Development of an experimental and computational platform for enhanced characterization of modified peptides and proteins in environmental proteomics

Over the last decade, mass spectrometry based proteomics has been established as the front-runner in systems-level protein expression studies. However, with the field progressing into research of more and more complex samples, novel challenges have been raised with respect to efficient protein extraction and computational matching. In this dissertation, various aspects in the proteomics workflow, including experimental and computational approaches, have been developed, optimized and systematically evaluated. In this work, some of the critical factors with respect to proteomics sample preparation, like available biomass, detergent removal methods, and intact protein fractionation to achieve deeper proteome measurements were evaluated. The presented work will help the broader scientific community to carefully design proteomics experiments especially in biomass limited samples. A second major area of focus in this dissertation is comprehensive characterization of post-translational modifications (PTMs) in different biological systems. PTMs are critical for functioning of both the prokaryotic and eukaryotic species and this dissertation will highlight some of the experimental strategies to explore the diversity of PTMs in microbial isolates via application of alternate protease and multiple fragmentation schemes. The PTM discovery approach will be further extended into a complex eukaryotic model trees species Populus trichocarpa using recently developed sequence tagging methods to carryout broad scale PTM search and a complete blind PTM search. Although the work presented in this dissertation mainly revolves around prokaryotic and eukaryotic species involved in environmental proteomics, the general considerations outlined in this work can be extended to every proteomics pipeline. Thus this dissertation will benefit the scientific community in carefully designing experiments before embarking on any research project involving mass spectrometry

Clinical profile of scrub typhus patients in a tertiary care centre in Himachal Pradesh, India

Background: Scrub typhus a zoonotic disease caused by gram negative bacteria O. tsutsugamushi, is endemic in Himachal Pradesh. This illness occurs mainly in monsoon and post monsoon season. study design of  this study was conducted in a tertiary care centre in Himachal Pradesh between July 2015 and June 2016. All the indoor patients with age above 18 years with a diagnosis of scrub typhus were included in this study.Results: Out of total 180 patients, 130 were female patients. Most patients were in the age group 21-30 (23.3%). All the patients presented with history of fever, but 54 patients presented with high grade fever. Other Most common symptom was chills and rigours (81%), followed by vomiting and headache each 32%, cough 31%. On examination 21% patients had eschar,14% patients had lymphadenopathy. Most number of patients presented in the month of September (51.6%), followed by August (33.3%).Conclusion: Scrub typhus being an important differential of acute undifferentiated fever in this region, should not be missed by primary care physicians, as once multi organ dysfunction sets in, mortality rate starts rising. So, there is a high need of sensitization of doctors and people about this illness so that early diagnosis and early treatment can be ensured

Cardiac disease in pregnancy: still an arduous conundrum for the obstetrician

Cardiac diseases, complicating about 1 percent of all pregnancies, account for significant maternal morbidity and mortality by being the leading cause of obstetrical intensive care unit admissions and of indirect maternal deaths. Of late, there has been observed a changing pattern in heart disease, the etiology having shifted from primarily rheumatic to predominantly congenital (75–82%), with shunt lesions preponderating (20–65%). Counseling and management of women of childbearing age with suspected cardiac disease ought to commence prior to conception; they should be managed by interdisciplinary teams; high risk patients must be treated in specialized facilities, and diagnostic procedures and interventions should be executed by mavens with profound expertise in the cardiovascular diseases and proficiency in treating pregnant women. This article provides a comprehensive review on management of cardiac disease in pregnancy to assist obstetricians in tackling this mystifying medical situation effortlessly, attaining a favorable feto-maternal outcome

Pattern of hepatitis B and C infection among gravid women and their newborns in a tertiary care infirmary in India

Background: The objective is to determine the prevalence of the hepatitis B and C virus among pregnant women, to assess impact of maternal hepatitis B virus (HBV) or hepatitis C virus (HCV) carrier status on pregnancy outcomes and to gauge the risk factors associated with them. Antenatal clinic attenders and women undergoing termination of pregnancy over three years.Methods: The study was conducted in Gian Sagar Medical College & Hospital, Patiala, Punjab, India. Hepatitis B antigen and Hepatitis C virus antibody testing of sera from specimens sent to the hospital laboratory for routine serological testing. The results were then linked to risk information, obstetric complications and pregnancy outcome.Results: Overall HBsAg and anti-hepatitis C antibody prevalence was 1.2% (33/2031). Increased risk of transmission was associated with sexually transmitted diseases and previous surgical procedures. High rates of preterm labor pains, CD (27.27%), and non-reassuring fetal heart rate patterns and meconium stained liquor were found in the seropositive patients.Conclusions: Maternal hepatitis B and C carrier status is an eminent risk factor for adverse pregnancy outcome.

Frequency of peripheral neuropathy in pre diabetics in sub Himalayan region: a cross sectional observational study

Background: Peripheral neuropathy in pre diabetics has been studied in various studies till now. Many are in support and many against. No data was available in any study using all three criteria i.e. impaired fasting glucose, impaired glucose tolerance and HbA1C. Aim was to study the frequency of peripheral neuropathy in pre diabetics in a tertiary health care centre in sub Himalayan region.Methods: A 50 patients of prediabetes were enrolled for this study; preformed proforma was used to collect the information, data on examination and investigations. Then these patients were subjected to nerve conduction studies.Results: Out of total 50 pre diabetic patients 9(18%) were diagnosed having peripheral neuropathy. Maximum number of pre diabetic patients were (26) in the age group 46-55 years with mean age of 44.49 years ±7.01 (S.D.). 28 (56%) were males with a female to male ratio of 1:1.27. 20% patients had complaint of polyuria, 12% presented with polydipsia, 14% of total pre diabetic patients had paresthesia on history. 6% patients had impaired vibration and position sense on clinical examination. Out of total 9 patients having evidence of Peripheral Neuropathy 6 (66.66%) were meeting all three criteria for Prediabetes while 8 (88.88%) had IFG, 7 patients had IGT. 42% of the patients were fulfilling the criteria of metabolic syndrome. 28 had raised TGs and out of them 5 (17.8%) had peripheral neuropathy. Out of 24 obese patients, 4 (16.6%) had peripheral neuropathy. Out of 9 patients with peripheral neuropathy 66.66% patients were considered to be suffering with peripheral neuropathy on the basis of sensory symptoms and 33.33% were considered on the basis of impaired vibration and position sense on examination, one patient diagnosed on the basis of nerve conduction studies. 38% were in high risk group of developing T2DM in future as per Indian diabetes risk score. Mean compound motor action potential (CMAP) and nerve conduction velocity (NCV) were less in patients with peripheral neuropathy in comparison to patients without peripheral neuropathy.Conclusions: Peripheral neuropathy can occur in prediabetes though it is difficult to confirm it. Most common is small fiber neuropathy which can be diagnosed on the basis of history and examination. But by diagnosing it early in the course of prediabetes, morbidity and mortality secondary to neuropathy can be prevented

Testosterone levels in men with type 2 diabetes mellitus

Background: To study testosterone levels in men with type 2 diabetes mellitus in age group of 30-50 years.Methods: In this cross sectional study of 193 type 2 diabetes men aged between 30-50 years, total and free testosterone levels were calculated along with other relevant clinical variables like hypertension, BMI, dyslipidemia, peripheral neuropathy, retinopathy.Results: The study group had study out of 193 patients 34.7% have low total testosterone levels, 29.53% have low free testosterone levels and 23.3% have both low and free testosterone levels. Maximum number of patients with low total testosterone levels were in the age group between 46-50 years (41.0%) and with low free total testosterone levels were in the age group between 36-40 years (41.8%).Conclusions: Type 2 diabetes mellitus is associated with low levels of total and free testosterone. Obesity and dyslipidemia are also associated with low testosterone levels

Impacts of chemical gradients on microbial community structure

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower’. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems

Role of aromatase inhibitors in managing hypogonadism in adult males related to obesity and aging: A systematic review and meta-analysis

No meta-analysis is available which has analysed the role of aromatase inhibitors (AIs) in hypogonadism in adult males related to obesity and aging. This meta-analysis intended to address this knowledge gap. Electronic databases were searched for studies involving adult males with hypogonadism. The primary outcomes were changes in total testosterone (TT). Secondary outcomes were alterations in oestradiol, luteinizing hormone (LH), and side-effect profile. From initially screened 177 articles, data from three randomised controlled trials(RCTs) (118 patients) and three uncontrolled studies(52 patients) were analysed. AIs were associated with significantly greater improvement in TT after three months [mean difference (MD) 7.08 nmol/L (95% Confidence Interval (CI): 5.92–8.24); P < 0.01; I2 = 0%], six months [MD 6.61 nmol/L (95% CI: 5.30–7.93); P < 0.01] and 12 months [MD 5.20 nmol/L (95% CI: 3.78–6.62); P < 0.01] therapy. AIs were associated with greater reduction in oestradiol after three months [MD -3.07 pmol/L (95% CI: -5.27– -0.87); P < 0.01; I2 = 40%], six months [MD -5.39 pmol/L (95% CI: -7.18– -3.60); P < 0.01] and 12 months [MD -8.3 pmol/L (95% CI: -15.97– -0.63); P = 0.03] therapy. AIs were associated with greater increase in LH after three months [MD 1.79 IU/L (95% CI: 0.77–2.81); P < 0.01; I2 = 0%], six months [MD 2.20 IU/L (95% CI: 0.29 – 4.11); P = 0.02] and 12 months [MD 1.70 IU/L (95% CI: 0.28–3.12); P = 0.02] therapy. Occurrence of treatment-emergent adverse events[Risk ratio (RR) 1.48 (95% CI: 0.47–4.66); P = 0.45; I2 = 0%] and severe adverse events[RR 2.48 (95% CI: 0.42–14.66); P = 0.32; I2 = 0%] were similar among AIs and controls. Following six-month treatment, AIs were associated with significantly lower bone mineral density (BMD) at lumbar-spine [MD -0.04 gm/cm2 (95% CI: -0.08– -0.01); P = 0.03], but not total hip [MD 0.01 gm/cm2 (95% CI: -0.02–0.04); P = 0.55] and femoral neck [MD 0.02 gm/cm2 (95% CI: -0.01–0.05); P = 0.12] compared to controls. This meta-analysis highlights the good efficacy of AIs in improving TT over 3–12 months of use. Adverse impact on spine bone density remains a concern in obese ageing males and warrants further evaluation

Pattern of hepatitis B and C infection among gravid women and their newborns in a tertiary care infirmary in India

Background: The objective is to determine the prevalence of the hepatitis B and C virus among pregnant women, to assess impact of maternal hepatitis B virus (HBV) or hepatitis C virus (HCV) carrier status on pregnancy outcomes and to gauge the risk factors associated with them. Antenatal clinic attenders and women undergoing termination of pregnancy over three years.Methods: The study was conducted in Gian Sagar Medical College &amp; Hospital, Patiala, Punjab, India. Hepatitis B antigen and Hepatitis C virus antibody testing of sera from specimens sent to the hospital laboratory for routine serological testing. The results were then linked to risk information, obstetric complications and pregnancy outcome.Results: Overall HBsAg and anti-hepatitis C antibody prevalence was 1.2% (33/2031). Increased risk of transmission was associated with sexually transmitted diseases and previous surgical procedures. High rates of preterm labor pains, CD (27.27%), and non-reassuring fetal heart rate patterns and meconium stained liquor were found in the seropositive patients.Conclusions: Maternal hepatitis B and C carrier status is an eminent risk factor for adverse pregnancy outcome.