Nuclear gyrB encodes a functional subunit of the Plasmodium falciparum gyrase that is involved in apicoplast DNA replication

The DNA replication machinery of the Plasmodium falciparum apicoplast is a validated drug target. Nuclear-encoded gyrase subunits are predicted to play a critical role in maintaining DNA topology during the D-loop/bi-directional ori replication process of the parasite. We show the presence of P. falciparum gyrase subunits in parasite lysates by using antibodies generated against recombinant gyrase A and B. The ATPase activity of PfGyrB was inhibited by novobiocin that also caused parasite death in culture. Reduction of apicoplast/nuclear DNA ratio in the presence of novobiocin indicated that the drug targets apicoplast DNA replication. Molecular modeling of gyrase A and B subunits revealed extensive fold conservation with the Escherichia coli counterparts as well as the presence of a long disordered loop adjacent to the ATPase domain of PfGyrB. Our results have implications for development of PfGyrB as a drug target against malaria.     

Production of infectious virus and degradation of APOBEC3G are separable functional properties of human immunodeficiency virus type 1 Vif

HIV-1 Vif regulates viral infectivity by inhibiting the encapsidation of APOBEC3G (APO3G) through proteasomal degradation of the protein. Here we compared various Vif proteins for their ability to induce APO3G degradation and rescue viral infectivity. We found that Vif expressed from proviral vectors caused relatively inefficient degradation of APO3G in HeLa cells yet was very effective in inhibiting APO3G's antiviral activity. On the other hand, Vif expressed autonomously from a codon-optimized vector caused very efficient APO3G degradation and also effectively inhibited APO3G's antiviral effects. In contrast, a Vif chimera containing an N-terminal fluorescent tag efficiently induced APO3G degradation but was unable to restore viral infectivity. The lack of a direct correlation between APO3G degradation and rescue of viral infectivity suggests that these two properties of Vif are functionally separable. Our data imply that intracellular degradation of APO3G may not be the sole activity of Vif required for the production of infectious virions from APO3G-expressing cells.     

Decorin inhibition of PDGF-stimulated vascular smooth muscle cell function: potential mechanism for inhibition of intimal hyperplasia after balloon angioplasty

Decorin is a small proteoglycan that binds to transforming growth factor-beta (TGF-beta) and inhibits its activity. However, its interaction with platelet-derived growth factor (PDGF), involved in arterial repair after injury, is not well characterized. The objectives of this study were to assess decorin-PDGF and decorin-PDGF receptor (PDGFR) interactions, the in vitro effects of decorin on PDGF-stimulated smooth muscle cell (SMC) functions and the in vivo effects of decorin overexpression on arterial repair in a rabbit carotid balloon-injury model. Decorin binding to PDGF was demonstrated by solid-phase binding and affinity cross-linking assays. Decorin potently inhibited PDGF-stimulated PDGFR phosphorylation. Pretreatment of rabbit aortic SMC with decorin significantly inhibited PDGF-stimulated cell migration, proliferation, and collagen synthesis. Decorin overexpression by adenoviral-mediated gene transfection in balloon-injured carotid arteries significantly decreased intimal cross-sectional area and collagen content by approximately 50% at 10 weeks compared to beta-galactosidase-transfected or balloon-injured, non-transfected controls. This study shows that decorin binds to PDGF and inhibits its stimulatory activity on SMCs by preventing PDGFR phosphorylation. Decorin overexpression reduces intimal hyperplasia and collagen content after arterial injury. Decorin may be an effective therapy for the prevention of intimal hyperplasia after balloon angioplasty.     

A meta-analysis on the efficacy and tolerability of natalizumab in relapsing multiple sclerosis

Introduction

Natalizumab is a new humanized monoclonal antibody used in multiple sclerosis (MS). The aim of this meta-analysis was to evaluate the efficacy and tolerability of this drug in relapsing MS. PubMed, Scopus, Web of Science, and Cochrane Central Register of Controlled Trials were searched for studies that investigated the efficacy and/or tolerability of natalizumab in MS. Data were collected from 1966 to 2008 (up to October).

Material and methods

The search terms were: “multiple sclerosis” or “MS” and “natalizumab”. “Mean change in Expanded Disability Status Scale (EDSS)”, “number of patients with at least one relapse”, and “number of patients with at least one new gadolinium (Gd)-enhancing lesion” were the key outcomes of interest for assessment of efficacy. “Any adverse events”, “serious adverse events”, “death”, and “withdrawal because of adverse events” were the key outcomes for tolerability. Among existing trials, four randomized placebo controlled clinical trials met our criteria and were included.

Results

Pooled relative risk for at least one relapse in four trials including all doses was 0.7, with a non-significant RR (95% CI: 0.42–1.17, p = 0. 17). Summary RR for at least one relapse in two trials in which doses of 3 mg/kg or 6 mg/kg or 300 mg every 4 weeks were administered gave a value of 0.5 asa significant RR (95% CI: 0.42–0.61, p < 0.0001). The summary RR for at least one new Gd-enhancing lesion was 0.22, a non-significant RR (95% CI: 0.05–1.01, p = 0.051). Three deaths were reported in the natalizumab group. Comparing adverse events between natalizumab and placebo yielded a non-significant RR of 0.99 (95% CI: 0.96–1.01, p = 0.34) for any adverse events (n = 3), and a significant RR of 0.39 (95% CI: 0.29–0.52, p < 0.0001) for serious adverse events (n = 2). The summary RR for withdrawal due to adverse events by natalizumab vs. placebo therapy between two trials was 1.43, a non-significant RR (95% CI: 0.68–3.02, p = 0.35).

Conclusions

It seems that using 3 or 6 mg/kg every 4 weeks is the best method of administration of natalizumab for preventing relapse and occurrence of new Gd-enhancing lesions. The current data on the efficacy and safety of natalizumab are insufficient to reach a convincing conclusion and thus further clinical trials are still needed.     

Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15

The maternal and paternal genomes possess distinct epigenetic marks that distinguish them at imprinted loci. In order to identify imprinted loci, we used a novel method, taking advantage of the fact that uniparental disomy (UPD) provides a system that allows the two parental chromosomes to be studied independently. We profiled the paternal and maternal methylation on chromosome 15 using immunoprecipitation of methylated DNA and hybridization to tiling oligonucleotide arrays. Comparison of six individuals with maternal versus paternal UPD15 revealed 12 differentially methylated regions (DMRs). Putative DMRs were validated by bisulfite sequencing, confirming the presence of parent-of-origin-specific methylation marks. We detected DMRs associated with known imprinted genes within the Prader-Willi/Angelman syndrome region, such as SNRPN and MAGEL2, validating this as a method of detecting imprinted loci. Of the 12 DMRs identified, eight were novel, some of which are associated with genes not previously thought to be imprinted. These include a site within intron 2 of IGF1R at 15q26.3, a gene that plays a fundamental role in growth, and an intergenic site upstream of GABRG3 that lies within a previously defined candidate region conferring an increased maternal risk of psychosis. These data provide a map of parent-of-origin-specific epigenetic modifications on chromosome 15, identifying DNA elements that may play a functional role in the imprinting process. Application of this methodology to other chromosomes for which UPD has been reported will allow the systematic identification of imprinted sites throughout the genome.Imprinting is a phenomenon in which the expression status of a gene is dependent on the sex of the parent from which it is inherited. Imprinted genes generally exhibit monoallelic expression accompanied by parent-of-origin-specific epigenetic marks such as differential DNA methylation and histone modifications that distinguish the maternal and paternal genomes at these loci (Reik and Walter 2001; Dindot et al. 2009). More than 60 imprinted genes have been identified in humans (http://www.geneimprint.com/), and their clustered nature suggests that many are regulated by regional control mechanisms.To date, the discovery of imprinted sites in both mouse and human has largely been driven through the use of phenotype-based approaches. The vast majority of loci subject to parent-of-origin effects were first recognized through the observation that maternal and paternal transmission of the same genetic mutation results in different phenotypes (Nicholls et al. 1989). For example, the identification of imprinted gene clusters in 15q11-q13 associated with Prader-Willi/Angelman syndrome, 11p11.5 associated with Beckwith-Wiedemann syndrome, and imprinted loci at 14q32, 6q24, and 20q13.2 were all catalyzed by the initial observation that genetic disease occurred specifically in patients with either uniparental disomy (UPD) or deletions of these regions of specific parental origin. In combination with chromosomal engineering techniques that can systematically generate defined aneuploidies, this notion has been applied to screen the mouse genome for imprinting with great success, resulting in the identification of more than 130 murine imprinted genes (Williamson et al. 2009). However, because this methodology relies on the recognition of overt phenotypic differences between individuals to detect imprinting, it is likely to miss imprinting that may cause subtle phenotype differences or those that manifest in ways that are not easily recognized by typical methods of phenotypic characterization. Further, imprinted genes will also be missed or masked by phenotypes that are lethal.In order to circumvent this limitation, a variety of genomic techniques have been developed to identify parent-of-origin effects. Several previous studies have attempted to detect imprinting based on the differential expression of parental alleles at imprinted loci. Studies using subtractive cDNA hybridization (Kaneko-Ishino et al. 1995) and high-throughput cDNA sequencing in hybrid mouse strains (Wang et al. 2008) have been used to detect imprinted expression with some success. However, these approaches are limited in that they can only assay the subset of genes expressed in the tissue(s) under investigation, and for some genes, imprinted expression is only observed in specific tissues or at certain developmental stages (Deltour et al. 1995; Rougeulle et al. 1997; Zhou et al. 2006). Furthermore, sequencing-based approaches are only able to assay allelic bias in genes containing transcribed polymorphisms (Daelemans et al. 2010).Alternative approaches to detect imprinting have used the fact that the maternal and paternal genomes have differential epigenetic marks at most imprinted loci. This approach has the advantage over expression-based methods, in that these differential methylation marks are generally conserved, even in tissues that lack imprinted expression (Dockery et al. 2009). The presence of overlapping euchromatin and heterochromatin marks has been used to highlight imprinted domains in human (Wen et al. 2008), and restriction landmark genome scanning (Hayashizaki et al. 1994) and methylation-sensitive representational difference analysis (Kelsey et al. 1999; Smith et al. 2003) have been applied as methods to detect differentially methylated regions in the mouse genome. However, the reliance of these latter techniques on restriction enzyme digestion means that they can only assay a small subset of CpGs that overlap the enzyme recognition site, and if used in outbred genomes, are liable to artifacts generated by the presence of single nucleotide variants that alter restriction patterns.Because one of the key features of imprinted genes is the presence of parent-of-origin-specific methylation, we hypothesized that the systematic comparison of DNA methylation patterns in maternal versus paternal chromosomes should represent an optimal method for the detection of imprinted loci. Based on this hypothesis, we have taken advantage of the fact that uniparental disomy provides a unique system that allows the separate study of chromosomes derived from a single parent and combined this with a methodology in which the methylation of entire chromosomes can be analyzed in an unbiased fashion. By analyzing methylation patterns in cases of maternal UPD15 (matUPD15) and paternal UPD15 (patUPD15) using immunoprecipitation of methylated DNA and high-density tiling arrays with complete coverage of human chromosome 15, we generated separate methylation profiles of the maternally and paternally derived alleles. Comparison of the two parental epigenotypes identifies numerous loci on chromosome 15 that show parent-of-origin-specific methylation differences, defining a set of DNA elements that are likely responsible for the establishment and/or maintenance of imprinting on this chromosome. We identify novel imprinted loci both within and outside of the known PWS/AS imprinted domain, suggesting candidate loci that may exert parent-of-origin effects in several human phenotypes.     

Development of Immunoglobulin M Memory to Both a T-Cell-Independent and a T-Cell-Dependent Antigen following Infection with Vibrio cholerae O1 in Bangladesh

Vibrio cholerae O1 can cause severe watery diarrhea that can be life-threatening without treatment. Infection results in long-lasting protection against subsequent disease. Development of memory B cells of the immunoglobulin G (IgG) and IgA isotypes to V. cholerae O1 antigens, including serotype-specific lipopolysaccharide (LPS) and the B subunit of cholera toxin (CTB), after cholera infection has been demonstrated. Memory B cells of the IgM isotype may play a role in long-term protection, particularly against T-cell-independent antigens, but IgM memory has not been studied in V. cholerae O1 infection. Therefore, we assayed acute- and convalescent-phase blood samples from cholera patients for the presence of memory B cells that produce cholera antigen-specific IgM antibody upon polyclonal stimulation in in vitro culture. We also examined the development of serological and antibody-secreting cell responses following infection. Subjects developed significant IgM memory responses by day 30 after infection, both to the T-cell-independent antigen LPS and to the T-cell-dependent antigen CTB. No significant corresponding elevations in plasma IgM antibodies or circulating IgM antibody-secreting cells to CTB were detected. In 17 subjects followed to day 90 after infection, significant persistence of elevated IgM memory responses was not observed. The IgM memory response to CTB was negatively correlated with the IgG plasma antibody response to CTB, and there was a trend toward negative correlation between the IgM memory and IgA plasma antibody responses to LPS. We did not observe an association between the IgM memory response to LPS and the vibriocidal titer.Vibrio cholerae continues to be a significant global health burden as a cause of severe secretory diarrhea, resulting in an estimated three to five million annual cases, with more than 100,000 deaths from rapid dehydration (47); cholera has recently become endemic in new regions (44, 45). V. cholerae is a noninvasive pathogen that colonizes the mucosal surface of the small intestine. Strains can be distinguished serologically by the O antigen of the lipopolysaccharide (LPS); V. cholerae O1 is the most common cause of cholera in South Asia as well as globally. The O1 serogroup has two major biotypes, El Tor and classical, and two major serotypes, Inaba and Ogawa (35). Natural infection with V. cholerae O1 El Tor induces protective immunity that lasts for at least 3 to 10 years in both areas where cholera is not endemic and areas where it is endemic (21). It remains unknown, however, what aspects of the adaptive immune response to cholera confer this long-term protection.V. cholerae-infected patients mount immunologic responses to both protein and polysaccharide antigens, including rises in both serum immunoglobulin G (IgG) and IgA antibodies (14). A number of these serological responses have been shown to correlate with protection against reinfection; these include the complement-dependent serum vibriocidal antibody (14) and IgA (but not IgG) responses to LPS, cholera toxin B subunit (CTB), and toxin coregulated pilus A (TcpA) (17). These serological responses, however, are short-lived (4, 32), and the association of the vibriocidal titer with protection is not absolute (36), suggesting that these responses may reflect protection from more recent exposure but that other immunologic mechanisms mediate longer-term protection. In addition to serological responses, development of mucosal immune responses to intestinal antigens can be detected in the blood, when B cells activated by antigen in the gut-associated lymphoid tissues circulate transiently in the blood as antibody-secreting cells (ASCs), before homing back to intestinal mucosal surfaces (11, 26). Circulation of ASCs specific to both LPS and CTB is seen after cholera infection, peaking around the seventh day after infection and declining by day 11 (32).Responses of the IgM isotype to cholera antigens have been less thoroughly investigated than the IgG and IgA responses. However, IgM defenses may be an important component of the overall immunologic response to cholera, since vibriocidal antibodies are principally of the IgM isotype (22) and IgM levels of pooled convalescent-phase serum samples correspond closely with vibriocidal activity (24), which in turn correlates with immunity (14). The pentameric structure of IgM facilitates strong cross-linking of antigens and activation of complement in the defense against other gram-negative enteric bacteria (2).We have recently shown development of memory B cells of both the IgG and IgA isotypes to LPS, CTB, and TcpA; these cells persisted in the circulation beyond 1 year for the protein antigens CTB and TcpA, but were not measurably above baseline levels by 9 to 12 months after infection for the polysaccharide-containing antigen LPS (16, 18). These circulating memory B cells can be detected by ex vivo polyclonal stimulation of peripheral blood mononuclear cells (PBMCs); stimulated memory B cells mature into ASCs detectable by enzyme-linked immunospot (ELISPOT) assay. Alternatively, memory B-cell responses can be detected by measuring antigen-specific antibodies secreted by maturing ASCs during the ex vivo stimulation of PBMCs in the memory B-cell assay (18).Memory B cells relevant for cholera immunity may include IgM⁺ as well as switched-memory (IgA⁺ and IgG⁺) populations. The majority of circulating IgM⁺ cells are naïve B cells, but some IgM⁺ cells bear the memory cell marker CD27⁺, and recent evidence suggests that these IgM⁺CD27⁺ cells are true memory B cells whose immunoglobulin variable region genes have undergone somatic hypermutation in response to antigen in early-stage germinal centers (39). IgM⁺ memory cells can undergo isotype switching to produce IgG, IgA, or IgE antibody, but they also have a role in producing rapid, high-affinity IgM antibody responses to acute infection (19, 37, 46). In this study, we have measured the development of memory B-cell responses of the IgA, IgG, and IgM isotypes to both a protein (CTB) and a nonprotein (LPS) antigen, and we compared these memory responses with other immunologic responses in patients after V. cholerae infection in Bangladesh.     

Evidence for genetic heterogeneity in D‐2‐hydroxyglutaric aciduria

We performed molecular, enzyme, and metabolic studies in 50 patients with D ‐2‐hydroxyglutaric aciduria (D ‐2‐HGA) who accumulated D ‐2‐hydroxyglutarate (D ‐2‐HG) in physiological fluids. Presumed pathogenic mutations were detected in 24 of 50 patients in the D ‐2‐hydroxyglutarate dehydrogenase (D2HGDH) gene, which encodes D ‐2‐hydroxyglutarate dehydrogenase (D ‐2‐HGDH). Enzyme assay of D ‐2‐HGDH confirmed that all patients with mutations had impaired enzyme activity, whereas patients with D ‐2‐HGA whose enzyme activity was normal did not have mutations. Significantly lower D ‐2‐HG concentrations in body fluids were observed in mutation‐positive D ‐2‐HGA patients than in mutation‐negative patients. These results imply that multiple genetic loci may be associated with hyperexcretion of D ‐2‐HG. Accordingly, we suggest a new classification: D ‐2‐HGA Type I associates with D ‐2‐HGDH deficiency, whereas idiopathic D ‐2‐HGA manifests with normal D ‐2‐HGDH activity and higher D ‐2‐HG levels in body fluids compared with Type I patients. It remains possible that several classifications for idiopathic D ‐2‐HGA patients with diverse genetic loci will be revealed in future studies. Hum Mutat 31:1–5, 2010. © 2009 Wiley‐Liss, Inc.     

Hepatitis B virus BCP,precore/core,X gene mutations/genotypes and the risk of hepatocellular carcinoma in India

The study aims to characterize mutations of the HBV genome involving BCP, Precore/core and X regions and also defines HBV genotypes in patients of hepatocellular carcinoma (HCC). The study involved 150 HBV‐related HCC cases and 136 HBV‐related chronic liver disease patients without HCC as controls. HBV DNA was subjected to mutational analysis using SSCP technique, genotyping by RFLP, and direct nucleotide sequencing. HBV DNA was found in 58.7% (88/150) of the HCC cases and 74.3% (101/136) of controls. HBV mutants were observed in 44.3% of HCC cases and 43.2% of controls. HBV/D was prevalent amongst the patients and controls, followed by HBV/A. The prevalence of the TT1504 mutation in the X gene, the V1753 and T1762/A1764 mutations in the BCP region, and G1914 mutation in the core gene were significantly higher in the HCC group than in the non‐HCC group. Multivariate analyses showed that the TT1504, V1753, A1762T/G1764A, and the G1914 mutations and the patient's age, sex, and HBeAg status increased the risk of HCC development significantly. Also, patients with HCC had lower levels of serum albumin, viral load, and platelet counts but higher values of alkaline phosphatase, alanine aminotransferase, aspartate aminotransferase, bilirubin, and Alpha feto‐protein than those of controls (P < 0.001 for all comparisons). HBV/D was the predominant genotype associated with HCC cases seen in India. The presence of different types of HBV mutations, age, sex, HBeAg status, and viral load was found to increase significantly the risk of HCC development in India. J. Med. Virol. 82: 1115–1125, 2010. © 2010 Wiley‐Liss, Inc.     

Clinical use of liver biopsy for the diagnosis and management of inactive and asymptomatic hepatitis B virus carriers in Bangladesh

Patients with inactive chronic hepatitis B virus (HBV) infection are assumed to be free from liver disease. Accordingly, antiviral drug treatment is not recommended for these patients. However, the extent of liver damage in these patients has not been evaluated fully. The aim of this study was to evaluate the extent of liver damage in patients with inactive HBV. Liver biopsy was conducted in 141 inactive HBV carriers [HBeAg‐negative, low levels of HBV DNA (≤10,000 copies/ml) and normal levels of serum alanine aminotransferase (ALT)]. The extent of hepatic inflammation and fibrosis was evaluated in these patients by examining liver biopsy specimens. Although the patients were inactive HBV carriers, mild to moderate levels of necroinflammation (HAI necroinflammation score HAI‐N1 ≥ 7) were detected in 36 of 141 (26%) patients. Seventeen patients had a severe degree of hepatic fibrosis (HAI fibrosis score HAI‐F ≥ 3). A total of 10 patients had both considerable necroinflammation (HAI‐N1≥7) and severe fibrosis (HAI‐F ≥3). All 10 patients with significant hepatic inflammation and fibrosis were male and older than 25 years. However, all were HBeAg‐negative and expressed low levels of HBV DNA and normal ALT levels. The study demonstrates that features of liver damage were present in a considerable number of the patients. Assessment of liver biopsy specimens in a larger cohort of inactive HBV carriers is necessary to establish management guidelines for such patients. J. Med. Virol. 82:1350–1354, 2010. © 2010 Wiley‐Liss, Inc.