VARIABLE RESPONSE OF THREE MORPHOTYPES OF TECOMELLA UNDULATA (SM.) SEEM TOWARDS HUMAN PATHOGENIC BACTERIA

Objective: Medicinal Tree Tecomella undulata [Sm.] Seem belonging to family Bignoniaceae has three distinct morphotypes. Present study was undertaken to assess antimicrobial potential of the three morphotypes of Tecomella undulata against human pathogenic bacteria to select suitable morphotype for medicinal use.Methods: Disc diffusion method was used to test and compare the antimicrobial activity exhibited by 13 populations belonging to three morphotypes of this tree against five human pathogenic bacteria i. e. Bacillus subtilis, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Staphylococcus aureus.Results: Methanol and acetone extract of bark of the tree showed considerable activity against all the five bacteria tested. Differences were observed in the activity not only between the morphotypes but also within the morphotypes against the bacteria tested. Out of the three morpho types yellow morphotypes showed the highest antimicrobial action against all the five bacteria which were comparable to standard antibiotic Chloramphenicol. The trend in antibacterial activity observed was yellow>red>orange in acetone extract and yellow>orange>red in methanol extract towards all microbes except against bacillus bacteria where it was yellow>orange>red [acetone] and orange>yellow>red [methanol].Conclusion: The experimental results of the present study revealed that Tecomella undulata plants show great intraspecific variability in their antibacterial potential. Hence there is need to evaluate germplasm to select superior genotype for medicinal, multiplication, conservation or plantation purpose.Â

Physico-chemical and enzymatic changes in peach (Prunus persica (L.) Batsch) fruit in response to sodium salts during low temperature storage

‘Shan-i-Punjab’ is a leading cultivar of peach (Prunus persica (L.) Batsch) in Punjab. After harvesting peach fruits cannot be stored for a longer period under ambient conditions. To prolong the post-harvest life of fruits, an experiment was conducted during the year 2014. Physiological mature fruits of peach cv. Shan-i-Punjab were harvested and subjected to various post-harvest dip treatments viz. sodium bicarbonate (@ 0.5 and 1%), sodium benzoate (@ 0.5 and 1%) for 5 mins. Treated and untreated (control) fruits were packed in Corrugated fibre board CFB boxes and kept under low temperature storage conditions (0-10 C and 90-95% RH) for 6 weeks. Stored fruits were analyzed for various physico-chemical characteristics after 2, 4, 5 and 6 weeks of storage. Fruits treated with 0.5% sodium bicarbonate showed better results in terms low PLW (5.05%), high palatability rating (7.66), TSS (11.26%), acidity (0.70%) and PME activity (1.28 ml of 0.02N NaOH used) upto 4 weeks of storage as compared to control. It can be concluded that peach fruits of the cultivar Shan-i-Punjab treated with sodium bicarbonate @ 0.5% can be safely stored upto 4 weeks with acceptable quality under low temperature conditions

A BAC-based physical map of the Hessian fly genome anchored to polytene chromosomes

<p>Abstract</p> <p>Background</p> <p>The Hessian fly (<it>Mayetiola destructor</it>) is an important insect pest of wheat. It has tractable genetics, polytene chromosomes, and a small genome (158 Mb). Investigation of the Hessian fly presents excellent opportunities to study plant-insect interactions and the molecular mechanisms underlying genome imprinting and chromosome elimination. A physical map is needed to improve the ability to perform both positional cloning and comparative genomic analyses with the fully sequenced genomes of other dipteran species.</p> <p>Results</p> <p>An FPC-based genome wide physical map of the Hessian fly was constructed and anchored to the insect's polytene chromosomes. Bacterial artificial chromosome (BAC) clones corresponding to 12-fold coverage of the Hessian fly genome were fingerprinted, using high information content fingerprinting (HIFC) methodology, and end-sequenced. Fluorescence <it>in situ </it>hybridization (FISH) co-localized two BAC clones from each of the 196 longest contigs on the polytene chromosomes. An additional 70 contigs were positioned using a single FISH probe. The 266 FISH mapped contigs were evenly distributed and covered 60% of the genome (95,668 kb). The ends of the fingerprinted BACs were then sequenced to develop the capacity to create sequenced tagged site (STS) markers on the BACs in the map. Only 3.64% of the BAC-end sequence was composed of transposable elements, helicases, ribosomal repeats, simple sequence repeats, and sequences of low complexity. A relatively large fraction (14.27%) of the BES was comprised of multi-copy gene sequences. Nearly 1% of the end sequence was composed of simple sequence repeats (SSRs).</p> <p>Conclusion</p> <p>This physical map provides the foundation for high-resolution genetic mapping, map-based cloning, and assembly of complete genome sequencing data. The results indicate that restriction fragment length heterogeneity in BAC libraries used to construct physical maps lower the length and the depth of the contigs, but is not an absolute barrier to the successful application of the technology. This map will serve as a genomic resource for accelerating gene discovery, genome sequencing, and the assembly of BAC sequences. The Hessian fly BAC-clone assembly, and the names and positions of the BAC clones used in the FISH experiments are publically available at <url>http://genome.purdue.edu/WebAGCoL/Hfly/WebFPC/</url>.</p

Urinary, Plasma, and Serum Biomarkers’ Utility for Predicting Acute Kidney Injury Associated With Cardiac Surgery in Adults: A Meta-analysis

BackgroundEarly accurate detection of acute kidney injury (AKI) occurring after cardiac surgery may improve morbidity and mortality. Although several novel biomarkers have been developed for the early detection of AKI, their clinical utility in the critical intraoperative and immediate postoperative period remains unclear.Study DesignSystematic review and meta-analysis.Setting & PopulationAdult patients having cardiac surgery.Selection Criteria for StudiesEMBASE, CINAHL, Cochrane Library, Scopus, and PubMed from January 1990 until January 2015 were systematically searched for cohort studies reporting the utility of novel biomarkers for the early diagnosis of AKI after adult cardiac surgery. Reviewers extracted data for study design, population, timing of biomarker measurement and AKI occurrence, biomarker performance (area under the receiver operating characteristic curve [AUROC]), and risk of bias.Index TestsNovel urine, plasma, and serum AKI biomarkers, measured intraoperatively and in the early postoperative period (<24 hours).Reference TestsAKI was defined according to the RIFLE, AKIN, or 2012 KDIGO criteria.ResultsWe found 28 studies reporting intraoperative and/or early postoperative measurement of urine (n=23 studies) or plasma or serum (n=12 studies) biomarkers. Only 4 of these studies measured biomarkers intraoperatively. Overall, intraoperative discrimination by the urine biomarkers neutrophil gelatinase-associated lipocalin (NGAL) and kidney injury marker 1 (KIM-1) demonstrated AUROCs<0.70, whereas N-acetyl-β-d-glucosaminidase (NAG) and cystatin C had AUROCs<0.75. In the immediate 24-hour postoperative period, the urine biomarkers NGAL (16 studies), KIM-1 (6 studies), and liver-type fatty acid binding protein (6 studies) exhibited composite AUROCs of 0.69 to 0.72. The composite AUROCs for postoperative urine cystatin C, NAG, and interleukin 18 were ≤0.70. Similarly, the composite AUROCs for postoperative plasma NGAL (6 studies) and cystatin-C (5 studies) were <0.70.LimitationsHeterogeneous AKI definitions.ConclusionsIn adults, known urinary, plasma, and serum biomarkers of AKI possess modest discrimination at best when measured within 24 hours of cardiac surgery

Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza

Bacterial artificial chromosome (BAC) fingerprint and end-sequenced physical maps representing the ten genome types of Oryza are presente

Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum

BACKGROUND: With the completion of the genome sequence for rice (Oryza sativa L.), the focus of rice genomics research has shifted to the comparison of the rice genome with genomes of other species for gene cloning, breeding, and evolutionary studies. The genus Oryza includes 23 species that shared a common ancestor 8–10 million years ago making this an ideal model for investigations into the processes underlying domestication, as many of the Oryza species are still undergoing domestication. This study integrates high-throughput, hybridization-based markers with BAC end sequence and fingerprint data to construct physical maps of rice chromosome 1 orthologues in two wild Oryza species. Similar studies were undertaken in Sorghum bicolor, a species which diverged from cultivated rice 40–50 million years ago. RESULTS: Overgo markers, in conjunction with fingerprint and BAC end sequence data, were used to build sequence-ready BAC contigs for two wild Oryza species. The markers drove contig merges to construct physical maps syntenic to rice chromosome 1 in the wild species and provided evidence for at least one rearrangement on chromosome 1 of the O. sativa versus Oryza officinalis comparative map. When rice overgos were aligned to available S. bicolor sequence, 29% of the overgos aligned with three or fewer mismatches; of these, 41% gave positive hybridization signals. Overgo hybridization patterns supported colinearity of loci in regions of sorghum chromosome 3 and rice chromosome 1 and suggested that a possible genomic inversion occurred in this syntenic region in one of the two genomes after the divergence of S. bicolor and O. sativa. CONCLUSION: The results of this study emphasize the importance of identifying conserved sequences in the reference sequence when designing overgo probes in order for those probes to hybridize successfully in distantly related species. As interspecific markers, overgos can be used successfully to construct physical maps in species which diverged less than 8 million years ago, and can be used in a more limited fashion to examine colinearity among species which diverged as much as 40 million years ago. Additionally, overgos are able to provide evidence of genomic rearrangements in comparative physical mapping studies

Comparative analysis of repetitive DNA sequences in genus Oryza

Repetitive DNA sequences play a major architectonic role in higher order physical structuring of genomes. To be able to understand how these sequences shape plant genomes during evolution, BAC-end sequences representing ∼10% of ten Oryza genomes were used to sample their repetitive fraction. 36-76% of these genomes was repetitive and was correlated to the genome size (r=0.96). Analysis of the largest and smallest diploid genomes indicated their role in determining genome size of a species. Repetitive sequences specific to each species were identified for potential use as molecular markers in practical breeding and cytogenetic studies. Comparison of orthologous regions identified genomic rearrangements and conserved/variable regions with implications for changes at these loci both pre and post-genome differentiation from a common ancestor. Fragments of transposable elements were also found associated with conserved noncoding sequences, some of which were mapped to the untranslated regions and introns of genes, implying possible roles in gene regulation. Thus, the data suggests an evolutionary as well as functional significance of transposable elements in the host genomes. These determinations will be used to improve our understanding of the processes that might have played a role in shaping Oryza genomes

Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome

Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is &gt;78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence