Genome-wide association analysis of body conformation traits in Mexican Holstein cattle using a mix of sampled and imputed SNP genotypes.

In arid and semi-arid zones, animal health and production are closely correlated with body conformation traits. These selected traits, in turn, allow livestock to adapt unfavorable soil and environmental conditions. The primary objective of this study was to perform a genome-wide association analysis for a set of sampled and imputed SNPs with 16 conformation traits in a population of Holstein cows from a desert area of Northwestern Mexico. Imputation from 6K to 50K SNPs was performed as a low-cost optimization strategy. Results show eight SNPs associated with two conformation traits. The Udder Depth trait resulted in seven associated SNPs from chromosome 10, that related to Marbling Score, Milk Yield, Fat Yield, Protein Yield, and Protein Percentage Quantitative Trait Loci (QTLs). The Body Depth trait resulted in one associated SNP from chromosome 2, although no QTL relation was found. The discovery of genes associated with conformation traits may be indicative of the adaptive selection pressures the Holstein breed has undergone in response to the extreme weather conditions found in the northwestern areas of Mexico. Results of this study indicate that traits such as stature and body depth may be used as indicators of cows' potential genetic merits for milk, fat, and protein production.

Genome-wide identification of copy number variations in Holstein cattle from Baja California, Mexico, using high-density SNP genotyping arrays.

Copy number variations (CNVs) are an important source of genomic structural variation, and can be used as markers to investigate phenotypic and economic traits. CNVs also have functional effects on gene expression and can contribute to disease susceptibility in mammals. Currently, single nucleotide polymorphism genotyping arrays (SNP chips) are the technology of choice for identifying CNV variations. Microarray technologies have recently been used to study the bovine genome. The objective of the present study was to develop CNVs in Holstein cows from the Northwest of Mexico using the Affymetrix Axiom Genome-Wide BOS 1 Array, which assays 648,315 SNPs and provides a wide coverage for genome-wide studies. We applied the two most widely used algorithms for the discovery of CNVs (PennCNV and QuantiSNP) and found 56 CNV regions (CNVRs) representing 0.33% of the bovine genome (8.46 Mb). These CNVRs ranged from 1.5 to 970.8 kb with an average length of 151 kb. They involved 103 genes and showed a 28% overlap with CNVRs already reported. Of the 56 CNVRs found, 20 were novel. In this study we present the first genomic analysis of CNVs in Mexican cattle using high-density SNP data. Our results provide a new reference basis for future genomic variation and association studies between CNVs and phenotypes, especially in Mexican cattle.

Self-energy on the low- to high-energy electronic structure of correlated metal SrVO3.

The correlated electronic structure of SrVO(3) has been investigated by angle-resolved photoemission spectroscopy using in situ prepared thin films. Pronounced features of band renormalization have been observed: a sharp kink ∼60 meV below the Fermi level (E(F)) and a broad so-called "high-energy kink" ∼0.3 eV below E(F) as in the high-T(c) cuprates, although SrVO(3) does not show magnetic fluctuations. We have deduced the self-energy in a wide energy range by applying the Kramers-Kronig relation to the observed spectra. The obtained self-energy clearly shows a large energy scale of ∼0.7 eV, which is attributed to electron-electron interaction and gives rise to the ∼0.3 eV kink in the band dispersion as well as the incoherent peak ∼1.5 eV below E(F). The present analysis enables us to obtain a consistent picture for both the incoherent spectra and the band renormalization.

Localization of structural polymers in the cell wall of Neurospora crassa.

The distribution and localization of structural polymers in the cell wall of Neurospora crassa has been studied by selective removal and light and electron microscope examination. Observations with the light microscope indicated that each polymer by itself can provide structural integrity to the cell wall. Examination by electron microscopy showed that the cell wall consists of an outer layer of thick fibrils, identified chemically as a glucan-peptide-galactosamine complex, and an inner layer made up of beta-1,3 glucan and thin fibrils of chitin.

Integrated management of filarial lymphedema for rural communities.

The Global Alliance for the Elimination of Lymphatic Filariasis (GAELF) has recommended exploring local health traditions of skin care and a low cost treatment paradigm for rural communities has been proposed by Vaqas and Ryan. Our case study incorporates these promising treatments for use in treating filariasis in rural communities. Patients having lymphedema of one or both lower limbs (skin: normal, thickened or with trophic/warty changes) received treatment components from ayurveda, yoga and biomedicine simultaneously: including soap wash, phanta soaking, Indian manual lymph drainage (IMLD), pre- and post-IMLD yoga exercises, and compression using bandages for 194 days, along with diet restrictions and oral herbal medicines indicated for "elephantiasis" in Ayurveda. Entry points when infected were treated with biomedical drugs. The study was conducted in the reverse pharmacology design. 112 patients and 149 lower limbs completed 194 days of treatment during 2003-2006. Significant improvements were observed in the limb circumference measurements and the frequency of acute dermatolymphangioadenitis, use of preventive antibiotics, and reduction in the number of entry points were also improved. The objective to obtain significant benefit for a common problem using locally available, sustainable and affordable means has been achieved. It has not been our purpose to show that the regimen employed is better than another but the results do pose the question--"Are there components of Ayurvedic medicine that deserve further study?" It is important to understand that the regimen has been delivered mostly at home and that participants we have treated, representing a population suffering from a common problem, have not had access to effective conservative therapy that is culturally acceptable, safe, and efficacious.

Intraductal papillary mucinous neoplasm in tropical chronic pancreatitis.

We report a 56-year-old man with chronic calcifying pancreatitis of the tropics (tropical calcific pancreatitis) who had been asymptomatic and on follow up developed a pancreatic mass that was identified as intraductal papillary mucinous neoplasm. He has been asymptomatic after distal pancreatectomy.

Multi-center prospective survey of inflammatory bowel diseases in Kerala: More than 2000 cases.

BACKGROUND: Inflammatory bowel disease (IBD) is considered uncommon in Asia. The aim of this study was to document the demographic characteristics and clinical aspects of ulcerative colitis (UC) and Crohn's disease (CD) in Kerala, India. METHODS: A survey of IBD in Kerala was performed. All gastroenterologists in the region were invited. From May 2013 to October 2015, data were collected in a standardized pro-forma. RESULTS: Forty-seven doctors in 34 centers contributed data. A total of 2142 patients were analyzed. This is the largest state-wide survey of IBD in India. Ulcerative colitis was diagnosed in 1112 (38 new), Crohn's disease in 980 (53 new), and 50 were unclassified (5 new). The district-wise distribution of IBD cases correlated with the District-wise Gross State Domestic Product (r = 0.69, p < 0.01). Three percent was below the age of 18. Patients with UC had more diarrhea (73% vs. 51%), bleeding PR (79% vs. 34%), and intermittent flares (35% vs. 13%) (all p < 0.01). Patients with CD had more abdominal pain (62% vs. 46%), weight loss (53% vs. 40%), fever (28% vs. 18%), and history of antituberculosis treatment (21% vs. 5%) (all p < 0.01). Compared to adults, children (below 18 years) were more likely to have extensive UC (58% vs. 34%, p < 0.01) and unclassified IBD (15% vs. 2%, p < 0.01). CONCLUSION: Inflammatory bowel disease is common in Kerala, India. The disease characteristics of patients with IBD are almost similar to those from other parts of the country. Both UC and CD were seen in equal proportion in Kerala.

Detailed study of survival of patients with renal cell carcinoma in India.

PURPOSE: Renal cell carcinoma (RCC) accounts for approximately 90% of all renal malignancies. The rates of kidney cancers are high in developed countries and low in eastern countries and Africa. The objective was to conduct a survival study among Indian population following nephrectomy for RCC as there was a paucity of Indian studies in medical literature. MATERIALS AND METHODS: We conducted a follow-up study of eighty RCC patients who had nephrectomy between January 2003 and December 2010. These patients had pathological diagnosis after nephrectomy. The follow-up was done up to December 2015. The survival statistics were compiled according to Kaplan-Meier survival curves. RESULTS: The overall survival of eighty patients was 77%. The patients with tumor size ≤7 cm and the patients with tumor size> 7 cm showed significant statistical difference at 5-year survival (P < 0.0001). The patients with low nuclear grade (1 and 2) and the patients with high nuclear grade (3 and 4) showed significant statistical difference at 5-year survival (P < 0.0001). The patients with tumor node metastasis stage below T3 and the patients with clinical stage above or equal to T3 showed significant statistical difference at 5-year survival (P = 0.003). CONCLUSION: This study has demonstrated the importance of factors such as tumor size, nuclear grade, and stage in the assessment of prognosis of RCC patients. More studies in India with more patients are needed to demonstrate the importance of these prognostic factors.

Effect of prostaglandin E2 and hyaluronan on mesangial cell proliferation. A potential contribution to glomerular hypercellularity in diabetes.

Proliferation of mesangial cells is a feature of several forms of human and experimental glomerulopathy, including that seen in diabetes. The nonsulfated glycosaminoglycan hyaluronan participates in the regulation of pericellular matrix assembly and is a mitogen in some cell types. We have shown previously that hyaluronan production is increased in the glomerulus in a glucose- and prostaglandin-dependent manner. We have investigated the effect of diabetes and of addition of hyaluronan and prostaglandin E2 (PGE2) on the uptake of [3H]thymidine by glomerular core preparations enriched in mesangial cells. When compared with nondiabetic controls, it was shown that [3H]thymidine uptake was significantly increased in glomerular core preparations from streptozotocin-induced diabetic rats (to 169 +/- 5%, P < 0.001). In glomerular cores from both experimental groups, hyaluronan (50-250 ng/ml) or PGE2 (10(-12) to 10(-8) mol/l) increased the uptake of [3H]thymidine. Further, mesangial cells from nondiabetic control glomerular cores, when maintained in culture in early passage, responded with increased [3H]thymidine uptake to raised glucose (5.6-25 mmol/l) and to added hyaluronan and PGE2. We propose that prostaglandin and hyaluronan production in response to a raised glucose environment in diabetes can contribute to mesangial hypercellularity.

Increasing cancer incidence in a tertiary care hospital in a developing country, India.

OBJECTIVE: Cancer is a major health problem in many countries including India. Since Cancer Registries are incomplete in India, only a few epidemiological studies have been done so far. The objective was to determine the leading causes of cancer in a tertiary care hospital and compare the incidences of different types of cancer with the incidences in India and developed countries. MATERIALS AND METHODS: An epidemiological study was done to collect data from pathology records of 1003 cancer cases during 6-month period in the year 2010. The data was collected in a computer and the data was utilized to make tables and histograms. RESULTS: Of the 1003 cases, the leading cancer site was breast, followed by colon and rectum, lymph node and stomach. The leading cancer site for men was colon and rectum and for women was breast. CONCLUSION: Cancer incidence is now low in India, a developing country, compared to developed Western countries. However, some cancers, like breast and colon and rectum cancers are increasing every year. IMPACT: The findings of this study support that cancer incidence is increasing in India and more epidemiological studies are needed.

Electronic structure of Sr2FeMoO6

We have analyzed the unusual electronic structure of Sr2FeMoO6 combining ab initio and model Hamiltonian approaches. Our results indicate that there are strong enhancements of the intra-atomic exchange strength at the Mo site as well as the antiferromagnetic coupling strength between Fe and Mo sites. We discuss the possibility of a negative effective Coulomb correlation strength ( U(eff)) at the Mo site due to these renormalized interaction strengths.

T lymphocyte reactivity of leprosy patients and healthy contacts from a leprosy-endemic population to delipidified cell components of Mycobacterium leprae.

In this study, we measured in vitro proliferative responses of peripheral blood mononuclear cells from both leprosy patients across the clinical spectrum and also healthy contacts from a leprosy-endemic population to delipidified cell components of Mycobacterium leprae (DCC) and Dharmendra lepromin. Dharmendra lepromin was poor in inducing in vitro T cell proliferation in all the study groups, even though it elicited marked in vivo skin test reaction in tuberculoid leprosy patients and healthy contacts. In contrast, Dharmendra preparation of BCG induced marked T-cell response in tuberculoid as well as bacterial index negative lepromatous patients. DCC induced a significantly higher lymphoproliferative response than Dharmendra lepromin in all study groups. A significant positive correlation was observed between the lymphoproliferative responses to DCC and BCG. The present study, based on a large number of leprosy patients and healthy contacts, clearly demonstrates that DCC, depleted of glycolipids and lipopolysaccharides, is a good antigenic preparation for evaluating T-cell reactivity to M. leprae.

Antigenic similarity of a cultivable acid fast bacterium to Mycobacterium leprae.

A cultivable acid fast stainable bacterium obtained from leprosy nodule showed similarity to M. leprae in antigenicity to serum antibodies of lepromatous leprosy patients. The antigenic similarity has been seen more clearly in the delipidified cell components of both these bacteria. An antigen of 35-38 kDa has been seen as a common antigen between M. leprae and the cultivable bacilli with binding ability to sera from leprosy patients. This cultivable bacterial component could be used for serodiagnosis of lepromatous leprosy.

Brunner's gland adenoma with circumferential duodenal involvement.

Brunner's gland adenoma is a benign tumor of the duodenum. We report a 58-year-old man who presented with abdominal pain, vomiting and weight loss. The patient underwent Whipple resection along with lymph node clearance. The resected tumor, 4 cm long, showed hypertrophied Brunner's glands.

A rapid method for viability and drug sensitivity of Mycobacterium leprae cultured in macrophages and using fluorescein diacetate.

The ability of viable M. leprae to hydrolyze Fluorescein diacetate and retain fluorescein inside the bacteria was used to identify viable M. leprae inside the cultured in vitro macrophages. The subjective microscopic count of the FDA test was demonstrated as useful routine test by confirming the results obtained therein with a quantitative and non subjective measurement of fluorescence in spectrofluorimeter. Using this method loss of viability of M. leprae in presence of dapsone and rifampicin was demonstrated. Such an assay, was well correlated with another in vitro assay, the Fc receptor test and also the in vivo mouse foot test. The drug resistance of clinical isolates of M. leprae demonstrated by mouse foot pad was also correlated with FDA test system. Thus we have reported a reliable, consistent and rapid in vitro test system for determining viability and drug sensitivity of M. leprae.

In vivo effect of delipidified cell component of Mycobacterium leprae in relation to infection with leprosy bacteria in mice.

The delipidified cell component (DCC) of Mycobacterium leprae was used as an immunomodulatory agent in Swiss white mice. The peritoneal macrophages of these mice were activated to produce increased amount of reactive oxygen intermediates like hydrogen peroxide (H2O2) and superoxide. These macrophages also attained the ability to kill M. Leprae in vitro as shown by several assay systems including the conventional mouse foot-pad technique. The increased levels of superoxide seem to be responsible for the killing of M. leprae as addition of the enzyme superoxide dismutase, which breaks down O2, resulted in survival of these bacilli inside the macrophages. The increased production of H2O2 does not seem to be responsible for killing M. leprae. The results indicate that the DCC of M. leprae acts as an effective immunomodulator in mice leading to the activation of macrophages with increased production of H2O2 and superoxide as well as enabling them to kill M. leprae via the action of superoxide anions.

Hydrolytic enzymes in macrophages from leprosy patients in presence of Mycobacterium leprae.

Presence of Mycobacterium leprae in association with in vitro cultured macrophages, from bacillary negative long term treated lepromatous leprosy patients, induces reduced level of protein and lowering of hydrolytic enzymes like p-glucuronidase, Lysozyme and Lactic dehydrogenase. Alkaline phosphatase, on the other hand is increased. In the macrophages from normal healthy individuals or tuberculoid leprosy patients, presence of M.leprae increases both protein and levels of all the above enzymes. This observation shows that macrophages from lepromatous leprosy patients are unable to manifest in presence of M. leprae, the key enzymes involved in degradation of complex biological entities phagocytosed by the cells.

Lipase activity in Mycobacterium leprae--an indicator of metabolic function.

Presence of lipase, in Mycobacterium leprae obtained from human nodules and infected armadillo tissues, has been detected by demonstrating the ability of the bacteria to hydrolyze tributyrin. This capacity is expressed during incubation of the bacteria with the substrate and needs a source of carbon and other energy metabolites. The activity is blocked by anti M. leprae drug rifampicin. It is concluded that expression of lipase activity is a metabolic event of M. leprae, while they are maintained in an energy providing medium.

Nature of peritoneal macrophages from DCC immunized mice.

Peritoneal macrophages from mice immunized with the delipidified cell component (DCC) of Mycobacterium leprae showed changes in various parameters such as increased protein synthesis, levels of hydrolytic enzyme and augmented phagocytic ability indicating activation of the cells. Furthermore, the surface structure of the cells were quite different from that of the macrophages of normal mice. These observations indicate that the peritoneal macrophages have been activated to phagocytose and kill M. leprae better in the immunized mice. The ability to kill the pathogen by these cells was reported by us earlier.

Correlation of in vitro Fc receptor assay with in vivo mouse foot pad method.

Resistant strains of M. leprae have been reported to the various antileprosy drugs. There is currently no accepted test to identify the susceptibility pattern of M. leprae to the drugs in a short period. The only accepted test is the mouse foot method which takes a long period to yield results. The Fc receptor assay using the ability of viable M. leprae to alter the membrane of the macrophage is well established. It takes only ten days and is inexpensive. In 6 cases of leprosy patients the susceptibility pattern was worked out both with the in vitro Fc receptor assay and the vivo in mouse foot method The results correlated very well leading to the fact that the assay system is reliable. Hence it can be used not only to study the status of a patient, but also to shortlist the number of compounds to be tested on the mouse foot pad as anti-leprosy drug candidates.