High-throughput SNP genotyping of modern and wild emmer wheat for yield and root morphology using a combined association and linkage analysis

Durum wheat (Triticum turgidum var. durum Desf.) is a major world crop that is grown primarily in areas of the world that experience periodic drought, and therefore, breeding climate-resilient durum wheat is a priority. High-throughput single nucleotide polymorphism (SNP) genotyping techniques have greatly increased the power of linkage and association mapping analyses for bread wheat, but as yet there is no durum wheat-specific platform available. In this study, we evaluate the new 384HT Wheat Breeders Array for its usefulness in tetraploid wheat breeding by genotyping a breeding population of F₆ hybrids, derived from multiple crosses between T. durum cultivars and wild and cultivated emmer wheat accessions. Using a combined linkage and association mapping approach, we generated a genetic map including 1345 SNP markers, and identified markers linked to 6 QTLs for coleoptile length (2), heading date (1), anthocyanin accumulation (1) and osmotic stress tolerance (2). We also developed a straightforward approach for combining genetic data from multiple families of limited size that will be useful for evaluating and mapping pre-existing breeding material.     

Emergence and spread of carbapenem-resistant Acinetobacter baumannii in a tertiary care hospital in Turkey

An intensive care unit (ICU)-based OXA-23-producing multiple-drug resistant Acinetobacter baumannii (MDRAB) outbreak was detected between October 2005 and October 2006. A total of 47 patients were infected/colonized with the outbreak strain. Clinical data were available from 37 patients. The all-cause mortality rate among the patients exposed to the epidemic strain was 35% (13/37). The outbreak strain and the resistance determinants were characterized both by microbiological methods and by molecular techniques. Cloning and sequencing experiments identified ISAbaI-associated bla(oxa-23) on the chromosome. Screening of imipenem-resistant Acinetobacter isolated from the ICU during the outbreak period with PCR identified 97 isolates as positive for the ISAbaI-bla(oxa-23) structure. Pulsed-field gel electrophoresis and plasmid analyses with selected nonrepetitive isolates revealed the clonality. Disk diffusion on cloxacillin-supplemented agar media and the real-time PCR experiments showed that outbreak isolates are overexpressing the ampC enzyme. This study highlights the occurrence of OXA-23-producing and ampC-overexpressing MDRAB in ICUs.     

Mapping by sequencing the Pneumocystis genome using the ordering DNA sequences V3 tool

A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits an integrated genome map to be stored, retrieved, viewed, and queried in a stand-alone capacity, in a client/server relationship with the Fungal Genome Database (FGDB), and as a web-browsing tool for the FGDB. In that ODS3 is programmed in Java, the tool promotes platform independence and supports export of integrated genome-mapping data in the extensible markup language (XML) for data interchange with other genome information systems. The tool ODS3 is used to create an initial integrated genome map of the AIDS-related fungal pathogen, Pneumocystis carinii. Contig dynamics would indicate that this physical map is approximately 50% complete with approximately 200 contigs. A total of 10 putative multigene families were found. Two of these putative families were previously characterized in P. carinii, namely the major surface glycoproteins (MSGs) and HSP70 proteins; three of these putative families (not previously characterized in P. carinii) were found to be similar to families encoding the HSP60 in Schizosaccharomyces pombe, the heat-shock psi protein in S. pombe, and the RNA synthetase family (i.e., MES1) in Saccharomyces cerevisiae. Physical mapping data are consistent with the 16S, 5.8S, and 26S rDNA genes being single copy in P. carinii. No other fungus outside this genus is known to have the rDNA genes in single copy.     

Effect of heteroatom-doped carbon quantum dots on the red emission of metal-conjugated phthalocyanines through hybridization

Quantum dots (QDs) are significant fluorescent materials for energy transfer studies with phthalocyanines (Pcs) and phthalocyanine (Pc)-like biomolecules (such as chlorophylls). Carbon-based QDs, especially, have been used in numerous studies concerning energy transfer with chlorophylls, but the numbers of studies concerning energy transfer between phthalocyanines and carbon-based QDs are limited. In this study, peripherally, hydroxythioethyl terminal group substituted metal-free phthalocyanine (H₂Pc) and zinc phthalocyanine (ZnPc) were noncovalently (electrostatic and/or π–π interaction) attached to carbon QDs containing boron and nitrogen to form QD-Pc nanoconjugates. The QD-Pc conjugates were characterized using different spectroscopic techniques (Fourier transform infrared spectroscopy and transmission electron microscopy). The absorption and fluorescence properties of QD-Pc structures in solution were studied. It was found that the quantum yields of the QDs slightly decreased from 30% to 25% upon doping the QDs with heteroatoms B and N. Förster resonance energy transfer efficiency was calculated as 33% for BCN-QD/ZnPc. For the other conjugates, almost no energy transfer from QDs to Pc cores was observed. It was shown that the energy transfer between QDs to Pc cores was completely different from the energy transfer between QDs and photosynthetic pigments, and therefore we concluded that heteroatom doping in the QD structure and the existence of zinc metal in the phthalocyanine structure is obligatory for an efficient energy transfer.     

Sequencing chromosome 5D of Aegilops tauschii and comparison with its allopolyploid descendant bread wheat (Triticum aestivum)

Flow cytometric sorting of individual chromosomes and chromosome‐based sequencing reduces the complexity of large, repetitive Triticeae genomes. We flow‐sorted chromosome 5D of Aegilops tauschii, the D genome donor of bread wheat and sequenced it by Roche 454 GS FLX platform to approximately 2.2x coverage. Repetitive sequences represent 81.09% of the survey sequences of this chromosome, and Class I retroelements are the prominent type, with a particular abundance of LTR/Gypsy superfamily. Nonrepetitive sequences were assembled to cover 17.76% of the total chromosome regions. Up to 6188 nonrepetitive gene loci were predicted to be encoded by the 5D chromosome. The numbers and chromosomal distribution patterns of tRNA genes suggest abundance in tRNA^Lys and tRNA^Met species, while the nonrepetitive assembly reveals tRNA^Ala species as the most abundant type. A comparative analysis of the genomic sequences of bread wheat and Aegilops chromosome 5D indicates conservation of gene content. Orthologous unique genes, matching Aegilops 5D sequences, numbered 3730 in barley, 5063 in Brachypodium, 4872 in sorghum and 4209 in rice. In this study, we provide a chromosome‐specific view into the structure and organization of the 5D chromosome of Ae. tauschii, the D genome ancestor of bread wheat. This study contributes to our understanding of the chromosome‐level evolution of the wheat genome and presents a valuable resource in wheat genomics due to the recent hybridization of Ae. tauschii genome with its tetraploid ancestor.     

Pretreatment with Proline or an Organic Bio-stimulant Induces Salt Tolerance in Wheat Plants by Improving Antioxidant Redox State and Enzymatic Activities and Reducing the Oxidative Stress

Journal of Plant Growth Regulation - In this study, the effects of seed soaking in proline (12 mM) or Moringa oleifera leaf extract (MLE; 6%) on the biomass, yield, and the antioxidant...     

A Wrench in the Works of Human Acetylcholinesterase: Soman Induced Conformational Changes Revealed by Molecular Dynamics Simulations

Irreversible inactivation of human acetylcholinesterase (hAChE) by organophosphorous pesticides (OPs) and chemical weapon agents (CWA) has severe morbidity and mortality consequences. We present data from quantum mechanics/molecular mechanics (QM/MM) and 80 classical molecular dynamics (MD) simulations of the apo and soman-adducted forms of hAChE to investigate the effects on the dynamics and protein structure when the catalytic Serine 203 is phosphonylated. We find that the soman phosphonylation of the active site Ser203 follows a water assisted addition-elimination mechanism with the elimination of the fluoride ion being the highest energy barrier at 6.5 kcal/mole. We observe soman-dependent changes in backbone and sidechain motions compared to the apo form of the protein. These alterations restrict the soman-adducted hAChE to a structural state that is primed for the soman adduct to be cleaved and removed from the active site. The altered motions and resulting structures provide alternative pathways into and out of the hAChE active site. In the soman-adducted protein both side and back door pathways are viable for soman adduct access. Correlation analysis of the apo and soman adducted MD trajectories shows that the correlation of gorge entrance and back door motion is disrupted when hAChE is adducted. This supports the hypothesis that substrate and product can use two different pathways as entry and exit sites in the apo form of the protein. These alternative pathways have important implications for the rational design of medical countermeasures.     

IL-10 and IL-6 gene polymorphisms as potential host susceptibility factors in Brucellosis

Several genes encoding for different cytokines may play crucial roles in host susceptibility to Brucellosis, since the cytokine production capacity varies among individuals and depends on the cytokine gene polymorphism. The association of the cytokine gene polymorphisms with the development of Brucellosis was investigated in this study. DNA samples were obtained from a Turkish population of 40 patients with Brucellosis, and 50 healthy control subjects. All genotyping (IL-6, IL10, IFN-gamma, TGF-beta and TNF-alpha) experiments were performed using sequence-specific primers PCR (PCR-SSP). When compared to the healthy controls, the frequencies of high/intermediate producing genotypes of IL-10 and high producing genotype of IL-6 were significantly more common in the patient group. These results suggest that IL-10 and IL-6 gene polymorphisms may affect susceptibility to Brucellosis and increase risk of developing the disease. In order to confirm the biological significance of our results, further studies should be performed in larger population groups.