Global Transcriptomics of Congenital Hepatic Fibrosis in Autosomal Recessive Polycystic Kidney Disease using PCK rats

Congenital hepatic fibrosis / Autosomal recessive polycystic kidney disease (CHF/ARPKD) is an inherited neonatal disease induced by mutations in the PKHD1 gene and characterized by cysts, and robust pericystic fibrosis in liver and kidney. The PCK rat is an excellent animal model which carries a Pkhd1 mutation and exhibits similar pathophysiology. We performed RNA-Seq analysis on liver samples from PCK rats over a time course of postnatal day (PND) 15, 20, 30, and 90 using age-matched Sprague-Dawley (SD) rats as controls to characterize molecular mechanisms of CHF/ARPKD pathogenesis. A comprehensive differential gene expression (DEG) analysis identified 1298 DEGs between PCK and SD rats. The genes overexpressed in the PCK rats at PND 30 and 90 were involved cell migration (e.g. Lamc2, Tgfb2 , and Plet1 ), cell adhesion (e.g. Spp1, Adgrg1 , and Cd44 ), and wound healing (e.g. Plat, Celsr1, Tpm1 ). Connective tissue growth factor ( Ctgf ) and platelet-derived growth factor ( Pdgfb ), two genes associated with fibrosis, were upregulated in PCK rats at all time-points. Genes associated with MHC class I molecules (e.g. RT1-A2 ) or involved in ribosome assembly (e.g. Pes1 ) were significantly downregulated in PCK rats. Upstream regulator analysis showed activation of proteins involved tissue growth (MTPN) and inflammation (STAT family members) and chromatin remodeling (BRG1), and inhibition of proteins involved in hepatic differentiation (HNF4α) and reduction of fibrosis (SMAD7). The increase in mRNAs of four top upregulated genes including Reg3b, Aoc1, Tm4sf20 , and Cdx2 was confirmed at the protein level using immunohistochemistry. In conclusion, these studies indicate that a combination of increased inflammation, cell migration and wound healing, and inhibition of hepatic function, decreased antifibrotic gene expression are the major underlying pathogenic mechanisms in CHF/ARPKD.

Comparison of machine learning and deep learning techniques in promoter prediction across diverse species

Gene promoters are the key DNA regulatory elements positioned around the transcription start sites and are responsible for regulating gene transcription process. Various alignment-based, signal-based and content-based approaches are reported for the prediction of promoters. However, since all promoter sequences do not show explicit features, the prediction performance of these techniques is poor. Therefore, many machine learning and deep learning models have been proposed for promoter prediction. In this work, we studied methods for vector encoding and promoter classification using genome sequences of three distinct higher eukaryotes viz. yeast (Saccharomyces cerevisiae), A. thaliana (plant) and human (Homo sapiens). We compared one-hot vector encoding method with frequency-based tokenization (FBT) for data pre-processing on 1-D Convolutional Neural Network (CNN) model. We found that FBT gives a shorter input dimension reducing the training time without affecting the sensitivity and specificity of classification. We employed the deep learning techniques, mainly CNN and recurrent neural network with Long Short Term Memory (LSTM) and random forest (RF) classifier for promoter classification at k-mer sizes of 2, 4 and 8. We found CNN to be superior in classification of promoters from non-promoter sequences (binary classification) as well as species-specific classification of promoter sequences (multiclass classification). In summary, the contribution of this work lies in the use of synthetic shuffled negative dataset and frequency-based tokenization for pre-processing. This study provides a comprehensive and generic framework for classification tasks in genomic applications and can be extended to various classification problems.

Snail induces epithelial cell extrusion by regulating RhoA contractile signalling and cell-matrix adhesion

Cell extrusion is a morphogenetic process that is implicated in epithelial homeostasis and elicited by stimuli ranging from apoptosis to oncogenic transformation. To explore whether the morphogenetic transcription factor Snail (SNAI1) induces extrusion, we inducibly expressed a stabilized Snail6SA transgene in confluent MCF-7 monolayers. When expressed in small clusters (less than three cells) within otherwise wild-type confluent monolayers, Snail6SA expression induced apical cell extrusion. In contrast, larger clusters or homogenous cultures of Snail6SA cells did not show enhanced apical extrusion, but eventually displayed sporadic basal delamination. Transcriptomic profiling revealed that Snail6SA did not substantively alter the balance of epithelial and mesenchymal genes. However, we identified a transcriptional network that led to upregulated RhoA signalling and cortical contractility in cells expressing Snail6SA Enhanced contractility was necessary, but not sufficient, to drive extrusion, suggesting that Snail collaborates with other factors. Indeed, we found that the transcriptional downregulation of cell-matrix adhesion cooperates with contractility to mediate basal delamination. This provides a pathway for Snail to influence epithelial morphogenesis independently of classic epithelial-to-mesenchymal transition.

Dynamic regulation of chromatin organizer SATB1 via TCR-induced alternative promoter switch during T-cell development

The chromatin organizer SATB1 is highly enriched in thymocytes and is essential for T-cell development. Although SATB1 regulates a large number of genes important for T-cell development, the mechanism(s) regulating expression of SATB1 during this process remain elusive. Using chromatin immune precipitation-seq-based occupancy profiles of H3K4me3 and H3Kme1 at Satb1 gene locus, we predicted four different alternative promoters of Satb1 in mouse thymocytes and characterized them. The expression of Satb1 transcript variants with distinct 5′ UTRs occurs in a stage-specific manner during T-cell development and is dependent on TCR signaling. The observed discrepancy between the expression levels of SATB1 mRNA and protein in developing thymocytes can be explained by the differential translatability of Satb1 transcript variants as confirmed by polysome profiling and in vitro translation assay. We show that Satb1 alternative promoters exhibit lineage-specific chromatin accessibility during T-cell development from progenitors. Furthermore, TCF1 regulates the Satb1 P2 promoter switch during CD4SP development, via direct binding to the Satb1 P2 promoter. CD4SP T cells from TCF1 KO mice exhibit downregulation of P2 transcript variant expression as well as low levels of SATB1 protein. Collectively, these results provide unequivocal evidence toward alternative promoter switch-mediated developmental stage-specific regulation of SATB1 in thymocytes.

Secukinumab for patients failing previous tumour necrosis factor-α inhibitor therapy: results of a randomized open-label study (SIGNATURE)

BACKGROUND

Efficacy data on therapies for patients with psoriasis who have failed tumour necrosis factor (TNF)-α inhibitor therapy is limited.

OBJECTIVES

To determine the effectiveness and tolerability of secukinumab, an interleukin (IL)-17A inhibitor, in patients with moderate/severe chronic plaque psoriasis with documented efficacy failure of TNF-α inhibitor therapy (SIGNATURE study).

METHODS

This was a randomized, open-label, noncomparator study in 53 dermatology centres in the U.K. and Republic of Ireland. Patients were randomized 1 : 1 to receive secukinumab 300 mg or 150 mg subcutaneously every week for 4 weeks, then 4-weekly thereafter. Patients were stratified by their prior efficacy failure with TNF-α inhibitors. Only patients who started and stayed on the same dose at each time point were included for efficacy assessments.

RESULTS

In total, 233 patients were analysed. The primary end point was met, with a statistically significant improvement in response rates [75% reduction in Psoriasis Area and Severity Index (PASI 75)] from baseline to week 16 in both secukinumab 300 mg and 150 mg dose groups [77 of 118 patients (65·3%) and 51 of 115 patients (44·3%), respectively; P < 0·0001]. After 72 weeks, in patients starting and remaining on 300 mg, 77% (54 of 70) achieved PASI 75. Improvements in Dermatology Life Quality Index from baseline to week 16 occurred and were maintained up to 72 weeks. The safety profile was generally consistent with previous secukinumab studies, although a higher incidence of some adverse events (e.g. candida infections) was observed.

CONCLUSIONS

This study provides evidence of efficacy and safety of secukinumab for treatment of patients with psoriasis who failed prior TNF-α inhibitor therapy. This study represents a 'real-world' population, providing reassurance that secukinumab is a treatment option in this difficult-to-treat population. What's already known about this topic? Conventional systemic nonbiological and tumour necrosis factor (TNF)-α inhibitor therapies for plaque psoriasis have not fully met patients' needs. There is a lack of data to support the treatment pathways for patients with psoriasis who have inadequate responses to TNF-α inhibitor therapy. Secukinumab, a recombinant high-affinity fully human monoclonal anti-human interleukin-17A antibody of the IgG1/κ-class, has shown excellent safety and efficacy in the treatment of moderate-to-severe psoriasis. What does this study add? This is the first study evaluating treatment with biologics after prior efficacy failure of TNF-α inhibitor therapy as defined by the U.K. National Institute for Health and Care Excellence criteria. Secukinumab is an effective treatment in this difficult-to-treat patient population. This study provides important practical information for clinicians managing psoriasis. Adverse events were consistent with the phase III programme for secukinumab, although some adverse events, e.g. candida, were increased.

GENERALIZED SYNTHETIC ESTIMATOR FOR DOMAIN MEAN IN TWO PHASE SAMPLING USING SINGLE AUXILIARY CHARACTER

In this paper, we have proposed a two phase sampling estimator for domain mean using auxiliary character with unknown X a domain mean. Also discussed properties of the proposed estimator for domain mean ps a T ,γ , using auxiliary character. Simulation study of the proposed estimator ps a T ,γ , has been made with conventional ratio synthetic estimator for domain mean ps a T ,−1, using auxiliary character in terms of simulated relative standard error (SRSE) and absolute relative bias (ARB). Simulation study shows that under synthetic assumption proposed estimator is more efficient than conventional ratio synthetic estimator for domain mean using auxiliary character.  

Primary Sjogren's syndrome presenting as hypokalemic paralysis: A case series

Primary Sjögren's syndrome (pSS) primarily involves exocrine glands, and renal tubular acidosis (RTA) is seen in one-third of the cases. RTA with hypokalemic paralysis as a presenting feature of pSS is described in few case reports in literature. We report 13 cases who presented as hypokalemic paralysis, and on evaluation were diagnosed to be pSS, as per the diagnostic criteria laid by the Sjögren's International Collaborative Clinical Alliance (2012). All patients were female, with a mean age at presentation being 33.1 ± 8.22 years (range, 25–48 years). Eleven patients had a complete distal RTA and two patients had incomplete distal RTA at the time of presentation. 62% (8/13) of patients had no signs and symptoms of exocrine gland involvement. All the cases were managed with oral alkali therapy, and six patients received additional immunomodulating agents. No improvement in renal tubular dysfunction (in the form of a reduction in the alkali dose) after immunomodulating therapy was observed over a mean follow-up of 2.8 years. Renal tubular dysfunction can be the presenting manifestation of pSS. It is important to consider the possible presence of this disorder in adults with otherwise unexplained distal RTA or hypokalemia.

Persistence of Corynebacterium diphtheriae in Delhi & National Capital Region (NCR)

Despite the introduction of mass immunization, diphtheria continues to play a major role as a potentially lethal infectious disease in many countries. Delay in the specific therapy of diphtheria may result in death and, therefore, accurate diagnosis of diphtheria is imperative. This study was carried out at National Centre for Disease Control (NCDC), Delhi, India, on samples of suspected diphtheria cases referred from various government hospitals of Delhi and neighbouring areas during 2012-2014. Primary identification of Corynebacterium diphtheriae was done by standard culture, staining and biochemical tests followed by toxigenicity testing by Elek's test on samples positive for C. diphtheriae. The results showed persistence of toxigenic C. diphtheriae in our community indicating the possibility of inadequate immunization coverage.

Abstract P2-12-02: Axillary reverse mapping: A feasibility study

Background

The mainstay of the therapy in breast cancer has been mastectomy or wide local excision along with axillary lymph node dissection (ALND). There are a lot of adverse effects associated with ALND, lymphedema being the most devastating. Sentinel lymph node biopsy (SLNB) can identify women who may or may not need axillary dissection and translate into a smaller number of patients undergoing axillary dissection. However, patients having positive lymph node on SLNB will still have to undergo ALND.

To reduce the occurrence of lymphedema and its associated complications the technique of Axillary Reverse Mapping (ARM) has been developed. It is based on the hypothesis that the lymphatic pathway of the arm is not involved by the metastasis of the breast primary and after accurately identifying and preserving the arm lymphatics, there would be risk of neither lymphedema, nor leaving behind metastatic cells in the lymph nodes. This prospective study was carried out to evaluate the feasibility of ARM in patients undergoing ALND.

Methods

This prospective study was carried out in the Department of General Surgery, PGIMER, from July 2010 to Dec 2011. There were seventy five Biopsy/FNAC confirmed breast cancer female patients between 18 to 75 years. All patients were undergoing ALND as part of their treatment. Patients with any prior surgical treatment for primary invasive breast cancer, bilateral breast cancer and metastatic breast disease were excluded. Patients with heart diseases, active or uncontrolled infection, dementia, altered mental status or any psychiatric condition, pregnant or lactating women and with known allergies to blue dye were also excluded.

All patients were treated as per the standard treatment for stage. All ALNDs were performed by a single surgeon. ARM was performed in all the patients by giving 5 ml of Isosulfan Blue Dye (Sterlized 1% solution) in the upper inner arm of the involved site approximately 60 minutes before exposure.

Results

The results were analyzed clinically during surgery and post-operatively by histo-pathological examination of lymphnodes. Intra-operatively, the identification of lymphnodes and lymphathics were noted in 17(22.7%) and 33 patients(44%) respectively. In none of the patient any attempt was made to preserve the blue nodes and all the lymph nodes were resected and sent for histopathological examination. In only 2 of 17 patients (11.76%) the lymph node was positive for malignant tumour cells. The tumour burden in both these patients was very high (more than 10 nodes involved). No association was found in the identification rates of ARM nodes and lymphatics to age, BMI, size of tumour, site of tumour, pathological status of axilla and timing of dye.

Conclusion

The identification rate of ARM lymphatics and nodes is low when only blue dye is used. The method appears it to be oncologically safe in patients with low tumour burden. However there is need for further studies will before this procedure can be universally applied without compromising the oncologic safety.

Once the technique is proven to be oncologically safe even in a selected group of patients, a large randomized trial will be needed to give a satisfactory answer whether the problem of lymphedema be eliminated or minimized in the patients in whom arm lymphatics are successfully preserved.

Citation Format: Khare S, Singh G, Das A, Bal A. Axillary reverse mapping: A feasibility study. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-12-02.

rmpM gene as a genetic marker for human bacterial meningitis

Meningitis is a bacterial, viral or fungal infection of the protective membrane meninges covering the brain and spinal cord. Viral and other forms of meningitis are mild and get cured within one or two week without any treatment. Whereas, bacterial meningitis can prove lethal if not being diagnosed or treated in time. Meningitis is a contagious infection and can spread from one person to another through coughing, sneezing or close contact. Usually the disease is diagnosed from cerebrospinal fluid (CSF) of the patients using culture, PCR, immunological and biochemical tests. All these methods suffer from one or more limitations. Our lab has developed a quick PCR based detection of Neisseria meningitidis (bacterial meningitis) directly from the patient CSF samples using specific primers of virulent rmpM gene. The overall analysis completes in 80 min for confirmation of the disease. Amplicon of 308 bp of rmpM gene does not show homology with other organisms and can be used as a genetic marker for human bacterial meningitis caused by Neisseria meningitidis.

speB gene as a specific genetic marker for early detection of rheumatic heart disease in human

Streptococcus pyrogenic exotoxin B gene (speB) is chromosomally encoded pyrogenic and cardiotoxic virulence factor of S. pyogenes. Exotoxin B is produced only in a secreted form, as a 40 KD proprotein, which is subsequently processed to 28 KD in the mature form. Streptococcus pyogenes infection in human, causes initially pharyngitis due to inhalation of aerosols emitted by infected persons, develops rheumatic fever which leads to the rheumatic heart disease (damage of heart valves). The available detection methods are bacterial culture, β-hemolysis, bacitracin sensitivity, hippurate test, phadebact test, CRP (C-reactive protein), ESR and PCR. All these methods are either expensive or non-confirmatory and have some limitations. Available PCR methods take more time and require other test to confirm the disease. Our PCR based detection of Streptococcus pyogenes in human using specific primers of speB gene completes overall analysis in 80 min which is the minimum time reported so far for the confirmation of the disease. Amplicon of 423bp of speB gene can be used as a specific genetic marker as it does not show homology with other organisms for early detection of rheumatic heart disease. Our method is specific virulence gene based which is quick, economical and more sensitive as compared with other methods.

sof gene as a specific genetic marker for detection of Streptococcus pyogenes causing pharyngitis and rheumatic heart disease

Streptococcus pyogenes is a human pathogen causing invasive and non&mdash;invasive diseases, as well as severe sequels, such as rheumatic fever. Rheumatic heart disease is a sequel of rheumatic fever results from an untreated strep throat causing damage of the heart valves. The usual detection methods of strep throat are culture, virulent test, antibiotic sensitivity, CRP, ESR and PCR. These methods are expensive, time consuming and have some limitations. All reported PCR methods are based on either 16S rRNA or specific gene based along with other methods to confirm the disease in more than 1h. Here, we have developed a PCR based diagnosis of streptococcus pyogenes using specific primers of virulent sof gene (serum opacity factor) of S. pyogenes. Our method is an improvement of the existing methods and the overall analysis completes in 1 h which is the least time reported so far for the confirmation of the disease. Amplicon of 228 bp of sof gene does not show homology with other organisms and can be used as genetic marker for S. pyogenes.

Diagnosis of Novel Pandemic Influenza Virus 2009 H1N1 in Hospitalized Patients

A real-time RT-PCR assay was standardized and evaluated for the detection of the recent pandemic 2009 H1N1 strain that circulated around the world causing colossal loss of human life. We amplified the conserved regions of the hemagglutinin (HA) gene of 438 clinical specimens using real-time RT-PCR assay for rapid identification of pandemic influenza virus. The real-time RT-PCR was optimized and the primers and probes were tested against a panel of known negative and positive controls. RNA isolated from the HeLa cell line served as quality control. The conventional RT-PCR which is an established method of influenza virus diagnosis was compared to real-time RT-PCR. Of 438 clinical specimens tested, 212 specimens were found positive for influenza A virus (SD 46.669) in which 139 specimens were diagnosed positive for the pandemic 2009 H1N1 while 73 were the seasonal influenza viruses. We report that the real-time RT-PCR assay offers both, a high sensitivity and specificity when compared with the traditional identification method. The real-time RT-PCR assay allows rapid identification of the pandemic swine 2009-H1N1 at very low viral loads that are negative by the traditional RT-PCR. This optimized assay can be a very useful tool to assist both epidemiologists and the clinicians.

Sprouty-2 controls c-Met expression and metastatic potential of colon cancer cells: sprouty/c-Met upregulation in human colonic adenocarcinomas

Sprouty negatively regulates receptor tyrosine kinase signals by inhibiting Ras/ERK pathways. Sprouty is down-regulated in breast, prostate and liver cancers and appears to function as a tumor suppressor. The role of Sprouty in colonic neoplasia, however, has not been investigated. Sprouty-2 protein and mRNA transcripts were significantly up-regulated in human colonic adenocarcinomas. Strikingly, the c-Met receptor was also upregulated in tumors with increased sprouty-2. To delineate a potential causal relationship between sprouty-2 and c-Met, K-ras mutant HCT-116 colon cancer cells were transduced with purified TAT-sprouty-2 protein or stably transfected with full-length human sprouty-2 gene. Sprouty-2 up-regulation significantly increased cell proliferation by accelerating cell cycle transition. Sprouty-2 transfectants demonstrated strong up-regulation of c-Met protein and mRNA transcripts and hepatocyte growth factor stimulated ERK and Akt phosphorylation and enhanced cell migration and invasion. In contrast, knockdown of c-Met by siRNA significantly decreased cell proliferation, migration and invasion in sprouty-2 transfectants. Further, knockdown of sprouty-2 by siRNA in parental HT-29 and LS-174T colon cancer cells also decreased cell invasion. Sprouty-2 transfectants formed significantly larger tumor xenografts and demonstrated increased proliferation and angiogenesis and suppressed apoptosis. Sprouty-2 tumors metastasized to liver from cecal orthotopic implants suggesting sprouty-2 might also enhance metastatic signals. Thus in colon cancer sprouty functions as an oncogene and its effects are mediated in part by c-Met up-regulation.

Characterization and evaluation of heavy metal tolerance of bacterial species from soil of waste area near Riyan steel rolling mills, Muzaffarnagar, India

The present study observed a variety of microorganisms from the soil of the waste area near Riyan Steel Rolling Mills , Muzaffarnagar. Among the microorganisms, 10 isolates of Bacillus subtilis, Pseudomonas aeruginosa and Staphylococcus aureus showed great potential against detrimental heavy metals like Hg, Pb, Zn. Out of these 10 isolates, only 2 isolates of Bacillus subtilis (N1A2, N1P2), one isolates of P. aeruginosa N1A4 and one isolates of S. aureus A1N3 showed tremendous tolerance against various heavy metals. Bacillus subtilis N1A2 showed15x109 cfu/ml in 100μg/ml of HgCl2 whereas B. subtilis N1P2 showed 15x109 cfu/ml in 400μg/ml of zinc acetatate. Similarily Pseudomonas aeruginosa N1A4 showed 11x109 cfu/ml in 150μg/ml of lead acetate. Staphylococcus aureus A1N3 showed great resistance towards 450μg/ml of zinc sulphate and maintain their growth up to 7x109 cfu/ml. strains were identified as Bacillus subtilis, Pseudomonas aeruginosa and Staphylococcus aureus on the basis of their morphological, physiological and biochemical and compared with their standard MTCC strains.

Direct detection and serogroup characterization of Neisseria meningitidis from outbreak of meningococcal meningitis in Delhi

BACKGROUND AND OBJECTIVES

Rapid clinical manifestation/progression of the meningococcal meningitis and lacunae in conventional bacteriological test often encourages indiscriminate use of antibiotics much before the etiology is established. Accordingly this study was planned to evaluate ctrA PCR for rapid molecular detection. In addition, multiplex PCR and sequencing was done for serogroup prediction to provide essential epidemiological and laboratory evidence for decision makers of health department of the country for choosing appropriate vaccine and phylogenetic analysis to establish its lineage.

MATERIALS AND METHODS

73 CSF samples, collected from equal number of suspected cases, were investigated by both bacteriological (microscopy, culture, LA and drug sensitivity testing) as well as molecular tests i.e. PCR targeting conserved ctrA gene, multiplex PCR for serogroup characterization and DNA sequencing.

RESULTS

ctrA PCR revealed sensitivity, specificity, positive predictive value and negative predictive values of 93.15%, 100%,100%, and 88.23% respectively. Multiplex PCR based genogrouping followed by DNA sequencing, BLAST and phylogenetic analysis revealed complete homology with earlier submitted Neisseria meningitidis serogroup A strain Z2491 to suggest the sole involvement of only serogroup A in the outbreak. Two strains showed resistance to cefuroxime, ciprofloxacin, nalidixic acid. Only one strain showed resistance to ciprofloxacin, emphasizing the need for a constant surveillance system.

CONCLUSION

These diagnostic molecular tools are of paramount importance in establishing etiology, serogrouping, and epidemiological surveillance especially in developing countries like India.

Morphologic and cytokine profile characterization of Salmonella enterica serovar typhimurium infection in calves with bovine leukocyte adhesion deficiency

The role of neutrophils in the pathogenesis of Salmonella enterica Typhimurium-induced ruminant and human enteritis and diarrhea has yet to be characterized with in vivo models. To address this question, the in vivo bovine ligated ileal loop model of nontyphoidal salmonellosis was used in calves with the naturally occurring bovine leukocyte adhesion deficiency (BLAD) mutation whose neutrophils are unable to extravasate and infiltrate the extravascular matrix. Data obtained from 4 BLAD Holstein calves homozygous for BLAD (CD18-), 1 to 5 weeks of age, were compared with 4 controls, age-matched Holstein calves negative for BLAD (CD18+). Morphologic studies revealed that infection of CD18- calves with S Typhimurium resulted in no significant tissue infiltration by neutrophils, less tissue damage, reduced luminal fluid accumulation, and increased bacterial invasion, when compared with CD18+ calves. Ultrastructurally, lesions in enterocytes induced by S Typhimurium infection in CD18- calves--including attachment and disruption of the brush border, apical membrane ruffling formation, and cellular degeneration--were similar to the ones reported in the literature for CD18- calves. Study of cytokine gene expression by quantitative real-time polymerase chain reaction revealed that early stages of acute infection (4-8 hours postinfection) were associated with increased interleukin 8 gene expression in the absence of tissue influx of neutrophils in CD18- calves, whereas later stages of infection (12 hours postinfection) were associated with increased expression of growth-related oncogene alpha in the presence of neutrophil influx in CD18+ calves. In contrast, the proinflammatory cytokines interleukin 1beta and tumor necrosis factor alpha were poorly correlated with the presence or absence of tissue neutrophils.

Characterization of RPO B gene for detection of rifampicin drug resistance by SSCP and sequence analysis

PURPOSE

Because of the emergence of multidrug-resistant tuberculosis in recent times, the rapid detection of resistance to the first-line anti-tuberculosis drug rifampicin was felt worldwide. Accordingly, this study was conducted to evaluate the diagnostic potential of polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) for checking its utility as a rapid screening test for determination of rifampicin drug resistance.

MATERIALS AND METHODS

A total of 34 isolates of Mycobacterium tuberculosis (M. tuberculosis) (22 rifampicin resistant, 11 rifampicin sensitive and one control H37Rv) strains were analysed by PCR-SSCP and DNA sequencing within the 157-bp region of the rpo B gene (Ala 500-Val 550).

RESULTS

Rifampicin resistance was detected successfully by PCR-SSCP in 20/22(90.90%) of rifampicin-resistant strains showing a total of nine different mutations in seven codon positions: codon 513 (CAA-->CCA), 516 (GAC-->GTC), 507 (GGC-->GAC), 526 (CAC-->GAC, TAC), 531 (TCG-->TTG, TGG), 522 (TCG-->TGG) and 533 (GTG-->CCG). Two rifampicin-resistant strains showed an identical PCR-SSCP pattern with the wild type H37Rv; 77.27% rifampicin-resistant strains showed a single point mutation and 9.09% had no mutation. Three rifampicin-resistant strains showed characteristic double mutations at codon positions 526 and 531. Sensitivity and specificity were calculated as 90.90% and 100%.

CONCLUSIONS

Rifampicin-resistant genotypes were mainly found in codon positions 516, 526 and 531. PCR-SSCP seems to be an efficacious method of predicting rifampicin resistance and substantially reduces the time required for susceptibility testing from 4 to 6 weeks to a few weeks.

Early phase morphological lesions and transcriptional responses of bovine ileum infected with Mycobacterium avium subsp. paratuberculosis

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of chronic enteritis in ruminants (Johne's disease) and a possible etiopathologic agent in human Crohn's disease. The host-pathogen interaction in this chronic disease has largely depended on the randomly collected static lesions studied in subclinically or clinically infected animals. We have established and utilized the neonatal calf ligated ileal loop model to study the early temporal host changes during MAP infection. After inoculation of ligated ileal loop with MAP, samples were analyzed for bacterial invasion, histologic and ultrastructural morphologic changes, and gene expression at several times (0.5-12 hours) postinfection. Our results indicate that MAP invades the intestinal mucosa as early as 0.5 hour postinoculation. Distribution and migration of neutrophils, monocytes/macrophages, and goblet cells were confirmed by histopathology, scanning and transmission electron microscopy. Coincident with the morphologic analysis, we measured by real-time polymerase chain reaction gene expression of various cytokines/chemokines that are involved in the recruitment of mononuclear and polymorphonuclear leukocytes to the site of infection. We also detected expression of several other genes, including intestinal-trefoil factor, profilin, lactoferrin, and enteric ss-defensin, which may play significant roles in the early MAP infection. Thus, the calf ligated intestinal loop model may be used as a human disease model to understand the role of MAP in the pathogenesis of Crohn's disease.

Diagnostic potential of IS6110, 38kDa, 65kDa and 85B sequence-based polymerase chain reaction in the diagnosis of Mycobacterium tuberculosis in clinical samples

PURPOSE

The correlation between the presence of specific gene sequence of M. tuberculosis and specific diagnosis of clinical tuberculosis is not known. This study compared the results of polymerase chain reaction (PCR) amplification of M. tuberculosis specific DNA sequences (IS6110, 65kDa, 38kDa and mRNA coding for 85B protein) from different clinical samples of pulmonary and extrapulmonary tuberculosis.

METHODS

One hundred and seventy-two clinical samples from suspected tuberculosis patients were tested for smear examination, culture (LJ and rapid BACTEC 460 TB system) and PCR. PCR was performed with specific primers for the targets: IS6110, 65 kDa, 38 kDa and 85 B.

RESULTS

Each PCR test was found to have a much higher positivity than conventional test and BACTEC culture (P < 0.05). Smear positive samples (56) and the samples (36) showing positive results by conventional methods (smear and LJ medium culture) and BACTEC were found to be positive by all PCR protocols. No significant difference was found between the four PCR protocols (P> 0.05). The primer specific for amplifying the 123bp IS6110 fragment gave the highest positivity (83%), followed by 65kDa, 38kDa and 85B RT-PCR in descending order.

CONCLUSIONS

These data suggest that the presence of IS6110 correlates more closely with the diagnosis of clinical tuberculosis than that of 65kDa, 38kDa and 85B proteins.

A polyherbal vaginal pessary with spermicidal and antimicrobial action: evaluation of its safety

A polyherbal vaginal pessary (Praneem) has been formulated that has antimicrobial properties against genital pathogens in addition to spermicidal action. Thus, it has dual potential as a barrier method for contraception and for providing protection against some sexually transmitted infections. The present study reports the findings of a multicentre trial that was conducted to evaluate the safety of this product. Trials were carried out in 23 women in three centres in India: the Postgraduate Institute of Medical Education and Research, Chandigarh; Safdarjang Hospital, New Delhi; and Kamla Nehru Memorial Hospital, Allahabad. Thorough clinical and pelvic examinations were carried out as well as cervical cytology, blood biochemistry and haematology before and after use of the polyherbal pessary intravaginally once daily for 7 consecutive days. No toxicity was observed on clinical examination or by laboratory investigations. Daily intravaginal use of this pessary for 7 days had no adverse effects on cervical cytology or on metabolic and organ functions.

Protein kinase C delta inhibits Caco-2 cell proliferation by selective changes in cell cycle and cell death regulators

PKC-delta is a serine/threonine kinase that mediates diverse signal transduction pathways. We previously demonstrated that overexpression of PKC-delta slowed the G1 progression of Caco-2 colon cancer cells, accelerated apoptosis, and induced cellular differentiation. In this study, we further characterized the PKC-delta dependent signaling pathways involved in these tumor suppressor actions in Caco-2 cells overexpressing PKC-delta using a Zn2+ inducible expression vector. Consistent with a G1 arrest, increased expression of PKC-delta caused rapid and significant downregulation of cyclin D1 and cyclin E proteins (50% decreases, P<0.05), while mRNA levels remained unchanged. The PKC agonist, phorbol 12-myristate 13-acetate (TPA, 100 nM, 4 h), induced two-fold higher protein and mRNA levels of p21(Waf1), a cyclin-dependent kinase (cdk) inhibitor in PKC-delta transfectants compared with empty vector (EV) transfected cells, whereas the PKC-delta specific inhibitor rottlerin (3 microM) or knockdown of this isoenzyme with specific siRNA oligonucleotides blocked p21(Waf1) expression. Concomitantly, compared to EV control cells, PKC-delta upregulation decreased cyclin D1 and cyclin E proteins co-immunoprecipitating with cdk6 and cdk2, respectively. In addition, overexpression of PKC-delta increased binding of cdk inhibitor p27(Kip1) to cdk4. These alterations in cyclin-cdks and their inhibitors are predicted to decrease G1 cyclin kinase activity. As an independent confirmation of the direct role PKC-delta plays in cell growth and cell cycle regulation, we knocked down PKC-delta using specific siRNA oligonucleotides. PKC-delta specific siRNA oligonucleotides, but not irrelevant control oligonucleotides, inhibited PKC-delta protein by more than 80% in Caco-2 cells. Moreover, PKC-delta knockdown enhanced cell proliferation ( approximately 1.4-2-fold, P<0.05) and concomitantly increased cyclin D1 and cyclin E expression ( approximately 1.7-fold, P<0.05). This was a specific effect, as nontargeted PKC-zeta was not changed by PKC-delta siRNA oligonucleotides. Consistent with accelerated apoptosis in PKC-delta transfectants, compared to EV cells, PKC-delta upregulation increased proapoptotic regulator Bax two-fold at mRNA and protein levels, while antiapoptotic Bcl-2 protein was decreased by 50% at a post-transcriptional level. PKC-delta specific siRNA oligonucleotides inhibited Bax protein expression by more than 50%, indicating that PKC-delta regulates apoptosis through Bax. Taken together, these results elucidate two critical mechanisms regulated by PKC-delta that inhibit cell cycle progression and enhance apoptosis in colon cancer cells. We postulate these antiproliferative pathways mediate an important tumor suppressor function for PKC-delta in colonic carcinogenesis.

Comparison of various microbiological tests including polymerase chain reaction for the diagnosis of osteoarticular tuberculosis

PURPOSE

To evaluate the utility of the polymerase chain reaction (PCR) test for diagnosing osteoarticular tuberculosis (TB).

METHODS

Clinical samples (synovial tissue and synovial fluid) obtained from 23 cases of suspected osteoarticular tuberculosis were subjected to Ziehl Neelsen (ZN) smear examination, radiometric BACTEC culture and PCR test for tuberculosis by amplifying 65 kDa antigen coding region of Mycobacterium tuberculosis (M.tb) genome.

RESULTS

PCR test was found to be much sensitive than the ZN smear examination and BACTEC culture (p<0.05) in the diagnosis of osteoarticular TB. In synovial fluid samples, PCR was positive in 73.9%, ZN smear examination in 17.39% and BACTEC culture in 39.13% of cases. The positivities were relatively lower with synovial tissue samples, the corresponding figures being 60.8, 8.6 and 26.08% respectively. Moreover, on combining the results of synovial fluid and tissues, the corresponding figures further increased to 78.2, 21.7 and 43.3% respectively. Further, sensitivity and specificity for PCR employing BACTEC culture as the "gold standard" was 100% respectively. Using BACTEC culture, the earliest positivity was seen in three days using synovial tissue specimen and 13 days with synovial fluid, the average detection times being 23.2 days and 32.6 days respectively. On the other hand, PCR test gave a positive result within 24 hours.

CONCLUSIONS

PCR test was shown to be much more sensitive than ZN smear examination and BACTEC culture test for diagnosing osteoarticular tuberculosis.

Molecular dynamics simulation of amyloid beta dimer formation

Recent experiments with amyloid beta (Abeta) peptide indicate that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce a molecular dynamics approach to study Abeta dimer formation. 1), We use discrete molecular dynamics simulations of a coarse-grained model to identify a variety of dimer conformations; and 2), we employ all-atom molecular mechanics simulations to estimate thermodynamic stability of all dimer conformations. Our simulations of a coarse-grained Abeta peptide model predicts 10 different planar beta-strand dimer conformations. We then estimate the free energies of all dimer conformations in all-atom molecular mechanics simulations with explicit water. We compare the free energies of Abeta(1-42) and Abeta(1-40) dimers. We find that 1), dimer conformations have higher free energies compared to their corresponding monomeric states; and 2), the free-energy difference between the Abeta(1-42) and the corresponding Abeta(1-40) dimer conformation is not significant. Our results suggest that Abeta oligomerization is not accompanied by the formation of thermodynamically stable planar beta-strand dimers.

Seroprevalence and incidence of rubella in and around Delhi (1988-2002)

National Institute of Communicable Diseases (NICD) has been engaged in rubella testing for serodiagnosis of the infection and screening for immunity status. The compiled and evaluated data of the work done on rubella testing for the past fifteen years has been presented here to show the trend and changing scenario of the disease in Delhi. Blood samples were from 7424 patients referred to NICD, Delhi for serodiagnosis of congenital Rubella syndrome (CRS) in malformed babies, in utero rubella infection in women and immunity status of pregnant women and women with bad obstetric history. They were tested for rubella IgG and/or rubella IgM antibodies using commercially available reagents and kits. The data from the 15 years of testing was then compiled and evaluated. From the available data it was seen that immunity status against rubella in childbearing age group of women increased steadily from 49% in 1988 to 87% in 2002. Reported cases of CRS at NICD are also on the decline over the time period. There is periodic indication of high incidence of rubella in the year 1988; 1991 and 1998 as the reported cases of acute rubella infection in childbearing age group is high during these years.

Comparison of the conventional diagnostic modalities, bactec culture and polymerase chain reaction test for diagnosis of tuberculosis

PURPOSE

To evaluate the performance of 65 kDa antigen based PCR assay in clinical samples obtained from pulmonary and extrapulmonary cases of tuberculosis.

METHODS

One hundred and fifty six samples were processed for detection of Mycobacterium tuberculosis by ZN smear examination, LJ medium culture, BACTEC radiometric culture and PCR tests.

RESULTS

A significant difference was seen in the sensitivities of different tests, the figures being 74.4% for PCR test, 33.79% for ZN smear examination, 48.9% for LJ culture and 55.8% for BACTEC culture (P< 0.05). However, there was no significant difference (P>0.05) as far as specificity of different tests was concerned. PCR test sensitivity in pulmonary and extrapulmonary clinical samples were 72.7% and 75.9% respectively and found to be significantly higher (P< 0.05) when compared with those of other tests. The mean detection time for M.tuberculosis was 24.03 days by LJ medium culture, 12.89 days by BACTEC culture and less than one day by PCR test.

CONCLUSIONS

PCR is a rapid and sensitive method for the early diagnosis of pulmonary and extrapulmonary tuberculosis.

Amplified fragment length polymorphism reveals genomic variability among Mycobacterium avium subsp. paratuberculosis isolates

Ninety-six primer sets were used for amplified fragment length polymorphism (AFLP) to characterize the genomes of 20 Mycobacterium avium subsp. paratuberculosis field isolates, 1 American Type Culture Collection (ATCC) M. avium subsp. paratuberculosis isolate (ATCC 19698), and 2 M. avium subsp. avium isolates (ATCC 35716 and Mac 104). AFLP analysis revealed a high degree of genomic polymorphism among M. avium subsp. paratuberculosis isolates that may be used to establish diagnostic patterns useful for the epidemiological tracking of M. avium subsp. paratuberculosis isolates. Four M. avium subsp. paratuberculosis-polymorphic regions revealed by AFLP were cloned and sequenced. Primers were generated internal to these regions for use in PCR analysis and applied to the M. avium subsp. paratuberculosis field isolates. An appropriate PCR product was obtained in 79 of 80 reactions, while the M. avium subsp. avium isolates failed to act as templates for PCR amplification in seven of eight reactions. This work revealed the presence of extensive polymorphisms in the genomes of M. avium subsp. paratuberculosis and M. avium subsp. avium, many of which are based on deletions. Of the M. avium subsp. paratuberculosis-specific sequences studied, one revealed a 5,145-bp region with no homologue in the M. avium subsp. avium genome. Within this region are genes responsible for integrase-recombinase function. Three additional M. avium subsp. paratuberculosis-polymorphic regions were cloned, revealing a number of housekeeping genes; all were evaluated for their diagnostic and epidemiological value.

Cold chain monitoring of OPV at transit levels in India: correlation of VVM and potency status

We have conducted a study to analyze monitoring of the cold chain of 674 OPV field samples collected at four different levels of vaccine distribution viz., immunization clinics, district stores, hospitals and Primary Health Centers (PHC) from states of Uttar Pradesh, Madhya Pradesh, and Delhi. The study design included: collection and scoring of vaccine vial monitor (VVM) status of the samples and testing for total oral polio virus concentration (TOPV) by standard WHO protocol. Ten samples each were exposed to 25 degrees C and 37 degrees C, and 10 samples as controls were kept at -20 degrees C. VVM were scored daily till they attained grade 4 and each sample was subsequently subjected to potency testing for individual polio serotypes 1, 2 and 3, and TOPV. Of the 674 samples tested it was observed that: samples from immunization clinics and district stores had an acceptable VVM score of grade 1 and 2; however the probable risk that a sub potent vaccine could have been administered was 2.15%. In 2.5% samples received from district stores vaccine had a VVM score of grade 3 (i.e., discard point), although vaccine when tested was found to be potent (i.e., leading to the vaccine wastage). With exposure to higher temperatures, VVM changed score to grade 2 and 3 when the vaccine was kept at 25 degrees C/37 degrees C, and the titres of individual serotypes 1, 2 and 3 and TOPV were beyond the acceptable limits. Important observations at the different levels of vaccine distribution network and correlation of VVM and potency status of OPV are discussed in the paper which will be of help to the EPI program managers at different transit levels.