Inter-comparison of high-resolution satellite precipitation products over Central Asia

This paper examines the spatial error structures of eight precipitation estimates derived from four different satellite retrieval algorithms including TRMM Multi-satellite Precipitation Analysis (TMPA), Climate Prediction Center morphing technique (CMORPH), Global Satellite Mapping of Precipitation (GSMaP) and Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks (PERSIANN). All the original satellite and bias-corrected products of each algorithm (3B42RTV7 and 3B42V7, CMORPH_RAW and CMORPH_CRT, GSMaP_MVK and GSMaP_Gauge, PERSIANN_RAW and PERSIANN_CDR) are evaluated against ground-based Asian Precipitation-Highly Resolved Observational Data Integration Towards Evaluation of Water Resources (APHRODITE) over Central Asia for the period of 2004 to 2006. The analyses show that all products except PERSIANN exhibit overestimation over Aral Sea and its surrounding areas. The bias-correction improves the quality of the original satellite TMPA products and GSMaP significantly but slightly in CMORPH and PERSIANN over Central Asia. 3B42RTV7 overestimates precipitation significantly with large Relative Bias (RB) (128.17%) while GSMaP_Gauge shows consistent high correlation coefficient (CC) (>0.8) but RB fluctuates between -57.95% and 112.63%. The PERSIANN_CDR outperforms other products in winter with the highest CC (0.67). Both the satellite-only and gauge adjusted products have particularly poor performance in detecting rainfall events in terms of lower POD (less than 65%), CSI (less than 45%) and relatively high FAR (more than 35%)

Rapid evolutionary change of common bean (Phaseolus vulgaris L) plastome, and the genomic diversification of legume chloroplasts

<p>Abstract</p> <p>Background</p> <p>Fabaceae (legumes) is one of the largest families of flowering plants, and some members are important crops. In contrast to what we know about their great diversity or economic importance, our knowledge at the genomic level of chloroplast genomes (cpDNAs or plastomes) for these crops is limited.</p> <p>Results</p> <p>We sequenced the complete genome of the common bean (<it>Phaseolus vulgari</it>s cv. Negro Jamapa) chloroplast. The plastome of <it>P. vulgaris </it>is a 150,285 bp circular molecule. It has gene content similar to that of other legume plastomes, but contains two pseudogenes, <it>rpl</it>33 and <it>rps</it>16. A distinct inversion occurred at the junction points of <it>trn</it>H-GUG/<it>rpl</it>14 and <it>rps</it>19/<it>rps</it>8, as in adzuki bean <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. These two pseudogenes and the inversion were confirmed in 10 varieties representing the two domestication centers of the bean. Genomic comparative analysis indicated that inversions generally occur in legume plastomes and the magnitude and localization of insertions/deletions (indels) also vary. The analysis of repeat sequences demonstrated that patterns and sequences of tandem repeats had an important impact on sequence diversification between legume plastomes and tandem repeats did not belong to dispersed repeats. Interestingly, <it>P. vulgaris </it>plastome had higher evolutionary rates of change on both genomic and gene levels than <it>G. max</it>, which could be the consequence of pressure from both mutation and natural selection.</p> <p>Conclusion</p> <p>Legume chloroplast genomes are widely diversified in gene content, gene order, indel structure, abundance and localization of repetitive sequences, intracellular sequence exchange and evolutionary rates. The <it>P. vulgaris </it>plastome is a rapidly evolving genome.</p

Isolation ofBdellovibriosp. from soil samples in Mexico and their potential applications in control of pathogens

In this study, two strains of Bdellovibrio were isolated from soil samples using the culture-dependent technique and two members of the family Enterobacteriaceae (Klebsiella sp. and Salmonella sp.) as prey. The Bdellovibrio strains were bacteriolytic, plaque-forming, and highly motile gram-negative bacteria. We identified and confirmed the Bdellovibrio strains using microscopy, PCR amplification, and sequencing of the 16S rRNA gene. They were observed to be different strains based on hit locus and prey range analyses. Here, the first report on Bdellovibrio strains isolated from soil in Mexico corroborates earlier report indicating that populations of Bdellovibrio found in soil are heterogeneous thereby the need to identify the various strains

New Implications on Genomic Adaptation Derived from the Helicobacter pylori Genome Comparison

BACKGROUND: Helicobacter pylori has a reduced genome and lives in a tough environment for long-term persistence. It evolved with its particular characteristics for biological adaptation. Because several H. pylori genome sequences are available, comparative analysis could help to better understand genomic adaptation of this particular bacterium. PRINCIPAL FINDINGS: We analyzed nine H. pylori genomes with emphasis on microevolution from a different perspective. Inversion was an important factor to shape the genome structure. Illegitimate recombination not only led to genomic inversion but also inverted fragment duplication, both of which contributed to the creation of new genes and gene family, and further, homological recombination contributed to events of inversion. Based on the information of genomic rearrangement, the first genome scaffold structure of H. pylori last common ancestor was produced. The core genome consists of 1186 genes, of which 22 genes could particularly adapt to human stomach niche. H. pylori contains high proportion of pseudogenes whose genesis was principally caused by homopolynucleotide (HPN) mutations. Such mutations are reversible and facilitate the control of gene expression through the change of DNA structure. The reversible mutations and a quasi-panmictic feature could allow such genes or gene fragments frequently transferred within or between populations. Hence, pseudogenes could be a reservoir of adaptation materials and the HPN mutations could be favorable to H. pylori adaptation, leading to HPN accumulation on the genomes, which corresponds to a special feature of Helicobacter species: extremely high HPN composition of genome. CONCLUSION: Our research demonstrated that both genome content and structure of H. pylori have been highly adapted to its particular life style

Virus del Dengue: estructura, serotipos y epidemiología molecular

Biotecnologí

Genome-wide comparison inferred the origin and evolution of B-cell epitopes on the proteins of human influenza A virus

Biotecnologí

A Viral-Human Interactome Based on Structural Motif- Domain Interactions Captures the Human Infectome

Biotecnologi

A Comprehensive Analysis of Codon Usage Patterns in Blunt Snout Bream (Megalobrama amblycephala) Based on RNA-Seq Data

Blunt snout bream (Megalobrama amblycephala) is an important fish species for its delicacy and high economic value in China. Codon usage analysis could be helpful to understand its codon biology, mRNA translation and vertebrate evolution. Based on RNA-Seq data for M. amblycephala, high-frequency codons (CUG, AGA, GUG, CAG and GAG), as well as low-frequency ones (NUA and NCG codons) were identified. A total of 724 high-frequency codon pairs were observed. Meanwhile, 14 preferred and 199 avoided neighboring codon pairs were also identified, but bias was almost not shown with one or more intervening codons inserted between the same pairs. Codon usage bias in the regions close to start and stop codons indicated apparent heterogeneity, which even occurs in the flanking nucleotide sequence. Codon usage bias (RSCU and SCUO) was related to GC3 (GC content of 3rd nucleotide in codon) bias. Six GO (Gene ontology) categories and the number of methylation targets were influenced by GC3. Codon usage patterns comparison among 23 vertebrates showed species specificities by using GC contents, codon usage and codon context analysis. This work provided new insights into fish biology and new information for breeding projects