PANNOTATOR: an automated tool for annotation of pan-genomes

Due to next-generation sequence technologies, sequencing of bacterial genomes is no longer one of the main bottlenecks in bacterial research and the number of new genomes deposited in public databases continues to increase at an accelerating rate. Among these new genomes, several belong to the same species and were generated for pan-genomic studies. A pan-genomic study allows investigation of strain phenotypic differences based on genotypic differences. Along with a need for good assembly quality, it is also fundamental to guarantee good functional genome annotation of the different strains. In order to ensure quality and standards for functional genome annotation among different strains, we developed and made available PANNOTATOR (http://bnet.egr.vcu.edu/iioab/agenote.php), a web-based automated pipeline for the annotation of closely related and well-suited genomes for pan-genome studies, aiming at reducing the manual work to generate reports and corrections of various genome strains. PANNOTATOR achieved 98 and 76% of correctness for gene name and function, respectively, as result of an annotation transfer, with a similarity cut-off of 70%, compared with a gold standard annotation for the same species. These results surpassed the RAST and BASys softwares by 41 and 21% and 66 and 17% for gene name and function annotation, respectively, when there were reliable genome annotations of closely related species. PANNOTATOR provides fast and reliable pan-genome annotation; thereby allowing us to maintain the research focus on the main genotype differences between strains.

Association of interleukin-4 and interleukin-17F polymorphisms in periodontitis in Dravidian ethnicity

BACKGROUND:

Complex network of pro and anti-inflammatory cytokines are known to act in inflamed periodontal tissue. This study explores the distribution of interleukin (IL)-4 (+33 C/T) and IL-17F (7383A/G, 7488A/G) gene polymorphism in chronic and aggressive periodontitis subjects of Dravidian ethnicity.

MATERIALS AND METHODS:

This case control study consisted of 124 periodontitis individuals comprising of 63 chronic and 61 aggressive periodontitis subjects as cases, and control group consisted of 101 healthy subjects. All subjects were genotyped for IL-4 + 33C/T, IL-17F 7383A/G, 7488A/G by polymerase chain reaction amplification followed by TaqMan assay for IL-4 + 33C/T, restriction enzyme digestion and gel electrophoresis for IL-17F 7383A/G and sequencing for IL-17F 7488A/G.

RESULTS:

IL-4 + 33C/T was significantly associated with periodontitis (P < 0.05) at both allelic and genotypic level. In subgroup analysis also significant difference (P < 0.05) in allelic distribution between aggressive periodontitis and control group for loci IL-4 + 33C/T was noted. However, there was a lack of association between IL-17F 7383A/G and IL-17F 7488A/G with periodontitis and its sub-groups at both allelic and genotypic levels.

CONCLUSIONS:

In Malayalam speaking Dravidian population IL-4 + 33C/T loci appears to be an important risk factor for periodontal disease with a leaning towards aggressive periodontitis. The association between IL-17F at 7383A/G and 7488A/G loci with either chronic or an aggressive periodontitis could not be ascertained.

Formulation and optimization of mucoadhesive nanodrug delivery system of acyclovir

Acyclovir is an antiviral drug used for the treatment of herpes simplex virus infections, with an oral bioavailability of only 10-20% [limiting absorption in gastrointestinal tract to duodenum and jejunum] and half-life of about 3 h, and is soluble only at acidic pH (pKa 2.27). Mucoadhesive polymeric nanodrug delivery systems of acyclovir have been designed and optimized using 2(3) full factorial design. Poly (lactic-co-glycolic acid) (PLGA) (50:50) was used as the polymer along with polycarbophil (Noveon AA-1) as the mucoadhesive polymer and pluronic F68 as the stabilizer. From the preliminary trials, the constraints for independent variables X(1) (amount of PLGA), X(2) (amount of pluronic F68) and X(3) (amount of polycarbophil) have been fixed. The dependent variables that were selected for study were particle size (Y(1)), % drug entrapment (Y(2)) and % drug release in 12 h (Y(3)). The derived polynomial equations were verified by check point formulation. The application of factorial design gave a statistically systematic approach for the formulation and optimization of nanoparticles with the desired particle size, % drug release and high entrapment efficiency. Drug: Polymer ratio and concentration of stabilizer were found to influence the particle size and entrapment efficiency of acyclovir-loaded PLGA nanoparticles. The release was found to follow Fickian as well as non-Fickian diffusion mechanism with zero-order drug release for all batches. In vitro intestinal mucoadhesion of nanoparticles increased with increasing concentration of polycarbophil. These preliminary results indicate that acyclovir-loaded mucoadhesive PLGA nanoparticles could be effective in sustaining drug release for a prolonged period.

Weight loss for reduction of proteinuria in diabetic nephropathy: Comparison with angiotensin-converting enzyme inhibitor therapy

Reduction of weight in obese type 2 diabetes mellitus (T2DM) individuals is emerging as a significant strategy in the reduction of proteinuria in diabetic nephropathy along with control of hyperglycemia, hypertension, and dyslipidemia. The objective was to evaluate the reduction in 24-h proteinuria in T2DM patients with nephropathy by weight loss, with conventional therapy (angiotensin-converting enzyme [ACE] inhibitors) as the control arm. A prospective, randomized controlled trial was conducted between June 2010 and May 2011. T2DM patients with confirmed nephropathy by 24-h urinary protein estimation with a body mass index (BMI) of >25 kg/m² were studied. Patients who had nondiabetic nephropathy, uncontrolled hypertension (>125/75 mmHg) irrespective of antihypertensive drugs, excess weight due to edema or obesity due to other specific diseases, alcoholics, smokers, and patients who were on hemodialysis were excluded from the study. The patients were divided into three groups, namely, group A, patients on ACE inhibitor therapy; group B, patients on lifestyle modifications for weight loss; and group C, patients on an antiobesity drug (orlistat) and lifestyle modifications. At the end of 6 months, all the three groups were compared. Data were analyzed using software SPSS version 15.0. This study encompassed a total of 88 patients; 12 patients were dropped during the study period and 76 (group A: 22, group B: 23, and group C: 31) patients remained. The mean age of the patients was 58.36 ± 10.87 years (range: 30-70 years). At baseline, age, gender, mean BMI, waist-to-hip ratio (WHR), and 24-h proteinuria did not vary significantly among the three groups. At 6 months, the mean BMI significantly decreased in group C (P < 0.001) compared to that in the other two groups. Among the parameters BMI and WHR, the proportional form of BMI correlated well with the degree of reduction in proteinuria (r = 0.397, P = 0.01). Reduction in weight using lifestyle modifications and antiobesity drugs might improve renal function and proteinuria safely as observed in obese patients with diabetic nephropathy.

Nanoparticles laden in situ gelling system for ocular drug targeting

Designing an ophthalmic drug delivery system is one of the most difficult challenges for the researchers. The anatomy and physiology of eye create barriers like blinking which leads to the poor retention time and penetration of drug moiety. Some conventional ocular drug delivery systems show shortcomings such as enhanced pre-corneal elimination, high variability in efficiency, and blurred vision. To overcome these problems, several novel drug delivery systems such as liposomes, nanoparticles, hydrogels, and in situ gels have been developed. In situ-forming hydrogels are liquid upon instillation and undergo phase transition in the ocular cul-de-sac to form viscoelastic gel and this provides a response to environmental changes. In the past few years, an impressive number of novel temperature, pH, and ion-induced in situ-forming systems have been reported for sustain ophthalmic drug delivery. Each system has its own advantages and drawbacks. Thus, a combination of two drug delivery systems, i.e., nanoparticles and in situ gel, has been developed which is known as nanoparticle laden in situ gel. This review describes every aspects of this novel formulation, which present the readers an exhaustive detail and might contribute to research and development.

Posttreatment evaluation of central nervous system gliomas

Although conventional contrast-enhanced MR imaging remains the standard-of-care imaging method in the posttreatment evaluation of gliomas, recent developments in therapeutic options such as chemoradiation and antiangiogenic agents have caused the neuro-oncology community to rethink traditional imaging criteria. This article highlights the latest recommendations. These recommendations should be viewed as works in progress. As more is learned about the pathophysiology of glioma treatment response, quantitative imaging biomarkers will be validated within this context. There will likely be further refinements to glioma response criteria, although the lack of technical standardization in image acquisition, postprocessing, and interpretation also need to be addressed.

Can Metabolic Factors be used Prognostically for Short-Term Mortality in HIV-Infected Patients?

BACKGROUND

Metabolic abnormalities are common throughout the course of human immunodeficiency virus (HIV) infection and may occur either due to HIV infection or as a result of side effects of antiretroviral therapy. It has been established that dyslipidemia and dysglycemia associated with HIV disease reduce the long-term survival of the patients, but their role for predicting prognosis of short-term mortality in HIV patients is unknown.

AIM

To study dyslipidemia and dysglycemia as a prognostic indicator for short-term mortality (<3 months) in HIV patients.

SUBJECTS AND METHODS

An observational, prospective study was conducted at a tertiary care center over a period of 6 months. Consecutive HIV-positive patients hospitalized (both, HIV status known prior to hospitalization and the diagnosis made for the first time at admission) in medical wards from March to May 2010 were studied. All patients had their random blood sugars, fasting blood sugars (if possible), fasting lipid profile, and cluster of differentiation 4 (CD4) counts tested at the time of enrollment. The patients were followed for a period of 3 months, at the end of which they were categorized as survivors and non-survivors, and the demographic, clinical, and investigational parameters were compared between the above groups. Data was analyzed by applying Mann-Whitney U test, two sample t-test, Fisher-Exact test, and stepwise logistic regression analysis of significance, using the computer-based program, Stata, version 11.1.

RESULTS

A total of 82 patients were enrolled for the study of which 64 (78.05%) were males and 18 (21.95%) were females, with a mean (SD) age of 34.00 (7.0) years. The mean CD4 count was 206.23 (129.5) cells/mm(3). The overall mortality within 3 months was 20.7% (17/82). Mycobacterium tuberculosis as opportunistic infection was found in 42 patients, out of which 13 expired (P=0.02). Patients with low high-density lipoprotein (HDL) and hypertriglyceridemia (adjusted OR = 22.92, P value = 0.03, adjusted OR = 3.4, P value = 0.02, respectively) had high likelihood of mortality within 3 months.

CONCLUSIONS

Low HDL and hypertriglyceridemia also appear to be promising short-term mortality markers in HIV patients apart from established factors like low CD4 counts, co-morbid conditions, and opportunistic infections like M. tuberculosis infection. This study warrants further studies with a larger sample size to establish HDL and triglyceride as markers of disease progression and short-term mortality in HIV-infection.

Study on Clinico-Laboratory Profile of Children with Scrub Typhus

Scrub typhus is an acute, febrile, infectious illness caused by Orientia (formerly Rickettsia) tsutsugamushi,an obligate intracellular gram-negative bacterium. Humans are accidental hosts in this zoonotic disease.The present retrospective study describes clinical profile of the children hospitalized in hospital with Scrub Typhus infection during period 2010-2011. 19 hospitalized children with clinical features suggestive of Rickettsial disease (fever, generalized rash) who tested ELISA positive for IgM against Scrub Typhus were included in the present study between the age of 1 years and 15 years. All children presented with fever (100%). 42.10% had lymphadenopathy, 47.36% had eschar and 57.89% patients had cough. 26.31, 21.05%, 10.52%, had hepatomegaly, pain abdomen, and respiratory distress and gastrointestinal bleed respectively. All of the children were investigated and treated with as per protocol. None of them died. We think that Rickettsial infection is not quite common in this region but study showed that it is not an uncommon entity and thus, high degree of suspicion, knowledge of geographical distribution and clinical features of Rickettsial disease helps in its early diagnosis and treatment. J Nepal Paediatr Soc 2012;32(2):187-192 doi: http://dx.doi.org/10.3126/jnps.v32i2.5683

Convergent functional genomics of schizophrenia: from comprehensive understanding to genetic risk prediction

We have used a translational convergent functional genomics (CFG) approach to identify and prioritize genes involved in schizophrenia, by gene-level integration of genome-wide association study data with other genetic and gene expression studies in humans and animal models. Using this polyevidence scoring and pathway analyses, we identify top genes (DISC1, TCF4, MBP, MOBP, NCAM1, NRCAM, NDUFV2, RAB18, as well as ADCYAP1, BDNF, CNR1, COMT, DRD2, DTNBP1, GAD1, GRIA1, GRIN2B, HTR2A, NRG1, RELN, SNAP-25, TNIK), brain development, myelination, cell adhesion, glutamate receptor signaling, G-protein-coupled receptor signaling and cAMP-mediated signaling as key to pathophysiology and as targets for therapeutic intervention. Overall, the data are consistent with a model of disrupted connectivity in schizophrenia, resulting from the effects of neurodevelopmental environmental stress on a background of genetic vulnerability. In addition, we show how the top candidate genes identified by CFG can be used to generate a genetic risk prediction score (GRPS) to aid schizophrenia diagnostics, with predictive ability in independent cohorts. The GRPS also differentiates classic age of onset schizophrenia from early onset and late-onset disease. We also show, in three independent cohorts, two European American and one African American, increasing overlap, reproducibility and consistency of findings from single-nucleotide polymorphisms to genes, then genes prioritized by CFG, and ultimately at the level of biological pathways and mechanisms. Finally, we compared our top candidate genes for schizophrenia from this analysis with top candidate genes for bipolar disorder and anxiety disorders from previous CFG analyses conducted by us, as well as findings from the fields of autism and Alzheimer. Overall, our work maps the genomic and biological landscape for schizophrenia, providing leads towards a better understanding of illness, diagnostics and therapeutics. It also reveals the significant genetic overlap with other major psychiatric disorder domains, suggesting the need for improved nosology.

Diagnosis and inflammatory response of patients with candiduria

Candiduria is common in hospitalised patients, but the clinical relevance is still unclear. This study was done to further our knowledge on detection of and host responses to candiduria. Urines and clinical data from 136 patients in whom presence of yeast was diagnosed by microscopic urinalysis were collected. Diagnosis by standard urine culture methods on blood and MacConkey agar as well as on fungal culture medium (Sabouraud dextrose agar) was compared. Inflammatory parameters (IL-6 and IL-17, Ig) were quantified in the urine and compared with levels in control patients without candiduria. Standard urine culture methods detected only 37% of Candida spp. in urine. Sensitivity was especially low (23%) for C. glabrata and was independent of fungal burden. Candida specific IgG but not IgA was significantly elevated when compared with control patients (P < 0.0001 and 0.07 respectively). In addition, urine levels of IL-6 and IL-17 were significantly higher in candiduric patients when compared with control patients (P < 0.001). Multivariate analysis documented an independent association between an increased IgG (odds ratio (OR) 136.0, 95% confidence interval (CI) 25.7-719.2; P < 0.0001), an increased IL-17 (OR 17.4, 95% CI 5.3-57.0; P < 0.0001) and an increased IL-6 level (OR 4.9, 95% CI 1.9-12.4; P = 0.001) and candiduria. In summary, our data indicate that clinical studies on candiduria should include fungal urine culture and that inflammatory parameters may be helpful to identify patients with clinically relevant candiduria.

Effect of gingivitis on azithromycin concentrations in gingival crevicular fluid

BACKGROUND

Macrolide antibiotics yield high concentrations in inflamed tissue, suggesting that their levels in gingival crevicular fluid (GCF) could be increased at gingivitis sites. However, the increased volume of GCF associated with gingivitis could potentially dilute macrolides. To determine whether these assumptions are correct, the bioavailability of systemically administered azithromycin was compared in GCF from healthy and gingivitis sites.

METHODS

Experimental gingivitis was induced in one maxillary posterior sextant in nine healthy individuals. Contralateral healthy sextants served as controls. Participants ingested 500 mg azithromycin, followed by a 250-mg dose 24 hours later. Four hours after the second dose, plaque was removed from experimental sites. GCF was collected from eight surfaces in both the experimental and control sextants and pooled separately. GCF samples were subsequently collected on days 2, 3, 8, and 15, and azithromycin content was determined by agar diffusion bioassay.

RESULTS

On days 2 and 3, the pooled GCF volume at experimental sites was significantly higher than at control sites (P <0.01), and the total azithromycin mass in 30-second GCF samples pooled from experimental sites was significantly higher than at control sites (P <0.02). However, there were no significant differences in azithromycin concentration between the experimental and control pools at any point. Concentrations exceeded 7.3 μg/mL on day 2 and 2.5 μg/mL on day 15.

CONCLUSION

Azithromycin concentrations are similar in GCF from gingivitis sites and healthy sites, suggesting that the processes that regulate GCF azithromycin concentration can compensate for local inflammatory changes.