Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach.

Small cardamom (Elettaria cardamomum), grown in limited coastal tropical countries is one of the costliest and widely exported agri-produce having global turnover of >10 billion USD. Mosaic/marble disease is one of the major impediments that requires understanding of disease at molecular level. Neither whole genome sequence nor any genomic resources are available, thus RNA seq approach can be a rapid and economical alternative. De novo transcriptome assembly was done with Illumina Hiseq data. A total of 5317 DEGs, 2267 TFs, 114 pathways and 175,952 genic region putative markers were obtained. Gene regulatory network analysis deciphered molecular events involved in marble disease. This is the first transcriptomic report revealing disease mechanism mediated by perturbation in auxin homeostasis and ethylene signalling leading to senescence. The web-genomic resource (SCMVTDb) catalogues putative molecular markers, candidate genes and transcript information. SCMVTDb can be used in germplasm improvement against mosaic disease in endeavour of small cardamom productivity. Availability of genomic resource, SCMVTDb: http://webtom.cabgrid.res.in/scmvtdb/.

Identification of stable reference gene for transcript normalization in black pepper-Phytophthora capsici pathosystem.

A systematic validation of reference genes is a pre-requisite for the proper normalization of gene transcripts. In the present study, the annotated sequences from black pepper (Piper nigrum L.) leaf transcriptome were used as reference genes namely actin (PnACT), glyceraldehyde phosphate dehydrogenase (PnGAPDH), ß-tubulin (PnTUB), ubiquitin conjugating enzyme (PnUBCE), 18srRNA and elongation factor-1-α (PnElF) to identify the stable reference gene. We focused the selection of stable reference gene on important biotic stress (Phytophthora) with different algorithms (geNorm, NormFinder and BestKeeper) along with Reffinder which resulted in identification of PnGAPDH and PnUBCE as stable genes. Norm qPCR (R package) was also used to estimate the stability of the selected genes. We elucidated the expression patterns of a target gene PnBGLU which codes for 1,3 beta glucanase with most stable as well as least stable reference genes by which the importance of selecting the stable gene for gene expression studies in this system was emphasized. The mean expression levels of PnBGLU was significantly overestimated and misinterpreted when least stable reference gene was used as normalizer. The selected reference genes on further analysis of the expression dynamics of PnBGLU among resistant and susceptible genotypes showed PnGAPDH as the suitable reference gene for P. nigrum-P. capsici pathosystem.

Proteomics assisted profiling of antimicrobial peptide signatures from black pepper (Piper nigrum L.).

Plant antimicrobial peptides are the interesting source of studies in defense response as they are essential components of innate immunity which exert rapid defense response. In spite of abundant reports on the isolation of antimicrobial peptides (AMPs) from many sources, the profile of AMPs expressed/identified from single crop species under certain stress/physiological condition is still unknown. This work describes the AMP signature profile of black pepper and their expression upon Phytophthora infection using label-free quantitative proteomics strategy. The differential expression of 24 AMPs suggests that a combinatorial strategy is working in the defense network. The 24 AMP signatures belonged to the cationic, anionic, cysteine-rich and cysteine-free group. As the first report on the possible involvement of AMP signature in Phytophthora infection, our results offer a platform for further study on regulation, evolutionary importance and exploitation of theses AMPs as next generation molecules against pathogens.

Influence of temperature on symptom expression, detection of host factors in virus infected Piper nigrum L.

Expression of symptoms in black pepper plants (Piper nigrum) infected with Piper yellow mottle virus (PYMoV) vary depending on the season, being high during summer months. Here, we explored the influence of temperature on symptom expression in PYMoV infected P. nigrum. Our controlled environment study revealed increase in virus titer, total proteins, IAA and reducing sugars when exposed to temperature stress. There was change in the 2-D separated protein before and after exposure. The 2-D proteomics LC-MS identified host and viral proteins suggesting virus-host interaction during symptom expression. The analysis as well as detection of host biochemical compounds may help in understanding the detailed mechanisms underlying the viral replication and damage to the crop, and thereby plan management strategies.

Rapid Genome-Wide Location-Specific Polymorphic SSR Marker Discovery in Black Pepper by GBS Approach.

Black pepper (Piper nigrum), the "King of Spices," is an economically important spice in India and is known for its medicinal and cultural values. SSRs, the tandem repeats of small DNA sequences, are often polymorphic in nature with diverse applications. For population structure, QTL/gene discovery, MAS, and diversity analysis, it is imperative to have their location specificity. The existing PinigSSRdb catalogs ~70K putative SSR markers but these are anonymous (unknown chromosomal location), based on 916 scaffolds rather than 26 chromosomes. Under this study, we generated ddRAD sequence data of 29 black pepper genotypes from all over India, being low-cost and most efficient technique for the identification of polymorphic markers. The major limitation of ddRAD with compromised/non-uniform coverage has been successfully overcome by taking advantage of chromosome-wise data availability. The latest black pepper genome assembly was used to extract genome-wide SSRs. A total of 276,230 genomic SSRs were mined distributed over 26 chromosomes, with relative density of 362.88 SSRs/Mb and average distance of 2.76 Kb between two SSRs. This assembly was also used to find the polymorphic SSRs in the generated GBS data of 29 black pepper genotypes utilizing rapid and cost-effective method giving 3,176 polymorphic SSRs, out of which 2015 were found to be hypervariable. The developed web-genomic resource, BlackP2MSATdb (http://webtom.cabgrid.res.in/blackp2msatdb/), is the largest and first reported web resource for genomic and polymorphic SSRs of black pepper, which is useful to develop varietal signature, coreset, physical map, QTL/gene identification, and MAS in endeavor of black pepper production.

Digital and advanced imaging in endodontics: a review.

This review provides an overview of digital radiography as it exists, including advanced imaging such as computed tomography (CT), cone beam volumetric imaging, and micro-CT as relevant to the practice of endodontics. An evidence-based approach to adoption of different imaging technologies is included to assist the practitioner with the selection process of imaging modalities. Commonly used imaging terminology is introduced, as well as the advantages and disadvantages of image processing. New image reconstruction techniques have been introduced that provide information three-dimensionally to the clinician for routine endodontic and surgical treatment planning. The age of three-dimensional imaging and image processing is here. Limitations and advantages of newly introduced imaging modalities are discussed briefly.

Prevalence of Middle Mesial Canals and Isthmi in the Mesial Root of Mandibular Molars: An In Vivo Cone-beam Computed Tomographic Study.

INTRODUCTION: Many studies have investigated the morphology of the mandibular molar, but the prevalence of the middle mesial (MM) canal in the mesial root of the mandibular molar is still the subject of controversy. In addition, in previous literature, a true MM canal has not been clearly distinguished from an isthmus between the mesiobuccal and mesiolingual canals. Therefore, the objectives of this study were 2-fold: METHODS: Ninety limited field of view cone-beam computed tomographic scans were observed. One hundred twenty-two mature mandibular first and second molars with no previous root canal treatment, no root resorption, and intact crowns were retrospectively evaluated. Data regarding the sex, age, presence of MM canals, and number of root canals in the mesial root were recorded. RESULT: Of the 122 teeth, 20 (16.4%) had true MM canals. The prevalence of MM canals was 26% in first molars and 8% in second molars (P < .05). The frequency of isthmi in the mesial roots was 64.7%. The frequency of isthmi was higher in second molars, but the difference was not statistically significant (P > .05). CONCLUSIONS: This study showed a high prevalence of mandibular molars with MM canals or isthmi. The detection and biomechanical cleaning of these areas during nonsurgical or surgical root canal treatment are critical.

Niosome encapsulated of vincristine sulfate: improved anticancer activity with reduced toxicity in mice.

Nonionic surfactant vesicles (niosomes) are promising drug carriers for anticancer drugs. Niosome encapsulated vincristine sulfate prepared by transmembrane pH gradient drug uptake process (remote loading method) was evaluated for toxicity and antitumour activity after administration to tumour bearing mice. The toxicity of vincristine sulfate was reduced after niosome encapsulation and anticancer activity improved, which may be due to better delivery of vincristine at the tumour site.

Effect of macrophage activation on plasma disposition of niosomal 3H-methotrexate in sarcoma-180 bearing mice.

Methotrexate niosomes were formed by reverse phase evaporation technique using sorbitan monostearate (Span 60) surfactant. The pharmacokinetic parameters of methotrexate (MTX) after macrophage activation via muramyl dipeptide gelatin conjugate were studied and the results compared with those obtained after free MTX and MTX niosomes without macrophage activation. In mice MTX concentrations and tumour regression were higher after macrophage activation.

Effect of iterative restoration on the detection of artificially induced vertical radicular fractures by Tuned Aperture Computed Tomography.

OBJECTIVE: The purpose of this study was to evaluate the effect of the number of iterative restorations (IR) on the diagnostic accuracy of Tuned Aperture Computed Tomography images (TACT) for detection of induced vertical/oblique root fractures in mandibular teeth. STUDY DESIGN: Fractures were induced in 28 single-rooted, endodontically treated cadaver mandibular teeth while another 26 such teeth served as controls. TACT slices reconstructed by using 9 arbitrary projections (angular disparity of 9 degrees -20 degrees) were iteratively restored 1, 2, and 3 times. Eight observers scored their diagnoses by using a confidence rating scale. Ground truth was available from direct examination with transillumination, following extraction. RESULTS: Mean areas under the representative ROC curves for the 3 operations were 0.96 (3 IRs), 0.87 (2 IRs), and 0.86 (1 IRs). Analysis of variance demonstrated significant differences between 3 and 1 to 2 IRs (P <.01), as well as between observers (P <.01). CONCLUSION: Diagnostic accuracy of TACT for vertical/oblique root fracture detection improved after 3 IRs.

Antitumor and antifertility activities of plumbagin controlled release formulations.

With a view to increase efficiency and reduce toxicity of Plumbagin, an attempt was made to formulate plumbagin as a controlled release preparation using various carriers and test for their antitumor and antifertility activities. Niosomes and albumin microspheres were used as carriers. In vitro data showed promising results for these formulations thus they were taken up for in vivo assessment. Given at a dose of 5 mg/kg, ip the albumin microspheres showed promising antitumor and antifertility activity when compared to the niosomes on control. Animal survival data also indicated slight improvement in survival rate and thus antitumoral activity. Also, an interesting point was that the antifertility activity was affected through an antiovulatory action as seen from histopathological studies.

Sero diagnosis of tuberculosis in children using two ELISA kits.

The diagnosis of childhood tuberculosis is based on circumstantial evidence in the absence of a gold standard in the majority of cases. Sero-diagnosis offers scope for an early diagnosis in a variety of clinical conditions and is simple to perform. A number of mycobacterial antigens have been used for antibody detection assays and several are available as kits in the market. This study was done to evaluate the value of antibody detection kits (ELISA) against the A60 antigen and 38 kDa antigen of Mycobacterium tuberculosis in the diagnosis of childhood tuberculosis at the outpatient department of the Institute of Social Paediatrics, Government Stanley Hospital in collaboration with Tuberculosis Research Centre, Chennai. Thirty five children with pulmonary tuberculosis, 7 with TB lymphadenitis and 22 healthy controls were studied. In addition to routine investigations including gastric lavage for AFB culture, serum antibodies against the A60 and 38 kDa antigens were assayed using commercially available ELISA kits. With A60, IgM serum levels were positive in 74% of pulmonary TB cases, 57% of TB lymphadenitis cases and 50% of controls. A60 IgG was positive in 17% of pulmonary TB, 86% of TB lymphadenitis and 14% of controls. The 38 kDa IgG antibody was positive in 37% of pulmonary and 86% of TB lymphadenitis cases and 27% of controls. Among 10 culture confirmed cases, A60 IgM was positive in 8, A60 IgG in 3 and 38 kDa IgG in 5 patients. The sensitivity of the tests ranged between 29% and 71% and specificity between 50% and 86%. Although the numbers are small, the results suggest that serodiagnosis using the currently available antigens of M. tuberculosis is unlikely to be a confirmatory test for tuberculosis in children.

Structure and NLO properties of halogen (F, Cl) substituted formic acid dimers.

In this work, using ab initio and density functional theory (DFT) methods halogen substituted formic acid (FA) dimer is studied. The dimer stability is due to the hydrogen bonds, either conventional (OH⋯O, OH⋯F, OH⋯Cl) or non-conventional (CH⋯O, CH⋯F, CH⋯Cl). Among all the dimers, trans-trans form is more stable than the trans-cis, and cis-cis form. Basis set extrapolated counterpoise corrected interaction energy results for the FA dimer are in excellent agreement with BSSE corrected MP2 interaction energy. Symmetry Adopted Perturbation Theory (SAPT) analysis reveals that the electrostatic effect plays a dominant role in stabilization among the dimers with maximum interaction energy. Chlorine substituted FA dimer has high hyperpolarizability, which makes them excellent candidate for nonlinear optical materials (NLO). The halogen substituted formic acid dimers have higher stability and polarizability value than the unsubstituted formic acid dimer. The hyperpolarizability values depend on the geometrical structures of halogenated formic acid dimers than the type of hydrogen bonds. The small excitation energy and HOMO-LUMO gap in the halogenated formic acid dimer has led to the strong nonlinear optical response. The depolarization ratio and Rayleigh scattering increases in formic acid dimer after the halogen atom substitution.

Effect of yoga therapy on anxiety and depressive symptoms and quality-of-life among caregivers of in-patients with neurological disorders at a tertiary care center in India: A randomized controlled trial.

CONTEXT: The concerns of caregivers of patients with neurological disorders have been a felt need for a long time, with many of them experiencing significant psychiatric morbidity. AIMS: This study aimed to find the effect of yoga in reducing anxiety and depression, as well as improving quality-of-life in caregivers of patients with neurological disorders. SETTINGS AND DESIGN: The study was conducted using a randomized controlled design, with yoga intervention and waitlisted controls. METHODOLOGY: SIXTY CONSENTING CAREGIVERS OF INPATIENTS IN NEUROLOGY WARDS WERE RANDOMIZED INTO TWO GROUPS: Yoga and control. Demographic variables except years of education and length of caretaking were comparable in the two groups, as also baseline scores of anxiety, depression and quality-of-life. A specific yoga module comprising yogasanas, pranayama, and chanting was taught to the participants in the yoga group by the researcher. At follow-up 43 patients (yoga n=20 and control group n=23) were available. Two-way repeated measures analysis of variance was used to test the change from pre-test to post-test scores within and between groups. Analysis of covariance was performed to compare the post-test scores between the groups adjusting for education and length of caretaking. RESULTS: Following one month intervention of yoga therapy, there was a significant (P<0.001) decrease in anxiety and depression scores, as well as improved quality-of-life among the participants in the yoga group as compared with the control group. CONCLUSION: This study highlights the usefulness of a yoga intervention for caregivers of inpatients with neurological problems. The small sample size and lack of blinding were some of the limitations of this study.

Configuration of the inferior alveolar canal as detected by cone beam computed tomography.

AIMS: The aim of this study is to evaluate the course of the inferior alveolar canal (IAC) including its frequently seen variations in relation to root apices and the cortices of the mandible at fixed pre-determined anatomic reference points using cone beam volumetric computed tomography (CBVCT). MATERIAL AND METHODS: This retrospective study utilized CBVCT images from 44 patients to obtain quantifiable data to localize the IAC. Measurements to the IAC were made from the buccal and lingual cortical plates (BCP/LCP), inferior border of the mandible and the root apices of the mandibular posterior teeth and canine. Descriptive analysis was used to map out the course of the IAC. RESULTS: IACs were noted to course superiorly toward the root apices from the second molar to the first premolar and closer to the buccal cortical plate anteriorly. The canal was closest to the LCP at the level of the second molar. In 32.95% of the cases, the canal was seen at the level of the canine. CONCLUSIONS: This study indicates that caution needs to be exercised during endodontic surgical procedures in the mandible even at the level of the canine. CBVCT seems to provide an optimal, low-dose, 3D imaging modality to help address the complexities in canal configuration.

Endodontic clinical management of a dens invaginatus case by using a unique treatment approach: a case report.

INTRODUCTION: Dens invaginatus is a developmental anomaly that poses treatment challenges when nonsurgical root canal therapy is deemed necessary. Teeth with complex root canal morphology often require a comprehensive treatment approach to effectively clean, shape, and disinfect the pulp canal space before obturation. Endodontic clinical management of a tooth with dens invaginatus might include using cone-beam computed tomography (CBCT) to aid in the diagnosis and treatment-planning phase and use of the surgical operating microscope in performing the clinical phase of treatment. A novel approach could include using the revascularization technique as the final treatment step in the management of a dens invaginatus case in which the root apex has not completed formation. METHODS: This case report will provide both an overview of the feasibility of using CBCT scans in diagnosis and treatment planning and a step-by-step clinical technique, by using surgical operating microscope and the revascularization technique, in the successful endodontic management of a complex dens invaginatus case. CONCLUSIONS: Five-month and 12-month follow-up clinical and radiographic findings will provide a candid view of inherent advantages and challenges of this technique.

The present scenario of cervical cancer control and HPV epidemiology in India: an outline.

OBJECTIVE: To give a clear picture with epidemiological evidence about the present scenario of cervical cancer control and HPV in India. DESIGN: Review of published studies, concentrating on recent systematic reviews, meta-analyses and large prospective studies. CONCLUSIONS AND RECOMMENDATIONS: Cervical cancer is unique among cancers in that it can largely be prevented through screening and removal of precursor lesions. It is the second most common cancer among women worldwide and is the most common malignancy in developing countries, particularly in India. Nowadays, cervical screening for women is necessary because there are no signs and symptoms of cervical precancers. The establishment of a prevention program is urgently required considering both screening and vaccination. But most women in India do not have access to effective screening programmes. It has been estimated that in India, even with a major effort to expand cytology services, it will not be possible to screen even one-fourth of the population once in a lifetime in the near future. New HPV vaccines will also help prevent HPV infection and the precancerous changes that lead to cervical cancer. The focus on detection and prevention of cervical cancer must be emphasized in a highly populated country like India to prevent its extensive spread.

Effect of gallic acid on xenobiotic metabolizing enzymes in 1,2-dimethyl hydrazine induced colon carcinogenesis in Wistar rats--a chemopreventive approach.

Colon cancer risk may be influenced by phase I and II xenobiotic-metabolizing enzyme systems. The chemopreventive agent gallic acid (GA), a plant polyphenol, is found in various natural products. Our aim was to evaluate the potential role of GA on drug-metabolizing enzymes in 1,2-dimethyl hydrazine (DMH) induced rat colon carcinogenesis. The total experimental duration was 30 weeks. The effect of GA (50 mg/kg b.w.) on the activities of phase I enzymes (cytochrome P450 and cytochrome b5) and phase II enzymes (glutathione S-transferase, DT-diaphorase and gamma glutamyl transpeptidase) were assessed in the liver and colonic mucosa and the colons were also examined visually. In DMH induced rats, there was a decrease in the activities of phase II enzymes and an increase in the activities of phase I enzymes. On GA supplementation, there was a significant increase in the activities of phase II enzymes and a significant decrease in the activities of phase I enzymes, in addition to the decreased tumor incidence. Histopathological changes also confirm this. Thus, the marked potential of GA in modulating the phase I and II xenobiotic-metabolizing enzymes suggests that GA may have a major impact on colon cancer chemoprevention.

Detection of vertical root fractures by using cone-beam computed tomography: a clinical study.

INTRODUCTION: Vertical root fractures of teeth (VRFs) often pose a diagnostic dilemma because of the difficulty in detection of these in intraoral radiographs except in certain cases with very distinct clinical findings. This often leads to unwarranted extraction of the tooth. Cone-beam computed tomography (CBCT) produces three-dimensional images and allows precise visualization and evaluation of VRFs or cracks in extracted teeth, as reported previously. This clinical pilot study was designed to determine the diagnostic accuracy of noninvasive CBCT for detection of suspected VRFs in endodontically treated teeth by using exploratory surgery to confirm the presence or absence of a fracture. METHODS: Thirty-two teeth in 29 patients with clinical signs and symptoms suggestive of VRF were included in the study after informed consent was obtained. They underwent a limited area CBCT evaluation. All CBCT studies were blinded, and 2 board-certified oral and maxillofacial radiologists assessed the presence or absence of VRF through sequential evaluation of the three-dimensional volume. Subjects underwent surgical exploration as part of treatment, which helped establish the presence or absence of VRF. RESULTS: Pearson correlation coefficient by using surgical finding to confirm presence/absence of fracture was 0.602, positive predictive value was 91%, and negative predictive value was 67%. The sensitivity was 88%, and specificity was 75%. CONCLUSIONS: This study revealed the superior diagnostic accuracy of CBCT for detection of VRF.