CoreGenes5.0: An Updated User-Friendly Webserver for the Determination of Core Genes from Sets of Viral and Bacterial Genomes

The determination of core genes in viral and bacterial genomes is crucial for a better understanding of their relatedness and for their classification. CoreGenes5.0 is an updated user-friendly web-based software tool for the identification of core genes in and data mining of viral and bacterial genomes. This tool has been useful in the resolution of several issues arising in the taxonomic analysis of bacteriophages and has incorporated many suggestions from researchers in that community. The webserver displays result in a format that is easy to understand and allows for automated batch processing, without the need for any user-installed bioinformatics software. CoreGenes5.0 uses group protein clustering of genomes with one of three algorithm options to output a table of core genes from the input genomes. Previously annotated "unknown genes" may be identified with homologues in the output. The updated version of CoreGenes is able to handle more genomes, is faster, and is more robust, providing easier analysis of custom or proprietary datasets. CoreGenes5.0 is accessible at coregenes.org, migrating from a previous site.

ICTV Virus Taxonomy Profile: Chaseviridae 2022

Members of the family Chaseviridae are lytic bacterial viruses infecting representatives of the bacterial class Gammaproteobacteria. Chaseviruses have a global distribution. Virions of members of this family have a myovirus morphology (icosahedral head with contractile tail). Genomes are dsDNA of 52-56 kbp with G+C content ranging from 39.3-52.5 %. Chaseviruses, like members of the family Autographiviridae, encode a large single subunit RNA polymerase, but unlike those viruses their promoter sequences have not yet been identified. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Chaseviridae, which is available at ictv.global/report/chaseviridae.

Spectral tuning and deactivation kinetics of marine mammal melanopsins

In mammals, the photopigment melanopsin (Opn4) is found in a subset of retinal ganglion cells that serve light detection for circadian photoentrainment and pupil constriction (i.e., mydriasis). For a given species, the efficiency of photoentrainment and length of time that mydriasis occurs is determined by the spectral sensitivity and deactivation kinetics of melanopsin, respectively, and to date, neither of these properties have been described in marine mammals. Previous work has indicated that the absorbance maxima (λmax) of marine mammal rhodopsins (Rh1) have diversified to match the available light spectra at foraging depths. However, similar to the melanopsin λmax of terrestrial mammals (~480 nm), the melanopsins of marine mammals may be conserved, with λmax values tuned to the spectrum of solar irradiance at the water's surface. Here, we investigated the Opn4 pigments of 17 marine mammal species inhabiting diverse photic environments including the Infraorder Cetacea, as well as the Orders Sirenia and Carnivora. Both genomic and cDNA sequences were used to deduce amino acid sequences to identify substitutions most likely involved in spectral tuning and deactivation kinetics of the Opn4 pigments. Our results show that there appears to be no amino acid substitutions in marine mammal Opn4 opsins that would result in any significant change in λmax values relative to their terrestrial counterparts. We also found some marine mammal species to lack several phosphorylation sites in the carboxyl terminal domain of their Opn4 pigments that result in significantly slower deactivation kinetics, and thus longer mydriasis, compared to terrestrial controls. This finding was restricted to cetacean species previously found to lack cone photoreceptor opsins, a condition known as rod monochromacy. These results suggest that the rod monochromat whales rely on extended pupillary constriction to prevent photobleaching of the highly photosensitive all-rod retina when moving between photopic and scotopic conditions.

From Orphan Phage to a Proposed New Family-the Diversity of N4-Like Viruses

Escherichia phage N4 was isolated in 1966 in Italy and has remained a genomic orphan for a long time. It encodes an extremely large virion-associated RNA polymerase unique for bacterial viruses that became characteristic for this group. In recent years, due to new and relatively inexpensive sequencing techniques the number of publicly available phage genome sequences expanded rapidly. This revealed new members of the N4-like phage group, from 33 members in 2015 to 115 N4-like viruses in 2020. Using new technologies and methods for classification, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) has moved the classification and taxonomy of bacterial viruses from mere morphological approaches to genomic and proteomic methods. The analysis of 115 N4-like genomes resulted in a huge reassessment of this group and the proposal of a new family "Schitoviridae", including eight subfamilies and numerous new genera.

Bacterial diversity in the clarki ecotype of the photosynthetic sacoglossan, Elysia crispata

Few studies have examined the bacterial communities associated with photosynthetic sacoglossan sea slugs. In this study, we determined the bacterial diversity in the clarki ecotype, Elysia crispata using 16S rRNA sequencing. Computational analysis using QIIME2 revealed variability between individual samples, with the Spirochaetes and Bacteroidetes phyla dominating most samples. Tenericutes and Proteobacteria were also found, among other phyla. Computational metabolic profiling of the bacteria revealed a variety of metabolic pathways involving carbohydrate metabolism, lipid metabolism, nucleotide metabolism, and amino acid metabolism. Although associated bacteria may be involved in mutually beneficial metabolic pathways, there was a high degree of variation in the bacterial community of individual slugs. This suggests that many of these relationships are likely opportunistic rather than obligate and that many of these bacteria may live commensally providing no major benefit to the slugs.

Nutritional assessment, phytochemical composition and antioxidant analysis of the pulp and seed of medjool date grown in Mexico

The aim of this study was the characterization of fatty acids, antioxidant activity, some physical properties, nutrient content, sugars, and minerals in the pulp and seeds of the date cultivar 'Medjool' (Phoenix dactylifera L.) grown in Mexico. The samples were obtained at maturity (Tamar) in the 2017 harvest season in the valleys of San Luis Rio Colorado and Mexicali, Mexico. The following average values were obtained on a % dry weight basis for pulp and seeds, respectively: protein, 3.14% and 4.84%; lipids, 0.75% and 9.94%; fiber, 6.34% and 66.79%; total sugars, 75.32% and 5.88%; reducing sugars, 70.26% and 4.40%; and sucrose, 5.06% and 1.46%. Analysis of the minerals revealed that the most abundant elements for the pulp were: potassium, 851.98 mg/100 g; magnesium, 142.97 mg/100 g; and phosphorus, 139.40 mg/100 g, whereas for the seeds, they were potassium, 413.36 mg/100 g; sulfur, 151.36 mg/100 g; and phosphorus, 92.42 mg/100 g. Gas chromatography-mass spectrometry analysis revealed that the major unsaturated fatty acid was oleic acid, at 52.34% and 45.92%, respectively, for pulp and seeds. The main saturated fatty acids were palmitic acid (6.75%) and lauric acid (17.24%) in pulp and seeds, respectively. The total phenolic content was 1.16 and 13.73 mg GAE/100 g for pulp and seeds, respectively. Finally, the antioxidant activities were: b-carotene, 65.50% and 47.75%; DPPH, 0.079 IC₅₀ g/L and 0.0046 IC₅₀ g/L; and ABTS, 13.72 IC₅₀ g/L and 0.238 IC₅₀ g/L, respectively. The results obtained in this study confirm that the 'Medjool' cultivar grown in Mexico has the same quality of nutrients and antioxidants as those grown in the other main date-producing countries.

Detailed study of survival of patients with renal cell carcinoma in India

PURPOSE

Renal cell carcinoma (RCC) accounts for approximately 90% of all renal malignancies. The rates of kidney cancers are high in developed countries and low in eastern countries and Africa. The objective was to conduct a survival study among Indian population following nephrectomy for RCC as there was a paucity of Indian studies in medical literature.

MATERIALS AND METHODS

We conducted a follow-up study of eighty RCC patients who had nephrectomy between January 2003 and December 2010. These patients had pathological diagnosis after nephrectomy. The follow-up was done up to December 2015. The survival statistics were compiled according to Kaplan-Meier survival curves.

RESULTS

The overall survival of eighty patients was 77%. The patients with tumor size ≤7 cm and the patients with tumor size> 7 cm showed significant statistical difference at 5-year survival (P < 0.0001). The patients with low nuclear grade (1 and 2) and the patients with high nuclear grade (3 and 4) showed significant statistical difference at 5-year survival (P < 0.0001). The patients with tumor node metastasis stage below T3 and the patients with clinical stage above or equal to T3 showed significant statistical difference at 5-year survival (P = 0.003).

CONCLUSION

This study has demonstrated the importance of factors such as tumor size, nuclear grade, and stage in the assessment of prognosis of RCC patients. More studies in India with more patients are needed to demonstrate the importance of these prognostic factors.

Multi-center prospective survey of inflammatory bowel diseases in Kerala: More than 2000 cases

BACKGROUND

Inflammatory bowel disease (IBD) is considered uncommon in Asia. The aim of this study was to document the demographic characteristics and clinical aspects of ulcerative colitis (UC) and Crohn's disease (CD) in Kerala, India.

METHODS

A survey of IBD in Kerala was performed. All gastroenterologists in the region were invited. From May 2013 to October 2015, data were collected in a standardized pro-forma.

RESULTS

Forty-seven doctors in 34 centers contributed data. A total of 2142 patients were analyzed. This is the largest state-wide survey of IBD in India. Ulcerative colitis was diagnosed in 1112 (38 new), Crohn's disease in 980 (53 new), and 50 were unclassified (5 new). The district-wise distribution of IBD cases correlated with the District-wise Gross State Domestic Product (r = 0.69, p < 0.01). Three percent was below the age of 18. Patients with UC had more diarrhea (73% vs. 51%), bleeding PR (79% vs. 34%), and intermittent flares (35% vs. 13%) (all p < 0.01). Patients with CD had more abdominal pain (62% vs. 46%), weight loss (53% vs. 40%), fever (28% vs. 18%), and history of antituberculosis treatment (21% vs. 5%) (all p < 0.01). Compared to adults, children (below 18 years) were more likely to have extensive UC (58% vs. 34%, p < 0.01) and unclassified IBD (15% vs. 2%, p < 0.01).

CONCLUSION

Inflammatory bowel disease is common in Kerala, India. The disease characteristics of patients with IBD are almost similar to those from other parts of the country. Both UC and CD were seen in equal proportion in Kerala.

Genome-wide association analysis of body conformation traits in Mexican Holstein cattle using a mix of sampled and imputed SNP genotypes

In arid and semi-arid zones, animal health and production are closely correlated with body conformation traits. These selected traits, in turn, allow livestock to adapt unfavorable soil and environmental conditions. The primary objective of this study was to perform a genome-wide association analysis for a set of sampled and imputed SNPs with 16 conformation traits in a population of Holstein cows from a desert area of Northwestern Mexico. Imputation from 6K to 50K SNPs was performed as a low-cost optimization strategy. Results show eight SNPs associated with two conformation traits. The Udder Depth trait resulted in seven associated SNPs from chromosome 10, that related to Marbling Score, Milk Yield, Fat Yield, Protein Yield, and Protein Percentage Quantitative Trait Loci (QTLs). The Body Depth trait resulted in one associated SNP from chromosome 2, although no QTL relation was found. The discovery of genes associated with conformation traits may be indicative of the adaptive selection pressures the Holstein breed has undergone in response to the extreme weather conditions found in the northwestern areas of Mexico. Results of this study indicate that traits such as stature and body depth may be used as indicators of cows' potential genetic merits for milk, fat, and protein production.

A Preliminary Molecular and Phylogenetic Analysis of the Genome of a Novel Endogenous Retrovirus in the Sea Slug Elysia chlorotica

An endogenous retrovirus that is present in the sea slug Elysia chlorotica is expressed in all individuals at the end of the annual life cycle. But the precise role of the virus, if any, in slug senescence or death is unknown. We have determined the genomic sequence of the virus and performed a phylogenetic analysis of the data. The 6060-base pair genome of the virus possesses a reverse transcriptase-domain-containing protein that shows similarity to retrotransposon sequences found in Aplysia californica and Strongylocentrotus purpuratus. However, nucleotide BLAST analysis of the whole genome resulted in hits to only a few portions of the genome, indicating that the Elysia chlorotica retrovirus is novel, has not been previously sequenced, and does not have great genetic similarity to other known viral species. When more invertebrate retroviral genomes are examined, a more precise phylogenetic placement of the Elysia chlorotica retrovirus can be determined.

An Analysis of Adenovirus Genomes Using Whole Genome Software Tools

The evolution of sequencing technology has lead to an enormous increase in the number of genomes that have been sequenced. This is especially true in the field of virus genomics. In order to extract meaningful biological information from these genomes, whole genome data mining software tools must be utilized. Hundreds of tools have been developed to analyze biological sequence data. However, only some of these tools are user-friendly to biologists. Several of these tools that have been successfully used to analyze adenovirus genomes are described here. These include Artemis, EMBOSS, pDRAW, zPicture, CoreGenes, GeneOrder, and PipMaker. These tools provide functionalities such as visualization, restriction enzyme analysis, alignment, and proteome comparisons that are extremely useful in the bioinformatics analysis of adenovirus genomes.

Increasing cancer incidence in a tertiary care hospital in a developing country, India

OBJECTIVE

Cancer is a major health problem in many countries including India. Since Cancer Registries are incomplete in India, only a few epidemiological studies have been done so far. The objective was to determine the leading causes of cancer in a tertiary care hospital and compare the incidences of different types of cancer with the incidences in India and developed countries.

MATERIALS AND METHODS

An epidemiological study was done to collect data from pathology records of 1003 cancer cases during 6-month period in the year 2010. The data was collected in a computer and the data was utilized to make tables and histograms.

RESULTS

Of the 1003 cases, the leading cancer site was breast, followed by colon and rectum, lymph node and stomach. The leading cancer site for men was colon and rectum and for women was breast.

CONCLUSION

Cancer incidence is now low in India, a developing country, compared to developed Western countries. However, some cancers, like breast and colon and rectum cancers are increasing every year.

IMPACT

The findings of this study support that cancer incidence is increasing in India and more epidemiological studies are needed.

Depletion of Olig2 in oligodendrocyte progenitor cells infected by Theiler's murine encephalomyelitis virus

Theiler's murine encephalomyelitis virus (TMEV) infects the central nervous system of mice and causes a demyelinating disease that is a model for multiple sclerosis. During the chronic phase of the disease, TMEV persists in oligodendrocytes and macrophages. Lack of remyelination has been attributed to insufficient proliferation and differentiation of oligodendrocyte progenitor cells (OPCs), but the molecular mechanisms remain unknown. Here, we employed pluripotent stem cell technologies to generate pure populations of mouse OPCs to study the temporal and molecular effects of TMEV infection. Global transcriptome analysis of RNA sequencing data revealed that TMEV infection of OPCs caused significant up-regulation of 1926 genes, whereas 1853 genes were significantly down-regulated compared to uninfected cells. Pathway analysis revealed that TMEV disrupted many genes required for OPC growth and maturation. Down-regulation of Olig2, a transcription factor necessary for OPC proliferation, was confirmed by real-time PCR, immunofluorescence microscopy, and western blot analysis. Depletion of Olig2 was not found to be specific to viral strain and did not require expression of the leader (L) protein, which is a multifunctional protein important for persistence, modulation of gene expression, and cell death. These data suggest that direct infection of OPCs by TMEV may inhibit remyelination during the chronic phase of TMEV-induced demyelinating disease.

Functional prediction of hypothetical proteins in human adenoviruses

Assigning functional information to hypothetical proteins in virus genomes is crucial for gaining insight into their proteomes. Human adenoviruses are medium sized viruses that cause a range of diseases. Their genomes possess proteins with uncharacterized function known as hypothetical proteins. Using a wide range of protein function prediction servers, functional information was obtained about these hypothetical proteins. A comparison of functional information obtained from these servers revealed that some of them produced functional information, while others provided little functional information about these human adenovirus hypothetical proteins. The PFP, ESG, PSIPRED, 3d2GO, and ProtFun servers produced the most functional information regarding these hypothetical proteins.

Genome-wide identification of copy number variations in Holstein cattle from Baja California, Mexico, using high-density SNP genotyping arrays

Copy number variations (CNVs) are an important source of genomic structural variation, and can be used as markers to investigate phenotypic and economic traits. CNVs also have functional effects on gene expression and can contribute to disease susceptibility in mammals. Currently, single nucleotide polymorphism genotyping arrays (SNP chips) are the technology of choice for identifying CNV variations. Microarray technologies have recently been used to study the bovine genome. The objective of the present study was to develop CNVs in Holstein cows from the Northwest of Mexico using the Affymetrix Axiom Genome-Wide BOS 1 Array, which assays 648,315 SNPs and provides a wide coverage for genome-wide studies. We applied the two most widely used algorithms for the discovery of CNVs (PennCNV and QuantiSNP) and found 56 CNV regions (CNVRs) representing 0.33% of the bovine genome (8.46 Mb). These CNVRs ranged from 1.5 to 970.8 kb with an average length of 151 kb. They involved 103 genes and showed a 28% overlap with CNVRs already reported. Of the 56 CNVRs found, 20 were novel. In this study we present the first genomic analysis of CNVs in Mexican cattle using high-density SNP data. Our results provide a new reference basis for future genomic variation and association studies between CNVs and phenotypes, especially in Mexican cattle.

Integration of genomic and proteomic analyses in the classification of the Siphoviridae family

Using a variety of genomic (BLASTN, ClustalW) and proteomic (Phage Proteomic Tree, CoreGenes) tools we have tackled the taxonomic status of members of the largest bacteriophage family, the Siphoviridae. In all over 400 phages were examined and we were able to propose 39 new genera, comprising 216 phage species, and add 62 species to two previously defined genera (Phic3unalikevirus; L5likevirus) grouping, in total, 390 fully sequenced phage isolates. Many of the remainders are orphans which the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) chooses not to ascribe genus status at the time being.

Evidence for a retroviral insertion in TRPM1 as the cause of congenital stationary night blindness and leopard complex spotting in the horse

Leopard complex spotting is a group of white spotting patterns in horses caused by an incompletely dominant gene (LP) where homozygotes (LP/LP) are also affected with congenital stationary night blindness. Previous studies implicated Transient Receptor Potential Cation Channel, Subfamily M, Member 1 (TRPM1) as the best candidate gene for both CSNB and LP. RNA-Seq data pinpointed a 1378 bp insertion in intron 1 of TRPM1 as the potential cause. This insertion, a long terminal repeat (LTR) of an endogenous retrovirus, was completely associated with LP, testing 511 horses (χ²=1022.00, p<<0.0005), and CSNB, testing 43 horses (χ²=43, p<<0.0005). The LTR was shown to disrupt TRPM1 transcription by premature poly-adenylation. Furthermore, while deleterious transposable element insertions should be quickly selected against the identification of this insertion in three ancient DNA samples suggests it has been maintained in the horse gene pool for at least 17,000 years. This study represents the first description of an LTR insertion being associated with both a pigmentation phenotype and an eye disorder.

CoreGenes3.5: a webserver for the determination of core genes from sets of viral and small bacterial genomes

Background

CoreGenes3.5 is a webserver that determines sets of core genes from viral and small bacterial genomes as an automated batch process. Previous versions of CoreGenes have been used to classify bacteriophage genomes and mine data from pathogen genomes.

Findings

CoreGenes3.5 accepts as input GenBank accession numbers of genomes and performs iterative BLASTP analyses to output a set of core genes. After completion of the program run, the results can be either displayed in a new window for one pair of reference and query genomes or emailed to the user for multiple pairs of small genomes in tabular format.

Conclusions

With the number of genomes sequenced increasing daily and interest in determining phylogenetic relationships, CoreGenes3.5 provides a user-friendly web interface for wet-bench biologists to process multiple small genomes for core gene determinations. CoreGenes3.5 is available at http://binf.gmu.edu:8080/CoreGenes3.5.

Self-energy on the low- to high-energy electronic structure of correlated metal SrVO3

The correlated electronic structure of SrVO(3) has been investigated by angle-resolved photoemission spectroscopy using in situ prepared thin films. Pronounced features of band renormalization have been observed: a sharp kink ∼60 meV below the Fermi level (E(F)) and a broad so-called "high-energy kink" ∼0.3 eV below E(F) as in the high-T(c) cuprates, although SrVO(3) does not show magnetic fluctuations. We have deduced the self-energy in a wide energy range by applying the Kramers-Kronig relation to the observed spectra. The obtained self-energy clearly shows a large energy scale of ∼0.7 eV, which is attributed to electron-electron interaction and gives rise to the ∼0.3 eV kink in the band dispersion as well as the incoherent peak ∼1.5 eV below E(F). The present analysis enables us to obtain a consistent picture for both the incoherent spectra and the band renormalization.

Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0

Background

The growing whole genome sequence databases necessitate the development of user-friendly software tools to mine these data. Web-based tools are particularly useful to wet-bench biologists as they enable platform-independent analysis of sequence data, without having to perform complex programming tasks and software compiling.

Findings

GeneOrder4.0 is a web-based "on-the-fly" synteny and gene order analysis tool for comparative bacterial genomics (ca. 8 Mb). It enables the visualization of synteny by plotting protein similarity scores between two genomes and it also provides visual annotation of "hypothetical" proteins from older archived genomes based on more recent annotations.

Conclusions

The web-based software tool GeneOrder4.0 is a user-friendly application that has been updated to allow the rapid analysis of synteny and gene order in large bacterial genomes. It is developed with the wet-bench researcher in mind.

Data mining pathogen genomes using GeneOrder and CoreGenes and CGUG: gene order, synteny and in silico proteomes

Sequence databases are growing exponentially due to 'next generation' DNA analysers and applications of these data. Databases include multiple sequences of previously sequenced organisms, particularly ones of consequence to human health. Applications are limited by tools available to mine them, particularly user-friendly tools that are useful for bench researchers. GeneOrder, CoreGenes and CGUG are web-based 'on-the-fly' tools that examine gene order and synteny, as well as proteomes for comparative genomics and for drug discovery and design targets. CoreGenes (CGUG) now allows analysis of genomes ranging up to 1.9 megabases. Many of these small genome bacteria have impacts on human health.

Classification of Myoviridae bacteriophages using protein sequence similarity

Background

We advocate unifying classical and genomic classification of bacteriophages by integration of proteomic data and physicochemical parameters. Our previous application of this approach to the entirely sequenced members of the Podoviridae fully supported the current phage classification of the International Committee on Taxonomy of Viruses (ICTV). It appears that horizontal gene transfer generally does not totally obliterate evolutionary relationships between phages.

Results

CoreGenes/CoreExtractor proteome comparison techniques applied to 102 Myoviridae suggest the establishment of three subfamilies (Peduovirinae, Teequatrovirinae, the Spounavirinae) and eight new independent genera (Bcep781, BcepMu, FelixO1, HAP1, Bzx1, PB1, phiCD119, and phiKZ-like viruses). The Peduovirinae subfamily, derived from the P2-related phages, is composed of two distinct genera: the "P2-like viruses", and the "HP1-like viruses". At present, the more complex Teequatrovirinae subfamily has two genera, the "T4-like" and "KVP40-like viruses". In the genus "T4-like viruses" proper, four groups sharing >70% proteins are distinguished: T4-type, 44RR-type, RB43-type, and RB49-type viruses. The Spounavirinae contain the "SPO1-"and "Twort-like viruses."

Conclusion

The hierarchical clustering of these groupings provide biologically significant subdivisions, which are consistent with our previous analysis of the Podoviridae.

CGUG: in silico proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to ca. 1.9 Mb

BACKGROUND

Viruses and small-genome bacteria (~2 megabases and smaller) comprise a considerable population in the biosphere and are of interest to many researchers. These genomes are now sequenced at an unprecedented rate and require complementary computational tools to analyze. "CoreGenesUniqueGenes" (CGUG) is an in silico genome data mining tool that determines a "core" set of genes from two to five organisms with genomes in this size range. Core and unique genes may reflect similar niches and needs, and may be used in classifying organisms.

FINDINGS

CGUG is available at http://binf.gmu.edu/geneorder.html as a web-based on-the-fly tool that performs iterative BLASTP analyses using a reference genome and up to four query genomes to provide a table of genes common to these genomes. The result is an in silico display of genomes and their proteomes, allowing for further analysis. CGUG can be used for "genome annotation by homology", as demonstrated with Chlamydophila and Francisella genomes.

CONCLUSION

CGUG is used to reanalyze the ICTV-based classifications of bacteriophages, to reconfirm long-standing relationships and to explore new classifications. These genomes have been problematic in the past, due largely to horizontal gene transfers. CGUG is validated as a tool for reannotating small genome bacteria using more up-to-date annotations by similarity or homology. These serve as an entry point for wet-bench experiments to confirm the functions of these "hypothetical" and "unknown" proteins.

Genomic and bioinformatics analyses of HAdV-14p, reference strain of a re-emerging respiratory pathogen and analysis of B1/B2

Unlike other human adenovirus (HAdV) species, B is divided into subspecies B1 and B2. Originally this was partly based on restriction enzyme (RE) analysis. B1 members, except HAdV-50, are commonly associated with respiratory diseases while B2 members are rarely associated with reported respiratory diseases. Recently two members of B2 have been identified in outbreaks of acute respiratory disease (ARD). One, HAdV-14, has re-emerged after an apparent 52-year absence. Genomic analysis and bioinformatics data are reported for HAdV-14 prototype for use as a reference and to understand and counter its re-emergence. The data complement and extend the original criteria for subspecies designation, unique amongst the adenoviruses, and highlight differences between B1 and B2, representing the first comprehensive analysis of this division. These data also provide finer granularity into the pathoepidemiology of the HAdVs. Whole genome analysis uncovers heterogeneous identity structures of the hexon and fiber genes amongst the HAdV-14 and the B1/B2 subspecies, which may be important in prescient vaccine development. Analysis of cell surface proteins provides insight into HAdV-14 tropism, accounting for its role as a respiratory pathogen. This HAdV-14 prototype genome is also a reference for applications of B2 adenoviruses as vectors for vaccine development and gene therapy.

Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools

We defined phage genera by measuring genome relationships by the numbers of shared homologous/orthologous proteins. We used BLAST-based tools (CoreExtractor.vbs and CoreGenes) to analyze 55 fully sequenced bacteriophage genomes from the NCBI and EBI databases. This approach was first applied to the T7-related phages. Using a cut-off score of 40% homologous proteins, we identified three genera within the T7-related phages, redefined the phi29-related phages, and introduced five novel genera. The T7- and phi29-related phages were given subfamily status and named "Autographivirinae" and "Picovirinae", respectively. Our results confirm and refine the ICTV phage classification, enable elimination of errors in public databases, and provide a straightforward tool for the molecular classification of new phage genomes.

Intraductal papillary mucinous neoplasm in tropical chronic pancreatitis

We report a 56-year-old man with chronic calcifying pancreatitis of the tropics (tropical calcific pancreatitis) who had been asymptomatic and on follow up developed a pancreatic mass that was identified as intraductal papillary mucinous neoplasm. He has been asymptomatic after distal pancreatectomy.

Isolated duodeno-pancreatic involvement due to metastatic dysgerminoma ovary and its management by a modified pancreatico-duodenal resection

Dysgerminomas of the ovary rarely metastasize to abdominal viscera and when they do, the involvement is a part of a disseminated disease. A 30-year-old woman developed isolated duodenopancreatic dysgerminoma 14 years after salpingo-oophorectomy. The clinical picture was complicated by the presence of tuberculous lesions in the liver which mimicked metastatic disease. Surgical excision was carried out using a modified pancreatic head resection.

Brunner's gland adenoma with circumferential duodenal involvement

Brunner's gland adenoma is a benign tumor of the duodenum. We report a 58-year-old man who presented with abdominal pain, vomiting and weight loss. The patient underwent Whipple resection along with lymph node clearance. The resected tumor, 4 cm long, showed hypertrophied Brunner's glands.

Spin, charge, and orbital ordering in La0.5Sr1.5Mno4

We have analyzed the experimental evidence of charge and orbital ordering in La0.5Sr1.5MnO4 using first principles band structure calculations. Our results suggest the presence of two types of Mn sites in the system. One of the Mn sites behaves as an Mn3+ ion, favoring a Jahn-Teller distortion of the surrounding oxygen atoms, while the distortion around the other is not a simple breathing mode kind. Band structure effects are found to dominate the experimental spectrum for orbital and charge ordering, providing an alternate explanation for the experimentally observed results.

Electronic structure of Sr2FeMoO6

We have analyzed the unusual electronic structure of Sr2FeMoO6 combining ab initio and model Hamiltonian approaches. Our results indicate that there are strong enhancements of the intra-atomic exchange strength at the Mo site as well as the antiferromagnetic coupling strength between Fe and Mo sites. We discuss the possibility of a negative effective Coulomb correlation strength ( U(eff)) at the Mo site due to these renormalized interaction strengths.

Production of hyaluronan by glomerular mesangial cells in response to fibronectin and platelet-derived growth factor

The formation of the non-sulphated glycosaminoglycan hyaluronan by cells of the renal glomerulus in diabetes may contribute to altered matrix composition. We describe an increased production of hyaluronan from mesangial cell-enriched glomerular cores from diabetic animals, and further show that increased hyaluronan production follows the exposure of non-diabetic and diabetic preparations to fibronectin and to platelet-derived growth factor in vitro. Hyaluronan production appeared dependent on protein kinase C activity, and could not be shown after prolonged phorbol ester preincubation. Stimulation by fibronectin was wholly dependent on cyclooxygenase activity and prior prostaglandin production, while the effect of platelet-derived growth factor showed only a partial dependence.

Effect of prostaglandin E2 and hyaluronan on mesangial cell proliferation. A potential contribution to glomerular hypercellularity in diabetes

Proliferation of mesangial cells is a feature of several forms of human and experimental glomerulopathy, including that seen in diabetes. The nonsulfated glycosaminoglycan hyaluronan participates in the regulation of pericellular matrix assembly and is a mitogen in some cell types. We have shown previously that hyaluronan production is increased in the glomerulus in a glucose- and prostaglandin-dependent manner. We have investigated the effect of diabetes and of addition of hyaluronan and prostaglandin E2 (PGE2) on the uptake of [3H]thymidine by glomerular core preparations enriched in mesangial cells. When compared with nondiabetic controls, it was shown that [3H]thymidine uptake was significantly increased in glomerular core preparations from streptozotocin-induced diabetic rats (to 169 +/- 5%, P < 0.001). In glomerular cores from both experimental groups, hyaluronan (50-250 ng/ml) or PGE2 (10(-12) to 10(-8) mol/l) increased the uptake of [3H]thymidine. Further, mesangial cells from nondiabetic control glomerular cores, when maintained in culture in early passage, responded with increased [3H]thymidine uptake to raised glucose (5.6-25 mmol/l) and to added hyaluronan and PGE2. We propose that prostaglandin and hyaluronan production in response to a raised glucose environment in diabetes can contribute to mesangial hypercellularity.

Increased hyaluronan production in the glomeruli from diabetic rats: a link between glucose-induced prostaglandin production and reduced sulphated proteoglycan

Exposure in vivo or in vitro to elevated glucose increases production of vasoactive prostaglandins by glomeruli and mesangial cells. This study aimed to determine whether this increased prostaglandin production could provide a link with later structural changes in diabetic nephropathy. Glomerular cores were prepared from control rats and streptozotocin-diabetic rats (3 weeks' duration). Over 24 h in culture hyaluronan production from diabetic glomerular cores was higher than production from control glomerular cores whether maintained in 5.6 mmol/l glucose (105.6 +/- 15.5 vs 53.6 +/- 8.5 ng hyaluronan per 250 glomerular cores, p < 0.001); in 25 mmol/l glucose (149.3 +/- 34.8 vs 62.7 +/- 7.8 ng hyaluronan per 250 glomerular cores, p < 0.01); or in 45 mmol/l glucose (176.8 +/- 23.3 vs 102.0 +/- 17.9 ng hyaluronan per 250 glomerular cores, p < 0.01). At 5.6 mmol/l glucose, exposure in vitro to prostaglandin E2 caused an increase in hyaluronan production [maximal at 10(-9) mol/l prostaglandin E2, 237 +/- 19 vs 42 +/- 4, ng hyaluronan per 250 glomerular cores, p < 0.001 (control) and 195 +/- 7 vs 103 +/- 5, ng hyaluronan per 250 glomerular cores, p < 0.001 (diabetic)]. In both control and diabetic glomerular cores hyaluronan production was reduced significantly by the cyclooxygenase inhibitor indomethacin (10(-5) mol/l) [24.7 +/- 3.33 vs. 40.25 +/- 4.11 ng hyaluronan per 250 glomerular cores, p < 0.05 (control) and 36.5 +/- 6.25 vs 118.0 +/- 22.6, p < 0.01 (diabetic)]. A direct spectrophotometric microassay was used to determine the concentration of sulphated glycosaminoglycans derived from papain-digested glomerular core proteoglycans.(ABSTRACT TRUNCATED AT 250 WORDS)