Evaluation of Bovine High-Density SNP Genotyping Array in Indigenous Dairy Cattle Breeds

In total 52 samples of Sahiwal ( 19 ), Tharparkar ( 17 ), and Gir ( 16 ) were genotyped by using BovineHD SNP chip to analyze minor allele frequency (MAF), genetic diversity, and linkage disequilibrium among these cattle. The common SNPs of BovineHD and 54K SNP Chips were also extracted and evaluated for their performance. Only 40%-50% SNPs of these arrays was found informative for genetic analysis in these cattle breeds. The overall mean of MAF for SNPs of BovineHD SNPChip was 0.248 ± 0.006, 0.241 ± 0.007, and 0.242 ± 0.009 in Sahiwal, Tharparkar and Gir, respectively, while that for 54K SNPs was on lower side. The average Reynold's genetic distance between breeds ranged from 0.042 to 0.055 based on BovineHD Beadchip, and from 0.052 to 0.084 based on 54K SNP Chip. The estimates of genetic diversity based on HD and 54K chips were almost same and, hence, low density chip seems to be good enough to decipher genetic diversity of these cattle breeds. The linkage disequilibrium started decaying (r² < 0.2) at 140 kb inter-marker distance and, hence, a 20K low density customized SNP array from HD chip could be designed for genomic selection in these cattle else the 54K Bead Chip as such will be useful.

Heteroleptic metal(II) complexes of hydrotris(methimazolyl)borate and diimines: Synthesis, theoretical calculations, antimicrobial, antioxidant, in vitro cytotoxicity and molecular docking studies

A series of heteroleptic metal(II) complexes of formulation [M(Tm)(diimine)](ClO₄) (1-8), [Tm = hydrotris(methimazolyl)borate, diimine = 2,2'-bipyridyl or 1,10-phenanthroline and M = Mn(II), Ni(II), Cu(II) or Zn(II)] have been synthesized and characterized by spectroscopic methods. The geometric parameters of the complexes were determined using UV-Vis spectroscopy and DFT calculations. The analyses of HOMO and LUMO have been used to explain the charge transfer within the molecule. Antimicrobial activity of the synthesized heteroleptic complexes were evaluated against two Gram (-ve) (Escherichia coli and Klebsiella pneumoniae) and two Gram (+ve) (Bacillus cereus and Staphylococcus aureus) bacterial, and three fungal (Candida albicans, Candida glabrata and Candida krusei) strains with respect to the standard drugs erythromycin and amphotericin-B. The copper(II) complex 6 showed better scavenging activity against DPPH when compared to other complexes. The cytotoxic activity of copper(II) complexes 5 and 6 against MCF-7 cell line was assessed by MTT assay, which showed exponential responses toward increasing concentration of complexes. In the molecular docking studies, the complexes showed π-π, σ-π, hydrogen bonding, van der Waals and electrostatic interactions with FGFR kinase receptor.

Assessment of Regional Pediatric Computed Tomography Dose Indices in Tamil Nadu

The aim of this article is to assess Tamil Nadu pediatric computed tomography (CT) diagnostic reference levels (DRLs) by collecting radiation dose data for the most commonly performed CT examinations. This work was performed for thirty CT scanners installed in various parts of the Tamil Nadu region. The patient cohort was divided into two age groups: <1 year, and 1-5 years. CT dose indices were measured using a 10 cm3 pencil ion chamber with pediatric head and body polymethyl methacrylate phantoms. Dose data such as volumetric CT dose index (CTDIv) and dose length product (DLP) on a minimum of twenty average-sized pediatric patients in each category were recorded to calculate a mean site CTDIv and DLP value. The rounded 75th percentile was used to calculate a pediatric DRL for each hospital, and then region by compiling all results. Data were collected for 3600 pediatric patients. Pediatric CT DRL for two age groups: <1 year (CTDIv and DLP of head [20 mGy, 352 mGy.cm], chest [7 mGy, 120 mGy.cm] and abdomen [12 mGy, 252 mGy.cm]), and 1-5 years (CTDIv and DLP of head [38 mGy, 505 mGy.cm], chest [8 mGy, 132 mGy.cm] and abdomen [14 mGy, 270 mGy.cm]) for select procedures have been calculated. Proposed pediatric DRLs of CTDIv and DLP for head procedure were lower, and for chest and abdomen procedures were higher than European pediatric DRLs for both age groups.

An education management information system with simultaneous monitoring of stress stimulators for students Mental Health management

Education Management Information System (EMIS) is a widely acceptable and developing technology within the Information Technology field. The advancement in technology in this century is being collaborated with scientific invention or explorer and information strengthening or development. This paper presents the results and experiences gained from applying students oriented EMIS for monitoring and managing mental health. The Mental Health of students depends on the acquiring adequate knowledge on basic concepts within a time period or academic schedule. It's obviously significance to evaluate and appraise the stress stimulators as a challenge or threat. The theoretical framework for the study was designed for analyzing the stress stimulators, academic performance and EMIS accessibility. The sample examined in this study was stratified random sample from 75 students specifically all engineering college in Dindigul District of Tamilnadu. The primary factor is the academic stress stimulators that form one module of EMIS for each of the key variable such as curriculum & instruction related stressors, placement related, teamwork related and assessment related. The Mental Health related stress stimulators namely curriculum & syllabus, placement related, assessment related and team work related have a significant influence on academic performance by students in various institution. The important factor leading to the EMIS application in monitoring stress stimulators is curriculum & syllabus related and assessment related.

Theoretical investigation, biological evaluation and VEGFR2 kinase studies of metal(II) complexes derived from hydrotris(methimazolyl)borate

The reaction of soft tripodal scorpionate ligand, sodium hydrotris(methimazolyl)borate with M(ClO4)2·6H2O [MMn(II), Ni(II), Cu(II) or Zn(II)] in methanol leads to the cleavage of B-N bond followed by the formation of complexes of the type [M(MeimzH)4](ClO4)2·H2O (1-4), where MeimzH=methimazole. All the complexes were fully characterized by spectro-analytical techniques. The molecular structure of the zinc(II) complex (4) was determined by X-ray crystallography, which supports the observed deboronation reaction in the scorpionate ligand with tetrahedral geometry around zinc(II) ion. The electronic spectra of complexes suggested tetrahedral geometry for manganese(II) and nickel(II) complexes, and square-planar geometry for copper(II) complex. Frontier molecular orbital analysis (HOMO-LUMO) was carried out by B3LYP/6-31G(d) to understand the charge transfer occurring in the molecules. All the complexes exhibit significant antimicrobial activity against Gram (-ve) and Gram (+ve) bacterial as well as fungal strains, which are quite comparable to standard drugs streptomycin and clotrimazole. The copper(II) complex (3) showed excellent free radical scavenging activity against DPPH in all concentration with IC50 value of 30μg/mL, when compared to the other complexes. In the molecular docking studies, all the complexes showed hydrophobic, π-π and hydrogen bonding interactions with BSA. The cytotoxic activity of the complexes against human hepatocellular liver carcinoma (HepG2) cells was assessed by MTT assay, which showed exponential responses toward increasing concentration of complexes.

Cost-effective pediatric head and body phantoms for computed tomography dosimetry and its evaluation using pencil ion chamber and CT dose profiler

In the present work, a pediatric head and body phantom was fabricated using polymethyl methacrylate (PMMA) at a low cost when compared to commercially available phantoms for the purpose of computed tomography (CT) dosimetry. The dimensions of head and body phantoms were 10 cm diameter, 15 cm length and 16 cm diameter, 15 cm length, respectively. The dose from a 128-slice CT machine received by the head and body phantom at the center and periphery were measured using a 100 mm pencil ion chamber and 150 mm CT dose profiler (CTDP). Using these values, the weighted computed tomography dose index (CTDIw) and in turn the volumetric CTDI (CTDIv) were calculated for various combinations of tube voltage and current-time product. A similar study was carried out using standard calibrated phantom and the results have been compared with the fabricated ones to ascertain that the performance of the latter is equivalent to that of the former. Finally, CTDIv measured using fabricated and standard phantoms were compared with respective values displayed on the console. The difference between the values was well within the limits specified by Atomic Energy Regulatory Board (AERB), India. These results indicate that the cost-effective pediatric phantom can be employed for CT dosimetry.

Effect of Mutagens on Quantitative Characters in M₂ and M₃ Generation of Sesame (<i>Sesamum indicum</i> L.)

The mutagenic effects of different dose/concentrations of gamma rays (30, 40 and 50 KR) and ethyl methane sulphonate (1.0, 1.5 and 2.0 mM) on sesame (Sesamum indicum L.) varieties VRI-1 were investigated. The characters studied include; days to first flower, plant height, number of branches per plant, number of capsule per plant, number of seeds per capsule and seed yield per plant in M2 and M3 generations. Both negative and positive shifts in mean values were recorded as a result of the physical and chemical treatments. The results indicate the possibilities of evolving higher yield variants through proper selection. Thus, economic traits like number of capsule per plant, number of seeds per capsule and hundred seed weight in M3 generation offer scope for selection and improvement.

Effect of Mutagens on Quantitative Characters in M₂ and M₃ Generation of Sesame (<i>Sesamum indicum</i> L.)

The mutagenic effects of different dose/concentrations of gamma rays (30, 40 and 50 KR) and ethyl methane sulphonate (1.0, 1.5 and 2.0 mM) on sesame (Sesamum indicum L.) varieties VRI-1 were investigated. The characters studied include; days to first flower, plant height, number of branches per plant, number of capsule per plant, number of seeds per capsule and seed yield per plant in M2 and M3 generations. Both negative and positive shifts in mean values were recorded as a result of the physical and chemical treatments. The results indicate the possibilities of evolving higher yield variants through proper selection. Thus, economic traits like number of capsule per plant, number of seeds per capsule and hundred seed weight in M3 generation offer scope for selection and improvement.

Comparative screening of single nucleotide polymorphisms in β-casein and κ-casein gene in different livestock breeds of India

The most polymorphic milk protein gene is β-casein; 13 protein variants are known in cattle. Milk protein genetic polymorphism has received considerable research interest in recent years because of possible associations between milk protein and economically important traits in livestock. The present study was undertaken to explore the genetic polymorphisms in exon 7 of β-casein and exon 4 of κ-casein genes in Arunachali yaks (Bos grunniens), Sahiwal (Bos indicus) cattle, malpura sheep (Ovis aries) and Gaddi goat (Capra hircus). Results of the study revealed presence of 11 SNP variants in all livestock species. Four SNPs were observed in Bos indicus; two SNPs in Bos grunniens; three SNPs in Ovis aries and three SNPs in Capra hircus. These variations are found to be synonymous in nature as these variations do not result in their corresponding amino acids. A total of five polymorphic sites have been described at the κ-casein (CSN3) locus in the Indian domestic Gaddi goat (Capra hircus) when compared with exotic goat (X60763) while sequence analysis of κ-casein gene in sheep showed three novel nucleotide changes in malpura sheep when compared with the exotic sheep (AY237637). These results highlight the importance of taking into consideration the CSN3 SNPs when performing selection for milk composition in dairy livestock breeds.

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This is first comparative sequence analysis of Beta casein and kappa casein genes in different livestock breeds of India.

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Total 11 SNPs variants were found in all livestock species studied, namely, Bos indicus, Bos grunniens, Ovis aries and Capra hircus.

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Four SNPs were observed in Bos indicus; two SNPs in Bos grunniens; three SNPs in Ovis aries and three SNPs in Capra hircus.

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Homology of 99% with Bos taurus and Bos indicus, 97% with Bubalus bubaline, 99% with Bos grunniens, 95% with Ovis aries, 95% with Capra hircus.

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Sequence analysis of κ-casein gene in sheep showed three novel nucleotide changes in malpura sheep when compared with the exotic sheep (AY237637).

Probing extracellular acidity of live cells in real time for cancer detection and monitoring anti-cancer drug activity

A multifunctional platform is presented which (a) allows determination of extracellular pH in real time, (b) detects cancer cells, down to 5 cells, and (c) enables evaluating the efficacy of glycolysis inhibiting drugs.

Spatiotemporal differences in the c-fos pathway between C57BL/6J and DBA/2J mice following flurothyl-induced seizures: A dissociation of hippocampal Fos from seizure activity

Significant differences in seizure characteristics between inbred mouse strains highlight the importance of genetic predisposition to epilepsy. Here, we examined the genetic differences between the seizure-resistant C57BL/6J (B6) mouse strain and the seizure-susceptible DBA/2J (D2) strain in the phospho-Erk and Fos pathways to examine seizure-induced neuronal activity to uncover potential mechanistic correlates to these disparate seizure responsivities. Expression of neural activity markers was examined following 1, 5, or 8 seizures, or after 8 seizures, a 28 day rest period, and a final flurothyl rechallenge. Two brain regions, the hippocampus and ventromedial nucleus of the hypothalamus (VMH), had significantly different Fos expression profiles following seizures. Fos expression was highly robust in B6 hippocampus following one seizure and remained elevated following multiple seizures. Conversely, there was an absence of Fos (and phospho-Erk) expression in D2 hippocampus following one generalized seizure that increased with multiple seizures. This lack of Fos expression occurred despite intracranial electroencephalographic recordings indicating that the D2 hippocampus propagated ictal discharge during the first flurothyl seizure suggesting a dissociation of seizure discharge from Fos and phospho-Erk expression. Global transcriptional analysis confirmed a dysregulation of the c-fos pathway in D2 mice following 1 seizure. Moreover, global analysis of RNA expression differences between B6 and D2 hippocampus revealed a unique pattern of transcripts that were co-regulated with Fos in D2 hippocampus following 1 seizure. These expression differences could, in part, account for D2's seizure susceptibility phenotype. Following 8 seizures, a 28 day rest period, and a final flurothyl rechallenge, ∼85% of B6 mice develop a more complex seizure phenotype consisting of a clonic-forebrain seizure that uninterruptedly progresses into a brainstem seizure. This seizure phenotype in B6 mice is highly correlated with bilateral Fos expression in the VMH and was not observed in D2 mice, which always express clonic-forebrain seizures upon flurothyl retest. Overall, these results illustrate specific differences in protein and RNA expression in different inbred strains following seizures that precede the reorganizational events that affect seizure susceptibility and changes in seizure semiology over time.

Locus minimization in breed prediction using artificial neural network approach

Molecular markers, viz. microsatellites and single nucleotide polymorphisms, have revolutionized breed identification through the use of small samples of biological tissue or germplasm, such as blood, carcass samples, embryos, ova and semen, that show no evident phenotype. Classical tools of molecular data analysis for breed identification have limitations, such as the unavailability of referral breed data, causing increased cost of collection each time, compromised computational accuracy and complexity of the methodology used. We report here the successful use of an artificial neural network (ANN) in background to decrease the cost of genotyping by locus minimization. The webserver is freely accessible (http://nabg.iasri.res.in/bisgoat) to the research community. We demonstrate that the machine learning (ANN) approach for breed identification is capable of multifold advantages such as locus minimization, leading to a drastic reduction in cost, and web availability of reference breed data, alleviating the need for repeated genotyping each time one investigates the identity of an unknown breed. To develop this model web implementation based on ANN, we used 51,850 samples of allelic data of microsatellite-marker-based DNA fingerprinting on 25 loci covering 22 registered goat breeds of India for training. Minimizing loci to up to nine loci through the use of a multilayer perceptron model, we achieved 96.63% training accuracy. This server can be an indispensable tool for identification of existing breeds and new synthetic commercial breeds, leading to protection of intellectual property in case of sovereignty and bio-piracy disputes. This server can be widely used as a model for cost reduction by locus minimization for various other flora and fauna in terms of variety, breed and/or line identification, especially in conservation and improvement programs.

Molecular structure, Mulliken charge, frontier molecular orbital and first hyperpolarizability analysis on 2-nitroaniline and 4-methoxy-2-nitroaniline using density functional theory

In the present study, we made an attempt to calculate the energy gap, molecular dipole moment and first hyperpolarizability of 2-nitroaniline (2NA) and 4-methoxy-2-nitroaniline (4M2N) with a basis set 6-31G (d, p) function has been employed at density functional theory (DFT) methods. Geometry optimizations was carried out with DFT-B3LYP/6-31G (d, p), the results have revealed that intramolecular hydrogen bonding present in both the molecular system. We analyzed the energy gap, molecular dipole moment and hyperpolarizability changes due to substitution effect of the methoxy group in 2NA molecule. It is confirmed that strong electron acceptor and donor groups in a material yield higher NLO response.

Establishment of diagnostic reference levels in computed tomography for select procedures in Pudhuchery, India

Computed tomography (CT) scanner under operating conditions has become a major source of human exposure to diagnostic X-rays. In this context, weighed CT dose index (CTDI_w), volumetric CT dose index (CTDI_v), and dose length product (DLP) are important parameter to assess procedures in CT imaging as surrogate dose quantities for patient dose optimization. The current work aims to estimate the existing dose level of CT scanner for head, chest, and abdomen procedures in Pudhuchery in south India and establish dose reference level (DRL) for the region. The study was carried out for six CT scanners in six different radiology departments using 100 mm long pencil ionization chamber and polymethylmethacrylate (PMMA) phantom. From each CT scanner, data pertaining to patient and machine details were collected for 50 head, 50 chest, and 50 abdomen procedures performed over a period of 1 year. The experimental work was carried out using the machine operating parameters used during the procedures. Initially, dose received in the phantom at the center and periphery was measured by five point method. Using these values CTDI_w, CTDI_v, and DLP were calculated. The DRL is established based on the third quartile value of CTDI_v and DLP which is 32 mGy and 925 mGy.cm for head, 12 mGy and 456 mGy.cm for chest, and 16 mGy and 482 mGy.cm for abdomen procedures. These values are well below European Commission Dose Reference Level (EC DRL) and comparable with the third quartile value reported for Tamil Nadu region in India. The present study is the first of its kind to determine the DRL for scanners operating in the Pudhuchery region. Similar studies in other regions of India are necessary in order to establish a National Dose Reference Level.

Comparative sequence analysis in the exon 5 of growth hormone gene in the various livestock species of India

The aim of the study was to identify genetic polymorphism in growth hormone (GH) gene locus of six different livestock species using PCR-Direct DNA sequencing method. In exon 5 of GH gene, 10 SNPs variants were identified in all livestock species studied, namely Bubalus bubalis, Bos indicus, Bos frontalis, Bos grunniens, Ovis aries, and Capra hircus. Four SNPs were observed in Bubalus bubalis, two SNPs in Bos indicus, one SNP in Ovis aries, and three SNPs in Capra hircus. No changes were observed in Bos grunniens and Bos frontalis when compared with the template sequence and the SNPs observed in the present investigation may be useful in the marker assisted selection.

Forward versus inverse planning in oropharyngeal cancer: A comparative study using physical and biological indices

CONTEXT

Possible benefits of inverse planning.

AIMS

To analyze possible benefits of inverse planning intensity modulated radiation therapy (IMRT) over field-in-field 3D conformal radiation therapy (FIF-3DCRT) and to evaluate the differences if any, between low (6 Million Volts) and high energy (15 Million Volts) IMRT plans.

MATERIALS AND METHODS

Ten patients with squamous cell carcinoma of oropharynx, previously treated with 6 MV step and shoot IMRT were studied. V100, V33, V66 , mean dose and normal tissue complication probabilities (NTCP) were evaluated for parotid glands. Maximum dose and NTCP were the parameters for spinal cord.

STATISTICAL ANALYSIS USED

A two-tailed t-test was applied to analyze statistical significance between the different techniques.

RESULTS

For combined parotid gland, a reduction of 4.374 Gy, 9.343 Gy and 7.883 Gy were achieved for D100, D66 and D33, respectively in 6 MV-IMRT when compared with FIF-3DCRT. Spinal cord sparing was better in 6 MV-IMRT (40.963 ± 2.650), with an average reduction of maximum spinal cord dose by 7.355 Gy from that using the FIF-3DCRT technique. The uncomplicated tumor control probabilities values were higher in IMRT plans thus leading to a possibility of dose escalation.

CONCLUSIONS

Though low-energy IMRT is the preferred choice for treatment of oropharyngeal cancers, FIF-3DCRT must be given due consideration as a second choice for its well established advantages over traditional conventioan technique.

Genetic structuring of nine Indian domestic goat breeds based on SNPs identified in IGF-1 gene

The caprine Insulin like Growth Factor1 (IGF1) gene was analyzed for identification of single nucleotide polymorphisms (SNPs) and genetic structuring of Indian goat breeds. A panel of 80 samples belonging to nine Indian goat breeds (Capra hircus) including three large sized breeds (Jamunapari, Beetal and Jakhrana); three medium sized breeds (Sirohi, Barbari, and Osmanabadi) and three small sized breeds (Black Bengal, Changthangi, and Gaddi) were screened for SNP identification and diversity analysis. The comparative gene sequence analysis of all the nine goat breeds studied revealed a total of 18 SNPs in IGF1 gene. All the nucleotide changes were found to be synonymous. The mean observed heterozygosity was found to be maximum (0.074) in Sirohi, Beetal, Osmanabadi, and Gaddi breeds of goat, whereas it is found to be minimum (0.019) in Black Bengal breed of goat. The rest of the breeds were intermediate in terms of heterozygosity. The same has been confirmed by allele frequency distribution across the studied loci. Barbari and Gaddi were found to be more differentiated (0.0123), Changthangi and Jamunapari were least differentiated (0.00110) based on Nei's genetic distance.