MicroRNA, miR-501 regulate the V(D)J recombination in B cells

The stringent regulation of RAGs (Recombination activating genes), the site-specific endonuclease responsible for V(D)J recombination, is important to prevent genomic rearrangements and chromosomal translocations in lymphoid cells. In the present study, we identify a microRNA, miR-501, which can regulate the expression of RAG1 in lymphoid cells. Overexpression of the pre-miRNA construct led to the generation of mature miRNAs and a concomitant reduction in RAG1 expression, whereas inhibition using anti-miRs resulted in its enhanced expression. The direct interaction of the 3'UTR of miR-501 with RAG1 was confirmed by the reporter assay. Importantly, overexpression of miRNAs led to inhibition of V(D)J recombination in B cells, revealing their impact on the physiological function of RAGs. Of interest is the inverse correlation observed for miR-501 with RAG1 in various leukemia patients and lymphoid cell lines, suggesting its possible use in cancer therapy. Thus, our results reveal the regulation of RAG1 by miR-501-3p in B cells and thus V(D)J recombination and its possible implications on immunoglobulin leukemogenesis.

Comparative efficacy of Micropore™ surgical dressing, Tegaderm™ and Lockit plus® for lumbar epidural catheter fixation in children: a prospective parallel group randomized controlled trial

BACKGROUND

Proper fixation of an epidural catheter is necessary for desired drug effect and to prevent catheter displacement. Different techniques have been used for epidural catheter fixation. The aim of the study was to compare the relative efficacy of Micropore™ surgical dressing, Tegaderm™, and Lockit plus® in preventing lumbar epidural catheter migration in children.

METHODS

We studied 167 patients aged 5-16 years, for up to 48 h. After the elective abdominal or lower limb surgery. Patients were randomly assigned to one of three groups: (1) Micropore™ surgical dressing (group M), (2) Tegaderm™ (group T), or (3) Lockit plus® (group L). Incidence and extent of epidural catheter migration in centimetres (cm); was compared at 24 and 48 h post epidural fixation. Correlation between epidural catheter migration and patient characteristics, and relative incidence of complications in three groups was also analysed.

RESULTS

Incidence of catheter migration was 9.6% at 24 h (group M: 7.1%, group T: 21.1% and group L: 0%) and 45.5% at 48 h (group M: 66.1%, group T: 45.6% and group L: 24.1%). After 48 h, absolute migration (mean migration rounded off to the nearest 0.5 cm) was least in patients in group L: 0.34 cm (1.39) compared to group M 1.22 cm (SD: 1.85) group T: 0.94 cm (1.94) (p = <0.001).

CONCLUSION

Up to 48 h after surgery, the Lockit plus® device demonstrated the less epidural catheter migration when compared to micropore surgical dressing or tegaderm in children undergoing elective abdominal or lower limb surgery.

Maternal Serum Vitamin E Levels and its Association with Cord Blood Telomere Length and Mitochondrial DNA Copy Number in Preterm Premature Rupture of Membranes

Background and Objective

Oxidative stress is one of the pathophysiological factors of pPROM and Vit. E being antioxidant may have preventive role. Study was conducted to estimate maternal serum vitamin E levels and cord blood oxidative stress markers in pPROM cases.

Methods

This was a case-control study including 40 pPROM cases and 40 controls. Maternal serum vitamin E levels were measured at recruitment. Cord blood was collected at delivery for estimation of telomere length and mtDNA copy number as oxidative stress markers. Levels were compared using student's t test or Mann Whitney test. For correlation Pearson coefficient was used.

Results

Maternal serum vitamin E levels were normal in pPROM cases. Cord blood telomere length was more in pPROM than controls (428.99 ± 290.65 vs 322.35 ± 180.33) (p value 0.05). Cord blood mtDNA copy number was more in pPROM than controls (516.46 ± 443.55 vs 384.77 ± 328.27) (p value 0.13) though it was not significant. mtDNA copy number had negative correlation with Vit. E levels but it was statistically not significant (p value 0.49). There was no association of vitamin E levels with telomere length (p value 0.95).

Interpretation and Conclusion

pPROM was not associated with vitamin E deficiency. There was insignificant oxidative stress in cord blood as measured by mtDNA copy number but cord blood telomere length measurement did not detect any oxidative stress in pPPROM cases.

Nonamer dependent RAG cleavage at CpGs can explain mechanism of chromosomal translocations associated to lymphoid cancers

Chromosomal translocations are considered as one of the major causes of lymphoid cancers. RAG complex, which is responsible for V(D)J recombination, can also cleave non-B DNA structures and cryptic RSSs in the genome leading to chromosomal translocations. The mechanism and factors regulating the illegitimate function of RAGs resulting in oncogenesis are largely unknown. Upon in silico analysis of 3760 chromosomal translocations from lymphoid cancer patients, we find that 93% of the translocation breakpoints possess adjacent cryptic nonamers (RAG binding sequences), of which 77% had CpGs in proximity. As a proof of principle, we show that RAGs can efficiently bind to cryptic nonamers present at multiple fragile regions and cleave at adjacent mismatches generated to mimic the deamination of CpGs. ChIP studies reveal that RAGs can indeed recognize these fragile sites on a chromatin context inside the cell. Finally, we show that AID, the cytidine deaminase, plays a significant role during the generation of mismatches at CpGs and reconstitute the process of RAG-dependent generation of DNA breaks both in vitro and inside the cells. Thus, we propose a novel mechanism for generation of chromosomal translocation, where RAGs bind to the cryptic nonamer sequences and direct cleavage at adjacent mismatch generated due to deamination of meCpGs or cytosines.

Environmental tracers and groundwater residence time indicators reveal controls of arsenic accumulation rates beneath a rapidly developing urban area in Patna, India

Groundwater security is a pressing environmental and societal issue, particularly due to significantly increasing stressors on water resources, including rapid urbanization and climate change. Groundwater arsenic is a major water security and public health challenge impacting millions of people in the Gangetic Basin of India and elsewhere globally. In the rapidly developing city of Patna (Bihar) in northern India, we have studied the evolution of groundwater chemistry under the city following a three-dimensional sampling framework of multi-depth wells spanning the central urban zone in close proximity to the River Ganges (Ganga) and transition into peri-urban and rural areas outside city boundaries and further away from the river. Using inorganic geochemical tracers (including arsenic, iron, manganese, nitrate, nitrite, ammonium, sulfate, sulfide and others) and residence time indicators (CFCs and SF₆), we have evaluated the dominant hydrogeochemical processes occurring and spatial patterns in redox conditions across the study area. The distribution of arsenic and other redox-sensitive parameters is spatially heterogenous, and elevated arsenic in some locations is consistent with arsenic mobilization via reductive dissolution of iron hydroxides. Residence time indicators evidence modern (<~60-70 years) groundwater and suggest important vertical and lateral flow controls across the study area, including an apparent seasonal reversal in flow regimes near the urban center. An overall arsenic accumulation rate is estimated to be ~0.003 ± 0.003 μM.yr^-1 (equivalent to ~0.3 ± 0.2 μg.yr^-1), based on an average of CFC-11, CFC-12 and SF₆-derived models, with the highest rates of arsenic accumulation observed in shallow, near-river groundwaters also exhibiting elevated concentrations of nutrients including ammonium. Our findings have implications on groundwater management in Patna and other rapidly developing cities, including potential future increased groundwater vulnerability associated with surface-derived ingress from large-scale urban abstraction or in higher permeability zones of river-groundwater connectivity.

Household and community systems for groundwater remediation in Bihar, India: Arsenic and inorganic contaminant removal, controls and implications for remediation selection

The presence of arsenic (As) and other inorganic contaminants in groundwater is a key public health issue in India and many other parts of the world. Whilst a broad range of remediation technologies exist, performance can be highly variable, and appropriate selection and management of remediation approaches remains challenging. Here, we have identified and tested the performance of a range of small-scale remediation technologies (e.g. sand filters, multi-stage filtration and reverse osmosis (RO)-based systems; n = 38) which have been implemented in Bihar, India. We have undertaken spot-assessments of system performance under typical operating conditions in household and non-household (e.g. community, hospital, hostel/hotel) settings. The removal of As and other inorganic contaminants varied widely (ranging from ~0-100%), with some solutes generally more challenging to remove than others. We have evaluated the relative importance of technology type (e.g. RO-based versus non-RO systems), implementation setting (e.g. household versus non-household) and source water geochemistry (particularly concentrations and ratios of As, Fe, P, Si and Ca), as potential controls on remediation effectiveness. Source water composition, particularly the ratio ([Fe] - 1.8[P])/[As], is a statistically significant control on As removal (p < 0.01), with higher ratios associated with higher removal, regardless of technology type (under the site-specific conditions observed). This ratio provides a theoretical input which could be used to identify the extent to which natural groundwater composition may be geochemically compatible with higher levels of As removal. In Bihar, we illustrate how this ratio could be used to identify spatial patterns in theoretical geochemical compatibility for As removal, and to identify where additional Fe may theoretically facilitate improved remediation. This geochemical approach could be used to inform optimal selection of groundwater remediation approaches, when considered alongside other important considerations (e.g. technical, managerial and socio-economic) known to impact the effective implementation and sustainability of successful groundwater remediation approaches.

A systematic approach to understand hydrogeochemical dynamics in large river systems: Development and application to the River Ganges (Ganga) in India

Large river systems, such as the River Ganges (Ganga), provide crucial water resources for the environment and society, yet often face significant challenges associated with cumulative impacts arising from upstream environmental and anthropogenic influences. Understanding the complex dynamics of such systems remains a major challenge, especially given accelerating environmental stressors including climate change and urbanization, and due to limitations in data and process understanding across scales. An integrated approach is required which robustly enables the hydrogeochemical dynamics and underpinning processes impacting water quality in large river systems to be explored. Here we develop a systematic approach for improving the understanding of hydrogeochemical dynamics and processes in large river systems, and apply this to a longitudinal survey (> 2500 km) of the River Ganges (Ganga) and key tributaries in the Indo-Gangetic basin. This framework enables us to succinctly interpret downstream water quality trends in response to the underpinning processes controlling major element hydrogeochemistry across the basin, based on conceptual water source signatures and dynamics. Informed by a 2019 post-monsoonal survey of 81 river bank-side sampling locations, the spatial distribution of a suite of selected physico-chemical and inorganic parameters, combined with segmented linear regression, reveals minor and major downstream hydrogeochemical transitions. We use this information to identify five major hydrogeochemical zones, characterized, in part, by the inputs of key tributaries, urban and agricultural areas, and estuarine inputs near the Bay of Bengal. Dominant trends are further explored by investigating geochemical relationships (e.g. Na:Cl, Ca:Na, Mg:Na, Sr:Ca and NO₃:Cl), and how water source signatures and dynamics are modified by key processes, to assess the relative importance of controls such as dilution, evaporation, water-rock interactions (including carbonate and silicate weathering) and anthropogenic inputs. Mixing/dilution between sources and water-rock interactions explain most regional trends in major ion chemistry, although localized controls plausibly linked to anthropogenic activities are also evident in some locations. Temporal and spatial representativeness of river bank-side sampling are considered by supplementary sampling across the river at selected locations and via comparison to historical records. Limitations of such large-scale longitudinal sampling programs are discussed, as well as approaches to address some of these inherent challenges. This approach brings new, systematic insight into the basin-wide controls on the dominant geochemistry of the River Ganga, and provides a framework for characterising dominant hydrogeochemical zones, processes and controls, with utility to be transferable to other large river systems.

Antibody conjugated magnetic nanoparticle based colorimetric assay for the detection and quantification of aflatoxin B1 in wheat grains

Aflatoxin B1 (AFB1) is a most potent carcinogenic secondary metabolite produced by Aspergillus flavus. As a food safety concern, development of a rapid, cost effective, sensitive and easy to use method for the detection of aflatoxin is of prime requirement. In this study, AFB1 was conjugated with bovine serum albumin (BSA), and AFB1-BSA conjugate was purified by HPLC. Purification was confirmed by UV-Vis spectroscopy, FTIR and MALDI-TOF mass spectrometry. The polyclonal antibody was raised against AFB1-BSA conjugate in rabbit and purified by protein A sepharose and BSA sepharose affinity columns. Iron oxide nanoparticles (MNPs) were synthesised by co-precipitation method and their surface was functionalised with (3-aminopropyl) triethoxysilane (APTES). Size of APTES conjugated MNPs was determined by electron microscopy, and characterised by several biophysical techniques. The purified anti-AFB1 antibody was conjugated with surface functionalised MNPs and the conjugation was confirmed by determining the sizes of free and antibody conjugated MNPs by field emission scanning electron microscope where increase of particle sizes from 10-20 to 40-50 nm was observed due to antibody conjugation. Anti-AFB1 antibody conjugated MNPs were used for capturing AFB1 from the aflatoxin spiked wheat grains with a recovery percentage of more than 80% and used effectively five times. The captured AFB1 was then quantified by a sensitive colorimetric assay where colourless AFB1 was first converted into coumaric acid by NaOH. Subsequently, coumaric acid reacted with 2,6-dibromoquinone-4-chloroimide (DBQC) to a green-coloured indophenol product which was quantified spectrophotometrically. AFB1 contamination as low as 2 μg/kg in wheat grains was detected by the developed technique suggesting its potential application for both qualitative and quantitative analysis of aflatoxins present in feed and food materials.

MicroRNA miR-29c regulates RAG1 expression and modulates V(D)J recombination during B cell development

Recombination activating genes (RAGs), consisting of RAG1 and RAG2, are stringently regulated lymphoid-specific genes, which initiate V(D)J recombination in developing lymphocytes. We report the regulation of RAG1 through a microRNA (miRNA), miR-29c, in a B cell stage-specific manner in mice and humans. Various lines of experimentation, including CRISPR-Cas9 genome editing, demonstrate the target specificity and direct interaction of miR-29c to RAG1. Modulation of miR-29c levels leads to change in V(D)J recombination efficiency in pre-B cells. The miR-29c expression is inversely proportional to RAG1 in a B cell developmental stage-specific manner, and miR-29c null mice exhibit a reduction in mature B cells. A negative correlation of miR-29c and RAG1 levels is also observed in leukemia patients, suggesting the potential use of miR-29c as a biomarker and a therapeutic target. Thus, our results reveal the role of miRNA in the regulation of RAG1 and its relevance in cancer.

Emerging organic contaminants in groundwater under a rapidly developing city (Patna) in northern India dominated by high concentrations of lifestyle chemicals

Aquatic pollution from emerging organic contaminants (EOCs) is of key environmental importance in India and globally, particularly due to concerns of antimicrobial resistance, ecotoxicity and drinking water supply vulnerability. Here, using a broad screening approach, we characterize the composition and distribution of EOCs in groundwater in the Gangetic Plain around Patna (Bihar), as an exemplar of a rapidly developing urban area in northern India. A total of 73 EOCs were detected in 51 samples, typically at ng.L^-1 to low μg.L^-1 concentrations, relating to medical and veterinary, agrochemical, industrial and lifestyle usage. Concentrations were often dominated by the lifestyle chemical and artificial sweetener sucralose. Seventeen identified EOCs are flagged as priority compounds by the European Commission, World Health Organisation and/or World Organisation for Animal Health: namely, herbicides diuron and atrazine; insecticides imidacloprid, thiamethoxam, clothianidin and acetamiprid; the surfactant perfluorooctane sulfonate (and related perfluorobutane sulfonate, perfluorohexane sulfonate, perfluorooctanoic acid and perfluoropentane sulfonate); and medical/veterinary compounds sulfamethoxazole, sulfanilamide, dapson, sulfathiazole, sulfamethazine and diclofenac. The spatial distribution of EOCs varies widely, with concentrations declining with depth, consistent with a strong dominant vertical flow control. Groundwater EOC concentrations in Patna were found to peak within ∼10 km distance from the River Ganges, indicating mainly urban inputs with some local pollution hotspots. A heterogeneous relationship between EOCs and population density likely reflects confounding factors including varying input types and controls (e.g. spatial, temporal), wastewater treatment infrastructure and groundwater abstraction. Strong seasonal agreement in EOC concentrations was observed. Co-existence of limited transformation products with associated parent compounds indicate active microbial degradation processes. This study characterizes key controls on the distribution of groundwater EOCs across the urban to rural transition near Patna, as a rapidly developing Indian city, and contributes to the wider understanding of the vulnerability of shallow groundwater to surface-derived contamination in similar environments.

Knowledge and Practices of Intensive Care Unit Nurses Related to Prevention of Ventilator Associated Pneumonia in Selected Intensive Care Units of a Tertiary Care Centre, India

Background:

Ventilator-Associated Pneumonia (VAP) is a recognized nosocomial infection and a leading cause of high morbidity and mortality. Intensive Care Unit (ICU) nurses are in the best position to put the known evidence-based strategies into practice to prevent VAP. The aim of the present study is to assess the knowledge and practices of ICU nurses related to prevention of VAP in selected ICUs of a tertiary care centre in India (2013–2014) and to find out the association between knowledge and practices.

Materials and Methods:

A descriptive survey was conducted in the different ICUs of a tertiary care hospital in India. Purposive sampling technique was used and 108 ICU staff nurses were enrolled during the period of data collection. The tool used for data collection was a self-developed valid and reliable knowledge-based questionnaire and an observational checklist. The descriptive (frequency and percentages) and inferential (Chi-square test) statistics was used.

Results

Out of the 108 nurses enrolled in the study, 82 (75.93%) had average, 24 (22.22%) had good and only 2 (1.85%) of the ICU nurses had poor knowledge. Assessment of the practices revealed that 68 (94.44%) nurses had average and only 4 (5.55%) nurses had good practice. There was no association between the knowledge and practices of ICU nurses related to prevention of VAP. (χ² = 0.14, p = 0.710).

Conclusions:

Although the nurses were having good to average knowledge scores, their practices were not associated with knowledge scores. There is a need to find out the ways that would help the nurses to adhere to good practices.

The peripheral immune response in hyperglycemic stroke

OBJECTIVES

Hyperglycemia is common in acute ischemic stroke patients and is associated with poor clinical outcome. However, aggressive reduction of post-stroke hyperglycemia did not improve clinical outcome, suggesting that other mechanisms are playing a detrimental role in hyperglycemic stroke. We hypothesize that the acute post-stroke immune response is altered in the hyperglycemic state leading to higher mortality and morbidity. The objective of this study was to characterize temporal changes in circulating immune cells after stroke and their association with clinical outcomes in hyperglycemic compared to euglycemic patients.

PATIENTS AND METHODS

This retrospective study included 97 (58 % euglycemic, 42 % hyperglycemic) patients presenting within 12 h of symptom onset of stroke. Blood neutrophil, monocyte and lymphocyte concentrations were measured sequentially for 96 h post stroke. Primary clinical outcome was the difference in the NIH stroke scale at admission compared to discharge. Secondary outcome measures included discharge disposition and the modified Rankin Scale (mRS) at 90 days.

RESULTS

Circulating neutrophils were significantly higher in hyperglycemic than in euglycemic patients within the first 48 h post stroke, while lymphocyte counts trended to be lower. Hyperglycemic patients had higher mortality rates, less favorable discharge disposition and worse neurological function at 90 days. In both groups, the neutrophil to lymphocytes ratio ((NLR) remained strongly associated with neurological function at discharge within the first 24 h (p < 0.001), and remained significant in hyperglycemic patients up to 48 h (p < 0.001). Multivariate regression analysis showed no confounding by other factors and a significant correlation with differences in NIHSS score (CI; - 9.287 to -1.46, p = 0.0077**) and NLR (CL; 0.6058-6.901, p = 0.0203*) in hyperglycemic patients.

CONCLUSIONS

Our data suggests that circulating immune cells play an important role in mediating poor clinical outcome in hyperglycemic patients following stroke. The NLR is a strong predictor of neurological outcomes in hyperglycemic patients. Thus, the modulation of immune cells may be a viable therapeutic approach to improve outcomes for this high risk group.

Autocyclized and oxidized forms of SCR7 induce cancer cell death by inhibiting nonhomologous DNA end joining in a Ligase IV dependent manner

Nonhomologous DNA end joining (NHEJ) is the major DNA double-strand break (DSB) repair pathway in mammals. Previously, we have described a small molecule inhibitor, SCR7, which can inhibit NHEJ in a Ligase IV-dependent manner. Administration of SCR7 within the cells resulted in the accumulation of DNA breaks, cell death, and inhibition of tumor growth in mice. In the present study, we report that parental SCR7, which is unstable, can be autocyclized into a stable form. Both parental SCR7 and cyclized SCR7 possess the same molecular weight (334.09) and molecular formula (C₁₈ H₁₄ N₄ OS), whereas its oxidized form, SCR7-pyrazine, possesses a different molecular formula (C₁₈ H₁₂ N₄ OS), molecular weight (332.07), and structure. While cyclized form of SCR7 showed robust inhibition of NHEJ in vitro, both forms exhibited efficient cytotoxicity. Cyclized and oxidized forms of SCR7 inhibited DNA end joining catalyzed by Ligase IV, whereas their impact was minimal on Ligase III, Ligase I, and T4 DNA Ligase-mediated joining. Importantly, both forms inhibited V(D)J recombination, although the effect was more pronounced for SCR7-cyclized. Both forms blocked NHEJ in a Ligase IV-dependent manner leading to the accumulation of DSBs within the cells. Although cytotoxicity due to SCR7-cyclized was Ligase IV specific, the pyrazine form exhibited nonspecific cytotoxicity at higher concentrations in Ligase IV-null cells. Finally, we demonstrate that both forms can potentiate the effect of radiation. Thus, we report that cyclized and oxidized forms of SCR7 can inhibit NHEJ in a Ligase IV-dependent manner, although SCR7-pyrazine is less specific to Ligase IV inside the cell.

Association of ITGAM, TNFSF4, TNFAIP3 and STAT4 gene polymorphisms with risk of systemic lupus erythematosus in a North Indian population

Several susceptibility genes have been associated with systemic lupus erythematosus (SLE) across different populations worldwide. However, data on association between genetic polymorphisms and SLE from Indian population is scarce. We aimed to replicate the association of single nucleotide polymorphisms (SNPs) in ITGAM, TNFSF4, TNFAIP3 and STAT4 genes with susceptibility to SLE in a North Indian population. Three hundred and ninety-four SLE patients and 583 unrelated healthy controls of the same ethnic background were enrolled. All samples were genotyped for SNPs in ITGAM (rs1143679), TNFSF4 (rs2205960), TNFAIP3 (rs5029939) and STAT4 (rs7574865) using TaqMan genotyping assay. At allele level, significant association with susceptibility to SLE was detected with polymorphisms in ITGAM (A vs. G, odds ratio (OR) = 1.73, 95% confidence interval (CI) = 1.30–2.30, p < 0.001), TNFSF4 (T vs. G, OR = 1.33, 95% CI = 1.08–1.64, p < 0.01), TNFAIP3 (G vs. C, OR = 1.91, 95% CI = 1.27–2.85, p < 0.01) and STAT4 (T vs. G, OR = 1.38, 95% CI = 1.13–1.69, p < 0.01). All four SNPs were associated with SLE under a dominant model with an OR of 1.47 (95% CI = 1.07–2.04, p < 0.05) for ITGAM, 1.30 (95% CI = 1.01–1.69, p < 0.05) for TNFSF4, 1.90 (95% CI = 1.25–2.90, p < 0.01) for TNFAIP3 and 1.38 (95% CI = 1.06–1.78, p < 0.05) for STAT4. Under a recessive model, significant association was found with ITGAM (OR = 4.87, 95% CI = 2.17–10.91, p < 0.001), TNFSF4 (OR = 1.84, 95% CI = 1.13–3.00, p < 0.05) and STAT4 (OR = 1.82, 95% CI = 1.19–2.77, p < 0.01). In conclusion, single nucleotide polymorphisms in ITGAM, TNFSF4, TNFAIP3 and STAT4 genes are associated with susceptibility to SLE in a North Indian population.

Stochasticity enables BCR-independent germinal center initiation and antibody affinity maturation

Two immunoglobulin (Ig) diversification mechanisms collaborate to provide protective humoral immunity. Combinatorial assembly of IgH and IgL V region exons from gene segments generates preimmune Ig repertoires, expressed as B cell receptors (BCRs). Secondary diversification occurs when Ig V regions undergo somatic hypermutation (SHM) and affinity-based selection toward antigen in activated germinal center (GC) B cells. Secondary diversification is thought to only ripen the antigen-binding affinity of Igs that already exist (i.e., cognate Igs) because of chance generation during preimmune Ig diversification. However, whether stochastic activation of noncognate B cells can generate new affinity to antigen in GCs is unclear. Using a mouse model whose knock-in BCR does not functionally engage with immunizing antigen, we found that chronic immunization induced antigen-specific serological responses with diverse SHM-mediated antibody affinity maturation pathways and divergent epitope targeting. Thus, intrinsic GC B cell flexibility allows for somatic, noncognate B cell evolution, permitting de novo antigen recognition and subsequent antibody affinity maturation without initial preimmune BCR engagement.

HIV integrase inhibitor, Elvitegravir, impairs RAG functions and inhibits V(D)J recombination

Integrase inhibitors are a class of antiretroviral drugs used for the treatment of AIDS that target HIV integrase, an enzyme responsible for integration of viral cDNA into host genome. RAG1, a critical enzyme involved in V(D)J recombination exhibits structural similarity to HIV integrase. We find that two integrase inhibitors, Raltegravir and Elvitegravir, interfered with the physiological functions of RAGs such as binding, cleavage and hairpin formation at the recombination signal sequence (RSS), though the effect of Raltegravir was limited. Circular dichroism studies demonstrated a distinct change in the secondary structure of RAG1 central domain (RAG1 shares DDE motif amino acids with integrases), and when incubated with Elvitegravir, an equilibrium dissociation constant (K_d) of 32.53±2.9 μM was determined by Biolayer interferometry, leading to inhibition of its binding to DNA. Besides, using extrachromosomal assays, we show that Elvitegravir inhibited both coding and signal joint formation in pre-B cells. Importantly, treatment with Elvitegravir resulted in significant reduction of mature B lymphocytes in 70% of mice studied. Thus, our study suggests a potential risk associated with the use of Elvitegravir as an antiretroviral drug, considering the evolutionary and structural similarities between HIV integrase and RAGs.

Effectiveness and tolerability of simeprevir and sofosbuvir in nontransplant and post-liver transplant patients with hepatitis C genotype 1

BACKGROUND

Hepatitis C virus genotype 1a (HCV-1a), prior treatment, cirrhosis and post-transplant status are historically associated with poor treatment responses. The new oral direct-acting agents appear to be effective and safe in these patients.

AIMS

To evaluate the effectiveness and tolerability of simeprevir and sofosbuvir in a diverse real-life cohort of patients, including difficult-to-treat patients.

METHODS

We conducted a retrospective cohort study in 198 consecutive patients with hepatitis C genotype 1 (148 nontransplant, 50 post transplant), who were treated with simeprevir and sofosbuvir for 12 weeks between December 2013 and December 2014. Primary outcome was sustained virological response with undetectable HCV RNA 12 weeks after completion of therapy (SVR12). Risk factors evaluated for lack of SVR12 included HCV 1a (vs. 1b), prior treatment (vs. none), and cirrhosis (vs. no cirrhosis).

RESULTS

SVR12 rates were similar in non- and post-transplant settings, 82% and 88%, respectively. There were no significant differences in adverse events in patients regardless of cirrhosis or transplant status. On multivariate analysis also inclusive of gender and liver transplant status, negative predictors of SVR12 were having at least 2 or 3 risk factors (OR 0.30, 95% CI 0.10-0.87, P = 0.027 or 0.29, 95% CI 0.09-0.85, P = 0.025, respectively).

CONCLUSION

Simeprevir and sofosbuvir combination is a safe and effective regimen for the treatment of non- and post-transplant patients with traditional risk factors for poor treatment response, unless more than 2 difficult-to-treat risk factors are present.

Detection of rifampicin resistance in tuberculosis by molecular methods: A report from Eastern Uttar Pradesh, India

Diagnosis of drug resistance tuberculosis (TB) by the gold standard method is labour intensive and time consuming. Hence, there is an urgent need for introduction of rapid diagnostic techniques. Line probe assay (LPA) and cartridge-based nucleic acid amplification test (CBNAAT) have been introduced in India under Revised National Tuberculosis Control Program. Spot and morning sputum samples of previously treated patients by anti-TB drugs were subjected to LPA or CBNAAT. Total 682/1253 (54.4%) were diagnosed as rifampicin-resistant. The patients could be diagnosed early by molecular methods and put on second line treatment.

Homology and enzymatic requirements of microhomology-dependent alternative end joining

Nonhomologous DNA end joining (NHEJ) is one of the major double-strand break (DSB) repair pathways in higher eukaryotes. Recently, it has been shown that alternative NHEJ (A-NHEJ) occurs in the absence of classical NHEJ and is implicated in chromosomal translocations leading to cancer. In the present study, we have developed a novel biochemical assay system utilizing DSBs flanked by varying lengths of microhomology to study microhomology-mediated alternative end joining (MMEJ). We show that MMEJ can operate in normal cells, when microhomology is present, irrespective of occurrence of robust classical NHEJ. Length of the microhomology determines the efficiency of MMEJ, 5 nt being obligatory. Using this biochemical approach, we show that products obtained are due to MMEJ, which is dependent on MRE11, NBS1, LIGASE III, XRCC1, FEN1 and PARP1. Thus, we define the enzymatic machinery and microhomology requirements of alternative NHEJ using a well-defined biochemical system.

Sofosbuvir and simeprevir combination therapy in the setting of liver transplantation and hemodialysis

We report safety, tolerability, and 12-week sustained virologic response with half-standard dose sofosbuvir and standard-dose simeprevir combination therapy in a hepatitis C virus genotype 1a-infected liver transplant recipient on hemodialysis - uncharted territory for sofosbuvir-based therapy. The patient was a non-responder to prior treatment with pegylated interferon plus ribavirin. Sofosbuvir efficacy was maintained despite pill-splitting and administration of half-standard dose, 200 mg per day. No drug-drug interactions were noted with tacrolimus-based immunosuppression. Laboratory tests remained stable or improved during therapy. Our observation, if reproduced in a larger study, may lead to significant improvement in clinical outcomes and cost savings in this patient population.

Structure-specific nuclease activity of RAGs is modulated by sequence, length and phase position of flanking double-stranded DNA

RAGs (recombination activating genes) are responsible for the generation of antigen receptor diversity through the process of combinatorial joining of different V (variable), D (diversity) and J (joining) gene segments. In addition to its physiological property, wherein RAG functions as a sequence-specific nuclease, it can also act as a structure-specific nuclease leading to genomic instability and cancer. In the present study, we investigate the factors that regulate RAG cleavage on non-B DNA structures. We find that RAG binding and cleavage on heteroduplex DNA is dependent on the length of the double-stranded flanking region. Besides, the immediate flanking double-stranded region regulates RAG activity in a sequence-dependent manner. Interestingly, the cleavage efficiency of RAGs at the heteroduplex region is influenced by the phasing of DNA. Thus, our results suggest that sequence, length and phase positions of the DNA can affect the efficiency of RAG cleavage when it acts as a structure-specific nuclease. These findings provide novel insights on the regulation of the pathological functions of RAGs.

Renal angioplasty for atherosclerotic renal artery stenosis: Cardiologist's perspective

Atherosclerotic renal artery stenosis (ARAS) is frequently associated with concomitant coronary and peripheral arterial disease with a significant impact on cardiovascular morbidity and mortality. Renal angioplasty of ARAS is more challenging because of increased incidence of technical failures, complications, and restenosis; while there is barely perceptible control of hypertension and only marginal improvement in renal function. This is because most of the patient population in recent randomized trials had unmanifested or clinically silent renovascular disease. Manifestations of RAS should be looked for and incorporated in the management plan particularly before deciding for revascularization. In the absence of clinical manifestation like renovascular hypertension, ischemic nephropathy, left ventricular failure, or unstable coronary syndromes; mere presence of RAS is analogous to presence of concomitant peripheral arterial disease which increases risk of adverse coronary events. Dormant-RAS in the absence of any manifestations can be managed with masterly inactivity. Chronological sequence of events and clinical condition of the patient help in decision making by identifying progressive renovascular disease. Selecting patients for renal artery stenting who actually will benefit from revascularization shall also decrease the unnecessary complications inherent with any interventional procedure. The present review is an attempt to analyze the current view on the diagnostic and management issues more specifically about the need and rationale behind angioplasty.

Keratometric astigmatism evaluation after trabeculectomy

INTRODUCTION

Post-operative astigmatism is one of the most important causes for diminution of vision after trabeculectomy.

OBJECTIVE

To evaluate the induced corneal astigmatism following trabeculectomy with the use of 8-0 silk suture.

MATERIALS AND METHODS

A prospective interventional study was done including 100 consecutive eyes of 84 patients who underwent trabeculectomy with the use of 8-0 silk suture. The postoperative induced astigmatism on the 1st post-operative day, 3rd week and after 6 months was determined.

STATISTICS

Vector analysis was performed on the data using a computerized method for calculating the surgically induced astigmatism (SIA) for each eye at every time point postoperatively. In order to analyze group changes, we also performed vector decomposition which gave us a mathematical expression of the changes in astigmatism "with the rule" (WTR) or "against the rule" (ATR).

RESULTS

The mean age of all the patients was 53.31 11.39 years. The mean 1st post-operative surgically induced astigmatism (SIA) was 2.73 D ( 99 degree ) which reduced to 0.41 D ( 58 degree) at the 3rd week and 0.43 ( 21 degree) at 6 months. The mean WTR astigmatism was 4.46 D and ART astigmatism was 1.42 D on the 1st post-operative day which was significantly high ( p less than 0.0001). At the 3rd week and 6 months WTR astigmatism ( 1.40 D and 1.08D ) and ATR astigmatism (1.27 D and 1.10 D) showed no significant changes (p=0.69,0.97 respectively.

CONCLUSION

Trabeculectomy with the use of 8/0 silk sutures showed significantly high 1st post-operative day SIA which nevertheless perished fast to a minimum amount at just 3 weeks.

Novel mutations in typical and atypical genetic loci through exome sequencing in autosomal recessive cerebellar ataxia families

Nearly a thousand mutations mapping to 60 different loci have been identified in cerebellar ataxias. However, almost 50% of the cases remain genetically uncharacterized and there is a difference in prevalence as well as in the phenotypic spectrum of ataxia among various geographical regions. This poses a challenge for setting up a genetic panel for screening ataxia. In our ataxic cohort of 1014 families, 61% are genetically uncharacterized (UC). We investigated the potential of whole exome sequencing in conjunction with homozygosity mapping (HM) to delineate the genetic defects in three uncharacterized families with recessive inheritance each manifesting some unusual phenotype: (i) infantile onset ataxia with hearing loss (IOAH), (ii) Juvenile onset cerebellar ataxia with seizures (JCS) and (iii) Friedreich ataxia-like (FA-like). We identified a novel missense mutation in c10orf2 in the family with IOAH, compound heterozygous mutations in CLN6 in the family with JCS and a homozygous frame-shift mutation in SACS in the FA-like patient. Phenotypes observed in our families were concordant with reported phenotypes of known mutations in the same genes thus obviating the need for functional validation. Our study revealed novel variations in three genes, c10orf2, CLN6, and SACS, that have so far not been reported in India. This study also demonstrates the utility of whole exome screening in clinics for early diagnosis.

Clinical predictors of influenza A(H1N1) in Kanpur, India

Influenza A (H1N1) commonly known as swine flu, has covered a large part of the globe rapidly since the outbreak started in Mexico on 18th March, 2009. Given the rapid worldwide spread of the virus, it is important to identify the symptoms that require screening for influenza A(H1N1). Therefore, this study was planned to determine the clinical predictors of influenza A(H1N1) in the population of Kanpur city. Study sample comprised all cases with flu-like symptoms suspected of having influenza A(H1N1) whose nasopharyngeal samples had been sent for laboratory examination. Of the 119 samples sent to the laboratory, 34 were found to be positive for influenza A(H1N1). Best predictors found were fever with shortness of breath (positive predictive value=87.5%) followed by fever with cough without other cold like features (positive predictive value=68.6%). None of the clinical signs had all the attributes of a good predictor of influenza A(H1N1). Fever with cough was the most sensitive (70.6%) and fever with shortness of breath was the most specific indicator (98.8%). Therefore, it was concluded that symptoms like fever with cough without other cold like features and fever with shortness of breath should not be ignored and require expert medical attention for screening of influenza A(H1N1).

Antibacterial Activity of Ethanol Extract of Andrographis paniculata

In the present study the ethanol extract of the aerial part of Andrographis paniculata was prepared and evaluated for antimicrobial activity against eleven bacterial strains by determining minimum inhibitory concentration and zone of inhibition. Minimum inhibitory concentration values were compared with control and zone of inhibition values were compared with standard ciprofloxacin in concentration 100 and 200 μg/ml. The results revealed that, the ethanol extract is potent in inhibiting bacterial growth of both Gram-negative and Gram positive bacteria.

Growth, yield and tuber quality of Solanum tuberosum L. under supplemental ultraviolet-B radiation at different NPK levels

In many areas, decreases in the stratospheric ozone layer have resulted in an increase in ultraviolet-B (UV-B, 280-315 nm) radiation reaching the Earth's surface. The present study was conducted to evaluate the interactive effects of supplemental UV-B (sUV-B) and mineral nutrients on a tuber crop, potato (Solanum tuberosum L. var Kufri Badshah), under natural field conditions in a dry tropical environment. The nutrient treatments were the recommended dose of NPK (F(o)), 1.5 times the recommended dose of NPK (F(1)), 1.5 times the recommended dose of N (F(2)) and 1.5 times the recommended dose of K (F(3)). The response of potato plants to sUV-B varied with nutrient treatment and concentration. sUV-B adversely affected growth, yield and quality of tubers, causing an increase in reducing sugars in the tubers and thus reducing the economic value. Growth and fresh weight of tubers was maximal with sUV-B at 1.5 times recommended NPK, but the dry weight of tubers were highest with the recommended NPK dose. Reducing sugar content was lower in potato plants treated with sUV-B and the recommended NPK than with sUV-B and 1.5 times the recommended NPK. This study thus clearly shows that growing potato with 1.5 times the recommended NPK or 1.5 times the recommended dose of N/K does not alleviate the sUV-B induced changes in yield and quality of tubers compared to the recommended NPK dose.