Microarray-based ultra-high resolution discovery of genomic deletion mutations

BACKGROUND: Oligonucleotide microarray-based comparative genomic hybridization (CGH) offers an attractive possible route for the rapid and cost-effective genome-wide discovery of deletion mutations. CGH typically involves comparison of the hybridization intensities of genomic DNA samples with microarray chip representations of entire genomes, and has widespread potential application in experimental research and medical diagnostics. However, the power to detect small deletions is low. RESULTS: Here we use a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection. We show that the power to detect smaller deletions (4, 28 and 104 bp) depends upon oligonucleotide density (essentially the number of genome-representative oligonucleotides on the microarray chip), and determine the oligonucleotide spacings necessary to guarantee detection of deletions of specified size. CONCLUSIONS: Our findings will enhance a wide range of research and clinical applications, and in particular will aid in the discovery of genomic deletions in the absence of a priori knowledge of their existence

Paddy Production Technology in Konkan Region of Maharashtra.

The study has assessed the economic analysis and impact assessment of production technology of paddy cultivation in Konkan region of Maharashtra for the year 2014-15, based on the data of costs and returns of crop. Apart from benefit-cost ratio (BCR), yield gap analysis, resource use efficiencies, adoption index and impact of improved paddy technology have been estimated in the study. It has shown that the per hectare cost ‘C’ was  49,393.85 and BCR is 1.41, whereas the per quintal cost production was  1,069.78 at the overall level for improved paddy cultivation methods. Further, there was a 16.59 per cent yield gap between actual yield  and yield of demonstration plot, in which cultural practices (11.58) have shown a stronger effect than input use (5.01). The composit index of technology adoption was worked out to 67.46 per cent indicated that the sample farmers adopted less than 30 per cent recommended paddy production technology and obtained 36.65 qtls/ha yield. The contribution of different components on impact of paddy production technology in Kokan region, net returns was maximum (44.22 per cent) followed by gross returns and main produce.                 The most important constraint in improved method of paddy cultivation has been identified as ‘high cost of seed, fertilizers and labour charges, lack of knowledge about fertilizers application, seed treatment small fragmented holding and low price to produce. The improved paddy production technology method being more skill oriented, the study has observed that yields can be made on adoption and impact sustainable if constraints are addressed on war-footing basis

Induction of Hemeoxygenase-1 Reduces Renal Oxidative Stress and Inflammation in Diabetic Spontaneously Hypertensive Rats

The renoprotective mechanisms of hemeoxygenase-1 (HO-1) in diabetic nephropathy remain to be investigated. We hypothesize that HO-1 protects the kidney from diabetic insult via lowering renal oxidative stress and inflammation. We used control and diabetic SHR with or without HO-1 inducer cobalt protoporphyrin (CoPP) treatment for 6 weeks. Urinary albumin excretion levels were significantly elevated in diabetic SHR compared to control and CoPP significantly attenuated albumin excretion. Immuno-histochemical analysis revealed an elevation in TGF-β staining together with increased urinary collagen excretion in diabetic versus control SHR, both of which were reduced with CoPP treatment. Renal oxidative stress markers were greater in diabetic SHR and reduced with CoPP treatment. The increase in renal oxidative stress was associated with an elevation in renal inflammation in diabetic SHR. CoPP treatment also significantly attenuated the markers of renal inflammation in diabetic SHR. In vitro inhibition of HO with stannous mesoporphyrin (SnMP) increased glomerular NADPH oxidase activity and inflammation and blocked the anti-oxidant and anti-inflammatory effects of CoPP. These data suggest that the reduction of renal injury in diabetic SHR upon induction of HO-1 are associated with decreased renal oxidative stress and inflammation, implicating the role of HO-1 induction as a future treatment of diabetic nephropathy

To evaluate the efficacy of Siravyadha and Basti in the management of Siraja Granthi (Varicose Vein) - A Comparative Clinical Study

Background: In this changed lifestyle of human beings, he has become a victim of several diseases, amongst them one is Varicose Veins, which are caused due to long standing or sitting in chairs which causes extra load on veins to pump the blood against gravity towards the Heart, especially the veins of the legs. Finally the veins get fatigued that leads to dilation and cause Varicosity in veins. Objectives: To compare the effect of Siravyadhana and Basti in the management of Siraja Granthi (Varicose Vein). Methods: Cases presenting with classical signs and symptoms of Siraja Granthi were randomly divided into 2 groups. Group A was treated with Siravyadhana and Group B were subjected for Sahacharadi Basti. The data was collected before treatment and after 8th day and 30th days. The obtained data was statistically analyzed. Results: 20 patients in Group A, 93.33% reduction was seen in Shoola, while 93.02% reduction was found in Group B. In Gaurava 86.36% reduction was found in Group A and 85.71% reduction was seen in Group B. Shotha was decreased by 67.74% in Group A, while 62.65% in Group B. In Sira Utseda, 54.05% reduction was seen in Group A and 47.36% reduction in Group B. Conclusion: Group A, cases showed better improvement. Out of 20 patients, 2 patients got complete remission in Group A, 2 patients showed excellent response, while in Group B, 6 patients showed excellent response, In Group A and B, 11 and 8 patients showed good response respectively. In Group A and B, 5 and 6 patients showed moderate response

Atrioventricular canal defect and genetic syndromes: the unifying role of sonic hedgehog

The atrioventricular canal defect (AVCD) is a congenital heart defect (CHD) frequently associated with extracardiac anomalies (75%). Previous observations from a personal series of patients with AVCD and "polydactyly syndromes" showed that the distinct morphology and combination of AVCD features in some of these syndromes is reminiscent of the cardiac phenotype found in heterotaxy, a malformation complex previously associated with functional cilia abnormalities and aberrant Hedgehog (Hh) signaling. Hh signaling coordinates multiple aspects of left-right lateralization and cardiovascular growth. Being active at the venous pole the secondary heart field (SHF) is essential for normal development of dorsal mesenchymal protrusion and AVCD formation and septation. Experimental data show that perturbations of different components of the Hh pathway can lead to developmental errors presenting with partially overlapping manifestations and AVCD as a common denominator. We review the potential role of Hh signaling in the pathogenesis of AVCD in different genetic disorders. AVCD can be viewed as part of a "developmental field," according to the concept that malformations can be due to defects in signal transduction cascades or pathways, as morphogenetic units which may be altered by Mendelian mutations, aneuploidies, and environmental causes

Epidemiology of Methicillin-resistant and Methicillin-sensitive Staphylococcus aureus infections in Lebanon

Background. Methicillin-resistant Staphylococcus aureus (MRSA) is a prevalent pathogen associated with significant morbidity and mortality. In Lebanon, MRSA rates have recently started to rise. We aimed to determine risk factors for acquiring MRSA and Methicillin-sensitive Staphylococcus aureus (MSSA) infections and identify independent risk factors for in-hospital mortality among patients with S. aureus infection. Methods. We used a case-case-control study design that included patients with infections and compared them to uninfected controls. Two multivariable regression models were constructed to determine variables associated with acquiring MRSA and MSSA infections. We explored independent predictors of mortality in the overall population compared with the MRSA subgroup. Results. 356 patients with S. aureus infections were identified and compared to 208 uninfected controls. A recent history of surgery and underlying diabetes were independent risk factors for acquiring both infections. Having a urinary catheter for more than 6 days and steroid therapy were unique risk factors for MRSA infection (aOR 28.1, 95% CI 3.5-223.6 and 3.7, 95% CI 1.6-8.7, respectively). Risk factors exclusively associated with MRSA infection included ICU admission, acute renal failure, and malignancy. Conclusions. Risk factors associated with MRSA infection are distinct from those associated with MSSA infection. This can be used to risk stratify patients and will aid in choosing empirical antibiotic therapy

First evidence of maternally inherited mosaicism in TGFBR1 and subtle primary myocardial changes in Loeys-Dietz syndrome: a case report

Background: Loeys-Dietz syndrome (LDS) is a rare multisystemic disorder characterized by vascular and skeletal abnormalities, with considerable intra- and interfamilial variability. Case presentation: We report the case of an 8-year-old male with clinical features of two distinct genetic disorders, namely LDS, manifesting in the first months by progressive aortic root dilatation, arterial tortuosity, bifid uvula, and inguinal hernias and oculocutaneous albinism (OCA) manifesting by white hair and skin that does not tan, nystagmus, reduced iris pigment with iris translucency, and reduced retinal pigment). We identified previously reported, homozygous mutations of TYR, c.1A > G (p.Met1Val) and heterozygous, missense mutation of TGFBR1, c.1460G > A (p.Arg487Gln). Family history revealed that his mother underwent multiple surgical repairs for recurrent hemorrhage originating from the buccal artery. Molecular studies confirmed a maternally inherited low grade TGFBR1 mutation somatic mosaicism (18% in peripheral blood leukocytes, 18% in buccal cells and 10% in hair root cells). Maternal cardiac investigations revealed peculiar cardiovascular features: mild tortuosity at the aortic arch, dilatation of the proximal abdominal aorta, multiple deep left ventricular myocardial crypts, and dysplastic mitral valve. TGFBR2 germline mosaicism has been described in three fathers of children carrying TGFBR2 mutations but, to the best of our knowledge, no case of maternally inherited TGFBR1 mutation mosaicism has been reported so far. Conclusions: This case report suggests that individuals with somatic mosaicism might be at risk for mild and unusual forms of LDS but germline mosaicism can lead to full blown picture of the disease in offspring

Gestational hypercalcemia: Prevalence and biochemical profile

Gestational hypercalcemia is associated with an increased risk of maternal, fetal and neonatal morbidity and mortality. Hypercalcemia may develop during pregnancy in individuals who were previously asymptomatic. The increased sensitivity during pregnancy may be related to physiological, gestational alterations in vitamin D and calcium metabolism and may be influenced by gene variants. The prevalence is unknown. We investigated the prevalence of hypercalcemia in trimester 3 (T3) in a population representative prospective cohort study (n = 1832) in South-West Sweden. Women with serum albumin (Alb) adjusted calcium (CaAlb) ≥ 2.65 mmol/L in T3 (n = 30) were matched to normo-calcemic controls, and markers of calcium and vitamin D metabolism were investigated in trimester 1 (T1) and T3. Serum concentrations of Ca, phosphate (P), Magnesium (Mg), Alb and creatinine (Cr), parathyroid hormone (PTH; T3 only), vitamin D metabolites (total 25(OH)D, 1,25(OH)2D, 24,25(OH)2D, and free 25(OH)D) were analysed in T1 and T3. CaAlb (Payne; inter-laboratory difference: UEA = 0.15 + 0.9*UGOT; UEA 2.54 = UGOT 2.65) and estimated glomerular filtration rate (eGFR; modified 4-variable MDRD) and vitamin D metabolites ratios (VMR) were calculated. Normally and non-normally distributed data were presented as mean (SD) or median (95%CI). Group differences in relationships between vitamin D metabolites and with PTH were investigated with multiple regression analyses. Hypercalcemia in T3 was found in 1.7% of women. PTH concentrations suggestive of primary hyperparathyroidism was found in 1 woman and none had 25(OH)D or 24,25(OH)2D concentrations in the toxicity range or suggestive of mutations in the CYP24A1 gene. CaAlb was significantly higher in hypercalcemic cases compared to controls in T1 (2.44 (2.30-2.80) vs 2.37 (2.25-2.49) mmol/L) and T3 (2.63 (2.52-2.78) vs 2.46 (2.31-2.58) mmol/L). Serum P was higher among cases than controls in T3 (1.12 (0.16) vs 1.07 (0.18) mmol/L) but not in T1 (1.12 (0.18) and 1.12 (0.16) mmol/L). PTH in T3 was lower in cases (1.6 (1.6-2.8) vs 2.3 (2.1-2.8) pmol/L) but 1,25(OH)2D concentrations were similar. There were no significant group differences in serum 25(OH)D, free 25(OH)D, 24,25(OH)2D, Mg, Alb, Cr and eGFR. Regression analyses did not show significant differences between cases and controls in relationships between vitamin D metabolites and with PTH, except for the free 25(OH)D-PTH relationship and a higher free:total 25(OH)D ratio in cases at T1. In conclusion, most common causes of hypercalcemia were excluded in the majority of women. Hypercalcemic women had a relatively high serum 1,25(OH)2D concentration despite an appropriately suppressed PTH, suggestive of abnormal gestational adaptions

Synthesis of Fluorine-18 Functionalized Nanoparticles for use as in vivo Molecular Imaging Agents

Nanoparticles containing fluorine-18 were prepared from block copolymers made by ring opening metathesis polymerization (ROMP). Using the fast initiating ruthenium metathesis catalyst (H_2IMes)(pyr)_2(Cl)_2Ru=CHPh, low polydispersity amphiphilic block copolymers were prepared from a cinnamoyl-containing hydrophobic norbornene monomer and a mesyl-terminated PEG-containing hydrophilic norbornene monomer. Self-assembly into micelles and subsequent cross-linking of the micelle cores by light-activated dimerization of the cinnamoyl groups yielded stable nanoparticles. Incorporation of fluorine-18 was achieved by nucleophilic displacement of the mesylates by the radioactive fluoride ion with 31% incorporation of radioactivity. The resulting positron-emitting nanoparticles are to be used as in vivo molecular imaging agents for use in tumor imaging