Anglo Irish Bank

About: Anglo Irish Bank is a based out in . It is known for research contribution in the topics: Diamino acid & Strain (chemistry). The organization has 113 authors who have published 130 publications receiving 1612 citations. The organization is also known as: IBRC.

SuperSAGE: the drought stress-responsive transcriptome of chickpea roots

Abstract: Drought is the major constraint to increase yield in chickpea (Cicer arietinum). Improving drought tolerance is therefore of outmost importance for breeding. However, the complexity of the trait allowed only marginal progress. A solution to the current stagnation is expected from innovative molecular tools such as transcriptome analyses providing insight into stress-related gene activity, which combined with molecular markers and expression (e)QTL mapping, may accelerate knowledge-based breeding. SuperSAGE, an improved version of the serial analysis of gene expression (SAGE) technique, generating genome-wide, high-quality transcription profiles from any eukaryote, has been employed in the present study. The method produces 26 bp long fragments (26 bp tags) from defined positions in cDNAs, providing sufficient sequence information to unambiguously characterize the mRNAs. Further, SuperSAGE tags may be immediately used to produce microarrays and probes for real-time-PCR, thereby overcoming the lack of genomic tools in non-model organisms. We applied SuperSAGE to the analysis of gene expression in chickpea roots in response to drought. To this end, we sequenced 80,238 26 bp tags representing 17,493 unique transcripts (UniTags) from drought-stressed and non-stressed control roots. A total of 7,532 (43%) UniTags were more than 2.7-fold differentially expressed, and 880 (5.0%) were regulated more than 8-fold upon stress. Their large size enabled the unambiguous annotation of 3,858 (22%) UniTags to genes or proteins in public data bases and thus to stress-response processes. We designed a microarray carrying 3,000 of these 26 bp tags. The chip data confirmed 79% of the tag-based results, whereas RT-PCR confirmed the SuperSAGE data in all cases. This study represents the most comprehensive analysis of the drought-response transcriptome of chickpea available to date. It demonstrates that – inter alias – signal transduction, transcription regulation, osmolyte accumulation, and ROS scavenging undergo strong transcriptional remodelling in chickpea roots already 6 h after drought stress. Certain transcript isoforms characterizing these processes are potential targets for breeding for drought tolerance. We demonstrate that these can be easily accessed by micro-arrays and RT-PCR assays readily produced downstream of SuperSAGE. Our study proves that SuperSAGE owns potential for molecular breeding also in non-model crops.

The Draft Genome of Hop ( Humulus lupulus ), an Essence for Brewing

Abstract: Thefemaleflowerofhop(Humuluslupulusvar.lupulus)isanessential ingredient that gives characteristic aroma, bitter-nessanddurability/stabilitytobeer.However,themoleculargeneticbasisforidentifyingDNAmarkersinhopforbreedingand to study its domestication has been poorly established.Here, we provide draft genomes for two hop cultivars [cv.Saazer (SZ) and cv. Shinshu Wase (SW)] and a Japanese wildhop [H. lupulus var. cordifolius; also known as Karahanasou(KR)]. Sequencing and de novo assembly of genomic DNAfrom heterozygous SW plants generated scaffolds with atotal size of 2.05Gb, corresponding to approximately 80%of the estimated genome size of hop (2.57Gb). The scaffoldscontained 41,228 putative protein-encoding genes. Thegenome sequences for SZ and KR were constructed by align-ing their short sequence reads to the SW reference genomeandthenreplacingthenucleotidesatsinglenucleotidepoly-morphism (SNP) sites. De novo RNA sequencing (RNA-Seq)analysis of SW revealed the developmental regulation ofgenes involved in specialized metabolic processes thatimpact taste and flavor in beer. Application of a novel bio-informatics tool, phylogenetic comparative RNA-Seq (PCP-Seq), which is based on read depth of genomic DNAs andRNAs, enabled the identification of genes related to the bio-synthesis of aromas and flavors that are enriched in SWcomparedtoKR.Ourresultsnotonlysuggestthesignificanceof historical human selection process for enhancing aromaandbitternessbiosynthesesinhopcultivars,butalsoserveascrucial information for breeding varieties with high qualityand yield.Keywords: Genomics Hop Humulus Specialized metab-olism Transcriptome.Abbreviations: BCCA, branched-chain amino acid; BWA,Burrows–Wheeler aligner; CCL, cytosolic CoA ligase; CNV,copy number variation; FPKM, fragments per kilobase ofexon model per million mapped reads; FPP, farnesyldiphosphate; gDNA, genomic DNA; GO, gene ontology;GPP, geranyl diphosphate; GPPS, GPP, geranyl diphosphatesynthase; ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphatesynthase; LSU, large subunit; LTR, long terminal repeat; MP,mate-pair; MTS, monoterpene synthase; NGS, next gener-ation sequencing; OMT, O-methyltransferase; PA, proantho-cyanidin; PCP-Seq, phylogenetic comparative RNAsequencing; PE, paired-end; qRT-PCR, quantitative reversetranscription–PCR; rbcL, ribulose-1,5-bisphosphate carboxyl-ase large subunit; RNA-Seq, RNA sequencing; SNP, single nu-cleotide polymorphism; VPS, valerophenone synthase; WGS,whole-genome sequencing.The nucleotide sequences described in this paper have beensubmitted to the DNA Databank of Japan (DDBJ) as aBioProject (hop: Humulus lupulus) with the accession number(PRJDB3233) (Supplementary information).

Efficient transformation of the edible basidiomycete Lentinus edodes with a vector using a glyceraldehyde-3-phosphate dehydrogenase promoter to hygromycin B resistance.

Abstract: To construct a vector for high-level expression of heterologous genes in Lentinus edodes, the L. edodes GPD promoter, which is expressed constitutively and strongly, was fused to a hygromycin B phosphotransferase gene (hph) derived from Escherichia coli as a selective marker. Using the resulting pLG-hph construct, L. edodes was efficiently transformed to hygromycin resistance by restriction enzyme-mediated integration (REMI). The restriction enzyme concentrations yielding the maximal numbers of transformants by the REMI method were 10 U per transformation in the case of BglII and 25–50 U in the case of HindIII. Southern analysis of the transformants indicated that some 50% of plasmid integrations were REMI-mediated events. These results indicate that pLG is a useful vector for transformation of L. edodes. Deletion analysis of the GPD promoter region suggested that the segment between positions −442 bp and −270 bp relative to the transcription start point may be essential for function.

Microbial diversity in the hypersaline Lake Meyghan, Iran.

Abstract: Lake Meyghan is one of the largest and commercially most important salt lakes in Iran. Despite its inland location and high altitude, Lake Meyghan has a thalassohaline salt composition suggesting a marine origin. Inputs of fresh water by rivers and rainfall formed various basins characterized by different salinities. We analyzed the microbial community composition of three basins by isolation and culturing of microorganisms and by analysis of the metagenome. The basins that were investigated comprised a green ~50 g kg−1 salinity brine, a red ~180 g kg−1 salinity brine and a white ~300 g kg−1 salinity brine. Using different growth media, 57 strains of Bacteria and 48 strains of Archaea were isolated. Two bacterial isolates represent potential novel species with less than 96% 16S rRNA gene sequence identity to known species. Abundant isolates were also well represented in the metagenome. Bacteria dominated the low salinity brine, with Alteromonadales (Gammaproteobacteria) as a particularly important taxon, whereas the high salinity brines were dominated by haloarchaea. Although the brines of Lake Meyghan differ in geochemical composition, their ecosystem function appears largely conserved amongst each other while being driven by different microbial communities.

A robust universal method for extraction of genomic DNA from bacterial species

Abstract: The intactness of DNA is the keystone of genome-based clinical investigations, where rapid molecular detection of life-threatening bacteria is largely dependent on the isolation of high-quality DNA. Various protocols have been so far developed for genomic DNA isolation from bacteria, most of which have been claimed to be reproducible with relatively good yields of high-quality DNA. Nonetheless, they are not fully applicable to various types of bacteria, their processing cost is relatively high, and some toxic reagents are used. The routine protocols for DNA extraction appear to be sensitive to species diversity, and may fail to produce high-quality DNA from different species. Such protocols remain time-consuming and tedious, thus to resolve some of these impediments, we report development of a very simple, rapid, and high-throughput protocol for extracting of high-quality DNA from different bacterial species. Based upon our protocol, interfering phenolic compounds were removed from extraction using polyvinylpyrrolidone (PVP) and RNA contamination was precipitated using LiCI. The UV spectrophotometric and gel electrophoresis analysis resulted in high A260/A280 ratio (>1.8) with high intactness of DNA. Subsequent evaluations were performed using some quality-dependent techniques (e.g., RAPD marker and restriction digestions). The isolated DNA from 9 different bacterial species confirmed the accuracy of this protocol which requires no enzymatic processing and accordingly its low-cost making it an appropriate method f r large-scale DNA isolation fromvarious bacterial species.