CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features

Background  

CTCF (CCCTC-binding factor) is an evolutionarily conserved zinc finger protein involved in diverse functions ranging from negative regulation of MYC, to chromatin insulation of the beta-globin gene cluster, to imprinting of the Igf2 locus. The 11 zinc fingers of CTCF are known to differentially contribute to the CTCF-DNA interaction at different binding sites. It is possible that the differences in CTCF-DNA conformation at different binding sites underlie CTCF's functional diversity. If so, the CTCF binding sites may belong to distinct classes, each compatible with a specific functional role.     

Characterisation of thermotolerant,ethanol tolerant fermentative <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> for ethanol production

Of the four thermotolerant, osmotolerant, flocculating yeasts (VS₁, VS₂, VS₃ and VS₄) isolated from the soil samples collected within the hot regions of Kothagudem Thermal Power Plant, located in Khammam Dt., Andhra Pradesh, India, VS₁ and VS₃ were observed as better performers. They were identified as Saccharomyces cerevisiae. VS₁ and VS₃ were tested for their growth characteristics and fermentation abilities on various carbon sources including molasses at 30v°C and 40v°C respectively. More biomass and fermentation was observed in sucrose, fructose and glucose. Maximum amount of ethanol produced by VS₃ containing 150 (g/l) of these substrates were 74, 73, and 72 (g/l) at 30v°C and 64, 61 and 63 (g/l) at 40v°C respectively. With molasses containing 14% sugar, the amount of ethanol produced by VS₃ was 53.2 and 45 (g/l) at 30v°C and 40v°C respectively. VS₃ strain showed 12% W/V ethanol tolerance. VS₃ strain was also characterised for its ethanol producing ability using various starchy substrates in solid state and submerged fermentation. More ethanol was produced in submerged than solid state fermentation.     

Phenolic compounds detected in rice blast lesions

Salicylic,p-coumaric, and ferulic acids were detected in the acetone-insoluble cell fraction, presumably protein, extracted from the brown discoloured tissues of rice (Oryza sativa L.) leaves infected withPyricularia oryzae Cav. but not from healthy leaves. It is proposed that these phenolic acids are oxidizedin vivo in blast diseased rice leaves, and forms a protein-quinone complex.     

In silico mining of microsatellites and analysis of genetic diversity among inter‐ and intra‐generic aphids of the subfamily Aphidinae

Nearly 5 000 aphid species damage crops, either by sucking plant sap or as disease‐transmitting vectors. Microsatellites are used for understanding molecular diversity and eco‐geographical relationships among aphid species. Expressed sequence tag (EST)‐microsatellite motifs were identified through an in silico approach using inbuilt simple sequence repeat mining tools in aphid EST dataset. Microsatellite mining revealed one in every five aphid genes as containing a repeat motif, and out of 9 290 EST microsatellites mined from Aphis gossypii Glover and Acyrthosiphon pisum (Harris) (both Hemiptera: Aphididae), 80% were of A and/or T (AT, ATA, AAT, AATA, and ATTT) motifs, and the rest contained G and/or C motifs. All microsatellite sequences were annotated using BLAST. Primers for EST microsatellites were designed using the Primer 3.0 tool. 106 primer pairs of both dinucleotide repeats (DNRs) and trinucleotide repeats (TNRs), representing open reading frames (ORFs) and untranslated regions (UTRs), were synthesized to amplify 15 aphid species belonging to the subfamily Aphidinae, collected from diverse hosts. Four hundred forty‐five polymorphic alleles were amplified. Fifty TNR and 23 DNR microsatellites amplified across the species studied. Polymorphism information content values of microsatellites ranged from 0.23 to 0.91, amplifying 2–16 alleles. Genetic similarity indices were estimated using the ‘NTSYS‐pc’ software package. Unweighted pair group with arithmetic mean and principal component analysis resolved taxonomic relationships of the aphid species studied. The new aphid microsatellites developed will provide valuable information to researchers to study Indian aphid species diversity and genetic relationships.     

Phytotransformation of Perchlorate and Identification of Metabolic Products in Myriophyllum aquaticum

The uptake and transformation of perchlorate in the presence of Myriophyllum aquaticum (parrot-feather) were examined in sand and aqueous treatments with concentrations between 0.2 to 20 ppm. Controls were included without plants to confirm the uptake of perchlorate by parrot-feather. The kinetic data followed a first-order reaction mechanism with rate constants ranging from 0.004 to 0.090, resulting in half-lives between 7 to 173 days. Uptake rates were five times higher in aqueous treatments than in sand treatments. The intermediates detected in the plant tissue suggest that perchlorate transformed in a step-wise fashion to form chloride. Accumulation of perchlorate in the plant tissues (1.2 g/kg) suggests that parrot-feather has a high capacity for accumulating this contaminant.     

Role of Immune Responses against the Envelope and the Core Antigens of Simian Immunodeficiency Virus SIVmne in Protection against Homologous Cloned and Uncloned Virus Challenge in Macaques

We previously showed that envelope (gp160)-based vaccines, used in a live recombinant virus priming and subunit protein boosting regimen, protected macaques against intravenous and intrarectal challenges with the homologous simian immunodeficiency virus SIVmne clone E11S. However, the breadth of protection appears to be limited, since the vaccines were only partially effective against intravenous challenge by the uncloned SIVmne. To examine factors that could affect the breadth and the efficacy of this immunization approach, we studied (i) the effect of priming by recombinant vaccinia virus; (ii) the role of surface antigen gp130; and (iii) the role of core antigens (Gag and Pol) in eliciting protective immunity. Results indicate that (i) priming with recombinant vaccinia virus was more effective than subunit antigen in eliciting protective responses; (ii) while both gp130 and gp160 elicited similar levels of SIV-specific antibodies, gp130 was not as effective as gp160 in protection, indicating a possible role for the transmembrane protein in presenting functionally important epitopes; and (iii) although animals immunized with core antigens failed to generate any neutralizing antibody and were infected upon challenge, their virus load was 50- to 100-fold lower than that of the controls, suggesting the importance of cellular immunity or other core-specific immune responses in controlling acute infection. Complete protection against intravenous infection by the pathogenic uncloned SIVmne was achieved by immunization with both the envelope and the core antigens. These results indicate that immune responses to both antigens may contribute to protection and thus argue for the inclusion of multiple antigens in recombinant vaccine designs.     

Quantitative trait loci for resistance to stripe rust of wheat revealed using global field nurseries and opportunities for stacking resistance genes

Key message

Quantitative trait loci controlling stripe rust resistance were identified in adapted Canadian spring wheat cultivars providing opportunity for breeders to stack loci using marker-assisted breeding.

Abstract

Stripe rust or yellow rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss., is a devastating disease of common wheat (Triticum aestivum L.) in many regions of the world. The objectives of this research were to identify and map quantitative trait loci (QTL) associated with stripe rust resistance in adapted Canadian spring wheat cultivars that are effective globally, and investigate opportunities for stacking resistance. Doubled haploid (DH) populations from the crosses Vesper/Lillian, Vesper/Stettler, Carberry/Vesper, Stettler/Red Fife and Carberry/AC Cadillac were phenotyped for stripe rust severity and infection response in field nurseries in Canada (Lethbridge and Swift Current), New Zealand (Lincoln), Mexico (Toluca) and Kenya (Njoro), and genotyped with SNP markers. Six QTL for stripe rust resistance in the population of Vesper/Lillian, five in Vesper/Stettler, seven in Stettler/Red Fife, four in Carberry/Vesper and nine in Carberry/AC Cadillac were identified. Lillian contributed stripe rust resistance QTL on chromosomes 4B, 5A, 6B and 7D, AC Cadillac on 2A, 2B, 3B and 5B, Carberry on 1A, 1B, 4A, 4B, 7A and 7D, Stettler on 1A, 2A, 3D, 4A, 5B and 6A, Red Fife on 2D, 3B and 4B, and Vesper on 1B, 2B and 7A. QTL on 1A, 1B, 2A, 2B, 3B, 4A, 4B, 5B, 7A and 7D were observed in multiple parents. The populations are compelling sources of recombination of many stripe rust resistance QTL for stacking disease resistance. Gene pyramiding should be possible with little chance of linkage drag of detrimental genes as the source parents were mostly adapted cultivars widely grown in Canada.