InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms.

Phasing of single nucleotide (SNV), and structural variations into chromosome-wide haplotypes in humans has been challenging, and required either trio sequencing or restricting phasing to population-based haplotypes. Selvaraj et al demonstrated single individual SNV phasing is possible with proximity ligated (HiC) sequencing. Here, we demonstrate HiC can phase structural variants into phased scaffolds of SNVs. Since HiC data is noisy, and SV calling is challenging, we applied a range of supervised classification techniques, including Support Vector Machines and Random Forest, to phase deletions. Our approach was demonstrated on deletion calls and phasings on the NA12878 human genome. We used three NA12878 chromosomes and simulated chromosomes to train model parameters. The remaining NA12878 chromosomes withheld from training were used to evaluate phasing accuracy. Random Forest had the highest accuracy and correctly phased 86% of the deletions with allele-specific read evidence. Allele-specific read evidence was found for 76% of the deletions. HiC provides significant read evidence for accurately phasing 33% of the deletions. Also, eight of eight top ranked deletions phased by only HiC were validated using long range polymerase chain reaction and Sanger. Thus, deletions from a single individual can be accurately phased using a combination of shotgun and proximity ligation sequencing. InPhaDel software is available at: http://l337x911.github.io/inphadel/

GREEN PHYTO-SYNTHESIS OF GOLD NANOPARTICLES USING ACHYRANTHES ASPERA LINN SEED-EPICOTYLS LAYER EXTRACTS AND ITS ANTICANCER ACTIVITY

In the recent past decades, green phyto-process for the synthesis of metal incorporated nanoparticles has been evolving into an imperative branch of nanotechnology. We have reported a rapid, expedient and extracellular method for the synthesis of gold nanoparticles by reducing gold chloride with the help of aqueous seed-epicotyls layer extracts of Achyranthes aspera Linn (Amarantheceae).  This approach is simple, economic, stable for a long time, reproducible at room temperature and is synthesized in an eco-friendly mode to obtain a self-assembly of gold nanoparticles (AuNPs).  The resulting gold nanoparticles were characterized using UV-Visible absorption spectroscopy, Scanning Electron Microscopy (SEM), X-ray Diffraction (XRD) and FT-IR spectroscopic techniques. The anticancer activity of the gold nanoparticles was studied against HeLa (Cervical) cancer cell lines. We herein report for the first time, Achyranthes aspera Seed-Epicotyls assisted synthesis of biogenic gold nanoparticles; the nanoparticles are conspicuously smaller and better faceted compared with those synthesized by A. aspera leaf extracts previously reported. Synthesized gold nanoparticles showed potent anticancer activity at 50μg/ml concentration against cervical cancer cell lines.Keywords: Gold nanoparticles, anticancer activity, Achyranthes Aspera Linn.  Aqueous leaves Extract, SEM, XRD, HeLa cancer cell line

Cognitive rehabilitation for adults with traumatic brain injury to improve occupational outcomes.

BACKGROUND: Cognitive impairment in people with traumatic brain injury (TBI) could affect multiple facets of their daily functioning. Cognitive rehabilitation brings about clinically significant improvement in certain cognitive skills. However, it is uncertain if these improved cognitive skills lead to betterments in other key aspects of daily living. We evaluated whether cognitive rehabilitation for people with TBI improves return to work, independence in daily activities, community integration and quality of life. OBJECTIVES: To evaluate the effects of cognitive rehabilitation on return to work, independence in daily activities, community integration (occupational outcomes) and quality of life in people with traumatic brain injury, and to determine which cognitive rehabilitation strategy better achieves these outcomes. SEARCH METHODS: We searched CENTRAL (the Cochrane Library; 2017, Issue 3), MEDLINE (OvidSP), Embase (OvidSP), PsycINFO (OvidSP), and clinical trials registries up to 30 March 2017. SELECTION CRITERIA: We identified all available randomized controlled trials of cognitive rehabilitation compared with any other non-pharmacological intervention for people with TBI. We included studies that reported at least one outcome related to : return to work, independence in activities of daily living (ADL), community integration and quality of life. DATA COLLECTION AND ANALYSIS: Two review authors independently selected trials. We used standard methodological procedures expected by Cochrane. We evaluated heterogeneity among the included studies and performed meta-analysis only when we could include more than one study in a comparison. We used the online computer programme GRADEpro to assess the quality of evidence, and generate 'Summary of findings' tables. MAIN RESULTS: We included nine studies with 790 participants. Three trials (160 participants) compared cognitive rehabilitation versus no treatment, four trials (144 participants) compared cognitive rehabilitation versus conventional treatment, one trial (120 participants) compared hospital-based cognitive rehabilitation versus home programme and one trial (366 participants) compared one cognitive strategy versus another. Among the included studies, we judged three to be of low risk of bias.There was no difference between cognitive rehabilitation and no intervention in return to work (risk ratio (RR) 1.80, 95% confidence interval (CI) 0.74 to 4.39, 1 study; very low-quality evidence). There was no difference between biweekly cognitive rehabilitation for eight weeks and no treatment in community integration (Sydney Psychosocial Reintegration Scale): mean difference (MD) -2.90, 95% CI -12.57 to 6.77, 1 study; low-quality evidence). There was no difference in quality of life between cognitive rehabilitation and no intervention immediately following the 12-week intervention(MD 0.30, 95% CI -0.18 to 0.78, 1 study; low-quality evidence). No study reported effects on independence in ADL.There was no difference between cognitive rehabilitation and conventional treatment in return to work status at six months' follow-up in one study (RR 1.43, 95% CI 0.87 to 2.33; low-quality evidence); independence in ADL at three to four weeks' follow-up in two studies (standardized mean difference (SMD) -0.01, 95% CI -0.62 to 0.61; very low-quality evidence); community integration at three weeks' to six months' follow-up in three studies (Community Integration Questionnaire: MD 0.05, 95% CI -1.51 to 1.62; low-quality evidence) and quality of life at six months' follow-up in one study (Perceived Quality of Life scale: MD 6.50, 95% CI -2.57 to 15.57; moderate-quality evidence).For active duty military personnel with moderate-to-severe closed head injury, there was no difference between eight weeks of cognitive rehabilitation administered as a home programme and hospital-based cognitive rehabilitation in achieving return to work at one year' follow-up in one study (RR 0.95, 95% CI 0.85 to 1.05; moderate-quality evidence). The study did not report effects on independence in ADL, community integration or quality of life.There was no difference between one cognitive rehabilitation strategy (cognitive didactic) and another (functional experiential) for adult veterans or active duty military service personnel with moderate-to-severe TBI (one study with 366 participants and one year' follow-up) on return to work (RR 1.10, 95% CI 0.83 to 1.46; moderate-quality evidence), or on independence in ADL (RR 0.90, 95% CI 0.75 to 1.08; low-quality evidence). The study did not report effects on community integration or quality of life.None of the studies reported adverse effects of cognitive rehabilitation. AUTHORS' CONCLUSIONS: There is insufficient good-quality evidence to support the role of cognitive rehabilitation when compared to no intervention or conventional rehabilitation in improving return to work, independence in ADL, community integration or quality of life in adults with TBI. There is moderate-quality evidence that cognitive rehabilitation provided as a home programme is similar to hospital-based cognitive rehabilitation in improving return to work status among active duty military personnel with moderate-to-severe TBI. Moderate-quality evidence suggests that one cognitive rehabilitation strategy (cognitive didactic) is no better than another (functional experiential) in achieving return to work in veterans or military personnel with TBI

Interleukin-12B & interleukin-10 gene polymorphisms in pulmonary tuberculosis

Background & objectives: Cytokines play an important role in anti-tuberculosis immune response. Skewing of immunity from protective to pathogenic may involve a shift in Th1-Th2 paradigm. Cytokine gene polymorphism is known to be associated with functional differences in cytokine regulation and altered clinical performance in a variety of diseases. The aim of this study was to know whether Interleukin-12B 3’ UTR (Taq1) (A/C) and Interleukin-10 (-1082 G/A) gene polymorphisms were associated with susceptibility to pulmonary tuberculosis. Methods: IL -10 (-1,082 G/A) and IL-12B gene polymorphisms were studied in132 pulmonary TB (PTB) patients and 143 normal healthy subjects (NHS), using DNA based polymerase chain reaction (PCR) with sequence specific primers and restriction digestion. Results: The allelic as well as genotypic frequencies of Interleukin -10 (-1082) and Interleukin -12B (3’UTR Taq 1) did not differ significantly between the patients and controls. Interpretation & conclusion: Our findings suggested that IL -10 (-1082 G/A) and IL -12B 3’UTR (Taq I) (A/C) gene polymorphisms were not associated either with susceptibility or resistance to pulmonary tuberculosis in the south Indian population

Interferon gamma (IFN -gamma) and interleukin -4 (IL-4) gene variants and cytokine levels in pulmonary tuberculosis. Indian Journal of Medical Research

Background & objectives: Cytokine gene polymorphisms may alter Th1/Th2 balance with major implications in tuberculosis. The aim of our study was to find out whether Interferon � +874A and IL-4 -590T polymorphisms were associated with susceptibility to pulmonary tuberculosis as well as the level of IFN� and IL-4 in south Indian population. Methods: Interferon � +874A and IL-4 -590T promoter polymorphisms were studied in 129 pulmonary tuberculosis (PTB) patients and 127 normal healthy subjects (NHS) and were associated with culture filtrate and live Mycobacterium tuberculosis induced IFN� and IL-4 production in peripheral blood mononuclear cells (PBMCs). IL-4 gene variants were also associated with IgG antibody levels against M. tuberculosis culture filtrate antigen. Results: The variant IFN� genotypes and IFN� levels between genotypes did not differ significantly in patients and controls. Significantly increased frequency of variant IL-4 ‘CT’ genotype in PTB patients (P<0.05) and ‘CC’ genotype in control group (P<0.01) was observed. IL-4 levels were detectable in very few subjects and the IgG levels did not differ between the three IL-4 genotypes. Interpretation & conclusion: The study suggests a lack of functional association of Interferon � +874A polymorphism in tuberculosis in south Indian population. The higher frequency of IL-4 ‘CT’ genotype in PTB suggests a possible association of IL-4 -590T promoter polymorphism with susceptibility to tuberculosis, and the ‘CC’ genotype may be associated with protection

Promoter polymorphism of IL-8 gene and IL-8 production in pulmonary tuberculosis

Interleukin-8 (IL-8) is a chemokine which functions as a potent chemo attractant for the recruitment of leucocytes to the inflammatory sites. A polymorphism in position –251 in the promoter region of the IL-8 gene has been shown to be associated with altered IL-8 production. IL-8-251A promoter polymorphism was studied in 127 pulmonary tuberculosis (PTB) patients and 124 normal healthy subjects (NHS). IL-8 gene variants were correlated with IL-8 levels from peripheral blood mononuclear cells stimulated with phytohaemagglutinin, culture filtrate antigen (CFA) of Mycobacterium tuberculosis and live M. tuberculosis. No difference was observed in the variant genotype frequencies of IL-8 gene and IL-8 levels between NHS and PTB patients. NHS positive for TT genotype showed a higher spontaneous IL-8 production than AA genotype (P = 0.05). Similarly, PTB patients with TT genotype showed significantly higher IL-8 production to CFA (P = 0.009) and live M. tuberculosis (P = 0.022), compared to patients with AA genotype. The study suggests that the variant genotypes of –251 promoter polymorphism of the IL-8 gene are not associated with susceptibility to PTB. Probably, TT genotype may be associated with higher IL-8 production and increased leucocyte accumulation and inflammation at the site of M. tuberculosis infection

On the Synergistic Catalytic Properties of Bimetallic Mesoporous Materials Containing Aluminum and Zirconium: The Prins Cyclisation of Citronellal

Bimetallic three-dimensional amorphous mesoporous materials, Al-Zr-TUD-1 materials, were synthesised by using a surfactant-free, one-pot procedure employing triethanolamine (TEA) as a complexing reagent. The amount of aluminium and zirconium was varied in order to study the effect of these metals on the Brønsted and Lewis acidity, as well as on the resulting catalytic activity of the material. The materials were characterised by various techniques, including elemental analysis, X-ray diffraction, high-resolution TEM, N2 physisorption, temperature-programmed desorption (TPD) of NH3, and 27Al MAS NMR, XPS and FT-IR spectroscopy using pyridine and CO as probe molecules. Al-Zr-TUD-1 materials are mesoporous with surface areas ranging from 700–900 m2 g−1, an average pore size of around 4 nm and a pore volume of around 0.70 cm3 g−1. The synthesised Al-Zr-TUD-1 materials were tested as catalyst materials in the Lewis acid catalysed Meerwein–Ponndorf–Verley reduction of 4-tert-butylcyclohexanone, the intermolecular Prins synthesis of nopol and in the intramolecular Prins cyclisation of citronellal. Although Al-Zr-TUD-1 catalysts possess a lower amount of acid sites than their monometallic counterparts, according to TPD of NH3, these materials outperformed those of the monometallic Al-TUD-1 as well as Zr-TUD-1 in the Prins cyclisation of citronellal. This proves the existence of synergistic properties of Al-Zr-TUD-1. Due to the intramolecular nature of the Prins cyclisation of citronellal, the hydrophilic surface of the catalyst as well as the presence of both Brønsted and Lewis acid sites synergy could be obtained with bimetallic Al-Zr-TUD-1. Besides spectroscopic investigation of the active sites of the catalyst material a thorough testing of the catalyst in different types of reactions is crucial in identifying its specific active sites

Effects of sacubitril/valsartan on serum lipids in heart failure with preserved ejection fraction

Background: Dyslipidemia is common in heart failure with preserved ejection fraction. Sacubitril/valsartan improves glycemic control and augments natriuretic peptide signaling, providing mechanisms by which sacubitril/valsartan may affect serum lipids. However, empiric data on these effects are lacking. Methods and Results: We analyzed 4774 participants from PARAGON‐HF (Prospective Comparison of Angiotensin Receptor–Neprilysin Inhibitor With Angiotensin‐Receptor Blockers Global Outcomes in Heart Failure With Preserved Ejection Fraction) with available screening lipids. During follow‐up visits, we analyzed the treatment effect on lipid levels and assessed for interaction by baseline lipid levels. At the 16‐week visit, we adjusted these treatment effects for the change in several biomarkers (including hemoglobin A1c and urinary cyclic guanosine monophosphate/creatinine [a biomarker of natriuretic peptide activation]). The average age was 73±8 years, 52% were women, 43% had diabetes mellitus, and 64% were on statin therapy. Compared with valsartan, sacubitril/valsartan reduced triglycerides −5.0% (95% CI, −6.6% to −3.5%), increased high‐density lipoprotein cholesterol +2.6% (95% CI, +1.7% to +3.4%), and increased low‐density lipoprotein cholesterol +1.7% (95% CI, +0.4% to +3.0%). Sacubitril/valsartan reduced triglycerides most among those with elevated baseline levels (triglycerides≥200 mg/dL) (P‐interaction&lt;0.001), and at 16 weeks by −13.0% (95% CI, −18.1% to −7.6%), or −29.9 (95% CI, −44.3 to −15.5) mg/dL, in this group. Adjusting for the change in urinary cyclic guanosine monophosphate/creatinine significantly attenuated treatment effects on triglycerides and high‐density lipoprotein cholesterol, but not low‐density lipoprotein cholesterol, while adjusting for other biomarkers did not significantly alter the treatment effects. Conclusions: Sacubitril/valsartan significantly reduces triglycerides compared with valsartan, an effect that was nearly threefold stronger in those with elevated baseline triglycerides. Modest increases in high‐density lipoprotein cholesterol and low‐density lipoprotein cholesterol cholesterol were also observed with therapy. The underlying mechanism(s) of changes in high‐density lipoprotein cholesterol and triglycerides are related to sacubitril/valsartan’s effects on natriuretic peptide activity. Registration: URL: https://www.clinicaltrials.gov; Unique identifier: NCT01920711

PolyGA targets the ER stress-adaptive response by impairing GRP75 function at the MAM in C9ORF72-ALS/FTD.

ER stress signaling is linked to the pathophysiological and clinical disease manifestations in amyotrophic lateral sclerosis (ALS). Here, we have investigated ER stress-induced adaptive mechanisms in C9ORF72-ALS/FTD, focusing on uncovering early endogenous neuroprotective mechanisms and the crosstalk between pathological and adaptive responses in disease onset and progression. We provide evidence for the early onset of ER stress-mediated adaptive response in C9ORF72 patient-derived motoneurons (MNs), reflected by the elevated increase in GRP75 expression. These transiently increased GRP75 levels enhance ER-mitochondrial association, boosting mitochondrial function and sustaining cellular bioenergetics during the initial stage of disease, thereby counteracting early mitochondrial deficits. In C9orf72 rodent neurons, an abrupt reduction in GRP75 expression coincided with the onset of UPR, mitochondrial dysfunction and the emergence of PolyGA aggregates, which co-localize with GRP75. Similarly, the overexpression of PolyGA in WT cortical neurons or C9ORF72 patient-derived MNs led to the sequestration of GRP75 within PolyGA inclusions, resulting in mitochondrial calcium (Ca2+) uptake impairments. Corroborating these findings, we found that PolyGA aggregate-bearing human post-mortem C9ORF72 hippocampal dentate gyrus neurons not only display reduced expression of GRP75 but also exhibit GRP75 sequestration within inclusions. Sustaining high GRP75 expression in spinal C9orf72 rodent MNs specifically prevented ER stress, normalized mitochondrial function, abrogated PolyGA accumulation in spinal MNs, and ameliorated ALS-associated behavioral phenotype. Taken together, our results are in line with the notion that neurons in C9ORF72-ALS/FTD are particularly susceptible to ER-mitochondrial dysfunction and that GRP75 serves as a critical endogenous neuroprotective factor. This neuroprotective pathway, is eventually targeted by PolyGA, leading to GRP75 sequestration, and its subsequent loss of function at the MAM, compromising mitochondrial function and promoting disease onset

Transcriptome response to heavy metal stress in Drosophila reveals a new zinc transporter that confers resistance to zinc

All organisms are confronted with external variations in trace element abundance. To elucidate the mechanisms that maintain metal homeostasis and protect against heavy metal stress, we have determined the transcriptome responses in Drosophila to sublethal doses of cadmium, zinc, copper, as well as to copper depletion. Furthermore, we analyzed the transcriptome of a metal-responsive transcription factor (MTF-1) null mutant. The gene family encoding metallothioneins, and the ABC transporter CG10505 that encodes a homolog of ‘yeast cadmium factor’ were induced by all three metals. Zinc and cadmium responses have similar features: genes upregulated by both metals include those for glutathione S-transferases GstD2 and GstD5, and for zinc transporter-like proteins designated ZnT35C and ZnT63C. Several of the metal-induced genes that emerged in our study are regulated by the transcription factor MTF-1. mRNA studies in MTF-1 overexpressing or null mutant flies and in silico search for metal response elements (binding sites for MTF-1) confirmed novel MTF-1 regulated genes such as ferritins, the ABC transporter CG10505 and the zinc transporter ZnT35C. The latter was analyzed in most detail; biochemical and genetic approaches, including targeted mutation, indicate that ZnT35C is involved in cellular and organismal zinc efflux and plays a major role in zinc detoxification