmid repository for Dictyostelium research, has relocated to Northwestern University in 2009. This allowed us integrating all Dictyostelium resources to better serve the research community. In this chapter, we will describe how to navigate the Web site and highlight some of our newer improvements.

DictyBase 2013: integrating multiple Dictyostelid species.

dictyBase (http://dictybase.org) is the model organism database for the social amoeba Dictyostelium discoideum. This contribution provides an update on dictyBase that has been previously presented. During the past 3 years, dictyBase has taken significant strides toward becoming a genome portal for the whole Amoebozoa clade. In its latest release, dictyBase has scaled up to host multiple Dictyostelids, including Dictyostelium purpureum [Sucgang, Kuo, Tian, Salerno, Parikh, Feasley, Dalin, Tu, Huang, Barry et al.(2011) (Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biol., 12, R20)], Dictyostelium fasciculatum and Polysphondylium pallidum [Heidel, Lawal, Felder, Schilde, Helps, Tunggal, Rivero, John, Schleicher, Eichinger et al. (2011) (Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication. Genome Res., 21, 1882-1891)]. The new release includes a new Genome Browser with RNAseq expression, interspecies Basic Local Alignment Search Tool alignments and a unified Basic Local Alignment Search Tool search for cross-species comparisons.

Follicular Dendritic Cell Sarcoma of Ileoceacal Region in a Young Woman: A Rare Case Report with Review of Literature.

Follicular dendritic cell sarcoma arises from the follicular dendritic cells present in the lymph nodes, especially of the head and neck area. Rarely, extranodal sites may be affected including tonsil, the oral cavity, liver, spleen and the gastrointestinal tract. Here, we report a case of intra-abdominal follicular dendritic cell sarcoma presenting as a huge mass in the ileocecal region of a 24-year young woman.

Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR.

WormBase, dictyBase and The Arabidopsis Information Resource (TAIR) are model organism databases containing information about Caenorhabditis elegans and other nematodes, the social amoeba Dictyostelium discoideum and related Dictyostelids and the flowering plant Arabidopsis thaliana, respectively. Each database curates multiple data types from the primary research literature. In this article, we describe the curation workflow at WormBase, with particular emphasis on our use of text-mining tools (BioCreative 2012, Workshop Track II). We then describe the application of a specific component of that workflow, Textpresso for Cellular Component Curation (CCC), to Gene Ontology (GO) curation at dictyBase and TAIR (BioCreative 2012, Workshop Track III). We find that, with organism-specific modifications, Textpresso can be used by dictyBase and TAIR to annotate gene productions to GO's Cellular Component (CC) ontology.

Basaloid squamous cell carcinoma of nasopharynx: an extremely rare variety of tumour of nasopharynx.

Nasopharyngeal carcinoma is the predominant tumour type arising in the nasopharynx with cervical lymphadenopathy present in 60-90% of all cases at the time of presentation. The most pathological varieties include squamous cell carcinoma well-differentiated keratinising, and moderately differentiated non-keratinising and an undifferentiated type. The rare variety of squamous cell carcinoma is basaloid type, according to the "WHO Classification of Tumours Pathology and Genetics: Head and Neck Tumours". In this study, we present a case of basaloid squamous cell carcinoma of nasopharynx in a 41-year female who presented with epistaxis and bilateral cervical lymphadenopathy.

Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum.

BACKGROUND: The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum. RESULTS: We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 × coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict. CONCLUSIONS: The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.

dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa.

dictyBase (http://www.dictybase.org), the model organism database for Dictyostelium, aims to provide the broad biomedical research community with well integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a 'reference genome' in the Amoebozoa clade. We highlight several new features in the present update: (i) new annotations; (ii) improved interface with web 2.0 functionality; (iii) the initial steps towards a genome portal for the Amoebozoa; (iv) ortholog display; and (v) the complete integration of the Dicty Stock Center with dictyBase.

Identification and characterization of phage PS166 lysogens from non-O1, O139 strains of Vibrio cholerae.

BACKGROUND: In recent years, non-O1, O139 serogroups of Vibrio cholerae have become a major source of pathogenic infection. However, the origin and acquisition of their virulence properties remain under explored. In this regard bacteriophages of Vibrio cholerae are well known to be the carriers of pathogenic traits across various strains. So, any possible association of vibriophages and non-O1, O139 serogroups would provide a deeper insight of their pathogenic threats. MATERIAL/METHODS: Ten non-O1, O139 clinical isolates of Vibrio cholerae were induced by mitomycin C. Virulence profiles of those isolates were determined by multiplex PCR. BglII, KpnI and HaeII were used to generate the restriction profile of isolated bacteriophage. Two of the phage harboring strains was ribotyped by Southern hybridization. RESULTS: In the present study, ten non-O1, O139 diarrheal isolates of Vibrio cholerae were examined for their ability to produce infectious phage particles out of which two strains, PG128 and PG130 were found to be positive. The host range and restriction profile of phage particles were identical to a biotype converting temperate vibriophage PS166. Both PG128 and PG130 carried unique ribotype pattern and lacked the major virulence determinants. But PG128 was found to carry hlyA, mshA, rtxC and toxR, a set of accessory virulence determinants. CONCLUSIONS: The evidences present here provide definite clues for a possible phage mediated emergence of newer Vibrio choleare pathogens.

dictyBase--a Dictyostelium bioinformatics resource update.

dictyBase (http://dictybase.org) is the model organism database for Dictyostelium discoideum. It houses the complete genome sequence, ESTs and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome. This dictyBase update describes the annotations and features implemented since 2006, including improved strain and phenotype representation, integration of predicted transcriptional regulatory elements, protein domain information, biochemical pathways, improved searching and a wiki tool that allows members of the research community to provide annotations.

A quantitative proteomic analysis of mitochondrial participation in p19 cell neuronal differentiation.

A quantitative proteomic analysis of changes in protein expression accompanying the differentiation of P19 mouse embryonal carcinoma cells into neuron-like cells using isobaric tag technology coupled with LC-MS/MS revealed protein changes reflecting withdrawal from the cell cycle accompanied by a dynamic reorganization of the cytoskeleton and an up-regulation of mitochondrial biogenesis. Further study of quantitative changes in abundance of individual proteins in a purified mitochondrial fraction showed that most mitochondrial proteins increased significantly in abundance. A set of chaperone proteins did not participate in this increase, suggesting that neuron-like cells are relatively deficient in mitochondrial chaperones. We developed a procedure to account for differences in recovery of mitochondrial proteins during purification of organelles from distinct cell or tissue sources. Proteomic data supported by RT-PCR analysis suggests that enhanced mitochondrial biogenesis during neuronal differentiation may reflect a large increase in expression of PGC-1alpha combined with down-regulation of its negative regulator, p160 Mybbp1a.

MiGenes: a searchable interspecies database of mitochondrial proteins curated using gene ontology annotation.

MOTIVATION: There has been an explosion of interest in the role of mitochondria in programmed cell death and other fundamental pathological processes underlying the development of human diseases. Nevertheless, the inventory of mitochondrial proteins encoded in the nuclear genome remains incomplete, providing an impediment to mitochondrial research at the interface with systems biology. We created the MiGenes database to further define the scope of the mitochondrial proteome in humans and model organisms including mice, rats, flies and worms as well as budding and fission yeasts. MiGenes is intended to stimulate mitochondrial research using model organisms. SUMMARY: MiGenes is a large-scale relational database that is automatically updated to keep pace with advances in mitochondrial proteomics and is curated to assure that the designation of proteins as mitochondrial reflects gene ontology (GO) annotations supported by high-quality evidence codes. A set of postulates is proposed to help define which proteins are authentic components of mitochondria. MiGenes incorporates >1160 new GO annotations to human, mouse and rat protein records, 370 of which represent the first GO annotation reflecting a mitochondrial localization. MiGenes employs a flexible search interface that permits batchwise accession number searches to support high-throughput proteomic studies. A web interface is provided to permit members of the mitochondrial research community to suggest modifications in protein annotations or mitochondrial status.

A prospective and randomized study of radiotherapy, sequential chemotherapy radiotherapy and concomitant chemotherapy-radiotherapy in unresectable non small cell carcinoma of the lung.

PURPOSE: Treatment of advanced Non small cell lung cancer (NSCLC) often produces dismal results. Combination of available treatment modalities has reportedly improved the outcome. A prospectively randomized trial was conducted, comparing combined treatment modalities versus radiotherapy alone, in treatment of unresectable NSCLC. MATERIALS AND METHODS: A total of 103 patients were randomized to three groups. In group 'A', 32 patients received radiotherapy alone (6500 cGy/30 fraction). In group 'B', 35 patients received neoadjuvant chemotherapy (Cisplatin 80 mg/m2 on day 1 and Etoposide 100 mg/m day 1-3 intravenously q3 weeks for 3 cycles), followed by radiotherapy (6000 cGy/30 fractions) and 3 more cycles of Chemotherapy, with the same regimen. In group 'C', 36 patients received radiotherapy (5000 cGy/25 fractions) with concurrent chemotherapy (cisplatin 20 mg/m2 + Etoposide 75 mg/m2 intravenously on day 1-5 and day 22-26), followed by 2 more cycles of chemotherapy, q3 weeks with the same regimen. RESULTS: Initial treatment responses were significantly higher in group 'B' (P < 0.05) and 'C' (P < 0.03), compared to group 'A'. Follow-up observations showed, that addition of chemotherapy brought down distant metastasis's from 62.5% (group 'A') to 48.6% (group 'B') and 44.4% (group 'C'). The median time to tumour progression also improved from 16 months (Group 'A') to 21 months (Group 'B' and 'C'). But 2 year follow up did not show any survival benefit. Acute toxicities were more frequent in group 'B' and 'C', but were manageable. CONCLUSION: Addition of chemotherapy with radiation in unresectable NSCLC improves response rates, time to tumour progression and disease free survival, though the same effect is not translated in overall survival.

Isolation and characterization of unserotypable lysogens of Vibrio cholerae phage PS166.

BACKGROUND: Temperate phages of Vibrio cholerae are the major force in the emergence of newer pathogenic clones. PS166, a temperate vibriophage, has the ability to convert pathogenic biotypes of the V. Cholerae O1 serogroup. During the conversion process, PS166 also tends to produce a group of lysogens neither reported nor characterized so far. Characterization of those lysogens may provide insight into the emergence of newer pathogenic clones of V. Cholerae. MATERIAL/METHODS: The V. cholerae eltor strain MAK757 was used to generate PS166 lysogens which were serotyped by using antisera specific to V. Cholerae O1 and O139 strains. Multiplex PCR was used to compare the status of various pathogenic markers of those lysogens. The outer membrane proteins (OMP) of the lysogens were determined by SDS-PAGE. RESULTS: Temperate phage PS166 infection of V. cholerae eltor MAK757 gave rise to a new kind of lysogens termed unserotypable due to their lack of reactivity to both O1 and O139 antisera. Moreover, these lysogens displayed a new phage sensitivity profile different from both classical and parental eltor biotypes. The genetic profiles of the CTX element and VPI region of these lysogens were found to be unaltered, together with the biotype-specific markers mshA and hlyA. Though the genetic loci of major outer membrane proteins did not change after lysogenization, the outer membrane protein profile of these lysogens showed the absence of a 40-kDa band corresponding to the toxR-controlled porin, ompT. CONCLUSIONS: We provide evidence for the vibriophage PS166-mediated lysogenic conversion of pathogenic cholera strains.