GenSeed-HMM: A Tool for Progressive Assembly Using Profile HMMs as Seeds and its Application in Alpavirinae Viral Discovery from Metagenomic Data.

This work reports the development of GenSeed-HMM, a program that implements seed-driven progressive assembly, an approach to reconstruct specific sequences from unassembled data, starting from short nucleotide or protein seed sequences or profile Hidden Markov Models (HMM). The program can use any one of a number of sequence assemblers. Assembly is performed in multiple steps and relatively few reads are used in each cycle, consequently the program demands low computational resources. As a proof-of-concept and to demonstrate the power of HMM-driven progressive assemblies, GenSeed-HMM was applied to metagenomic datasets in the search for diverse ssDNA bacteriophages from the recently described Alpavirinae subfamily. Profile HMMs were built using Alpavirinae-specific regions from multiple sequence alignments (MSA) using either the viral protein 1 (VP1; major capsid protein) or VP4 (genome replication initiation protein). These profile HMMs were used by GenSeed-HMM (running Newbler assembler) as seeds to reconstruct viral genomes from sequencing datasets of human fecal samples. All contigs obtained were annotated and taxonomically classified using similarity searches and phylogenetic analyses. The most specific profile HMM seed enabled the reconstruction of 45 partial or complete Alpavirinae genomic sequences. A comparison with conventional (global) assembly of the same original dataset, using Newbler in a standalone execution, revealed that GenSeed-HMM outperformed global genomic assembly in several metrics employed. This approach is capable of detecting organisms that have not been used in the construction of the profile HMM, which opens up the possibility of diagnosing novel viruses, without previous specific information, constituting a de novo diagnosis. Additional applications include, but are not limited to, the specific assembly of extrachromosomal elements such as plastid and mitochondrial genomes from metagenomic data. Profile HMM seeds can also be used to reconstruct specific protein coding genes for gene diversity studies, and to determine all possible gene variants present in a metagenomic sample. Such surveys could be useful to detect the emergence of drug-resistance variants in sensitive environments such as hospitals and animal production facilities, where antibiotics are regularly used. Finally, GenSeed-HMM can be used as an adjunct for gap closure on assembly finishing projects, by using multiple contig ends as anchored seeds.

Chelonid herpesvirus 5 in secretions and tumor tissues from green turtles (Chelonia mydas) from Southeastern Brazil: A ten-year study.

Fibropapillomatosis (FP), a neoplastic disease characterized by the formation of multiple tumors affecting different species of sea turtles and, most often, the green turtle (Chelonia mydas), is considered one of the major threats to the survival of this species. Recent studies indicate that Chelonid herpesvirus (ChHV5) is the etiological agent of this disease, though its association with anthropogenically altered environments and the immune status of these animals also appears to contribute to disease expression and tumor formation. In this study, tumor biopsy and secretions from green turtles captured off the coast of São Paulo State, Brazil, were used in histological and molecular analyses to detect and characterize circulating ChHV5. In 40.9% of cases, the tumor histopathological findings revealed focal ballooning degeneration with intranuclear inclusion bodies, results which are suggestive of viral infection. ChHV5 was detected using polymerase chain reaction (PCR) on the animals' skin, ocular tumor biopsies, and ocular and oral secretions. The analysis of the detected ChHV5 sequences revealed two distinct genetic sequences together. Phylogenetic analysis indicated that Brazilian samples were similar to ChHV5 samples described for the Atlantic phylogeographic group and are therefore part of the same clade as the Gulf of Guinea and Puerto Rico samples. This similarity suggests a possible flow of the virus between these three regions.

Phylodynamics and movement of Phycodnaviruses among aquatic environments.

Phycodnaviruses have a significant role in modulating the dynamics of phytoplankton, thereby influencing community structure and succession, nutrient cycles and potentially atmospheric composition because phytoplankton fix about half the carbon dioxide (CO(2)) on the planet, and some algae release dimethylsulphoniopropionate when lysed by viruses. Despite their ecological importance and widespread distribution, relatively little is known about the evolutionary history, phylogenetic relationships and phylodynamics of the Phycodnaviruses from freshwater environments. Herein we provide novel data on Phycodnaviruses from the largest river system on earth--the Amazon Basin--that were compared with samples from different aquatic systems from several places around the world. Based on phylogenetic inference using DNA polymerase (pol) sequences we show the presence of distinct populations of Phycodnaviridae. Preliminary coarse-grained phylodynamics and phylogeographic inferences revealed a complex dynamics characterized by long-term fluctuations in viral population sizes, with a remarkable worldwide reduction of the effective population around 400 thousand years before the present (KYBP), followed by a recovery near to the present time. Moreover, we present evidence for significant viral gene flow between freshwater environments, but crucially almost none between freshwater and marine environments.

Cultured epithelial cells response to phototherapy with low intensity laser.

BACKGROUND AND OBJECTIVES: Little is known about the intracellular response of epithelial cells to phototherapy. The aim of this in vitro study was to analyze the effect of phototherapy with low-energy lasers with different wavelengths and powers on cultured epithelial cell growth under different nutritional conditions. STUDY DESIGN/MATERIALS AND METHODS: Epithelial cell cultures (Vero cell line) grown in nutritional deficit in culture medium supplemented with 2% fetal bovine serum (FBS) were irradiated with low-energy laser from one to three times with a GaAlAs laser (660 nm) and InGaAlP (780 nm), 40 and 70 mW, respectively, with 3 or 5 J/cm2. Cell growth was indirectly assessed by measuring the cell mitochondrial activity. RESULTS: Nonirradiated cell cultures grown in nutritional regular medium supplemented with 10% FBS produced higher cell growth than all cultures grown in nutritional deficit irradiated or not. The overall cell growth of cultures grown under nutritionally deficit conditions was significantly improved especially when irradiated with 780 nm for three times. CONCLUSIONS: Phototherapy with the laser parameters tested increases epithelial cell growth rate for cells stressed by growth under nutritionally deficient states. This cell growth improvement is directly proportional to the number of irradiations; however, was not enough to reach the full cell growth potential rate of Vero epithelial cell line observed when growing under nutritional regular condition.

Molecular epidemiology of human adenovirus isolated from children hospitalized with acute respiratory infection in São Paulo, Brazil.

In a study of acute respiratory disease, two collections of nasopharyngeal aspirates (NPA) were obtained from children hospitalized at the Pediatric Clinic of the University Hospital, São Paulo, in 1995 and 2000. Adenovirus was detected in 33 (8.2%) of 401 children followed. These viruses were isolated in HEp-2, HEK-293, or NCI-H292 cells and serotyped by neutralization. The genome types were determined after restriction analyses of the genomic DNA extracted from infected cells. Nineteen isolates were characterized as Human adenovirus B, genome types HAdV-3a, HAdV-7h, and HAdV-7h1; 11 as Human adenovirus C, genome types HAdV-1D10, HAdV-2D25, HAdV-5D2, and HAdV-6D3. Our findings show that species C adenoviruses present an endemic infection pattern, with co-circulation of different serotypes and genome types; no new genomic variant was observed. Species B adenoviruses showed epidemic infection patterns, with shifts in the predominant genome type. The isolates from 1995 belong to genome type 7h, or the variant 7h1, with a clear substitution of the type 7b, prevalent in São Paulo for more then 10 years. In 2000, the variant 7h1 predominated and the emergence of the type 3a was observed. Almost 10 years passed between the identification of HAdV-7h in Argentina and its detection in São Paulo. The geographic isolation of these two countries was reduced by the increase in population mobility due to growing commercial relationships.