Association mapping for protein, total soluble sugars, starch, amylose and chlorophyll content in rice.

BACKGROUND: Protein, starch, amylose and total soluble sugars are basic metabolites of seed that influence the eating, cooking and nutritional qualities of rice. Chlorophyll is responsible for the absorption and utilization of the light energy influencing photosynthetic efficiency in rice plant. Mapping of these traits are very important for detection of more number of robust markers for improvement of these traits through molecular breeding approaches. RESULTS: A representative panel population was developed by including 120 germplasm lines from the initial shortlisted 274 lines for mapping of the six biochemical traits using 136 microsatellite markers through association mapping. A wide genetic variation was detected for the traits, total protein, starch, amylose, total soluble sugars, chlorophyll a, and chlorophyll b content in the population. Specific allele frequency, gene diversity, informative markers and other diversity parameters obtained from the population indicated the effectiveness of utilization of the population and markers for mapping of these traits. The fixation indices values estimated from the population indicated the existence of linkage disequilibrium for the six traits. The population genetic structure at K = 3 showed correspondence with majority of the members in each group for the six traits. The reported QTL, qProt1, qPC6.2, and qPC8.2 for protein content; qTSS8.1 for total soluble sugar; qAC1.2 for amylose content; qCH2 and qSLCHH for chlorophyll a (Chl. a) while qChl5D for chlorophyll b (Chl. b) were validated in this population. The QTL controlling total protein content qPC1.2; qTSS7.1, qTSS8.2 and qTSS12.1 for total soluble sugars; qSC2.1, qSC2.2, qSC6.1 and qSC11.1 for starch content; qAC11.1, qAC11.2 and qAC11.3 for amylose content; qChla8.1 for Chl. a content and qChlb7.1 and qChlb8.1 for Chl. b identified by both Generalized Linear Model and Mixed Linear Model were detected as novel QTL. The chromosomal regions on chromosome 8 at 234 cM for grain protein content and total soluble sugars and at 363 cM for Chl. a and Chl. b along with the position at 48 cM on chromosome 11 for starch and amylose content are genetic hot spots for these traits. CONCLUSION: The validated, co-localized and the novel QTL detected in this study will be useful for improvement of protein, starch, amylose, total soluble sugars and chlorophyll content in rice.

Genome-wide analysis and characterization of heat shock transcription factors (Hsfs) in common bean (Phaseolus vulgaris L.).

Heat shock transcription factors (Hsfs) play an essential role as transcriptional regulatory proteins against heat stress by controlling the expression of heat-responsive genes. Common bean is a highly thermosensitive crop, and, therefore, its genome sequence information is segregated, characterized here in terms of heat shock transcription factors and its evolutionary significance. In this study, a complete comprehensive set of 29 non-redundant full-length Hsf genes were identified and characterized from Phaseolus vulgaris L. (PvHsf) genome sequence. Detailed gene information such as chromosomal localization, domain position, motif organization, and exon-intron identification were analyzed. All the 29 PvHsf genes were mapped on 8 out of 11 chromosomes, indicating the gene duplication occurred in the common bean genome. Motif analysis and exon-intron structure were conserved in each group, which showed that the cytoplasmic proteins highly influence the conserved structure of PvHsfs and heat-induced response. The HSF genes were grouped into three classes, i.e., A to C and 14 groups, based on structural features and phylogenetic relationships. Only one pair of paralog sequences suggests that it may be derived from the duplication event during evolution. A comparative genomics study indicated the influence of whole-genome duplication and purifying selection on the common bean genome during development. In silico expression analysis showed the active role of class A and B family during abiotic stress conditions and higher expression in floral organs. The qRT-PCR analysis revealed PvHSFA8 as the master regulator and PvHSFB1A and PvHSFB2A induction during heat exposure in French beans.

Population genetic structure and association mapping for iron toxicity tolerance in rice.

Iron (Fe) toxicity is a major abiotic stress which severely reduces rice yield in many countries of the world. Genetic variation for this stress tolerance exists in rice germplasms. Mapping of gene(s)/QTL controlling the stress tolerance and transfer of the traits into high yielding rice varieties are essential for improvement against the stress. A panel population of 119 genotypes from 352 germplasm lines was constituted for detecting the candidate gene(s)/QTL through association mapping. STRUCTURE, GenAlEx and Darwin softwares were used to classify the population. The marker-trait association was detected by considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) analyses. Wide genetic variation was observed among the genotypes present in the panel population for the stress tolerance. Linkage disequilibrium was detected in the population for iron toxicity tolerance. The population was categorized into three genetic structure groups. Marker-trait association study considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) showed significant association of leaf browning index (LBI) with markers RM471, RM3, RM590 and RM243. Three novel QTL controlling Fe-toxicity tolerance were detected and designated as qFeTox4.3, qFeTox6.1 and qFeTox10.1. A QTL reported earlier in the marker interval of C955-C885 on chromosome 1 is validated using this panel population. The present study showed that QTL controlling Fe-toxicity tolerance to be co-localized with the QTL for Fe-biofortification of rice grain indicating involvement of common pathway for Fe toxicity tolerance and Fe content in rice grain. Fe-toxicity tolerance QTL qFeTox6.1 was co-localized with grain Fe-biofortification QTLs qFe6.1 and qFe6.2 on chromosome 6, whereas qFeTox10.1 was co-localized with qFe10.1 on chromosome 10. The Fe-toxicity tolerance QTL detected from this mapping study will be useful in marker-assisted breeding programs.

Synthesis of drug conjugated magnetic nanocomposite with enhanced hypoglycemic effects.

In the present study, a magnetic nanocomposite (magnetite Fe3O4 and hematite Fe2O3) has been successfully synthesized by the sol-gel method and coated with polyvinyl alcohol (PVA) followed by conjugation of anti-diabetic drug metformin. Detailed structural and microstructural characterization of the nanocomposite (NP) and drug conjugated nanocomposite (NP-DC) are analyzed by the Rietveld refinement of respective XRD patterns, FTIR analysis, UV-Vis spectroscopy, SEM and TEM results. SEM and TEM image analyses reveal the spherical morphology and average size of NP, PVA coated nanoparticles (NP-PVA) and NP-DC samples, indicating a suitable size to be a nanocarrier. The biocompatibility of NP and NP-DC was carried out in NIH/3T3 and J774A. 1 cells. The enhanced activity of the drug, when conjugated with nanocomposite, is confirmed after the treatment of both the pure drug and NP-DC sample on the 18 h fasted normoglycemic and hyperglycemic mice. The blood glucose level of the mice is effectively decreased with the same concentration of the pure drug and NP-DC sample. It proves the increased activity of the NP-DC sample, as only 5 wt% drug is present that shows the same efficiency as the pure drug. This study suggests excellent biocompatibility and cytocompatibility of NP and NP-DC besides the critical property as a hypoglycemic agent. It is the first time approach of conjugating metformin with a magnetic nanocomposite for a significant increment of its hypoglycemic activity, which is very important to reduce the side effect of metformin for its prolonged use.

Linkage disequilibrium mapping for grain Fe and Zn enhancing QTLs useful for nutrient dense rice breeding.

BACKGROUND: High yielding rice varieties are usually low in grain iron (Fe) and zinc (Zn) content. These two micronutrients are involved in many enzymatic activities, lack of which cause many disorders in human body. Bio-fortification is a cheaper and easier way to improve the content of these nutrients in rice grain. RESULTS: A population panel was prepared representing all the phenotypic classes for grain Fe-Zn content from 485 germplasm lines. The panel was studied for genetic diversity, population structure and association mapping of grain Fe-Zn content in the milled rice. The population showed linkage disequilibrium showing deviation of Hardy-Weinberg's expectation for Fe-Zn content in rice. Population structure at K = 3 categorized the panel population into distinct sub-populations corroborating with their grain Fe-Zn content. STRUCTURE analysis revealed a common primary ancestor for each sub-population. Novel quantitative trait loci (QTLs) namely qFe3.3 and qFe7.3 for grain Fe and qZn2.2, qZn8.3 and qZn12.3 for Zn content were detected using association mapping. Four QTLs, namely qFe3.3, qFe7.3, qFe8.1 and qFe12.2 for grain Fe content were detected to be co-localized with qZn3.1, qZn7, qZn8.3 and qZn12.3 QTLs controlling grain Zn content, respectively. Additionally, some Fe-Zn controlling QTLs were co-localized with the yield component QTLs, qTBGW, OsSPL14 and qPN. The QTLs qFe1.1, qFe3.1, qFe5.1, qFe7.1, qFe8.1, qZn6, qZn7 and gRMm9-1 for grain Fe-Zn content reported in earlier studies were validated in this study. CONCLUSION: Novel QTLs, qFe3.3 and qFe7.3 for grain Fe and qZn2.2, qZn8.3 and qZn12.3 for Zn content were detected for these two traits. Four Fe-Zn controlling QTLs and few yield component QTLs were detected to be co-localized. The QTLs, qFe1.1, qFe3.1, qFe5.1, qFe7.1, qFe8.1, qFe3.3, qFe7.3, qZn6, qZn7, qZn2.2, qZn8.3 and qZn12.3 will be useful for biofortification of the micronutrients. Simultaneous enhancement of Fe-Zn content may be possible with yield component traits in rice.

Association mapping reveals multiple QTLs for grain protein content in rice useful for biofortification.

Rice is the staple food for majority of the global population. But, rice grain has low protein content (PC). Mapping of QTLs controlling grain PC is essential for enhancement of the trait through breeding programs. A shortlisted panel population for grain protein content was studied for genetic diversity, population structure and association mapping for grain PC. Phenotyping results showed a wide variation for grain PC. The panel population showed a moderate level of genetic diversity estimated through 98 molecular markers. AMOVA and structure analysis indicated linkage disequilibrium for grain PC and deviation of Hardy-Weinberg's expectation. The analysis showed 15% of the variation among populations and 73% among individuals in the panel population. STRUCTURE analysis categorized the panel population into three subpopulations. The analysis also revealed a common primary ancestor for each subpopulation with few admix individuals. Marker-trait association using 98 molecular markers detected 7 strongly associated QTLs for grain PC by both MLM and GLM analysis. Three novel QTLs qPC3.1, qPC5.1 and qPC9.1 were detected for controlling the grain PC. Four reported QTLs viz., qPC3, QPC8, qPC6.1 and qPC12.1 were validated for use in breeding programs. Reported QTLs, qPC6, qPC6.1 and qPC6.2 may be same QTL controlling PC in rice. A very close marker RM407 near to protein controlling QTL, qProt8 and qPC8, was detected. The study provided clue for simultaneous improvement of PC with high grain yield in rice. The strongly associated markers with grain PC, namely qPC3, qPC3.1, qPC5.1, qPC6.1, qPC8, qPC9.1 and qPC12.1, will be useful for their pyramiding for developing protein rich high yielding rice.

Structural and thermal characterization of PHAs produced by Lysinibacillus sp. through submerged fermentation process.

In this investigation an attempt has been made to characterize and identify Lysinibacillus sp. 3HHX by 16S-rDNA sequencing. The bacterium exhibited occurrence of PHAs granules on an average 11±1 per cell of 1.0µm length and breadth 0.72µm, revealed from TEM studies. Under optimized condition, 4.006gm/L of PHAs was extracted using hypochlorite digestion and multi-solvent extraction process. PhaC gene of ∼540bp and higher PHA synthase activity was detected at 48h of cultivation. The extracted PHAs was structurally characterized by GC-MS and 1H NMR reported to be P(3HB-co-3HDD-co-3HTD) and amorphous in nature with 112°C melting point, -11.0°C glass transition point and 114.76°C decomposition temperature detected by DSC & TGA respectively. The C/O of biopolymer disc was 1:65 as revealed from C1s and O1s spectra of XPS, that was completely biodegradable within 30 days. This biopolymer was observed to be non-cytotoxic to NIH 3T3 mouse fibroblast cells. The report is of its kind in establishing the abilities of Lysinibacillus sp. 3HHX for non-growth associated PHA co-polymer production. Moreover the biocompatible and biodegradable nature of the biopolymer conferred to its substantial biomedical applications.

Mechanical preparation of nanocrystalline biocompatible single-phase Mn-doped A-type carbonated hydroxyapatite (A-cHAp): effect of Mn doping on microstructure.

Nanocrystalline biocompatible single-phase Mn-doped A-type carbonated hydroxyapatite (A-cHAp) powder has been synthesized by mechanical alloying of a stoichiometric mixture of CaCO3, CaHPO4·2H2O and MnO powder for 10 h at room temperature under open air. The A-type carbonation in HAp (substitution of CO3(2-) for OH(-)) is confirmed by FTIR analysis. Microstructure characterization in terms of lattice imperfections and phase quantification of ball milled samples are made by analyzing XRD patterns employing the Rietveld structure refinement method. Rietveld analysis of XRD patterns recorded from Mn-doped HAp samples has been used to locate Mn(2+) cations in HAp. The Ca2 vacancy site is found to be more favorable for Mn substitution. Microstructure characterization by HRTEM corroborates the findings of the X-ray analysis where the presence of a significant amount of amorphous phase of HAp analogous to indigenous bone mineral is clearly found. MTT assay shows sufficiently high percentage cell viability confirming the cytocompatibility of the sample.

Effects of monovalent cation doping on the structure, microstructure, lattice distortion and magnetic behavior of single crystalline NdMnO3 compounds.

Pure and 15 mol% Na, K-doped NdMnO3 compounds with perovskite structures are prepared by sol-gel method. Tiny single crystals are formed after sintering the compounds at 1000 °C. The effect of Na and K doping as well as the effect of sintering temperature on the formation and microstructure of NdMnO3 are studied in detail by the Rietveld refinement technique using X-ray powder diffraction data. Single phase formation and single crystalline growth are also confirmed by high resolution transmission electron microscopy (HRTEM). Bond angles and bond lengths are calculated and shown by 3D diagrams. Monovalent doping induces noticeable changes in the microstructure and yields better structural stability in these compounds. Doping results in the change of Mn-O, Nd-O and Mn-O-Mn bond lengths which in turn reduces the lattice and octahedral distortion in the system along with an increase in the tolerance factor. The magnetic properties of these compounds are also modified as a result of doping. The temperature dependent magnetization results show that the Neel temperature of antiferromagnetic NdMnO3 compound is 67.2 K and the Curie temperatures of ferromagnetic Nd0.85Na0.15MnO3 and Nd0.85K0.15MnO3 compounds are 99.1 K and 98.6 K respectively. Both 15% Na and K doping results in a similar TC in doped NdMnO3 compounds.

Early seedling vigour, an imperative trait for direct-seeded rice: an overview on physio-morphological parameters and molecular markers.

MAIN CONCLUSION: Rapid uniform germination and accumulation of biomass during initial phase of seedling establishment is an essential phenotypic trait considered as early seedling vigour for direct seeded situation in rice irrespective of environment. Enhanced role of carbohydrate, amylase, growth hormones, antioxidant enzymes and ascorbic acid brings changes in vigour and phenotype of seedling. Early establishment and demanding life form dominate the surroundings. Crop plant that has better growth overdrives the weed plant and suppresses its growth. Seedling early vigour is the characteristic of seed quality and describes the rapid, uniform germination and the establishment of strong seedlings in any environmental condition. The phenotype of modern rice varieties has been changed into adaptable for transplanted rice with thirst toward water and selection pressure for semi-dwarf architecture resulting in reduced early vigour. Decreasing freshwater availability and rising labour cost drives the search for a suitable alternative management system to enhance grain yield productivity for the burgeoning world population. In view of these issues, much attention has been focused on dry direct-seeded rice, because it demands low input. A rice cultivar with a strong seedling vigour trait is desirable in case of direct seeding. However, seedling vigour has not been selected in crop improvement programmes in conventional breeding due to its complex nature and quantitative inheritance. Molecular markers have been proven effective in increasing selection efficiency, particularly for quantitative traits that are simply inherited. Marker-assisted selection approach has facilitated efficient and precise transfer of genes/QTL(s) into many crop species and suggests a speedy and efficient technique over conventional breeding and selection methods. In this review, we present the findings and investigations in the field of seedling vigour in rice that includes the nature of inheritance of physio-morphological and biochemical traits and QTLs to assist plant breeders who work for direct-seeded rice.

Effect of feeding Jerusalem artichoke (Helianthus tuberosus) root as prebiotic on nutrient utilization, fecal characteristics and serum metabolite profile of captive Indian leopard (Panthera pardus fusca) fed a meat-on-bone diet.

An experiment was conducted to determine the effect of incorporating Jerusalem artichoke (JA) as a prebiotic in the diet of Indian leopards (n = 11 adults) fed a meat-on-bone diet. The trial consisted of three periods (A1 , B, and A2 ). Each period comprised 17 days of adaptation and four days of collection. During the control periods (A1 and A2 ), the leopards were fed their normal zoo diets of 2.5-3 kg of buffalo meat-on-bone six days a week without any supplement. During trial B, meat-on-bone diets of the leopards were supplemented with JA at 2% of dietary dry matter (DM). Meat consumption was similar among the treatments. Supplementation of JA decreased the digestibility of crude protein (P < 0.01). Digestibilities of organic matter and ether extract were similar among the treatments. Serum concentrations of urea and triglycerides were lower (P < 0.05) when JA was added to the diet. Incorporation of JA to the basal diet increased fecal concentrations of acetate (P < 0.01), butyrate (P < 0.01), lactate (P < 0.01), Lactobacillus spp., and Bifidobacterium spp. (P < 0.01) with a simultaneous decrease in the concentration of ammonia (P < 0.01), Clostridia spp. (P < 0.01), and fecal pH (P < 0.01). Fecal microbial profiles and hind gut fermentation were improved, without any adverse effects on feed consumption, nutrient utilization, and serum metabolite profiles. Results of this experiment showed that feeding JA at 2% DM in the whole diet could be potentially beneficial for captive Indian leopards fed meat-on-bone diets.

Biocompatible nanocrystalline natural bonelike carbonated hydroxyapatite synthesized by mechanical alloying in a record minimum time.

Single phase nanocrystalline biocompatible A-type carbonated hydroxyapatite (A-cHAp) powder has been synthesized by mechanical alloying the stoichiometric mixture of CaCO3 and CaHPO4.2H2O powders in open air at room temperature within 2h of milling. The A-type carbonation in HAp is confirmed by FTIR analysis. Structural and microstructure parameters of as-milled powders are obtained from both Rietveld's powder structure refinement analysis and transmission electron microscopy. Size and lattice strain of nanocrystalline HAp particles are found to be anisotropic in nature. Mechanical alloying causes amorphization of a part of crystalline A-cHAp which is analogous to native bone mineral. Some primary bond lengths of as-milled samples are critically measured. MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] assay test reveals high percentage of cell viability and hence confirms the biocompatibility of the sample. The overall results indicate that the processed A-cHAp has a chemical composition very close to that of biological apatite.

Investigation of an outbreak of infectious pustular balanoposthitis in cattle breeding bulls at a frozen semen bank.

Infectious pustular balanoposthitis (IPB) is one of the reproductive disorders caused by bovine herpesvirus 1 (BoHV1) that can be transmitted through artificial insemination. A herd of 63 breeding bulls at a frozen semen bank in Odisha state in India experienced a suspected outbreak of IPB, with 11 bulls showing clinical signs of the infection. Clinical signs were noticed in two bulls initially and a few days after in the other nine animals. Serum samples from 53 bulls were examined for anti-BoHV1 antibodies using a virus neutralisation test (VNT) and a competitive enzyme-linked immunosorbent assay (cELISA); the remaining ten bulls were not included in the study because it was difficult to restrain them at that time. Paired serum samples were collected 21 days apart from ten clinically affected bulls (the eleventh clinically affected bull was not included in the study for the reason stated above). In the neutralisation test, the paired serum samples showed a two- to fourfold increase in anti-BoHV1 antibody titre; in the cELISA, the paired samples were also found positive for anti-BoHV1 antibodies. Serum samples from 43 in-contact bulls were collected about day 22 after the first observation of clinical infection in the herd. Among these serum samples, a total of 30 were found positive for anti-BoHV1 antibodies in the VNT and a total of 30 were found positive in cELISA. Ten samples were positive in one test but not the other and 25 tested positive in both tests. In all, 35 serum samples from in-contact bulls tested positive in either one or both of the two types of test. An overall agreement of 76.74% was found in detection of anti-BoHV1 antibodies in the two tests. Sensitivity was higher than specificity in detection of anti-BoHV1 antibodies in the serum samples. The glycoprotein C region of the genomic DNA of BoHV1 was amplified from semen samples by polymerase chain reaction. The findings from the outbreak indicate that continuous monitoring of breeding bulls at frozen semen banks is warranted to avoid the risks associated with artificial insemination.

Structural and microstructural characterizations of nanocrystalline hydroxyapatite synthesized by mechanical alloying.

Single phase nanocrystalline hydroxyapatite (HAp) powder has been synthesized by mechanical alloying the stoichiometric mixture of CaCO3 and CaHPO4 powders in open air at room temperature, for the first time, within 2 h of milling. Nanocrystalline hexagonal single crystals are obtained by sintering of 2h milled sample at 500 °C. Structural and microstructural properties of as-milled and sintered powders are revealed from both the X-ray line profile analysis and transmission electron microscopy. Shape and lattice strain of nanocrystalline HAp particles are found to be anisotropic in nature. Particle size of HAp powder remains almost invariant up to 10h of milling and there is no significant growth of nanocrystalline HAp particles after sintering at 500 °C for 3 h. Changes in lattice volume and some primary bond lengths of as-milled and sintered are critically measured, which indicate that lattice imperfections introduced into the HAp lattice during ball milling have been reduced partially after sintering the powder at elevated temperatures. We could achieve ~96.7% of theoretical density of HAp within 3h by sintering the pellet of nanocrystalline powder at a lower temperature of 1000 °C. Vickers microhardness (VHN) of the uni-axially pressed (6.86 MPa) pellet of nanocrystalline HAp is 4.5 GPa at 100 gm load which is close to the VHN of bulk HAp sintered at higher temperature. The strain-hardening index (n) of the sintered pellet is found to be >2, indicating a further increase in microhardness value at higher load.

Persistent left fifth aortic arch with pentalogy of Fallot.

Congenital double-lumen aortic arch resulting from persistence of the fifth aortic arterial arch (PFAA) is a rare congenital anomaly. It appears as a vascular structure running inferior and parallel to the "real" aortic arch from the innominate artery to the left subclavian artery. We report a case of persistent fifth aortic arch (systemic-to-systemic arterial connection) with pentalogy of Fallot in a patient who underwent successful intracardiac repair with a transannular patch with very proximal aortic cannulation for cardiopulmonary bypass (CPB).

A community based study of health related quality of life of the elderly in urban India.

The increasing population of elderly and emergence of chronic diseases, which adversely affects their quality of life, have implications in form of rising burden on the health systems in developing countries like India. A study was conducted to know the common morbidities and their effect on the health related quality of life (HRQOL) of the elderly. A community based cross-sectional study was conducted and 200 subjects, selected by cluster sampling from central Delhi, India, were studied from April 2005-February 2006. A pretested, semi-structured questionnaire along with short form-36 (SF-36) survey was used for data collection. The data was analysed using Chi-square and Student's 't' test on SPSS 12 statistical software. There were 89 males and 111 females, majority (64.5%) between 60 and 69 years of the age, were included in the study; 68.0% men and 37.8% of the women were married at the time of the study. Mean number of morbidities was 2.25 and 71.5% subjects had at least one disability/impairment. Around 2.5% subjects reported their health being poor and, another 50% of worsening of their health in last one year. HRQOL score for people with and without chronic morbidity/disability was 51.8 and 73.5 respectively with mean being at 56.7 (p < 0.05). Most commonly affected HRQOL domains were role physical, physical functioning and general health. Scores decreased as the age increased with females having less mean scores than males (p < 0.05). The quality of life of elderly in urban India is severely affected by the disabilities, impairments and chronic morbidities. There is an immediate need for specific preventive and rehabilitative measures targeted on elderly to maintain their quality of life in this population in Delhi.

Public health impact of plastics: An overview.

Plastic, one of the most preferred materials in today's industrial world is posing serious threat to environment and consumer's health in many direct and indirect ways. Exposure to harmful chemicals during manufacturing, leaching in the stored food items while using plastic packages or chewing of plastic teethers and toys by children are linked with severe adverse health outcomes such as cancers, birth defects, impaired immunity, endocrine disruption, developmental and reproductive effects etc. Promotion of plastics substitutes and safe disposal of plastic waste requires urgent and definitive action to take care of this potential health hazard in future.