Biological and Integrated Control of Botrytis Bunch Rot of Grape UsingTrichodermaspp.

Field trials were carried out in upstate New York in 1990, 1992, 1993, and 1994 and in Chile in 1992–1993 and 1993–1994 in order to evaluate the ability of various strains ofTrichodermaspp. to control bunch rot of grape, to assess the compatibility and possible additive effects of selected biocontrol fungi and dicarboximide fungicides, and to determine factors affecting biocontrol efficacy. In 1990, three strains ofTrichodermaspp. were evaluated for their biocontrol ability, and all provided significant control ofBotrytis cinerea.As few as two late applications of the biocontrol fungi were nearly as effective as up to five applications throughout bloom and fruit development. Trials in New York in 1992 and in Chile in 1992–1993 indicated thatTrichoderma harzianumcould replace some applications of iprodione or vinclozolin with little reduction in efficacy. In New York in 1993, we found that applications ofT. harzianumat bloom and early fruit development followed by a tank-mix application ofT. harzianumand half rates of iprodione gave extremely effective control of bunch rot. In 1994, less effective control was obtained than in earlier years. Addition of a nutritive adhesive (Pelgel, a mixture of carboxymethyl cellulose and gum arabic) applied with the biocontrol agent tended to improve results. Thus, biological control of bunch rot of grape withT. harzianumcan be an effective method of management of this disease.     

Proposal of Corynebacterium propinquum sp. nov. for Corynebacterium group ANF-3 strains

Abstract Chemotaxonomic and genomic studies were performed on seven Corynebacterium group ANF-3 strains isolated from human sources. All these strains possess cell wall component type IV ( meso -diaminopimelic acid, arabinose and galactose), corynemycolic acids and a G+C content of DNA of 57 to 59 mol%. These results confirm that they can be placed in the genus Corynebacterium . Six of these strains were found to constitute a tight hybridization group distinct from named Corynebacterium species or related organisms. This genomic group constitutes a new species which can be identified within the genus Corynebacterium by ribotyping or phenotypic tests and for which the name Corynebacterium propinquum is proposed. The type strain is strain B 77159 (= Collection of the Institut Pasteur CIP 103792).     

Intraspecific DNA sequence variation of the mitochondrial control region of white sturgeon (Acipenser transmontanus)

Intraspecific sequence variation in the D-loop region of mtDNA in white sturgeon (Acipenser transmontanus), a relict North American fish species, was examined in 27 individuals from populations of the Columbia and Fraser rivers. Thirty-three varied nucleotide positions were present in a 462-nucleotide D-loop sequence, amplified using the polymerase chain reaction. Bootstrapped neighbor-joining and maximum- parsimony trees of sequences from 19 haplotypes suggest that the two populations have recently diverged. This is consistent with the hypothesis that the Columbia River, a Pleistocene refugium habitat, was the source of founders for the Fraser River after the last glacial recession. On the basis of a divergence time of 10-12 thousand years ago, the estimated substitution rate of the white sturgeon D-loop region is 1.1-1.3 x 10(-7) nucleotides/site/year, which is comparable to rates for hypervariable sequences in the human D-loop region. Furthermore, the ratio of mean percent nucleotide differences in the D- loop (2.27%) to that in whole mtDNA (0.54%, as estimated from restriction-enzyme data) is 4.3, which is similar to the fourfold-to- fivefold-higher substitution rate estimated for the human D-loop. The high nucleotide substitution rate of the hypervariable region indicates that the vertebrate D-loop has potential as a genetic marker in molecular population studies.      

SHEAR: sample heterogeneity estimation and assembly by reference

Background

Personal genome assembly is a critical process when studying tumor genomes and other highly divergent sequences. The accuracy of downstream analyses, such as RNA-seq and ChIP-seq, can be greatly enhanced by using personal genomic sequences rather than standard references. Unfortunately, reads sequenced from these types of samples often have a heterogeneous mix of various subpopulations with different variants, making assembly extremely difficult using existing assembly tools. To address these challenges, we developed SHEAR (Sample Heterogeneity Estimation and Assembly by Reference; http://vk.cs.umn.edu/SHEAR), a tool that predicts SVs, accounts for heterogeneous variants by estimating their representative percentages, and generates personal genomic sequences to be used for downstream analysis.

Results

By making use of structural variant detection algorithms, SHEAR offers improved performance in the form of a stronger ability to handle difficult structural variant types and better computational efficiency. We compare against the lead competing approach using a variety of simulated scenarios as well as real tumor cell line data with known heterogeneous variants. SHEAR is shown to successfully estimate heterogeneity percentages in both cases, and demonstrates an improved efficiency and better ability to handle tandem duplications.

Conclusion

SHEAR allows for accurate and efficient SV detection and personal genomic sequence generation. It is also able to account for heterogeneous sequencing samples, such as from tumor tissue, by estimating the subpopulation percentage for each heterogeneous variant.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-84) contains supplementary material, which is available to authorized users.     

Comparison of Variable-Number Tandem-Repeat Markers typing and IS1245 Restriction Fragment Length Polymorphism fingerprinting of Mycobacterium avium subsp. hominissuis from human and porcine origins

Background  

Animal mycobacterioses are regarded as a potential zoonotic risk and cause economical losses world wide. M. avium subsp. hominissuis is a slow-growing subspecies found in mycobacterial infected humans and pigs and therefore rapid and discriminatory typing methods are needed for epidemiological studies. The genetic similarity of M. avium subsp. hominissuis from human and porcine origins using two different typing methods have not been studied earlier. The objective of this study was to compare the IS1245 RFLP pattern and MIRU-VNTR typing to study the genetic relatedness of M. avium strains isolated from slaughter pigs and humans in Finland with regard to public health aspects.     

De novo sequencing and development of EST-SSR for Gevuina avellana (Proteaceae), a nut tree from South America

?Premise of the study: The aim of this study was to develop molecular tools to investigate the genetic structure and diversity of natural populations of Gevuina avellana (Molina, Proteaceae), the Chilean hazelnut. Simple sequence repeats (SSRs) derived from expressed sequence tags (EST-SSRs) were developed, optimized, and characterized. ?Methods and Results: The microsatellite-containing sequences were selected from a cDNA library developed from the nut. The eight marker loci showed two to seven alleles in 60 unrelated trees, from two different natural populations. The observed heterozygosity (H(o)) was 0.44, ranging from 0.07 to 0.92 for different loci. When the multilocus genotype of the eight EST-SSRs was considered, all trees could be differentiated. ?Conclusions: The newly identified EST-SSRs in G. avellana and the multi-pooling strategy involving eight markers will facilitate future studies of clone identification, genetic structure, and diversity.