From QTL to variety-harnessing the benefits of QTLs for drought, flood and salt tolerance in mega rice varieties of India through a multi-institutional network.

Rice is a staple cereal of India cultivated in about 43.5Mha area but with relatively low average productivity. Abiotic factors like drought, flood and salinity affect rice production adversely in more than 50% of this area. Breeding rice varieties with inbuilt tolerance to these stresses offers an economically viable and sustainable option to improve rice productivity. Availability of high quality reference genome sequence of rice, knowledge of exact position of genes/QTLs governing tolerance to abiotic stresses and availability of DNA markers linked to these traits has opened up opportunities for breeders to transfer the favorable alleles into widely grown rice varieties through marker-assisted backcross breeding (MABB). A large multi-institutional project, "From QTL to variety: marker-assisted breeding of abiotic stress tolerant rice varieties with major QTLs for drought, submergence and salt tolerance" was initiated in 2010 with funding support from Department of Biotechnology, Government of India, in collaboration with International Rice Research Institute, Philippines. The main focus of this project is to improve rice productivity in the fragile ecosystems of eastern, northeastern and southern part of the country, which bear the brunt of one or the other abiotic stresses frequently. Seven consistent QTLs for grain yield under drought, namely, qDTY1.1, qDTY2.1, qDTY2.2, qDTY3.1, qDTY3.2, qDTY9.1 and qDTY12.1 are being transferred into submergence tolerant versions of three high yielding mega rice varieties, Swarna-Sub1, Samba Mahsuri-Sub1 and IR 64-Sub1. To address the problem of complete submergence due to flash floods in the major river basins, the Sub1 gene is being transferred into ten highly popular locally adapted rice varieties namely, ADT 39, ADT 46, Bahadur, HUR 105, MTU 1075, Pooja, Pratikshya, Rajendra Mahsuri, Ranjit, and Sarjoo 52. Further, to address the problem of soil salinity, Saltol, a major QTL for salt tolerance is being transferred into seven popular locally adapted rice varieties, namely, ADT 45, CR 1009, Gayatri, MTU 1010, PR 114, Pusa 44 and Sarjoo 52. Genotypic background selection is being done after BC2F2 stage using an in-house designed 50K SNP chip on a set of twenty lines for each combination, identified with phenotypic similarity in the field to the recipient parent. Near-isogenic lines with more than 90% similarity to the recipient parent are now in advanced generation field trials. These climate smart varieties are expected to improve rice productivity in the adverse ecologies and contribute to the farmer's livelihood.

Primary CNS lymphoma as second malignancy in a case of carcinoma larynx treated with chemoradiation.

A 66-year-old male was diagnosed as carcinoma larynx in the year April 2004. He was treated with concurrent chemoradiation and remained disease free for three consecutive years. After 3 years he suddenly complained of giddiness and seizures. Magnetic Resonance Imaging of brain showed features of primary CNS lymphoma (PCNSL) which was confirmed by histopathology test. To the best of our knowledge PCNSL as second malignancy in a case of carcinoma of head and neck has not been reported till date. The PCNSL in this patient may have resulted from depressed immunity due to previous radiotherapy. Whatever may be the predisposing cause, this case is most probably the first reported case of PCNSL in a patient of squamous cell carcinoma of larynx.

Antifungal activity of Agapanthus africanus extractives.

The ethanolic extract of the rhizomes of Agapanthus africanus showed antifungal activity. In bioassay guided fractionation, n-butanol fraction exhibited significant activity against human pathogens. A saponin, (25R)-spirost-7-en-2alpha,3beta,5alpha-triol-3-O-[alpha-L-rhamnopyranosyl(1-->2)-[beta-D-galactopyranosyl (1-->3)] beta-D-glucopyranoside (1), responsible for the antifungal activity and having MIC value of 15.6 microg/ml against Trychophyton mentagrophytes and Sporothrix schenekii, was isolated and identified as active constituent of the plant.

Prediction of ingredient quality and the effect of a combination of xylanase, amylase, protease and phytase in the diets of broiler chicks. 1. Growth performance and digestible nutrient intake.

1. A total of 2208 broiler chicks were used in two growth experiments (8 treatments and 12 replicate pens in each experiment) to assess the effects of xylanase, amylase, protease and phytase in maize-based diets. 2. A positive control diet was formulated containing adequate nutrient concentrations. A negative control diet was formulated to contain approximately 628 kJ/kg, 0.13%, 0.12% and 1 to 2% less metabolisable energy (ME), phosphorus (P), calcium (Ca) and amino acids, respectively, than the positive control. In addition, two further negative control diets that contained 167 or 334 kJ/kg more ME, respectively, than negative control 1 were formulated. 3. A further 4 dietary treatments were made by supplementing each of the 4 negative control diets with a combination of xylanase, amylase, protease and phytase, resulting in 8 dietary treatments in a 4 by 2 factorial arrangement. 4. The scale of the removal of energy, P, Ca and amino acids from the positive control diet was determined using least square models based on in vivo data for both the xylanase/amylase/protease cocktail and for phytase and it was predicted that performance of birds fed on negative control 1 would be returned by supplemental enzymes to that of those fed on the positive control. 5. In both experiments there was a significantly poorer performance in birds fed on the negative control 1 than in those fed on the positive control. The poorer weight gain and feed conversion ratio could be attributed in part to a reduced intake of digestible energy, P, nitrogen (N) and amino acids associated with birds fed on the negative control diet. 6. Supplementation of the negative control diets with the enzyme combination returned performance to that of the positive control in both experiments. 7. These data indicate that exogenous xylanase, amylase, protease and phytase can be used successfully in a strategically formulated low nutrient density diet to maintain performance to that of birds fed on a nutritionally adequate diet.

Prediction of ingredient quality and the effect of a combination of xylanase, amylase, protease and phytase in the diets of broiler chicks. 2. Energy and nutrient utilisation.

1. In order to investigate the effects of xylanase, amylase, protease and phytase in the diets of broiler chickens containing graded concentrations of metabolisable energy (ME), two 42-d experiments were conducted using a total of 2208 broiler chicks (8 treatments with 12 replicate pens in each experiment). 2. Four diets including one positive and three negative control diets were used. Three maize/soybean meal-based negative control (NC) diets were formulated to be identical in available phosphorus (P), calcium (Ca) and amino acids but NC1 contained approximately 0.17 MJ/kg less ME than NC2 and approximately 0.34 MJ/kg less ME than NC3. A positive control (PC) was fed for comparison and was formulated to be adequate in all nutrients, providing approximately 0.63 MJ/kg ME, 0.13% available P, 0.12% Ca and 1 to 2% amino acids more than NC1. 3. The reduction in nutrient density between NC1 and PC was determined using ingredient quality models Avichecktrade mark Corn and Phychecktrade mark that can predict the response to exogenous enzymes in maize/soybean meal-based broiler diets. Supplementation of each diet with or without a cocktail of xylanase, amylase, protease and phytase gave a total of 8 dietary treatments in a 4 x 2 factorial arrangement. The same treatments and diet designs were used in both experiments but conducted in different locations using different batches of maize, soybean meal and minor ingredients. 4. In both experiments, digestibility was improved by the addition of exogenous enzymes, particularly those for P, Ca and certain amino acids. In addition, the supplementation of the PC with enzymes elicited a positive response indicating that over-the-top addition of xylanase, amylase, protease and phytase may offer a nutritionally and economically viable alternative to feed cost reduction. 5. It can be concluded that the digestibility of nutrients by broilers fed on maize/soybean meal-based diets can be improved by the use of a combination of xylanase, amylase, protease and phytase.

Antifungal anthraquinones from Saprosma fragrans.

A new 3,4-dihydroxy-1-methoxy anthraquinone-2-corboxaldehyde (1) together with a known anthraquinone, damnacanthal (2), were isolated from the chloroform fraction of the aerial part (whole plant without root) of Saprosma fragrans. The isolated anthraquinones (1) and (2) were found to exhibit antifungal activity against Trichophyton mentagrophytes and Sporitrichum schenckii. Their structures were established by chemical and spectral analysis.

Squamous cell carcinoma over a nevus: a rare case.

Malignant melanoma and basal cell carcinoma are more common over a preexisting nevus. But squamous cell carcinoma over a nevus is a rare phenomenon. A 55-year-old male presented with a slow growing noduloulcerative lesion on a preexisting nevus over scalp. For that he had undergone excisional biopsy. Biopsy came out to be a squamous cell carcinoma with lateral margin positive for tumor. So postoperative radiotherapy given by means of HDR brachytherapy. Now he is on follow-up.

A novel technique for monitoring contaminant transport through soils.

An experimental setup which is capable of simulation as well as monitoring contaminant transport through soil mass has been developed. Efficiency of the experimental setup has been demonstrated by comparing the results obtained from the argentometric method. Reynolds number (R(e)) and the Peclet number (P(e)) have been found to be less than unity. This indicates that flow of the solute through soil mass is laminar and the dominant contaminant transport mechanism is diffusion.

Experimental methodology to assess contaminant diffusion in rock mass.

Monitoring changes in electrical conductivity (EC) of aqueous phase, due to contaminant diffusion through porous media, is one of the techniques followed by researchers to understand the migration mechanism. However, the contaminant diffusion in the rock mass is a slow process and hence detecting small changes in conductivity with the help of conventional laboratory conductivity meters is quite difficult. With this in view, an experimental methodology to monitor diffusion of contaminant(s) through the intact and fractured rock mass, with the help of a USDTS (Ultra-Sensitive Devices and Technical Services) conductivity meter, has been developed. Results have been validated with those obtained from the ion chromatograph (IC) technique and a good agreement has been noted. The study demonstrates usefulness of the proposed methodology for online monitoring of contaminant migration through the porous media.

Functional analysis of polar amino-acid residues in membrane associated regions of the NHE1 isoform of the mammalian Na+/H+ exchanger.

The NHE1 isoform of the Na+/H+ exchanger is a ubiquitous plasma membrane protein that regulates intracellular pH in mammalian cells. Site-specific mutagenesis was used to examine the functional role of conserved, polar amino-acid residues occurring in segments of the protein associated with the membrane. Seventeen mutant proteins were assessed by characterization of intracellular pH changes in stably transfected cells that lacked an endogenous Na+/H+ exchanger. All of the mutant proteins were targeted correctly to the plasma membrane and were expressed at similar levels. Amino-acid residues Glu262 and Asp267 were critical to Na+/H+ exchanger activity while mutation of Glu391 resulted in only a partial reduction in activity. The Glu262-->Gln mutant was expressed partially as a deglycosylated protein with increased sensitivity to trypsin treatment in presence of Na+. Substitution of mutated Glu262, Asp267 and Glu391 with alternative acidic residues restored Na+/H+ exchanger activity. The Glu262-->Asp mutant had a decreased affinity for Li+, but its activity for Na+ and H+ ions was unaffected. The results support the hypothesis that side-chain oxygen atoms in a few, critically placed amino acids are important in Na+/H+ exchanger activity and the acidic amino-acid residues at positions 262, 267 and 391 are good candidates for being involved in Na+ coordination by the protein.

Laser Raman and IR spectra and force fields for 2,4-dichlorobenzonitrile.

Raman spectrum of 2,4-dichlorobenzonitrile (2,4-DCBN) in powder form has been recorded in the region 50-4000 cm(-1) on a Jasco K-500 Raman spectrophotometer using the 488.0 nm radiation from an argon laser. FTIR spectra in the region 200-4000 cm(-1) have been recorded in KBr pellet and nujol mull on a Nicolet DX spectrometer. Using the observed Raman and IR frequencies, normal co-ordinate analysis has been carried out to support the vibrational analysis and to determine the planar and non-planar force fields.

Post-operative radiotherapy in carcinoma of buccal mucosa, a prospective randomized trial.

Squamous cell carcinoma of the buccal mucosa is a common cancer in India. We are referred a large number of locally advanced lesions where curative surgery is still possible. The objective of this study is to determine the role of post-operative radiotherapy in enhancing disease-free survival. Patients with stages III and IV cancer of the buccal mucosa potentially curable by surgery were randomized to surgery only or post-operative radiotherapy. Patients were followed up for 3 years. The clinico-pathological features in both arms were comparable. Disease-free survival at the end of the study was found to be 38% and 68% (P<0.005) respectively. Post-operative radiotherapy was thus seen to improve disease-free survival in squamous cell carcinoma of the buccal mucosa.

Immunocytochemical localization of PHF-TAU in clinically diagnosed non-demented aged human brain - abstract

Paired helical filament (PHF), a molecular component of Alzheimer's Neurofibrillary Tangles, was immunocytochemically detected in clinically non-demented human brain. Brains from both sexes were examined. Cryostat cut sections from the cerebral hemisphere were stained with antibodies raised against PHF and TAU, and Thioflavine-D and examined with a microscope (Riechert-Jung), equipped for light and fluorescence transmission viewing. Several regions of the cerebral hemisphere reacted positively to all antibodies used and Thioflavine-S. Neurons in the stratum pyramidale of the hippocampus in all brains showed consistent and significant staining profiles. PHF-TAU molecules were observed in the cytoplasm and axoplasm of a large population of stratum pyramidale neurons. In some neurons, the entire cytoplasm and axoplasm were invaded by these molecules. PHF-TAU molecules also appeared in the adventitia of small blood vessels in the hippocampus and to a lesser extent in blood vessels of other regions. It was not possible to delineate or identify whether these vascular associated PHF-TAU molecules were present in perivascular nerve or glial processes or in the extracellular space. This may be the first indication that perivascular astrocytic processes may sequester PHF-TAU molecules. The hippocampus has been reported to be implicated in both long- and short-term memory. The present study has shown that neurons in the stratum pyramidale are structurally and metabolically affected by PHF-TAU molecules which may be the most important cause of cell damage, thus propagating memory impairment. It is not known what role the vascular associated molecules play in the pathology of Alzheimer's disease (AU)

Anthropometric and craniofacial patterns in mentally retarded males with emphasis on the fragile X syndrome.

Anthropometric and craniofacial profile patterns indicating the percent difference from the overall mean were developed on 34 physical parameters with 31 white, mentally retarded males (23 adults and 8 children) with the fra(X) syndrome matched for age with 31 white, mentally retarded males without a known cause of their retardation. The fra(X) syndrome males consistently showed larger dimensions for all anthropometric variables, with significant differences for height, sitting height, arm span, hand length, middle finger length, hand breadth, foot length, foot breadth, and testicular volume. A craniofacial pattern did emerge between the two groups of mentally retarded males, but with overlap of several variables. Significant differences were noted for head circumference, head breadth, lower face height, bizygomatic diameter, inner canthal distance, ear length and ear width, with the fra(X) syndrome males having larger head dimensions (head circumference, head breadth, head length, face height and lower face height), but smaller measurements for minimal frontal diameter, bizygomatic diameter, bigonial diameter, and inner canthal distance. Several significant correlations were found with the variables for both mentally retarded males with and without the fra(X) syndrome. In a combined anthropometric and craniofacial profile of 19 variables comparing 26 white fra(X) syndrome males (13 with high expression (> 30%) and 13 with low expression (< 30%), but matched for age), a relatively flat profile was observed with no significant differences for any of the variables. Generally, fra(X) syndrome males with increased fragile X chromosome expression have larger amplifications of the CGG trinucleotide repeat of the FMR-1 gene. No physical differences were detectable in our study between fra(X) males with high expression and apparently larger amplifications of the CGG trinucleotide repeats compared with those patients with low expression. Our research illustrates the use of anthropometry in identifying differences between mentally retarded males with or without the fra(X) syndrome and offers a comprehensive approach for screening males for the fra(X) syndrome and selecting those individuals for cytogenetic and/or molecular genetic testing.

Clinical and cytogenetic survey of institutionalized mentally retarded patients with emphasis on the fragile-X syndrome.

A detailed clinical and cytogenetic survey for the fragile-X syndrome was undertaken on 201 institutionalized mentally retarded males with no previously recognized cause of retardation, and the causes of mental retardation were summarized from a total of 595 institutionalized male and female patients after the review of their medical records including clinical and cytogenetic data. Among the 201 males clinically and cytogenetically examined, five (2.5%) had abnormal chromosome findings with four (2%) having the fragile-X syndrome. Twelve of the males (6.0%) were diagnosed with a single gene disorder. In the present study, mental retardation was classified as possibly due to multifactorial causes when a genetic syndrome, chromosome abnormality or environmental insult was not identified, but mental retardation was present in one or more first and/or second degree relatives, but did not follow a recognizable inheritance pattern. Hence, mental retardation was recorded in other family members and may indicate possible multifactorial causes in 45 males (22.4%). An environmental insult was noted in 25 males (12.4%); unexplained birth defects in three males (1.5%); a specific condition or diagnosis identified, but cause unknown (e.g. Rubinstein-Taybi syndrome) in 10 males (5%); and no diagnosis made in the remaining 101 males (50.2%). Of all 595 patients (334 males and 261 females), including the 201 males who had undergone a detailed clinical and cytogenetic evaluation, 39 (6.6%) had abnormal chromosome findings, with Down's syndrome noted in 31 of the patients. Twenty-five patients (4.2%) were diagnosed with a single gene disorder while mental retardation was noted in other family members and may indicate possible multifactorial causes in 64 patients (10.8%). An environmental insult was noted in 170 patients (28.6%); unexplained birth defects in 17 patients (2.9%); a specific condition or diagnosis but cause unknown in 27 patients (4.5%); and no diagnosis made in 253 patients (42.5%). Clinical and cytogenetic screening of mentally retarded patients for the fragile-X syndrome and other causes of mental retardation is helpful in identifying individuals and their families who may benefit from genetic services such as counseling and treatment. This study was performed over an approximate 2 year period from 1987 to 1989.

A 15-item checklist for screening mentally retarded males for the fragile X syndrome.

A 15-item checklist, including physical and behavioral features frequently observed in fragile X syndrome, was used in a prospective study of 188 mentally retarded males in order to identify males at risk for this syndrome. Of the 188 males, 19 were found to have the fragile X syndrome, while the remaining 169 males had no recognizable cause of their mental retardation, including normal chromosomes. Significant differences (p less than 0.01) were found between mentally retarded males with and without the fragile X syndrome with increased hyperactivity; shorter attention span; more tactile defensiveness, hand-flapping, perseverative speech, and hyperextensibility; large ears and testes; higher frequency of simian creases or Sydney lines and plantar creases; and more positive family histories of mental retardation in the fragile X syndrome males. Multiple regression and discriminant analyses of the 188 males indicated several physical features were useful predictors for inclusion in the fragile X syndrome group. An overall correct classification rate of 93% was achieved based on 6 variables (plantar crease, simian crease, hyperflexibility, large testes, large ears, and a positive family history of mental retardation) that were entered into the discriminant equation. Therefore, our experience with a 15-item checklist suggests the potential of screening for the fragile X syndrome in mentally retarded males and that 6 of the 15 variables were particularly good predictors of this syndrome.

Anthropometric comparison of mentally retarded males with and without the fragile X syndrome.

An anthropometric survey of 41 variables (weight, height, 10 linear, 4 breadth, 22 craniofacial, 2 skinfold, and testicular volume), including multivariate discriminant analysis, was undertaken on 110 mentally retarded males (39 with and 71 without the fra(X) syndrome). The mean Z scores of the fra(X) syndrome males fell between -2.00 and 8.38 for bizygomatic diameter and testicular volume, respectively, and the range of the mean Z scores of the non-fra(X) males was from -2.64 to 2.26 for hand breadth and testicular volume, respectively. There was a statistically significant difference (P less than .05) between fra(X) and non-fra(X) males for 18 measurements (weight, height, 7 linear, 2 breadth, 5 craniofacial, 1 skinfold, and testicular volume), with the greater measurements (excluding bizygomatic diameter) found in fra(X) males. Sitting height, knee-buttock length, middle finger length, and hand length were negatively correlated (P less than .05) with age, whereas bizygomatic diameter, ear length, and ear width were positively correlated (P less than .05) with age and head circumference, head length, and outer canthal distance were positively correlated (P less than .05) with fra(X) chromosome expression in the fra(X) males. Triceps and subscapular skinfold thicknesses were negatively correlated (P less than .05) with age, whereas ankle breadth, ear length, ear width, and nose length were positively correlated (P less than .05) in the non-fra(X) males. Discriminant analysis of 34 fra(X) and 71 non-fra(X) males resulted in a discriminant function based on 6 of 17 anthropometric variables and age.(ABSTRACT TRUNCATED AT 250 WORDS)

Chromosomal mapping and nucleotide sequence of a human DNA autonomously replicating sequence.

A 1.1-kb human DNA fragment (ARSH1) capable of functioning as a putative origin of replication in yeast cells has been characterized both by in situ hybridization to human metaphase chromosomes and by DNA sequencing. Our hybridization studies show a preferential localization of ARSH1 in chromosome regions 1p34-36 and 2q34-37. DNA sequence analysis indicates that in addition to the consensus sequence required for ARS function in yeast cells, nuclear matrix-associated DNA motifs are also present in the 1.1-kb fragment. These results suggest that ARSH1 sequences may serve as points of anchorage to the nuclear matrix for chromosomes 1 and 2.