Generation of LexA enhancer-trap lines in Drosophila by an international scholastic network

Conditional gene regulation in Drosophila through binary expression systems like the LexA-LexAop system provides a superb tool for investigating gene and tissue function. To increase the availability of defined LexA enhancer trap insertions, we present molecular, genetic, and tissue expression studies of 301 novel Stan-X LexA enhancer traps derived from mobilization of the index SX4 line. This includes insertions into distinct loci on the X, II, and III chromosomes that were not previously associated with enhancer traps or targeted LexA constructs, an insertion into ptc, and seventeen insertions into natural transposons. A subset of enhancer traps was expressed in CNS neurons known to produce and secrete insulin, an essential regulator of growth, development, and metabolism. Fly lines described here were generated and characterized through studies by students and teachers in an international network of genetics classes at public, independent high schools, and universities serving a diversity of students, including those underrepresented in science. Thus, a unique partnership between secondary schools and university-based programs has produced and characterized novel resources in Drosophila, establishing instructional paradigms devoted to unscripted experimental science.

Impact of Undernutrition on Tuberculosis Treatment Outcomes in India: A Multicenter, Prospective, Cohort Analysis

BACKGROUND

Undernutrition is the leading risk factor for tuberculosis (TB) globally. Its impact on treatment outcomes is poorly defined.

METHODS

We conducted a prospective cohort analysis of adults with drug-sensitive pulmonary TB at 5 sites from 2015-2019. Using multivariable Poisson regression, we assessed associations between unfavorable outcomes and nutritional status based on body mass index (BMI) nutritional status at treatment initiation, BMI prior to TB disease, stunting, and stagnant or declining BMI after 2 months of TB treatment. Unfavorable outcome was defined as a composite of treatment failure, death, or relapse within 6 months of treatment completion.

RESULTS

Severe undernutrition (BMI <16 kg/m2) at treatment initiation and severe undernutrition before the onset of TB disease were both associated with unfavorable outcomes (adjusted incidence rate ratio [aIRR], 2.05; 95% confidence interval [CI], 1.42-2.91 and aIRR, 2.20; 95% CI, 1.16-3.94, respectively). Additionally, lack of BMI increase after treatment initiation was associated with increased unfavorable outcomes (aIRR, 1.81; 95% CI, 1.27-2.61). Severe stunting (height-for-age z score <-3) was associated with unfavorable outcomes (aIRR, 1.52; 95% CI, 1.00-2.24). Severe undernutrition at treatment initiation and lack of BMI increase during treatment were associated with a 4- and 5-fold higher rate of death, respectively.

CONCLUSIONS

Premorbid undernutrition, undernutrition at treatment initiation, lack of BMI increase after intensive therapy, and severe stunting are associated with unfavorable TB treatment outcomes. These data highlight the need to address this widely prevalent TB comorbidity. Nutritional assessment should be integrated into standard TB care.

Aloe vera and its two bioactive constituents in alleviation of diabetes -proteomic & mechanistic insights

ETHNOPHARMACOLOGICAL RELEVANCE

Aloe barbadensis Miller, commonly known as Aloe vera has been used since time immemorial for treatment of various diseases such as cancer, inflammatory disorders, diabetes, wound healing etc. AIM: Diabetes mellitus is a complex disorder and understanding the molecular mechanisms involved is a key to identify different markers for early diagnosis of the disease. The proteomic approach offers a plethora of opportunities to identify markers and targets involved in pathogenesis of diabetes. The present study was undertaken to understand the mechanism of action of Aloe vera and its two constituents (Carbohydrates and Polypeptides) in the alleviation of diabetes in streptozotocin-induced diabetic rats through a proteomics approach.

METHODS

Different groups of rats were fed with Aloe vera extract, carbohydrate fraction and peptide/polypeptide fraction for three weeks. The diabetic rats fed with Aloe vera and its two fractions restored the glucose and insulin levels to normal. The plasma of the rats was depleted with IgG and albumin and proteomic analysis was carried out. Apolipoproteins (dyslipidemia), complement factors (inflammatory pathways), zonulin (intestinal permeability), anti-oxidant related proteins were selected in this study as these are involved in the progression of diabetes.

RESULTS

It was observed that Aloe vera extract is involved in the alleviation of diabetes through these pathways while the carbohydrate fraction alleviates diabetes through an anti-oxidant mechanism and glucose uptake while the polypeptide fraction alleviates diabetes through the restoration of intestinal permeability by reduced zonulin levels.

CONCLUSION

The constituents of Aloe vera works different pathways involved in diabetes and the synergistic effect of these constituents make Aloe vera extract a prospective candidate, which can alleviate diabetes through regulation of the pathways involved in the progression of diabetes.

Development and Validation of a LC-MS/MS Method for the Profiling of Impurities Formed during Stress Study of Antifungal Agent-Efinaconazole

Liquid chromatography interfaced with mass spectroscopy (LC-MS) is a sensitive and effective analytical method that combines high-resolution separation as well as specific mass detection of impurities in formulated products and as well as in active pharmaceutical ingredient (API). In this study, LC-MS/MS was used to determine impurities formed during the stability period of Efinaconazole (EFZ, a triazole antifungal agent). The method was validated for its assay parameters such as specificity, linearity, accuracy, precision and also for solution stability. The calibration curve was found to be linear for the concentration range from 0.5 μg/mL to 30 μg/mL. A thorough investigation was performed by exposing Efinaconazole (1 mg/mL) to various stress conditions such as hydrolysis (acid and alkaline), oxidation, photolysis and temperature at various time intervals to achieve 10% degradation. The impurities formed during forced degradation were separated using high-performance liquid chromatography later it was identified using LC-MS/MS technique. The obtained results showed that EFZ is prone to oxidation when exposed to a 3% aqueous medium of hydrogen peroxide solution and quite stable in all the remaining stress conditions for a longer period.

Role of zonulin and GLP-1/DPP-IV in alleviation of diabetes mellitus by peptide/polypeptide fraction of Aloe vera in streptozotocin- induced diabetic wistar rats

ETHNO-PHARMACOLOGICAL RELEVANCE

The genus Aloe has a long history of usage in medicine. Aloe barbadensis Miller, commonly known as Aloe vera, is said to possess anti-diabetic, anti-inflammatory, anti-cancer, anti-microbial, immunomodulation, wound healing properties.

AIM OF THE STUDY

In diabetes mellitus, loss in intestinal permeability is observed with high levels of zonulin and low levels of glucagon-like peptide-1 (GLP-1) leading to hyperglycemia. The aim of the study was to understand the role of peptide/polypeptide fraction (PPF) of Aloe vera in the alleviation of diabetes through maintaining the intestinal permeability by regulating the zonulin and GLP-1 levels.

MATERIALS AND METHODS

The PPF of Aloe vera was obtained through trichloroacetic acid precipitation. The anti-diabetic potential of the PPF was tested through DPP-IV inhibition, glucose diffusion assay, and by using Rin-m5F cells. The anti-diabetic potential of the PPF was tested at a dose of 0.450 mg/kg bw in vivo using streptozotocin-induced diabetic Wistar rats. The effect of PPF on fasting plasma glucose, insulin, glucagon, Zonulin, GLP-1, DPP-IV, levels were studied in diabetic rats. The histopathological studies of the pancreas, small intestine, and liver were carried out for organ-specific effects.

RESULTS

PPF has the ability to reduce fasting plasma glucose levels with concomitant increase in insulin levels in streptozotocin-induced diabetic rats. It was also observed that increase in GLP-1 levels with a decrease in DPP-IV and zonulin levels thereby mitigating the loss of intestinal permeability. These findings correlate with the small intestine's histopathological observation where the excessive proliferation of epithelium in the small intestine of diabetic rats was reduced after PPF treatment.

CONCLUSION

These results suggest that the PPF of Aloe vera alleviates diabetes through islet cell rejuvenation via GLP-1/DPP-IV pathway and thereby suggesting the usage of PPF as an alternate medicine for diabetes mellitus with the possibility to reduce the intestinal permeability and zonulin levels.

Different coordination geometries of lighter lanthanates driven by the symmetry of guanidines as charge compensators

Six and nine coordination geometries of lighter lanthanates have been successfully synthesized using a controlled process under oil-bath conditions.

Comorbidities in pulmonary tuberculosis cases in Puducherry and Tamil Nadu, India: Opportunities for intervention

Background

We aimed to define characteristics of TB patients in Puducherry and two districts of Tamil Nadu, India and calculate the population attributable fractions (PAF) of TB from malnutrition and alcohol.

Methods

New smear-positive TB cases were enrolled into the Regional Prospective Observational Research for Tuberculosis (RePORT India) cohort. Census and National Family Health Survey data were used for comparisons.

Results

Data were analyzed for 409 participants enrolled between May 2014-June 2016; 307 (75.1%) were male, 60.2% were malnourished (body mass index [BMI] <18.5 kg/m²), and 29.1% severely malnourished (BMI <16). “Hazardous” alcohol use (based on AUDIT-C score) was reported by 155/305 (50.8%) of males. Tuberculosis cases were more likely than the Puducherry population to be malnourished (62.6% v 10.2% males and 71.7% v 11.3% of females; both p<0.001), and male cases were more likely to use alcohol than male non-cases (84.4% v 41%; p < .001). The PAF of malnutrition was 57.4% in males and 61.5% in females; the PAF for alcohol use was 73.8% in males and 1.7% in females.

Conclusions

Alcohol use in men and malnutrition are helping drive the TB epidemic in Southern India. Reducing the TB burden in this population will require efforts to mitigate these risk factors.

Leptin receptor antagonism of iNKT cell function: a novel strategy to combat multiple myeloma

A hallmark of bone marrow changes with aging is the increase in adipocyte composition, but how this impacts development of multiple myeloma (MM) is unknown. Here, we report the role of the adipokine leptin as master regulator of anti-myeloma tumor immunity by modulating the invariant natural killer T (iNKT) cell function. A marked increase in serum leptin levels and leptin receptor (LR) expression on iNKT cells in MM patients and the 5T33 murine MM model was observed. MM cells and leptin synergistically counteracted anti-tumor functionality of both murine and human iNKT cells. In vivo blockade of LR signaling combined with iNKT stimulation resulted in superior anti-tumor protection. This was linked to persistent IFN-γ secretion upon repeated iNKT cell stimulation and a restoration of the dynamic antigen-induced motility arrest as observed by intravital microscopy, thereby showing alleviation of iNKT cell anergy. Overall our data reveal the LR axis as novel therapeutic target for checkpoint inhibition to treat MM.

A comparison of 7-day versus 10-day course of low-dose dexamethasone for chronically ventilated preterm infants

OBJECTIVE

The objective of the study was to compare the effect of two different dexamethasone regimens on respiratory outcomes of ventilator-dependent preterm infants.

STUDY DESIGN

Retrospective study of ventilated preterm infants <29 weeks gestational age treated with either 7-day or 10-day dexamethasone course. Primary outcome was days to successful extubation. Other outcomes included rate of successful extubation and need for repeat steroid therapy.

RESULTS

Fifty-nine infants were identified; 32 (54%) received 7 days of dexamethasone and 27 (46%) received 10 days of dexamethasone. Both groups had comparable baseline demographics and clinical characteristics. Mean time to successful extubation was similar between the two groups (5.1±2.7 days in 7-day group and 6.0±3.7 days in 10-day group, P=0.42). Successful extubation by end of treatment (56% versus 67%, P=0.44) and need for repeat steroid therapy (47% versus 33%, P=0.43) were also similar.

CONCLUSION

7-day and 10-day course of dexamethasone have comparable efficacy in facilitating extubation of ventilator-dependent preterm infants.

MDR-TB in Puducherry, India: reduction in attrition and turnaround time in the diagnosis and treatment pathway

Setting: A mixed-methods operational research (OR) study was conducted to examine the diagnosis and treatment pathway of patients with presumptive multidrug-resistant tuberculosis (MDR-TB) during 2012-2013 under the national TB programme in Puducherry, India. High pre-diagnosis and pre-treatment attrition and the reasons for these were identified. The recommendations from this OR were implemented and we planned to assess systematically whether there were any improvements. Objectives: Among patients with presumptive MDR-TB (July-December 2014), 1) to determine pre-diagnosis and pre-treatment attrition, 2) to determine factors associated with pre-diagnosis attrition, 3) to determine the turnaround time (TAT) from eligibility to testing and from diagnosis to treatment initiation, and 4) to compare these findings with those of the previous study (2012-2013). Design: This was a retrospective cohort study based on record review. Results: Compared to the previous study, there was a decrease in pre-diagnosis attrition from 45% to 24% (P < 0.001), in pre-treatment attrition from 29% to 0% (P = 0.18), in the TAT from eligibility to testing from a median of 11 days to 10 days (P = 0.89) and in the TAT from diagnosis to treatment initiation from a median of 38 days to 19 days (P = 0.04). There is further scope for reducing pre-diagnosis attrition by addressing the high risk of patients with human immunodeficiency virus and TB co-infection or those with extra-pulmonary TB not undergoing drug susceptibility testing. Conclusion: The implementation of findings from OR resulted in improved programme outcomes.

Structural and anti-oxidant properties of guanidinium pyrazole-3,5-dicarboxylates

Multicomponent crystals (either salts or co-crystals) of pyrazole-3,5-dicarboxylic acid (H₃pzdc) with the nitrogen-containing organic bases guanidine (Gun), aminoguanidine (Agun), diaminoguanidine (Dagun) and triaminoguanidine (Tagun) have been synthesized and characterized by IR spectroscopy, TG-DTA, and single-crystal X-ray diffraction.

MDR-TB screening in a setting with molecular diagnostic techniques: who got tested, who didn't and why?

SETTING

The Revised National Tuberculosis Control Programme, Puducherry, India, which has facilities for molecular diagnostic technique.

OBJECTIVE

To determine pre-diagnostic and pre-treatment attrition among presumptive multidrug-resistant tuberculosis (MDR-TB) patients and reasons for attrition.

METHODS

In this mixed-methods study, the quantitative component consisted of retrospective cohort analysis through record review of all presumptive MDR-TB patients recorded between October 2012 and September 2013. The qualitative component included in-depth interviews with key informants involved in programmatic management of drug-resistant tuberculosis services.

RESULTS

Of 341 eligible presumptive MDR-TB patients, pre-diagnostic and pre-treatment attrition was respectively 45.5% (155/341) and 29% (2/7). Patients with extra-pulmonary TB (RR = 2.3), those with human immuno-deficiency and TB co-infection (RR = 1.7), those registered during October-December 2012 (RR = 1.3) and those identified from primary/secondary health centres (RR = 1.8) were less likely to be tested. Themes that emerged during the analysis of the qualitative data were 'lack of a systematic mechanism to track referrals for culture and drug susceptibility testing', 'absence of courier service to transport sputum', 'lack of knowledge and ownership among staff of general health system', 'shortage of diagnostic kits' and 'patient non-adherence'.

CONCLUSION

Despite the introduction of molecular diagnostic techniques, operational issues in MDR-TB screening remain a concern and require urgent attention.

Uptake of HIV testing and HIV positivity among presumptive tuberculosis patients at Puducherry, South India

SETTING

Puducherry, a district in South India with a low prevalence of human immunodeficiency virus (HIV) infection (<1% among antenatal women).

OBJECTIVES

1) To estimate the proportion of patients with known HIV status who were HIV-positive, 2) to describe the demographic and clinical characteristics of patients with unknown HIV status among presumptive TB patients, and 3) to assess the additional workload at HIV testing centres.

DESIGN

In this cross-sectional study, consecutive presumptive TB patients attending microscopy centres for diagnosis during March-May 2013 were asked if they knew their HIV status. Patients with unknown HIV status were offered voluntary counselling and HIV testing.

RESULTS

Of 1886 presumptive TB patients, HIV status was ascertained for 842 (44.6%); 28 (3.3%) were HIV-positive. The uptake of HIV testing was significantly higher in younger age groups, males, residents of Puducherry and smear-positive TB patients. The median increase in the number of clients tested for HIV per day per testing centre was 1 (range 0-6).

CONCLUSION

The uptake of HIV testing was low. HIV prevalence was higher among presumptive TB patients than in antenatal women, and as high as in TB patients. With minimal increase in workload at HIV testing centres, HIV testing could be implemented using existing resources.

Autophagy inhibits oxidative stress and tumor suppressors to exert its dual effect on hepatocarcinogenesis

The role of autophagy in carcinogenesis is controversial and apparently complex. By using mice with hepatocyte-specific knockout of Atg5, a gene essential for autophagy, we longitudinally studied the role of autophagy in hepatocarcinogenesis. We found that impairing autophagy in hepatocytes would induce oxidative stress and DNA damage, followed by the initiation of hepatocarcinogenesis, which could be suppressed by the antioxidant N-acetylcysteine. Interestingly, these mice developed only benign tumors with no hepatocellular carcinoma (HCC), even after the treatment with diethylnitrosamine, which induced HCC in wild-type mice. The inability of mice to develop HCC when autophagy was impaired was associated with the induction of multiple tumor suppressors including p53. Further analysis indicated that the induction of p53 was associated with the DNA-damage response. Tumorigenesis studies using an established liver tumor cell line confirmed a positive role of autophagy in tumorigenesis and a negative role of p53 in this process when autophagy was impaired. Our studies thus demonstrate that autophagy is required to maintain healthy mitochondria and to reduce oxidative stress and DNA damage to prevent the initiation of hepatocarcinogenesis. However, once hepatocarcinogenesis has been initiated, its presence is also required to suppress the expression of tumor suppressors to promote the development of HCC.

Prevalence of Diabetes Mellitus among Tuberculosis Patients in Urban Puducherry

Background:

Diabetes and Tuberculosis often present together and complicate each other at many levels. A collaborative framework for care and control of diabetes and tuberculosis developed by World Health Organisation and International Union against Tuberculosis and Lung Diseases emphasizes routine bi-directional screening for the two diseases.

Aims:

The study was to assess the prevalence of diabetes in tuberculosis patients currently on treatment.

Materials and Methods:

This facility-based cross-sectional study was undertaken in four randomly selected peripheral health institutions providing directly observed treatment short-course, treatment for tuberculosis patients. All cases of tuberculosis, more than 18 years of age were screened for diabetes. Risk factors like age, sex, family history of diabetes, alcohol, smoking and obesity were assessed.

Results:

The prevalence of diabetes in tuberculosis patients was found to be 29% (known diabetics - 20.7%, new Diabetes cases - 8.3%). Diabetes was significantly associated with older age, family history of diabetes, consumption of alcohol and sputum positivity.

Conclusions:

Screening patients with Tuberculosis for fasting blood sugar estimation will help in early detection of diabetes

Bone mineral density in patients with end-stage renal disease and its evolution after kidney transplantation

Renal transplantation is associated with abnormalities of the structure and function of the musculoskeletal system. No data are available on bone health in Indian patients with end-stage renal disease (ESRD) and its evolution after transplantation. Consecutive ESRD patients who underwent living donor renal transplantation were studied prospectively. Bone mineral density (BMD) was measured at lumbar vertebrae using quantitative computed tomography (CT) scan before transplantation and after 3 and 6 months. T and Z scores were calculated by comparing with normal control data, and values were correlated with various clinical and biochemical parameters. Of the 56 patients enrolled (mean age, 33.7 years; 47 males), 40 completed the 6-month follow-up. The vertebral trabecular bone density at the time of transplantation was 172±53 mg/cc and the average Z score was 0.26±1.7. There was a significant decline in BMD at 3 months (11.8%; P<0.0001) and 6 months (16%; P<0.0001) after transplantation. Both T and Z scores showed a significant decline at 3 and 6 months. There was a significant decline in intact parathormone (iPTH) levels after transplantation, but 15 (37.5%) patients continued to have raised iPTH 6 months after transplantation. The iPTH levels at 6 months had significant correlation with BMD decline (r=0.43, P=0.006). We conclude that Indian ESRD patients have relatively well-preserved BMD, but the density declines rapidly after transplantation. A significant proportion of patients exhibit persistent hyperparathyroidism 6 months after transplantation, which correlates with bone loss.

Smoking as an independent risk factor for hepatocellular carcinoma: the Singapore Chinese Health Study

Background:

Given the close correlation between smoking and alcohol intake in most epidemiologic studies, it is difficult to exclude the residual confounding effect of alcohol in the association between smoking and hepatocellular carcinoma (HCC).

Method:

We evaluated the association between smoking and risk of HCC in the Singapore Chinese Health Study, a prospective cohort with a low prevalence of alcohol intake. Information on cigarette smoking and alcohol consumption was obtained through in-person interviews conducted at enrolment.

Results:

After a mean of 11.5 years of follow-up, there were 394 incident cases of HCC. Participants who consumed more than two alcoholic drinks per day showed an increased risk for HCC (hazard ratio (HR)=2.24; 95% confidence interval (CI)=1.46–3.41). After adjusting for alcohol consumption and other potential confounders, current vs never smokers had a statistically significant, increased risk of HCC (HR=1.63; 95% CI=1.27–2.10) that was dose-dependent (number of cigarettes per day, P for trend<0.001). The observed tobacco–HCC association also was duration-dependent (years of smoking in ever smokers, P for trend=0.002). When we excluded daily drinkers from the analysis, all risk estimates remained essentially the same and statistically significant.

Conclusion:

Our findings strongly implicate tobacco smoke as a causal factor of HCC development.

Piperazinediium dioxamate

The title compound, C₄H₁₂N₂²⁺·2C₂H₂NO₃⁻, contains a network of doubly protanated piperazinium cations (lying about centres of inversion) and dioxamate anions. The piperazinium dication adopts a typical chair conformation. The crystal structure is stabilized by cation–to–anion N—H⋯O and anion–to–anion N—H⋯O hydrogen bonds.

Amino-guanidinium hydrogen succinate

The title compound, CH₇N₄⁺·C₄H₅O₄⁻, is a molecular salt containing discrete amino­guanidinium and succinate ions. The amino­guanidinium cation is nearly planar, with a maximum deviation of 0.035 (1) Å. The dihedral angle between the amino­guanidinium cation and the succinate anion is 3.35 (6)°. The crystal packing exhibits inter­molecular N—H⋯O and O—H⋯·O hydrogen bonds.

Histological benefits of virological response to peginterferon alfa-2a monotherapy in patients with hepatitis C and advanced fibrosis or compensated cirrhosis

BACKGROUND

Patients with chronic hepatitis C virus and advanced fibrosis or cirrhosis are at risk for disease progression and hepatic decompensation.

AIM

To determine the effects on hepatic histology of treatment with peginterferon alfa-2a (90 or 180 mug/week) or interferon alfa-2a (3 million units three times weekly) for 48 weeks in patients with paired biopsies.

METHODS

Liver biopsies were obtained at baseline and 6 months after end of treatment. Histological and virological responses were compared.

RESULTS

Patients attaining sustained virological response (n = 40) demonstrated the greatest improvements in fibrosis (-1.0, P < 0.0001) and inflammation (-0.65, P < 0.0001). Patients who cleared hepatitis C virus during treatment, but later relapsed (n = 59), experienced less improvement in fibrosis (-0.04, P < 0.0001) and inflammation (-0.14, P = 0.0768). Nonresponders (n = 85) showed no significant improvement in inflammation or fibrosis. Multiple regression analysis showed that the only factors contributing to improvement in fibrosis were sustained virological response (vs. nonresponder, P = 0.0005; vs. relapse, P = 0.7525) and body mass index < or =30 kg/m2 (P = 0.0995).

CONCLUSIONS

These findings indicate that virological response to peginterferon alfa-2a improves inflammation and fibrosis in hepatitis C virus patients with advanced fibrosis or cirrhosis. Improving virological response and maintaining ideal body weight are critical for achieving optimal histological outcomes in hepatitis C virus patients.

Hepatic steatosis in chronic hepatitis C: baseline host and viral characteristics and influence on response to therapy with peginterferon alpha-2a plus ribavirin

Hepatic steatosis is common in hepatitis C virus (HCV)-infected patients and may be associated with the metabolic syndrome. We studied steatosis in patients treated with peginterferonalpha-2a plus ribavirin. Forty-five of 207 patients (22%) had >5% hepatic steatosis at baseline. Significantly more patients with steatosis than without were HCV genotype 3 (51%vs 14%; P < 0.0001) had higher HCV-RNA (P = 0.0045), body weight (P = 0.0176), body mass index (BMI, P = 0.0352) and serum triglycerides (TG) (P = 0.0364), hypertriglyceridaemia (P = 0.0009), elevated blood pressure/history of hypertension (P = 0.0229) and lower cholesterol (P = 0.0009). Significant steatosis predictors were genotype 3 (OR 9.04, 95% CI 3.85-21.21, P < 0.0001), HCV-RNA (OR 2.96, 1.49-5.88, P = 0.0019) and triglycerides (OR 1.06, 1.02-1.11, P = 0.0071). In genotype 3 patients, HCV-RNA was the only significant predictor (OR 11.15, 2.60-47.81, P = 0.0012). In non-genotype 3 patients, hypertriglyceridaemia was the only significant predictor (OR 1.07, 1.02-1.12, P = 0.0041). 134 of 207 patients (65%) achieved an sustained virological response (SVR) with peginterferon alpha-2a plus ribavirin, similar to the overall response rate. In genotype 3 patients with an SVR, steatosis decreased from 48% to 13% (baseline to end-point). No change was seen in the steatosis rate in non-genotype 3 patients with an SVR. This large and comprehensive analysis of a large data base from a multinational trial further adds to the observations that chronic HCV is associated with hepatic steatosis in approximately a fifth of patients. Further, features of the metabolic syndrome are associated with hepatic steatosis in most of these patients. Steatosis is significantly more common in genotype 3 compared with other genotypes, and in these patients, an SVR is associated with steatosis clearance.

Intrahepatic lymphocyte phenotypes in hepatitis C virus infection: a comparison between cirrhotic and non-cirrhotic livers

AIM

The pathogenesis of viral hepatitis involves the activation of cellular immunity, including intrahepatic lymphocytes (IHL). Lym-phocyte phenotypes play a fundamental role in the pathogenesis of chronic hepatitis C virus (HCV) infection, the progression of liver fibrosis and subsequent hepatocellular carcinoma. The aim of this study was to evaluate the frequency of intrahepatic mononuclear cell phenotypes in patients with chronic HCV. Another aim was to assess the relationship of nonparenchymal cells with liver fibrosis.

METHODS

Liver fibrosis was evaluated with the Histologic Activity Index. Fourteen liver biopsies showed mild fibrosis (group 1), and 11 bridging fibrosis (group 2). Fourteen samples were explants from HCV patients who underwent liver transplantation (group 3). CD4 and CD8 T-lymphocytes, CD20 (B lymphocytes), CD16 (macrophage), and CD57 (NK) cells were detected using monoclonal antibodies on paraffin-embedded tissue.

RESULTS

A minority of lobular cells stained for T- or B-lymphocytes. Most lobular cells stained with macrophage antibodies, and were more common in bridging fibrosis, compared to mild fibrosis. The percentages of lobular CD4 and CD8 cells were significantly lower in regenerative nodules of cirrhotic livers. There was a strong negative correlation between lobular CD8 and fibrosis score (R= -0.65), and a strong positive correlation between CD16-stained mononuclear cells (macrophages) and fibrosis score (R=0.66). In portal and periportal areas, CD4 but not CD8 lymphocytes decreased in parallel with fibrosis. B-lymphocytes were more commonly found in the portal areas than in the lobule. CD57-positive cells were rare in both lobule and portal areas, and their frequency was not different in the three groups studied.

CONCLUSIONS

In hepatitis C, lobular mononuclear cells are mostly macrophages and appear associated with bridging fibrosis. Cirrhotic livers display significantly lower numbers of lobular CD4 and CD8 lymphocytes. This finding could help explain a decrease in immune surveillance and the promotion of neoplastic growth in HCV-associated cirrhosis.

A multicentre study of the usefulness of liver biopsy in hepatitis C

The role of liver biopsy in the assessment of chronic hepatitis C is generally accepted yet there is no prospective data available to quantify its contribution. A previous single centre pilot study suggested that the clinician could predict the amount of fibrosis and to a lesser extent, inflammation with moderate accuracy. The 2002 National Institute of Health Hepatitis C Consensus Conference recommended further study of the role of liver biopsy. Our objective was to compare a prediction of biopsy findings by expert clinicians using usually available clinical and laboratory data to actual biopsy results in order to determine whether biopsy is required routinely. This was a prospective observational study conducted at seven university centres in which the accuracy of clinician's predictions of the degree of inflammation and fibrosis were compared with the actual liver biopsy using an adaptation of a standard histological scoring system. We studied 81 adults with previously untreated chronic hepatitis C, raised serum transaminases and positive HCV-RNA in serum. Clinicians predicted the inflammatory grade in 44 of 80 cases (55%) and the fibrosis stage in 46 of 81 cases (57%). Nine of 17 cirrhotic cases were predicted (sensitivity 53%, specificity 56%). No unexpected additional diagnoses were made on the biopsies. Thus despite knowledge of the clinical and laboratory investigations of patients with hepatitis C, clinicians are unable to accurately predict the hepatic inflammatory grade and fibrotic stage. Liver biopsy is an essential investigation to accurately evaluate the grade and stage of liver disease patients with hepatitis C.

The Adaptive Evolution Database (TAED)

BACKGROUND

Developing an understanding of the molecular basis for the divergence of species lies at the heart of biology. The Adaptive Evolution Database (TAED) serves as a starting point to link events that occur at the same time in the evolutionary history (tree of life) of species, based upon coding sequence evolution analyzed with the Master Catalog. The Master Catalog is a collection of evolutionary models, including multiple sequence alignments, phylogenetic trees, and reconstructed ancestral sequences, for all independently evolving protein sequence modules encoded by genes in GenBank [1].

RESULTS

We have estimated from these models the ratio of nonsynonymous to synonymous nucleotide substitution (Ka/Ks), for each branch in their respective evolutionary trees of every subtree containing only chordata or only embryophyta proteins. Branches with high Ka/Ks values represent candidate episodes in the history of the family where the protein may have undergone positive selection, a phenomenon in molecular evolution where the mutant form of a gene must have conferred more fitness than the ancestral form. Such episodes are frequently associated with change in function. We have found that an unexpectedly large number of families (between 10 and 20% of those families examined) have at least one branch with a notably high Ka/Ks value (putative adaptive evolution). As a resource for biologists wishing to understand the interaction between protein sequences and the Darwinian processes that shape these sequences, we have collected these into The Adaptive Evolution Database (TAED).

CONCLUSIONS

Placed in a phylogenetic perspective, candidate genes that are undergoing evolution at the same time in the same lineage can be viewed together. This framework based upon coding sequence evolution can be readily expanded to include other types of evolution. In its present form, TAED provides a resource for bioinformaticists interested in data mining and for experimental evolutionists seeking candidate examples of adaptive evolution for further experimental study.

Recombinant hepatitis E virus genomes infectious for primates: importance of capping and discovery of a cis-reactive element

Hepatitis E virus recombinant genomes transcribed in vitro from two cDNA clones differing by two nucleotides were infectious for chimpanzees. However, one cDNA clone encoded a virus that was attenuated for chimpanzees and unable to infect rhesus monkeys. The second cDNA clone encoded a virus that infected both chimpanzees and rhesus monkeys and caused acute hepatitis in both. One mutation differentiating the two clones identified a cis-reactive element that appeared to overlap the 3' end of the capsid gene and part of the 3' noncoding region. Capping of the RNA transcripts was essential for infectivity.

Immunogenicity and protective efficacy of a vaccine prepared from 53 kDa truncated hepatitis E virus capsid protein expressed in insect cells

Hepatitis E virus (HEV) is an enterically transmitted virus that causes acute hepatitis. Expression of recombinant HEV capsid protein in insect cells results in two major proteolytically-processed products of 56 and 53kDa which consist of amino acids (aa) 112-607 and 112-578, respectively. The only neutralization epitope identified to date is located at least partially between amino acids 578 and 607 meaning it should be present only in the 56 and not in the 53kDa protein. Previously, it was shown that vaccination with the 56kDa protein greatly reduced virus shedding and protected Rhesus monkeys from hepatitis E when challenged with a high intravenous dose of homologous or heterologous HEV. To evaluate the immunogenicity and protective efficacy of the 53kDa protein, we vaccinated Rhesus monkeys with this protein and challenged them with a high or low dose of homologous virus. Vaccination with the 53kDa protein greatly reduced virus shedding but did not protect against hepatitis following the high dose challenge. Virus was not detected in the vaccinated animals following the low dose challenge, suggesting that sterilizing immunity may have been achieved.

Host range studies of GB virus-B hepatitis agent, the closest relative of hepatitis C virus, in New World monkeys and chimpanzees

GB virus-B (GBV-B) is a member of the Flaviviridae family of viruses. This RNA virus causes acute resolving hepatitis in experimentally infected tamarins, but its natural host remains unknown. GBV-B and a related virus, GBV-A, were recovered from serum containing the "GB agent," which was believed to have originated from a surgeon (initials: GB) with acute hepatitis. GBV-B has special interest because it is the virus related most closely to hepatitis C virus, which is an important cause of acute and chronic liver disease in humans. In the present study, we found that the host range of GBV-B includes owl monkeys. Tamarins and owl monkeys belong to two different families of New World monkeys. The natural history of GBV-B in the two owl monkeys studied was similar to that previously found for tamarins and was characterized by early appearance of viremia and viral clearance. However, the peak viral titers of GBV-B observed in owl monkeys (10(5) genome equivalents [GE] /ml) were lower than those observed in experimentally infected tamarins (10(7)-10(8) GE/ml) and acute hepatitis was observed in only one animal. If GBV-B were indeed a virus of humans, it would be expected to infect chimpanzees, a surrogate of humans, because all recognized human hepatitis viruses are transmissible to chimpanzees and cause hepatitis. However, in the present study, we failed to transmit GBV-B to a naive chimpanzee. In addition, a second naive chimpanzee transfected intrahepatically with RNA transcripts from an infectious clone of GBV-B did not become infected. Thus, chimpanzees are apparently not susceptible to GBV-B. Finally, we failed to detect GBV-B in acute-phase serum from surgeon GB. Our data suggest that GBV-B is not a human virus and that GBV-B, like GBV-A, is a virus of New World monkeys.

Extracellular nicotinamide adenine dinucleotide induces t cell apoptosis in vivo and in vitro

Incubation of mouse T cells expressing the cell surface enzyme ADP ribosyltransferase with nicotinamide adenine dinucleotide (NAD) had been reported to cause ADP ribosylation of cell surface molecules, inhibition of transmembrane signaling, and suppression of immune responses. In this study, we analyze the reasons for these effects and report that contact of T cells with NAD causes cell death. Naive T cells when incubated with NAD and adoptively transferred into semiallogeneic mice fail to cause graft-vs-host disease, and when injected into syngeneic, T cell-deficient recipients do not reconstitute these mice. Rather, they accumulate in the liver, leading to an increase of apoptotic lymphocytes in this organ. Similar effects are induced by injection of NAD, shown to cause a dramatic increase of apoptotic CD3(+), CD4(+), and CD8(+) cells in the liver. Consistent with this, in vitro incubation of naive T cells with NAD is shown to induce apoptosis. In contrast, no cell death is demonstrable when T cells are activated before incubation with NAD. It is concluded that ecto-NAD, as substrate of ADP ribosyltransferase, acts on naive, but not on activated CD69(+) T cells.

Exploration of sequence space for protein engineering

The process of protein engineering is currently evolving towards a heuristic understanding of the sequence-function relationship. Improved DNA sequencing capacity, efficient protein function characterization and improved quality of data points in conjunction with well-established statistical tools from other industries are changing the protein engineering field. Algorithms capturing the heuristic sequence-function relationships will have a drastic impact on the field of protein engineering. In this review, several alternative approaches to quantitatively assess sequence space are discussed and the relatively few examples of wet-lab validation of statistical sequence-function characterization/correlation are described.

Chronic hepatitis C in ethnic minority patients evaluated in Los Angeles County

OBJECTIVE

The aim of this study was to compare demographic, clinical, and histological features of hepatitis C in four ethnic groups seen at the Los Angeles County/University of Southern California Hepatitis Clinic.

METHODS

We evaluated 256 patients with chronic hepatitis C, with 132 (52%) receiving a liver biopsy as part of their evaluation. We estimated fibrosis progression in 103 patients with known duration of disease.

RESULTS

Asians (6%) were underrepresented in the hepatitis C cohort, whereas Latinos (51%) were overrepresented, as compared with the entire county population. A history of injection drug use was more frequent in whites (65%) than in African Americans (45%, p = 0.05), Latinos (47%, p = 0.01), or Asians (0%) and more frequent in Latinos (59%) than in Latinas (26%, p = 0.003). Such a gender difference was not found in African Americans or whites. Baseline laboratory values were comparable. The amount of alcohol consumed daily was higher in African Americans than in Asians (p = 0.0001) and whites (p = 0.10). African Americans (0.077 fibrosis stages/yr) and whites (0.084/yr) had significantly lower mean estimated progression of liver fibrosis than Latinos (0.215/yr) with hepatitis C virus infection (ps = 0.03 and 0.02, respectively): this was likely related to their longer estimated duration of disease.

CONCLUSION

Minorities represent the majority of chronic hepatitis C cases in the Los Angeles County Hepatitis Clinic. Asians, Latinas, and African Americans are less likely to report injection drug use as a risk factor for hepatitis C virus. Latinos seem to have faster liver fibrosis progression rates than either African Americans or whites.

Advances in directed protein evolution by recursive genetic recombination: applications to therapeutic proteins

Recent developments in directed evolution technologies combined with innovations in robotics and screening methods have revolutionized protein engineering. These methods are being applied broadly to many fields of biotechnology, including chemical engineering, agriculture and human therapeutics. More specifically, DNA shuffling and other methods of genetic recombination and mutation have resulted in the improvement of proteins of therapeutic interest. Optimizing genetic diversity and fitness through iterative directed evolution will accelerate improvements in engineered protein therapeutics.

Failure to infect rhesus monkeys with hepatitis C virus strains of genotypes 1a, 2a or 3a

The chimpanzee is the only recognized animal model for the study of hepatitis C virus (HCV). However, recently it was reported that rhesus monkeys were susceptible to HCV and developed hepatitis during infection. In the present study, we inoculated two rhesus monkeys each with HCV strain H77 (genotype 1a), strain HC-J6 (genotype 2a) or strain S52 (genotype 3a). Weekly serum samples were tested for liver enzyme values, HCV antibodies and HCV RNA. We did not find evidence of HCV infection in any of the monkeys during 24 weeks of follow-up. Our study demonstrates that rhesus monkeys are not readily infected with HCV and apparently do not represent a useful animal model for the study of HCV.

Fas-mediated apoptosis causes elimination of virus-specific cytotoxic T cells in the virus-infected liver

Immunity to allogeneic MHC Ags is weak in rodent livers, raising questions as to the mechanisms that might control responses in this organ. Infection with an adenovirus vector reveals that T cell-mediated immunity to nonself-Ags in the liver is self-limiting. Virus-induced liver injury decreases and coincides with disappearance of virus-specific CTL, concomitant to an increase of apoptotic T cells early after infection. But whereas death in CD4 cells is independent of Fas, perforin, and TNF-alpha, that of CD8 cells requires Fas and not perforin or TNF-alpha pathways. Fas ligand is expressed on liver-infiltrating cells, pointing to death by fratricide that causes almost complete disappearance of virus-specific CTL 4 wk after infection. CTL elimination is virus dose dependent, and high doses induced high alanine aminotransferase values, elevated expression of Fas ligand on CD8 cells, and increased CD8 cell migration into the infected liver.

The adaptive evolution database (TAED)

BACKGROUND

The Master Catalog is a collection of evolutionary families, including multiple sequence alignments, phylogenetic trees and reconstructed ancestral sequences, for all protein-sequence modules encoded by genes in GenBank. It can therefore support large-scale genomic surveys, of which we present here The Adaptive Evolution Database (TAED). In TAED, potential examples of positive adaptation are identified by high values for the normalized ratio of nonsynonymous to synonymous nucleotide substitution rates (KA/KS values) on branches of an evolutionary tree between nodes representing reconstructed ancestral sequences.

RESULTS

Evolutionary trees and reconstructed ancestral sequences were extracted from the Master Catalog for every subtree containing proteins from the Chordata only or the Embryophyta only. Branches with high KA/KS values were identified. These represent candidate episodes in the history of the protein family when the protein may have undergone positive selection, where the mutant form conferred more fitness than the ancestral form. Such episodes are frequently associated with change in function. An unexpectedly large number of families (between 10% and 20% of those families examined) were found to have at least one branch with high KA/KS values above arbitrarily chosen cut-offs (1 and 0.6). Most of these survived a robustness test and were collected into TAED.

CONCLUSIONS

TAED is a raw resource for bioinformaticists interested in data mining and for experimental evolutionists seeking candidate examples of adaptive evolution for further experimental study. It can be expanded to include other evolutionary information (for example changes in gene regulation or splicing) placed in a phylogenetic perspective.