The histochemical assessment of sulpho-, sialo-, and neutral-mucosubstances in fetal gastric mucosa

Background: Mucins are complex composition of carbohydrates and may be present as a mixture of different types. Normal distribution of mucin and its alteration in various inflammatory, benign and malignant lesions of gastrointestinal tract has aroused interest in the field of histochemistry. The main purpose of present work is to study the staining pattern and distribution of cells in different parts of fetal gastric mucosa and to correlate the nature of gastric mucins and its functional significance.  Methods: A total of 25 fetus stomach specimens (total 75 samples) one sample each from different parts of the stomach like fundus, body and pylorus, from fresh specimens. The samples were washed in normal saline, fixed in 2% calcium acetate in 10% formalin. These tissues were routinely processed and paraffin blocks were prepared. 6 m sections of these blocks were taken for histological and different histochemical staining.Results: Fetal fundic part of stomach shows increased neutral mucin in surface epithelium and foveolar cells. With combined AB pH 2.5 - PAS technique increased neutral mucin and small amount of acid mucins are observed. With AB pH 1, surface epithelium and deep glands show negative staining. Moderate alcinophilia is observed in deep foveolar cells and glandular cells. AB pH 2.5 shows alcinophilia in surface epithelium, foveolar cells and mucous neck cells indicating presence of sialomucin. Fetal pyloric part of stomach shows increased acid and neutral mucins. With pH 2.5 - PAS staining, purple staining is observed in surface epithelium, deep foveolar and pyloric glands.  Conclusion: All types of mucosubstances - neutral, sialo and sulpho-mucins, are secreted in relatively increased amounts by the surface epithelium and the glands of the stomach of the human fetus and neonate. Sulphomucin is seen mainly in the cells of the surface epithelium.  

Extraction of manganese from Ferro-manganese slag

In the present investigation an attempt has been made to recover manganese from ferro-manganese slag of ferro-alloy plant. Roasting and leaching are the techniques used to recover- manganese. Roasting has been carried out by mixing the slag with CaO and CaCO3, at 1200Cfor 2 hours. The leaching of the roasted mass has been carried out in ferric chloride solution alone, as well as in presence of sucrose in ferric chloride solution. The optimum condit-ions have been established by varying the parameters like concentration of leaching agent, percent solids, particle size of the slag, temperature and time of leaching. It is possible to recover 87% of manganese from the ferro-manganese slag of 200# at a temperature of 80°C, 2 hours of leaching time and 5% solids in 0. 154 M ferric chloride solution. It has been found that the presence of sucrose in ferric chloride solution enhances the rate & recovery)recovery of manganese from slag

Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array

<p>Abstract</p> <p>Background</p> <p>Cowpea (<it>Vigna unguiculata </it>L. Walp) is an important food and fodder legume of the semiarid tropics and subtropics worldwide, especially in sub-Saharan Africa. High density genetic linkage maps are needed for marker assisted breeding but are not available for cowpea. A single feature polymorphism (SFP) is a microarray-based marker which can be used for high throughput genotyping and high density mapping.</p> <p>Results</p> <p>Here we report detection and validation of SFPs in cowpea using a readily available soybean (<it>Glycine max) </it>genome array. Robustified projection pursuit (RPP) was used for statistical analysis using RNA as a surrogate for DNA. Using a 15% outlying score cut-off, 1058 potential SFPs were enumerated between two parents of a recombinant inbred line (RIL) population segregating for several important traits including drought tolerance, <it>Fusarium </it>and brown blotch resistance, grain size and photoperiod sensitivity. Sequencing of 25 putative polymorphism-containing amplicons yielded a SFP probe set validation rate of 68%.</p> <p>Conclusion</p> <p>We conclude that the Affymetrix soybean genome array is a satisfactory platform for identification of some 1000's of SFPs for cowpea. This study provides an example of extension of genomic resources from a well supported species to an orphan crop. Presumably, other legume systems are similarly tractable to SFP marker development using existing legume array resources.</p

Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array

<p>Abstract</p> <p>Background</p> <p>A large number of genetic variations have been identified in rice. Such variations must in many cases control phenotypic differences in abiotic stress tolerance and other traits. A single feature polymorphism (SFP) is an oligonucleotide array-based polymorphism which can be used for identification of SNPs or insertion/deletions (INDELs) for high throughput genotyping and high density mapping. Here we applied SFP markers to a lingering question about the source of salt tolerance in a particular rice recombinant inbred line (RIL) derived from a salt tolerant and salt sensitive parent.</p> <p>Results</p> <p>Expression data obtained by hybridizing RNA to an oligonucleotide array were analyzed using a statistical method called robustified projection pursuit (RPP). By applying the RPP method, a total of 1208 SFP probes were detected between two presumed parental genotypes (Pokkali and IR29) of a RIL population segregating for salt tolerance. We focused on the <it>Saltol </it>region, a major salt tolerance QTL. Analysis of FL478, a salt tolerant RIL, revealed a small (< 1 Mb) region carrying alleles from the presumed salt tolerant parent, flanked by alleles matching the salt sensitive parent IR29. Sequencing of putative SFP-containing amplicons from this region and other positions in the genome yielded a validation rate more than 95%.</p> <p>Conclusion</p> <p>Recombinant inbred line FL478 contains a small (< 1 Mb) segment from the salt tolerant parent in the <it>Saltol </it>region. The Affymetrix rice genome array provides a satisfactory platform for high resolution mapping in rice using RNA hybridization and the RPP method of SFP analysis.</p

Recent Ancestry of Kyasanur Forest Disease Virus

Clinicians in Asia should consider this disease when diagnosing acute febrile illnesses

Breeding tomato (Solanum lycopersicum L.) for resistance to biotic and abiotic stresses

Tomato (Solanum lycopersicum L.) is an important vegetable crop cultivated in the tropical and sub-tropical regions of the world. Low productivity in India is due to occurrence of both biotic and abiotic stresses. Among the biotic stresses, tomato leaf curl disease, bacterial wilt, early blight and Groundnut Bud Necrosis Virus disease have become serious production constraints causing considerable yield loss in the major tomato growing areas of the country. Adoption of multiple disease resistant varieties or F1 hybrids would be the most appropriate way to address these diseases. At ICAR-IIHR, Bengaluru systematic breeding strategies were employed to pyramid genes for resistance to early blight, bacterial wilt and tomato leaf curl diseases and to develop advanced breeding lines&amp; F1 hybrids with triple disease resistance. Stable source of resistance to early blight and bi-partite begomo-virus (Tomato Leaf Curl New Delhi Virus) has been identified in Solanum habrochaites LA-1777. Validation with molecular markers linked to tomato leaf curl virus resistance revealed that LA-1777 carryTy2 and other putative resistant genes. Several high yielding dual purpose hybrids were also developed for fresh market and processing with high level of resistance to multiple diseases. Cherry tomato lines have also been bred for high TSS, total carotenoids, total phenols, flavonoids, vitamin C, acidity and lycopene content. IIHR-249-1, IIHR-2101 (Solanum habrochaites LA-1777), IIHR- 2866 and IIHR-2864 recorded high values for quality parameters like total carotenoids, lycopene, vitamin C, total phenols, flavonoids and TSS. Drought tolerant root stock has been developed by an interspecific cross between S. habrochaites LA-1777 and S. lycopersicum (15 SB SB). Resistant sources have also been identified against Tuta absoluta, a serious insect pest reported from major tomato growing areas in the country in recent time. High temperature tolerant breeding lines are in pipe line

Sequencing of 15 622 Gene-bearing BACs Clarifies the Gene-dense Regions of the Barley Genome

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley–Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant

Mapping translocation breakpoints using a wheat microarray

We report mapping of translocation breakpoints using a microarray. We used complex RNA to compare normal hexaploid wheat (17 000 Mb genome) to a ditelosomic stock missing the short arm of chromosome 1B (1BS) and wheat-rye translocations that replace portions of 1BS with rye 1RS. Transcripts detected by a probe set can come from all three Triticeae genomes in ABD hexaploid wheat, and sequences of homoeologous genes on 1AS, 1BS and 1DS often differ from each other. Absence or replacement of 1BS therefore must sometimes result in patterns within a probe set that deviate from hexaploid wheat. We termed these ‘high variance probe sets’ (HVPs) and examined the extent to which HVPs associated with 1BS aneuploidy are related to rice genes on syntenic rice chromosome 5 short arm (5S). We observed an enrichment of such probe sets to 15–20% of all HVPs, while 1BS represents ∼2% of the total genome. In total 257 HVPs constitute wheat 1BS markers. Two wheat-rye translocations subdivided 1BS HVPs into three groups, allocating translocation breakpoints to narrow intervals defined by rice 5S coordinates. This approach could be extended to the entire wheat genome or any organism with suitable aneuploid or translocation stocks

Development and implementation of high-throughput SNP genotyping in barley

<p>Abstract</p> <p>Background</p> <p>High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource.</p> <p>Results</p> <p>Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM.</p> <p>Conclusion</p> <p>The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material.</p