Identification and mapping of yield and yield related QTLs from an Indian accession of Oryza rufipogon

BACKGROUND: Cultivated rice (Oryza sativa L.) is endowed with a rich genetic variability. In spite of such a great diversity, the modern rice cultivars have narrow genetic base for most of the agronomically important traits. To sustain the demand of an ever increasing population, new avenues have to be explored to increase the yield of rice. Wild progenitor species present potential donor sources for complex traits such as yield and would help to realize the dream of sustained food security. RESULTS: Advanced backcross method was used to introgress and map new quantitative trait loci (QTLs) relating to yield and its components from an Indian accession of Oryza rufipogon. An interspecific BC(2) testcross progeny (IR58025A/O. rufipogon//IR580325B///IR58025B////KMR3) was evaluated for 13 agronomic traits pertaining to yield and its components. Transgressive segregants were obtained for all the traits. Thirty nine QTLs were identified using interval mapping and composite interval mapping. In spite of it's inferiority for most of the traits studied, O. rufipogon alleles contributed positively to 74% of the QTLs. Thirty QTLs had corresponding occurrences with the QTLs reported earlier, indicating that these QTLs are stable across genetic backgrounds. Nine QTLs are novel and reported for the first time. CONCLUSION: The study confirms that the progenitor species constitute a prominent source of still unfolded variability for traits of complex inheritance like yield. With the availability of the complete genome sequence of rice and the developments in the field of genomics, it is now possible to identify the genes underlying the QTLs. The identification of the genes constituting QTLs would help us to understand the molecular mechanisms behind the action of QTLs

Growing Pleurotus ostreatus (ex. Fr) Kummer Using Gamma Radiation in Southern Ghana and its Associated Pests

Pests have been implicated in causing severe damage to food crops including mushrooms, thereby increasing the incidence of postharvest loss. This study investigated the various pests involved in the cultivation of gamma radiation aided cultivated Pleurotus ostreatus. Pests were isolated and identified by the procedure described by the Entomological Society of Canada. Cultivation of Pleurotus ostreatus was achieved by pre-treating composted sawdust substrates and spawn preparation with a gamma radiation dose of 15 kGy from a Cobalt 60 source (SLL 515, Hungary) at a dose rate of 1.7 kGyh-1 in air. A total of five pests were recorded while cropping, namely; Drosophila melanogaster (Fruit fly), Blatta germanica (cockroach), Archachatina marginata (giant snail), and Doratogonus meridionalis (millipede) and Cryptophlebia leucotreta (False codling moth). The predominant pest was Drosophila melanogaster (Fruit fly) (97%). Results recorded over four flush periods were 378g, 0.63, and 63% for Total yield, biological yield, Biological Efficiency (%), respectively. The average stipe length and pileus diameter were recorded and showed no statistical differences (p>0.05) observed in the different weeks. Other growth parameters (mushroom size, total number of primordia, total number of fruitbodies etc.) recorded showed some significant differences (p<0.05). Pests identified contributed to yield reduction and product quality

Engineering Silicon Nanocrystals: Theoretical study of the effect of Codoping with Boron and Phosphorus

We show that the optical and electronic properties of nanocrystalline silicon can be efficiently tuned using impurity doping. In particular, we give evidence, by means of ab-initio calculations, that by properly controlling the doping with either one or two atomic species, a significant modification of both the absorption and the emission of light can be achieved. We have considered impurities, either boron or phosphorous (doping) or both (codoping), located at different substitutional sites of silicon nanocrystals with size ranging from 1.1 nm to 1.8 nm in diameter. We have found that the codoped nanocrystals have the lowest impurity formation energies when the two impurities occupy nearest neighbor sites near the surface. In addition, such systems present band-edge states localized on the impurities giving rise to a red-shift of the absorption thresholds with respect to that of undoped nanocrystals. Our detailed theoretical analysis shows that the creation of an electron-hole pair due to light absorption determines a geometry distortion that in turn results in a Stokes shift between adsorption and emission spectra. In order to give a deeper insight in this effect, in one case we have calculated the absorption and emission spectra going beyond the single-particle approach showing the important role played by many-body effects. The entire set of results we have collected in this work give a strong indication that with the doping it is possible to tune the optical properties of silicon nanocrystals.Comment: 14 pages 19 figure

Enterotoxin genes, enterotoxin production, and methicillin resistance in Staphylococcus aureus isolated from milk and dairy products in Central Italy

AbstractA total of 227 Staphylococcus aureus colonies, isolated from 54 samples of raw milk and dairy products of bovine, ovine, caprine and bubaline origin were tested for the presence of genes coding for staphylococcal enterotoxins (SEs/SEls) and for methicillin resistance. Ninety-three colonies, from 31 of the 54 samples (57.4%) and from 18 (69.2%) of the 26 farms of origin tested positive for SEs/SEls genes. Most isolates harboured more than one toxin gene and 15 different toxinotypes were recorded. The most frequent were “sec” gene alone (28.6%), “sea, sed, ser, selj” (20%), “seg, sei” and “seh” (8.6%). The 77 colonies harbouring “classical enterotoxins” genes (sea-sed) were further tested for enterotoxin production, which was assessed for 59.2% of the colonies. Three methicillin-resistant S. aureus (MRSA) isolates were detected in three different ovine milk/dairy product samples (1.3%). All isolates belonged to spa type t127, sequence type 1, clonal complex 1, SCCmec type IVa

Discovering study-specific gene regulatory networks

This article has been made available through the Brunel Open Access Publishing Fund.Microarrays are commonly used in biology because of their ability to simultaneously measure thousands of genes under different conditions. Due to their structure, typically containing a high amount of variables but far fewer samples, scalable network analysis techniques are often employed. In particular, consensus approaches have been recently used that combine multiple microarray studies in order to find networks that are more robust. The purpose of this paper, however, is to combine multiple microarray studies to automatically identify subnetworks that are distinctive to specific experimental conditions rather than common to them all. To better understand key regulatory mechanisms and how they change under different conditions, we derive unique networks from multiple independent networks built using glasso which goes beyond standard correlations. This involves calculating cluster prediction accuracies to detect the most predictive genes for a specific set of conditions. We differentiate between accuracies calculated using cross-validation within a selected cluster of studies (the intra prediction accuracy) and those calculated on a set of independent studies belonging to different study clusters (inter prediction accuracy). Finally, we compare our method's results to related state-of-the art techniques. We explore how the proposed pipeline performs on both synthetic data and real data (wheat and Fusarium). Our results show that subnetworks can be identified reliably that are specific to subsets of studies and that these networks reflect key mechanisms that are fundamental to the experimental conditions in each of those subsets

The Qatar Biobank: background and methods

Background: The Qatar Biobank aims to collect extensive lifestyle, clinical, and biological information from up to 60,000 men and women Qatari nationals and long-term residents (individuals living in the country for ≥15 years) aged ≥18 years (approximately one-fifth of all Qatari citizens), to follow up these same individuals over the long term to record any subsequent disease, and hence to study the causes and progression of disease, and disease burden, in the Qatari population. Methods: Between the 11th-December-2012 and 20th-February-2014, 1209 participants were recruited into the pilot study of the Qatar Biobank. At recruitment, extensive phenotype information was collected from each participant, including information/measurements of socio-demographic factors, prevalent health conditions, diet, lifestyle, anthropometry, body composition, bone health, cognitive function, grip strength, retinal imaging, total body dual energy X-ray absorptiometry, and measurements of cardiovascular and respiratory function. Blood, urine, and saliva were collected and stored for future research use. A panel of 66 clinical biomarkers was routinely measured on fresh blood samples in all participants. Rates of recruitment are to be progressively increased in the coming period and the recruitment base widened to achieve a cohort of consented individuals broadly representative of the eligible Qatari population. In addition, it is planned to add additional measures in sub-samples of the cohort, including Magnetic Resonance Imaging (MRI) of the brain, heart and abdomen. Results: The mean time for collection of the extensive phenotypic information and biological samples from each participant at the baseline recruitment visit was 179 min. The 1209 pilot study participants (506 men and 703 women) were aged between 28–80 years (median 39 years); 899 (74.4 %) were Qatari nationals and 310 (25.6 %) were long-term residents. Approximately two-thirds of pilot participants were educated to graduate level or above. Conclusions: The pilot has proven that recruitment of volunteers into the Qatar Biobank project with intensive baseline measurements of behavioural, physical, and clinical characteristics is well accepted and logistically feasible. Qatar Biobank will provide a powerful resource to investigate the major determinants of ill-health and well-being in Qatar, providing valuable insights into the current and future public health burden that faces the country.Qatar Foundation for Education, Science and Community Development and the Supreme Council of Healt

Hematological and Genetic Markers in the Rational Approach to Patients With HCV Sustained Virological Response With or Without Persisting Cryoglobulinemic Vasculitis

Background and Aims: Direct-acting antivirals (DAAs) usually lead to improvement/remission of cryoglobulinemic vasculitis (CV), although symptoms may persist/recur after a sustained virological response (SVR). We evaluated hematological and genetic markers in patients with HCV-SVR vasculitis with and without persisting/recurring symptoms to early predict the CV outcome. Approach and Results: Ninety-eight patients with HCV-CV were prospectively enrolled after a DAA-induced SVR: Group A: 52 with complete clinical response; Group B: 46 with symptom maintenance/recurrence. Monoclonal B-cell lymphocytosis, t(14;18) translocation, and abnormal free light chains κ/λ ratios were detected by flow cytometry or nested-PCR or nephelometry in 4% Group A versus 17% Group B (P = 0.04) patients, 17% Group A versus 40% Group B patients (P = 0.02), and 17% Group A versus 47% Group B (P = 0.003) patients, respectively. At least 1 out of 3 clonality markers was altered/positive in 29% of Group A versus 70% of Group B patients (P < 0.0001). When available, pretherapy samples were also tested for t(14;18) translocation (detected in 12/37 [32%] Group A and 21/38 [55%] Group B) and κ/λ ratios (abnormal in 5/35 [14%] Group A and 20/38 [53%] Group B) (P = 0.0006), whereas at least one clonality marker was detected/altered in 16/37 (43%) Group A and 30/38 (79%) Group B (P = 0.002). CV-associated single-nucleotide polymorphisms were tested by real-time PCR. Among them, notch4 rs2071286 T minor allele and TT genotype showed a higher frequency in Group B versus Group A (46% vs. 29%, P = 0.01, and 17% vs. 2%, P = 0.006, respectively). Conclusions: Hematological or genetic analyses could be used to foresee the CV clinical response after DAA therapy and could be valuable to assess a rational flowchart to manage CV during follow-up

Biochemical Composition and Disease Resistance in Newly Synthesized Amphidiploid and Autotetraploid Peanuts

Genetic diversity in peanut (Arachishypogaea L.) is narrow due to its evolution and domestication processes. Amphidiploids and autotetraploids (newly synthesized tetraploids) were created to broaden its genetic base. Molecular analysis has shown that the newly synthesized tetraploids had broader genetic base; and were genetically divergent when compared to cultivated peanut. Nutritional composition relative to oil, fatty acid composition, O/L ratio, protein, iodine value and presence of plant proteinase inhibitors such as trypsin and chymotrypsin inhibitors were studied in the synthesized tetraploids. Some of the newly synthesized tetraploids had higher amounts of proteinase inhibitors. Evaluation of newly synthesized tetraploids revealed several lines resistant to late leaf spot (LLS) and peanut bud necrosis disease (PBND)

Surfactant protein D inhibits HIV-1 infection of target cells via interference with gp120-CD4 interaction and modulates pro-inflammatory cytokine production

© 2014 Pandit et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Surfactant Protein SP-D, a member of the collectin family, is a pattern recognition protein, secreted by mucosal epithelial cells and has an important role in innate immunity against various pathogens. In this study, we confirm that native human SP-D and a recombinant fragment of human SP-D (rhSP-D) bind to gp120 of HIV-1 and significantly inhibit viral replication in vitro in a calcium and dose-dependent manner. We show, for the first time, that SP-D and rhSP-D act as potent inhibitors of HIV-1 entry in to target cells and block the interaction between CD4 and gp120 in a dose-dependent manner. The rhSP-D-mediated inhibition of viral replication was examined using three clinical isolates of HIV-1 and three target cells: Jurkat T cells, U937 monocytic cells and PBMCs. HIV-1 induced cytokine storm in the three target cells was significantly suppressed by rhSP-D. Phosphorylation of key kinases p38, Erk1/2 and AKT, which contribute to HIV-1 induced immune activation, was significantly reduced in vitro in the presence of rhSP-D. Notably, anti-HIV-1 activity of rhSP-D was retained in the presence of biological fluids such as cervico-vaginal lavage and seminal plasma. Our study illustrates the multi-faceted role of human SPD against HIV-1 and potential of rhSP-D for immunotherapy to inhibit viral entry and immune activation in acute HIV infection. © 2014 Pandit et al.The work (Project no. 2011-16850) was supported by Medical Innovation Fund of Indian Council of Medical Research, New Delhi, India (www.icmr.nic.in/)

Differential expression of collectins in human placenta and role in inflammation during spontaneous Labor.

© 2014 Yadav et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Collectins, collagen-containing Ca2+ dependent C-type lectins and a class of secretory proteins including SP-A, SP-D and MBL, are integral to immunomodulation and innate immune defense. In the present study, we aimed to investigate their placental transcript synthesis, labor associated differential expression and localization at feto-maternal interface, and their functional implication in spontaneous labor. The study involved using feto-maternal interface (placental/decidual tissues) from two groups of healthy pregnant women at term (≥37 weeks of gestation), undergoing either elective C-section with no labor ('NLc' group, n = 5), or normal vaginal delivery with spontaneous labor ('SLv' group, n = 5). The immune function of SP-D, on term placental explants, was analyzed for cytokine profile using multiplexed cytokine array. SP-A, SP-D and MBL transcripts were observed in the term placenta. The 'SLv' group showed significant up-regulation of SP-D (p = 0.001), and down-regulation of SP-A (p = 0.005), transcripts and protein compared to the 'NLc' group. Significant increase in 43 kDa and 50 kDa SP-D forms in placental and decidual tissues was associated with the spontaneous labor (p<0.05). In addition, the MMP-9-cleaved form of SP-D (25 kDa) was significantly higher in the placentae of 'SLv' group compared to the 'NLc' group (p = 0.002). Labor associated cytokines IL-1α, IL-1β, IL-6, IL-8, IL-10, TNF-α and MCP-1 showed significant increase (p<0.05) in a dose dependent manner in the placental explants treated with nSP-D and rhSP-D. In conclusion, the study emphasizes that SP-A and SP-D proteins associate with the spontaneous labor and SP-D plausibly contributes to the pro-inflammatory immune milieu of feto-maternal tissues.Funding provided by BT/PR15227/BRB/10/906/2011) Department of Biotechnology (DBT), Government of India http://dbtindia.nic.in/index.asp (TM) and Indian Council of Medical Research (ICMR) Junior Research Fellowship (JRF)/Senior Research Fellowship (SRF), Government of India, www.icmr.nic.in (AKY)