Identification of group specific motifs in Beta-lactamase family of proteins

<p>Abstract</p> <p>Background</p> <p>Beta-lactamases are one of the most serious threats to public health. In order to combat this threat we need to study the molecular and functional diversity of these enzymes and identify signatures specific to these enzymes. These signatures will enable us to develop inhibitors and diagnostic probes specific to lactamases. The existing classification of beta-lactamases was developed nearly 30 years ago when few lactamases were available. DLact database contain more than 2000 beta-lactamase, which can be used to study the molecular diversity and to identify signatures specific to this family.</p> <p>Methods</p> <p>A set of 2020 beta-lactamase proteins available in the DLact database <url>http://59.160.102.202/DLact</url> were classified using graph-based clustering of Best Bi-Directional Hits. Non-redundant (> 90 percent identical) protein sequences from each group were aligned using T-Coffee and annotated using information available in literature. Motifs specific to each group were predicted using PRATT program.</p> <p>Results</p> <p>The graph-based classification of beta-lactamase proteins resulted in the formation of six groups (Four major groups containing 191, 726, 774 and 73 proteins while two minor groups containing 50 and 8 proteins). Based on the information available in literature, we found that each of the four major groups correspond to the four classes proposed by Ambler. The two minor groups were novel and do not contain molecular signatures of beta-lactamase proteins reported in literature. The group-specific motifs showed high sensitivity (> 70%) and very high specificity (> 90%). The motifs from three groups (corresponding to class A, C and D) had a high level of conservation at DNA as well as protein level whereas the motifs from the fourth group (corresponding to class B) showed conservation at only protein level.</p> <p>Conclusion</p> <p>The graph-based classification of beta-lactamase proteins corresponds with the classification proposed by Ambler, thus there is no need for formulating a new classification. However, further characterization of two small groups may require updating the existing classification scheme. Better sensitivity and specificity of group-specific motifs identified in this study, as compared to PROSITE motifs, and their proximity to the active site indicates that these motifs represents group-specific signature of beta-lactamases and can be further developed into diagnostics and therapeutics.</p

Histopathological alterations in testicular tissue of male rats exposed to arsenic

The present study was designed to investigate the adverse effect of arsenic on testicular tissue of Swiss albino male rats. Sodium arsenite was administered to adult male rats by gavage at the doses 1, 2 and 3 mg/kg body weight for 30 days. After the treatment, the testis were processed for histopathological observations. Sodium arsenite caused remarkable reduction in testicular weight (P&lt;0.05), while the body weight of experimental animals were reduced but not significantly (P&lt;0.05). Histological evaluation revealed dose-dependent, gradual destruction in histoarchitecture of testicular tissue. Sodium arsenite exposure caused complete arrest of spermatogenesis with disfigured seminiferous tubules in the testes .The lumens of the tubules were devoid of spermatids and were in places filled with cellular debris. The germinal epithelium was distorted. At places interstitial odema was also evident. Sertoli and Leydig cells were damaged. Along with structural alterations, fertility rate in experimental animals was significantly decreased at higher doses i.e. 2 and 3 mg/kg, as 100% infertility was observed. After withdrawal of the treatment over a period of 30 days, recovery was observed in low dose groups as few female rats became pregnant. The study concluded that exposure of arsenic causes testicular toxicity in male albino rat

Smart Beta Investing: An Alternative Investment Paradigm in Emerging Indian Equity Market

This paper fundamentally looks at the novel concept of Smart Beta investing in constructing a more efficient and well-diversified alternative investment. Smart beta has been a popular investment philosophy, although emerging countries have been slower to adopt and execute it. In this way, the study investigates the existence, performance, and robustness of smart beta strategies in a divergent financial market. Moreover, it is an initial attempt to integrate the framework of stock selection and stock weighting to construct and test smart beta strategies against the traditional Indian market benchmark (S&amp;P BSE 500). The findings show that smart beta investing results in a better risk-return profile on an absolute and risk-adjusted basis. Furthermore, the results demonstrate the consistency and robustness of smart beta strategies in different market conditions and display their outperformance even in bearish market conditions

Survival, attachment and internalization of Salmonella agona and Salmonella gaminara on orange surfaces

Salmonella outbreaks associated with orange juices have been reported in the past. Though there have been studies on the internalization of Salmonella into oranges there is inadequate information on the ability of this pathogen to survive on orange surfaces, become internalized, and survive the low pH internal conditions. The objective of this work was to study the survival of Salmonella gaminara and Salmonella agona on oranges obtained from the field and retail outlets and investigate their attachment and internalization potential. These studies showed that oranges obtained from both the field and retail outlets harbored relatively high concentrations of aerobic heterotrophic bacterial populations. There were significant differences in the survival of Salmonella agona and Salmonella gaminara at 4??C, room temperature (25??C) and 37??C. Survival was highest at 37??C and lowest at 4??C for both Salmonella gaminara and Salmonella agona. Salmonella agona and Salmonella gaminara showed significant differences in recovery when the cells were treated with pH 4.0, 7.0 and 9.5 buffers. The internalization studies suggest that a negative temperature differential favors the internalization of Salmonella cells into the fruit. Significant differences in the internalization of Salmonella into field and market oranges were observed with more internalization in the field oranges as compared to the market oranges. These results suggest that to prevent Salmonella contamination of orange juices adequate pre-harvest protection against pathogen contamination and post-harvest cleaning and disinfection strategies need to be employed

A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group

BACKGROUND: Dictyostelia are a well-studied group of organisms with colonial multicellularity, which are members of the mostly unicellular Amoebozoa. A phylogeny based on SSU rDNA data subdivided all Dictyostelia into four major groups, but left the position of the root and of six group-intermediate taxa unresolved. Recent phylogenies inferred from 30 or 213 proteins from sequenced genomes, positioned the root between two branches, each containing two major groups, but lacked data to position the group-intermediate taxa. Since the positions of these early diverging taxa are crucial for understanding the evolution of phenotypic complexity in Dictyostelia, we sequenced six representative genomes of early diverging taxa. RESULTS: We retrieved orthologs of 47 housekeeping proteins with an average size of 890 amino acids from six newly sequenced and eight published genomes of Dictyostelia and unicellular Amoebozoa and inferred phylogenies from single and concatenated protein sequence alignments. Concatenated alignments of all 47 proteins, and four out of five subsets of nine concatenated proteins all produced the same consensus phylogeny with 100% statistical support. Trees inferred from just two out of the 47 proteins, individually reproduced the consensus phylogeny, highlighting that single gene phylogenies will rarely reflect correct species relationships. However, sets of two or three concatenated proteins again reproduced the consensus phylogeny, indicating that a small selection of genes suffices for low cost classification of as yet unincorporated or newly discovered dictyostelid and amoebozoan taxa by gene amplification. CONCLUSIONS: The multi-locus consensus phylogeny shows that groups 1 and 2 are sister clades in branch I, with the group-intermediate taxon D. polycarpum positioned as outgroup to group 2. Branch II consists of groups 3 and 4, with the group-intermediate taxon Polysphondylium violaceum positioned as sister to group 4, and the group-intermediate taxon Dictyostelium polycephalum branching at the base of that whole clade. Given the data, the approximately unbiased test rejects all alternative topologies favoured by SSU rDNA and individual proteins with high statistical support. The test also rejects monophyletic origins for the genera Acytostelium, Polysphondylium and Dictyostelium. The current position of Acytostelium ellipticum in the consensus phylogeny indicates that somatic cells were lost twice in Dictyostelia. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-016-0825-7) contains supplementary material, which is available to authorized users

Challenges in involvement of male spouse in family planning program in rural areas of Varanasi

Background: Globally, men have not shared equally with women the responsibility for fertility regulation. While family planning efforts have been directed almost toward women, the lack of male involvement may also reflect the limited options available to men. Current methods for men are condom, withdrawal, or permanent, such as vasectomy. The success of family planning depends on the involvement of couples but this hardly happen especially in rural areas. It is the belief, though erroneously among most males that the practice of family planning should be the sole responsibility of the female. The present study was a community based cross sectional study with the objective to assess challenges in involvement of male spouse in family planning program in rural areas.Methods: This is a community based and cross-sectional study was undertaken in randomly selected 4 villages of Kashi vidyapeeth block, Varanasi. Total enumeration of women from the selected villages delivered within last 3 years was done and their husbands were interviewed by using a pre-designed, pre-tested interview schedule. Chi-square test was applied to find out any association between the variables. P<0.05 was considered to be statistically significant, data was analyzed with statistical package for the social sciences (SPSS) 20 trial version.Results: These preliminary findings are part of thesis shows that out of 130 interviewed respondents, majority (89.5%) had aware about family planning and two third (66.2%) of the respondents said that either they or their wives are using family planning. More than half of the respondents were aware about male sterilization but none of them were using male sterilization. Majority (77.7%) of the respondents said that human immunodeficiency virus-acquired immune deficiency syndrome (HIV-AIDS) and 45.4% were said that sexually transmitted diseases or sexually transmitted infections (STDs/STIs) can be prevented by use of condom. More than half (53.8%) of the respondents were sole of the decision maker regarding the use of family planning.Conclusions: The present study concludes that the majority of the respondents were awareness about the family planning but practices of family planning is low in the study area. Health workers should educate the eligible couples for use of contraceptive methods. Promotion of male contraceptive usage should be done by intense awareness campaigns

Assessment of Stock Market Liquidity and Efficiency: Evidence from an Emerging Country

The study examines the market efficiency, multi-dimensions of liquidity, and their interconnectedness for the Emerging Indian Stock Market. In contrast to the extant literature, the current study involves testing the market liquidity considering multi-dimensions such as depth, breadth, immediacy, tightness, and resiliency. Second, the study used a battery of tests to determine efficiency, including the Ljung and Box, runs test, Bartel test, Variance ratio, and BDS tests. Furthermore, using five quintiles classified by market depth, the linkage of market efficiency and liquidity is also being investigated. The findings show that during the pandemic, the Indian stock market has been proven to be efficient, suggesting that there are no abnormal returns. Moreover, the research demonstrates that during the COVID-19 pandemic, large volumes of securities are traded quickly and at a lower price effect, but with higher trading costs for completing a market transaction. However, it is worth noting that increased liquidity equates to greater efficiency, while lower liquidity equates to inefficiency. &nbsp

Post partum headache: a case series

Postpartum headache is the complaint of head, neck, or shoulder pain occurring during the first 6 weeks following delivery. Among the women who underwent neuraxial aneasthesia Post Dural puncture headache is one of the most common presentations. However, physicians should be aware that post Dural puncture headache is not the only cause of postpartum headache. Authors present a series of four cases that had varied presentation of post partum headache with varied diagnosis, the first case was of subdural haematoma where CT scan revealed an acute on chronic SDH. The second case was diagnosed as meningitis and the CSF for culture sensitivity grew Streptococcus Pneumoniae .In our third case of cortical vein  thrombosis , NCCT followed by MR venogram  revealed left transverse venous sinus thrombosis and our last case in the series was of posterior reversible encephalopathy syndrome where MRI confirmed the findings of typical findings are symmetric edema involving the white matter of the posterior regions of the cerebral hemispheres. The diagnostic dilemma was resolved by neuroimaging because the clinical presentation was not making us reach a satisfactory diagnosis of the cause of headache. Early resort to neuroimaging and multidisciplinary team effort paved way to early diagnosis and appropriate recovery of the patients

Association of serum cytokines IL-6, TNF-α, PTX-3 and progesterone modulation in cases of recurrent pregnancy loss

Background: Cytokines are major immune regulators, which play a critical role in the pathophysiology of unexplained recurrent pregnancy loss. Th1 class of cytokines has been shown to exert deleterious effects on pregnancy causing early loss.Methods: The changeover in the levels of Th1 cytokines was studied in two major groups; Gp I (N=30) comprised of RPL subjects with two or more consecutive spontaneous miscarriages history and Gp II (N=30) comprised of normal pregnancy controls .The efficacy of oral micronized progesterone was assessed in regulation of cytokine levels ,with Gp Ia (N=15) treated with 200 mg oral micronized progesterone and Gp Ib (N=15) comprised of untreated RPL subjects and its role in improving pregnancy outcome was also determined. The present study determined the levels of cytokine TNF-α, IL-6 and PTX-3 in serum samples for all the subjects at three time points at the time of enrolment, with (GpIa) or without (Gp Ib) progesterone administration at 20 weeks or abortion if earlier and at the time of delivery. Results: The results indicated that the levels of Th1 cytokines (TNF-α [37.80 versus 78.09], IL-6 [16.93 versus 81.12] and PTX-3 [17.42 versus 73.53]) was found to be reduced at every time point in the treated cases with an RPL history as compared to untreated ones. Further, the cases treated with with oral micronized progesterone were found to have better pregnancy outcomes (p<0.005 significant number of live births).Conclusions: The levels of interlukins, TNF-α, IL-6, PTX-3 in cases of RPL may not have a major contributory role in predicting outcome, however exogenous progesterone decreases the Th1 pro inflammatory response and efficiently improves the pregnancy outcomes by modulation of cytokine levels

Comparative Study of Colour Doppler versus Non Stress Test as a predictor of Perinatal outcome in PIH and IUGR

Background: Hypertensive disorders and intrauterine growth restriction are common complications encountered during pregnancy. This study was conducted to observe the usefulness of systolic/ diastolic (S/D) ratio in umbilical artery as compared with non-stress test (NST) to predict perinatal outcome in pregnancies complicated with hypertensive disorders and intrauterine growth restriction (IUGR). Methods: It was a prospective observational which was conducted on patients undergoing antenatal visits at the department of obstetrics and gynaecology, Army hospital research and referral, New Delhi from May 2017 to April 2019. NST was started at 32 weeks twice weekly in all patients. All patients were subjected to umbilical artery Doppler velocimetry waveform on weekly basis or every third day in cases of nonreactive NST. Results: Out of 140 patients, 53 patients (37.9%) had PIH and 44 (31.4%) had IUGR. 43 cases (30.7%) had both PIH and IUGR. Among the 140 patients, 40 patients (28.6%) had non-reactive NST and 60 patients (42.9%) of the patients had abnormal doppler. Abnormal doppler and non-reactive NST were associated with APGAR score of less than 7 at 5 minutes in the newborn. Abnormal perinatal outcome was more in abnormal doppler than normal doppler and the finding was statistically significant (p&lt;0.05). Conclusions: Overall sensitivity and diagnostic accuracy of Doppler is better as compared to that of NST in terms of detecting adverse perinatal outcomes