High GILT Expression Is Associated with Improved Survival in Metastatic Melanoma Patients Treated with Immune Checkpoint Inhibition.

Gamma-interferon-inducible lysosomal thiol reductase (GILT) is critical for MHC class II restricted presentation of multiple melanoma antigens. There is variable GILT protein expression in malignant melanocytes in melanoma specimens. High GILT mRNA expression in melanoma specimens is associated with improved overall survival, before the advent of immune checkpoint inhibitors (ICI). However, the association of GILT in metastatic melanoma with survival in patients treated with ICI and the cell type expressing GILT associated with survival have not been determined. Using RNA sequencing datasets, high GILT mRNA expression in metastatic melanoma specimens was associated with improved progression-free and overall survival in patients treated with ICI. A clinical dataset of metastatic melanoma specimens was generated and annotated with clinical information. Positive GILT immunohistochemical staining in antigen presenting cells and melanoma cells was observed in 100% and 65% of metastatic melanoma specimens, respectively. In the subset of patients treated with ICI in the clinical dataset, high GILT protein expression within melanoma cells was associated with improved overall survival. The association of GILT mRNA and protein expression with survival was independent of cancer stage. These studies support that high GILT mRNA expression in bulk tumor samples and high GILT protein expression in melanoma cells is associated with improved survival in ICI-treated patients. These findings support further investigation of GILT as a biomarker to predict the response to ICI.

Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis.

Chlamydia trachomatis remains a leading cause of bacterial sexually transmitted infections and preventable blindness worldwide. There are, however, limited in vitro models to study the role of host genetics in the response of macrophages to this obligate human pathogen. Here, we describe an approach using macrophages derived from human induced pluripotent stem cells (iPSdMs) to study macrophage-Chlamydia interactions in vitro. We show that iPSdMs support the full infectious life cycle of C. trachomatis in a manner that mimics the infection of human blood-derived macrophages. Transcriptomic and proteomic profiling of the macrophage response to chlamydial infection highlighted the role of the type I interferon and interleukin 10-mediated responses. Using CRISPR/Cas9 technology, we generated biallelic knockout mutations in host genes encoding IRF5 and IL-10RA in iPSCs, and confirmed their roles in limiting chlamydial infection in macrophages. This model can potentially be extended to other pathogens and tissue systems to advance our understanding of host-pathogen interactions and the role of human genetics in influencing the outcome of infections.

Leptomeningeal dissemination of a low-grade lumbar paraganglioma: case report.

Leptomeningeal dissemination of paraganglioma is rare, with only 2 prior cases in the literature. The authors present the case of a metastatic low-grade lumbar paraganglioma via leptomeningeal dissemination. This report emphasizes the utility of 3,4-dihydroxy-6-18F-fluoro-l-phenylalanine (18F-FDOPA) PET scanning for diagnosis, as well as the combination of radiation therapy and alkylating chemotherapeutic agents for the treatment of this rare phenomenon. The patient was a 61-year-old woman who presented with low-back pain and was found to have an isolated L-3 intrathecal tumor on MRI. Sixteen months after gross-total en bloc resection of the paraganglioma, the patient again became symptomatic with new neurological symptoms. MRI findings revealed enhancing leptomeningeal nodules throughout the spine. 18F-FDOPA PET/CT scanning was used to confirm the diagnosis of disseminated paraganglioma. Intrathecal thiotepa, radiation therapy, and systemic therapy with capecitabine and temozolomide have been used sequentially over a 2-year period, with each able to stabilize tumor growth for several months. The authors also summarize the 2 other reports of leptomeningeal dissemination of paragangliomas in the literature and compare the course and management of the 3 cases.

What's in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B.

UNLABELLED: For 100 years, it has been obvious that Salmonella enterica strains sharing the serotype with the formula 1,4,[5],12:b:1,2-now known as Paratyphi B-can cause diseases ranging from serious systemic infections to self-limiting gastroenteritis. Despite considerable predicted diversity between strains carrying the common Paratyphi B serotype, there remain few methods that subdivide the group into groups that are congruent with their disease phenotypes. Paratyphi B therefore represents one of the canonical examples in Salmonella where serotyping combined with classical microbiological tests fails to provide clinically informative information. Here, we use genomics to provide the first high-resolution view of this serotype, placing it into a wider genomic context of the Salmonella enterica species. These analyses reveal why it has been impossible to subdivide this serotype based upon phenotypic and limited molecular approaches. By examining the genomic data in detail, we are able to identify common features that correlate with strains of clinical importance. The results presented here provide new diagnostic targets, as well as posing important new questions about the basis for the invasive disease phenotype observed in a subset of strains. IMPORTANCE: Salmonella enterica strains carrying the serotype Paratyphi B have long been known to possess Jekyll and Hyde characteristics; some cause gastroenteritis, while others cause serious invasive disease. Understanding what makes up the population of strains carrying this serotype, as well as the source of their invasive disease, is a 100-year-old puzzle that we address here using genomics. Our analysis provides the first high-resolution view of this serotype, placing strains carrying serotype Paratyphi B into the wider genomic context of the Salmonella enterica species. This work reveals a history of disease dating back to the middle ages, caused by a group of distinct lineages with various abilities to cause invasive disease. By quantifying the key genomic differences between the invasive and noninvasive populations, we are able to identify key virulence-related targets that can form the basis of simple, rapid, point-of-care tests.

Maintenance eculizumab dose adjustment in the treatment of atypical hemolytic uremic syndrome: a case report and review of the literature.

Atypical hemolytic uremic syndrome (aHUS) patients treated with eculizumab may require higher doses to achieve and maintain optimal clinical response. Further studies are warranted to elucidate optimal dosing regimens of eculizumab in aHUS patients, and whether dosing regimens can be predicted based on mutational status, eculizumab levels, or other testing.

Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling.

Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA elements in bacterial and archaeal genomes is hampered by the difficulty of de novo identification. The emergence of new technologies for characterizing transcriptome outputs, notably RNA-seq, are improving noncoding RNA identification and expression quantification. However, a major challenge is to robustly distinguish functional outputs from transcriptional noise. To establish whether annotation of existing transcriptome data has effectively captured all functional outputs, we analysed over 400 publicly available RNA-seq datasets spanning 37 different Archaea and Bacteria. Using comparative tools, we identify close to a thousand highly-expressed candidate noncoding RNAs. However, our analyses reveal that capacity to identify noncoding RNA outputs is strongly dependent on phylogenetic sampling. Surprisingly, and in stark contrast to protein-coding genes, the phylogenetic window for effective use of comparative methods is perversely narrow: aggregating public datasets only produced one phylogenetic cluster where these tools could be used to robustly separate unannotated noncoding RNAs from a null hypothesis of transcriptional noise. Our results show that for the full potential of transcriptomics data to be realized, a change in experimental design is paramount: effective transcriptomics requires phylogeny-aware sampling.

Comparative genomics of Shiga toxin encoding bacteriophages.

BACKGROUND: Stx bacteriophages are responsible for driving the dissemination of Stx toxin genes (stx) across their bacterial host range. Lysogens carrying Stx phages can cause severe, life-threatening disease and Stx toxin is an integral virulence factor. The Stx-bacteriophage vB_EcoP-24B, commonly referred to as Ф24B, is capable of multiply infecting a single bacterial host cell at a high frequency, with secondary infection increasing the rate at which subsequent bacteriophage infections can occur. This is biologically unusual, therefore determining the genomic content and context of Ф24B compared to other lambdoid Stx phages is important to understanding the factors controlling this phenomenon and determining whether they occur in other Stx phages. RESULTS: The genome of the Stx2 encoding phage, Ф24B was sequenced and annotated. The genomic organisation and general features are similar to other sequenced Stx bacteriophages induced from Enterohaemorrhagic Escherichia coli (EHEC), however Ф24B possesses significant regions of heterogeneity, with implications for phage biology and behaviour. The Ф24B genome was compared to other sequenced Stx phages and the archetypal lambdoid phage, lambda, using the Circos genome comparison tool and a PCR-based multi-loci comparison system. CONCLUSIONS: The data support the hypothesis that Stx phages are mosaic, and recombination events between the host, phages and their remnants within the same infected bacterial cell will continue to drive the evolution of Stx phage variants and the subsequent dissemination of shigatoxigenic potential.

Assessing the impact of harm reduction programs on law enforcement in Southeast Asia: a description of a regional research methodology.

For over 15 years the Australian Agency for International Development (AusAID) has been a leading donor for harm reduction projects in Southeast Asia. The recent AusAID-supported harm reduction projects of greatest significance have included the Asia Regional HIV/AIDS Project (AHRP), from 2002 until 2007,1 and the HIV/AIDS Asia Regional Program (HAARP), from 2007 until 2015.2 Both projects included in their design specific strategies for engaging with law enforcement agencies at country level. The main focus of these strategies has been to develop law enforcement harm reduction policy and curriculum, and the design and implementation of specific harm reduction training for law enforcement officers.In July 2008, the Australian Development Research Awards (ADRA) funded the Nossal Institute for Global Health at the University of Melbourne to establish a research project created to assess the influence of harm reduction programs on the policy and operational practices of law enforcement agencies in Southeast Asia, known as the LEHRN Project (Law Enforcement, Harm Reduction, Nossal Institute Project). The ADRA is a unique grant research mechanism that specifically funds development research to improve the understanding and informed decision making of the implementation of Australian aid effectiveness.While the need to engage law enforcement when establishing harm reduction programs was well documented, little was known about the impact or influence of harm reduction programs on policy and practices of law enforcement agencies. The LEHRN Project provided the opportunity to assess the impact of harm reduction programs on law enforcement in Southeast Asia, with a focus on Vietnam, Cambodia and Lao PDR.

Harm reduction in Cambodia: a disconnect between policy and practice.

In 2003 the Government of Cambodia officially began to recognise that harm reduction was an essential approach to preventing HIV among people who use drugs and their sexual partners. Several programs aiming to control and prevent HIV among drug users have been implemented in Cambodia, mostly in the capital, Phnom Penh. However, there have been ongoing tensions between law enforcement and harm reduction actors, despite several advocacy efforts targeting law enforcement. This study attempts to better understand the implementation of harm reduction in Cambodia and how the policy environment and harm reduction program implementation has intersected with the role of law enforcement officials in Cambodia.

The village/commune safety policy and HIV prevention efforts among key affected populations in Cambodia: finding a balance.

The Village/Commune Safety Policy was launched by the Ministry of Interior of the Kingdom of Cambodia in 2010 and, due to a priority focus on "cleaning the streets", has created difficulties for HIV prevention programs attempting to implement programs that work with key affected populations including female sex workers and people who inject drugs. The implementation of the policy has forced HIV program implementers, the UN and various government counterparts to explore and develop collaborative ways of delivering HIV prevention services within this difficult environment. The following case study explores some of these efforts and highlights the promising development of a Police Community Partnership Initiative that it is hoped will find a meaningful balance between the Village/Commune Safety Policy and HIV prevention efforts with key affected populations in Cambodia.

Zyxin phosphorylation at serine 142 modulates the zyxin head-tail interaction to alter cell-cell adhesion.

Zyxin is an actin regulatory protein that is concentrated at sites of actin-membrane association, particularly cell junctions. Zyxin participates in actin dynamics by binding VASP, an interaction that occurs via proline-rich N-terminal ActA repeats. An intramolecular association of the N-terminal LIM domains at or near the ActA repeats can prevent VASP and other binding partners from binding full-length zyxin. Such a head-tail interaction likely accounts for how zyxin function in actin dynamics, cell adhesion, and cell migration can be regulated by the cell. Since zyxin binding to several partners, via the LIM domains, requires phosphorylation, it seems likely that zyxin phosphorylation might alter the head-tail interaction and, thus, zyxin activity. Here we show that zyxin point mutants at a known phosphorylation site, serine 142, alter the ability of a zyxin fragment to directly bind a separate zyxin LIM domains fragment protein. Further, expression of the zyxin phosphomimetic mutant results in increased localization to cell-cell contacts of MDCK cells and generates a cellular phenotype, namely inability to disassemble cell-cell contacts, precisely like that produced by expression of zyxin mutants that lack the entire regulatory LIM domain region. These data suggest that zyxin phosphorylation at serine 142 results in release of the head-tail interaction, changing zyxin activity at cell-cell contacts.

Predictors and consequences of incarceration among a sample of young Thai methamphetamine users.

INTRODUCTION AND AIMS: Our study examined the incidence of arrest and incarceration, investigated predictors of incarceration and explored the persistence of depression, alcohol use and drug use after incarceration among young methamphetamine users from Thailand. DESIGN AND METHODS: Participants were aged 18-25 years old and were a part of a 12 month randomised social network trial that aimed to reduce sexual risk and methamphetamine use. Estimates of the incidence of arrest and incarceration over 12 months were calculated. A matched case-control study (n = 73 cases; n = 223 controls) was performed to examine incarceration risk factors using conditional logistic regression. Persistence of drug-risk behaviours were explored after incarceration. RESULTS: Study participants (n = 950) were 72% male, with a median age of 19 years and a median of 9 years of schooling. Frequent drug and alcohol use were reported at baseline. In total, 35% of the sample reported ever having been arrested and 22% reported ever having been incarcerated at baseline. During the 12 month follow up, 16% of the sample was arrested. In univariate analyses, risk factors for incarceration included frequent drug and alcohol use, being less educated, and a history of arrest and incarceration. A high prevalence of drug and alcohol use and involvement in the drug economy persisted after arrest. DISCUSSION AND CONCLUSIONS: The study indicates a high prevalence of recidivism among this young sample, with continued involvement in drug-risk behaviours after incarceration. Appropriate interventions are needed to address root causes of arrest, largely related to substance use.

DNAPlotter: circular and linear interactive genome visualization.

UNLABELLED: DNAPlotter is an interactive Java application for generating circular and linear representations of genomes. Making use of the Artemis libraries to provide a user-friendly method of loading in sequence files (EMBL, GenBank, GFF) as well as data from relational databases, it filters features of interest to display on separate user-definable tracks. It can be used to produce publication quality images for papers or web pages. AVAILABILITY: DNAPlotter is freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/circular/

Meeting report: the fourth Genomic Standards Consortium (GSC) workshop.

This meeting report summarizes the proceedings of the "eGenomics: Cataloguing our Complete Genome Collection IV" workshop held June 6-8, 2007, at the National Institute for Environmental eScience (NIEeS), Cambridge, United Kingdom. This fourth workshop of the Genomic Standards Consortium (GSC) was a mix of short presentations, strategy discussions, and technical sessions. Speakers provided progress reports on the development of the "Minimum Information about a Genome Sequence" (MIGS) specification and the closely integrated "Minimum Information about a Metagenome Sequence" (MIMS) specification. The key outcome of the workshop was consensus on the next version of the MIGS/MIMS specification (v1.2). This drove further definition and restructuring of the MIGS/MIMS XML schema (syntax). With respect to semantics, a term vetting group was established to ensure that terms are properly defined and submitted to the appropriate ontology projects. Perhaps the single most important outcome of the workshop was a proposal to move beyond the concept of "minimum" to create a far richer XML schema that would define a "Genomic Contextual Data Markup Language" (GCDML) suitable for wider semantic integration across databases. GCDML will contain not only curated information (e.g., compliant with MIGS/MIMS), but also be extended to include a variety of data processing and calculations. Further information about the Genomic Standards Consortium and its range of activities can be found at http://gensc.org.

Meeting report: the fifth Genomic Standards Consortium (GSC) workshop.

This meeting report summarizes the proceedings of the fifth Genomic Standards Consortium (GSC) workshop held December 12-14, 2007, at the European Bioinformatics Institute (EBI), Cambridge, UK. This fifth workshop served as a milestone event in the evolution of the GSC (launched in September 2005); the key outcome of the workshop was the finalization of a stable version of the MIGS specification (v2.0) for publication. This accomplishment enables, and also in some cases necessitates, downstream activities, which are described in the multiauthor, consensus-driven articles in this special issue of OMICS produced as a direct result of the workshop. This report briefly summarizes the workshop and overviews the special issue. In particular, it aims to explain how the various GSC-led projects are working together to help this community achieve its stated mission of further standardizing the descriptions of genomes and metagenomes and implementing improved mechanisms of data exchange and integration to enable more accurate comparative analyses. Further information about the GSC and its range of activities can be found at http://gensc.org.

Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation.

The methodologies used to generate genome and metagenome annotations are diverse and vary between groups and laboratories. Descriptions of the annotation process are helpful in interpreting genome annotation data. Some groups have produced Standard Operating Procedures (SOPs) that describe the annotation process, but standards are lacking for structure and content of these descriptions. In addition, there is no central repository to store and disseminate procedures and protocols for genome annotation. We highlight the importance of SOPs for genome annotation and endorse an online repository of SOPs.

Pd-mBDPP-catalyzed regioselective internal arylation of electron-rich olefins by aryl halides.

meso-2,4-Bis(diphenylphosphino)pentane (mBDPP) has proved to be an effective regiocontrolling ligand for palladium-catalyzed internal arylation by aryl bromides of electron-rich olefins in a common solvent DMSO with no need for any halide scavengers. The arylation of the benchmark electron-rich olefin butyl vinyl ether took place smoothly to afford exclusively alpha-arylated product with high isolated yields. The better performance of mBDPP, compared with that of the commonly used DPPP [1,3-bis(diphenylphosphino)propane], highlights the important but subtle effect of ligand on the regioselectivity of the Heck arylation reactions.