Non-coding nucleotides and amino acids near the active site regulate peptide deformylase expression and inhibitor susceptibility in Chlamydia trachomatis

Chlamydia trachomatis, an obligate intracellular bacterium, is a highly prevalent human pathogen. Hydroxamic-acid-based matrix metalloprotease inhibitors can effectively inhibit the pathogen both in vitro and in vivo, and have exhibited therapeutic potential. Here, we provide genome sequencing data indicating that peptide deformylase (PDF) is the sole target of the inhibitors in this organism. We further report molecular mechanisms that control chlamydial PDF (cPDF) expression and inhibition efficiency. In particular, we identify the σ66-dependent promoter that controls cPDF gene expression and demonstrate that point mutations in this promoter lead to resistance by increasing cPDF transcription. Furthermore, we show that substitution of two amino acids near the active site of the enzyme alters enzyme kinetics and protein stability

A shifting enemy: analysing the BBC’s representations of “al-Qaeda” in the aftermath of the September 11th 2001 attacks

This article seeks to explore how the BBC made sense of the al-Qaeda phenomenon in its flagship “News at Ten” bulletin during the aftermath of the September 11th 2001 attacks. Using Critical Multimodal Discourse Analysis, it shows how the BBC’s representations function as a dynamic and continually shifting site upon which a range of fears, identities, discourses and forms of knowledge and power struggle and contend, and through which a number of different “al-Qaedas” manifest themselves. In particular, three shifting modes of visual and verbal representation are identified within the BBC’s coverage which each correspond to a separate understanding of al-Qaeda: the “Islamic” mode, the “Personalised” mode and the “Elusive” mode. These representations both draw upon and challenge the dominant discourses surrounding Islam, non-state terrorism and the identities of terrorist suspects, providing audiences with a variety of often conflicting ways of seeing and speaking about this entity. As such, the article provides insight into the complex nature of the BBC’s representations of al-Qaeda during its coverage of the September 11th 2001 attacks, and shows how such complexity serves, albeit inadvertently, to legitimise the far-reaching counterterrorism policies that were enacted in the aftermath of these attacks

The cyclic-di-GMP signaling pathway in the Lyme disease spirochete,

In nature, the Lyme disease spirochete Borrelia burgdorferi cycles between the unrelated environments of the Ixodes tick vector and mammalian host. In order to survive transmission between hosts, B. burgdorferi must be able to not only detect changes in its environment, but also rapidly and appropriately respond to these changes. One manner in which this obligate parasite regulates and adapts to its changing environment is through cyclic-di-GMP (c-di-GMP) signaling. c-di-GMP has been shown to be instrumental in orchestrating the adaptation of B. burgdorferi to the tick environment. B. burgdorferi possesses only one set of c-di-GMP-metabolizing genes (one diguanylate cyclase and two distinct phosphodiesterases) and one c-di-GMP-binding PilZ-domain protein designated as PlzA. While studies in the realm of c-di-GMP signaling in B. burgdorferi have exploded in the last few years, there are still many more questions than answers. Elucidation of the importance of c-di-GMP signaling to B. burgdorferi may lead to the identification of mechanisms that are critical for the survival of B. burgdorferi in the tick phase of the enzootic cycle as well as potentially delineate a role (if any) c-di-GMP may play in the transmission and virulence of B. burgdorferi during the enzootic cycle, thereby enabling the development of effective drugs for the prevention and/or treatment of Lyme disease

Transcriptional control in the prereplicative phase of T4 development

Control of transcription is crucial for correct gene expression and orderly development. For many years, bacteriophage T4 has provided a simple model system to investigate mechanisms that regulate this process. Development of T4 requires the transcription of early, middle and late RNAs. Because T4 does not encode its own RNA polymerase, it must redirect the polymerase of its host, E. coli, to the correct class of genes at the correct time. T4 accomplishes this through the action of phage-encoded factors. Here I review recent studies investigating the transcription of T4 prereplicative genes, which are expressed as early and middle transcripts. Early RNAs are generated immediately after infection from T4 promoters that contain excellent recognition sequences for host polymerase. Consequently, the early promoters compete extremely well with host promoters for the available polymerase. T4 early promoter activity is further enhanced by the action of the T4 Alt protein, a component of the phage head that is injected into E. coli along with the phage DNA. Alt modifies Arg265 on one of the two α subunits of RNA polymerase. Although work with host promoters predicts that this modification should decrease promoter activity, transcription from some T4 early promoters increases when RNA polymerase is modified by Alt. Transcription of T4 middle genes begins about 1 minute after infection and proceeds by two pathways: 1) extension of early transcripts into downstream middle genes and 2) activation of T4 middle promoters through a process called sigma appropriation. In this activation, the T4 co-activator AsiA binds to Region 4 of σ70, the specificity subunit of RNA polymerase. This binding dramatically remodels this portion of σ70, which then allows the T4 activator MotA to also interact with σ70. In addition, AsiA restructuring of σ70 prevents Region 4 from forming its normal contacts with the -35 region of promoter DNA, which in turn allows MotA to interact with its DNA binding site, a MotA box, centered at the -30 region of middle promoter DNA. T4 sigma appropriation reveals how a specific domain within RNA polymerase can be remolded and then exploited to alter promoter specificity

Fine-Scale Mapping of the 4q24 Locus Identifies Two Independent Loci Associated with Breast Cancer Risk

Background: A recent association study identified a common variant (rs9790517) at 4q24 to be associated with breast cancer risk. Independent association signals and potential functional variants in this locus have not been explored. Methods: We conducted a fine-mapping analysis in 55,540 breast cancer cases and 51,168 controls from the Breast Cancer Association Consortium. Results: Conditional analyses identified two independent association signals among women of European ancestry, represented by rs9790517 [conditional P = 2.51 × 10−4; OR, 1.04; 95% confidence interval (CI), 1.02–1.07] and rs77928427 (P = 1.86 × 10−4; OR, 1.04; 95% CI, 1.02–1.07). Functional annotation using data from the Encyclopedia of DNA Elements (ENCODE) project revealed two putative functional variants, rs62331150 and rs73838678 in linkage disequilibrium (LD) with rs9790517 (r2 ≥ 0.90) residing in the active promoter or enhancer, respectively, of the nearest gene, TET2. Both variants are located in DNase I hypersensitivity and transcription factor–binding sites. Using data from both The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), we showed that rs62331150 was associated with level of expression of TET2 in breast normal and tumor tissue. Conclusion: Our study identified two independent association signals at 4q24 in relation to breast cancer risk and suggested that observed association in this locus may be mediated through the regulation of TET2. Impact: Fine-mapping study with large sample size warranted for identification of independent loci for breast cancer risk

European consensus statement on diagnosis and treatment of adult ADHD: The European Network Adult ADHD.

BACKGROUND: Attention deficit hyperactivity disorder (ADHD) is among the most common psychiatric disorders of childhood that persists into adulthood in the majority of cases. The evidence on persistence poses several difficulties for adult psychiatry considering the lack of expertise for diagnostic assessment, limited treatment options and patient facilities across Europe. METHODS: The European Network Adult ADHD, founded in 2003, aims to increase awareness of this disorder and improve knowledge and patient care for adults with ADHD across Europe. This Consensus Statement is one of the actions taken by the European Network Adult ADHD in order to support the clinician with research evidence and clinical experience from 18 European countries in which ADHD in adults is recognised and treated. RESULTS: Besides information on the genetics and neurobiology of ADHD, three major questions are addressed in this statement: (1) What is the clinical picture of ADHD in adults? (2) How can ADHD in adults be properly diagnosed? (3) How should ADHD in adults be effectively treated? CONCLUSIONS: ADHD often presents as an impairing lifelong condition in adults, yet it is currently underdiagnosed and treated in many European countries, leading to ineffective treatment and higher costs of illness. Expertise in diagnostic assessment and treatment of ADHD in adults must increase in psychiatry. Instruments for screening and diagnosis of ADHD in adults are available and appropriate treatments exist, although more research is needed in this age group

Clinical and biomarker changes in premanifest Huntington disease show trial feasibility: A decade of the PREDICT-HD study

There is growing consensus that intervention and treatment of Huntington disease (HD) should occur at the earliest stage possible. Various early-intervention methods for this fatal neurodegenerative disease have been identified, but preventive clinical trials for HD are limited by a lack of knowledge of the natural history of the disease and a dearth of appropriate outcome measures. Objectives of the current study are to document the natural history of premanifest HD progression in the largest cohort ever studied and to develop a battery of imaging and clinical markers of premanifest HD progression that can be used as outcome measures in preventive clinical trials. Neurobiological predictors of Huntington’s disease is a 32-site, international, observational study of premanifest HD, with annual examination of 1013 participants with premanifest HD and 301 gene-expansion negative controls between 2001 and 2012. Findings document 39 variables representing imaging, motor, cognitive, functional, and psychiatric domains, showing different rates of decline between premanifest HD and controls. Required sample size and models of premanifest HD are presented to inform future design of clinical and preclinical research. Preventive clinical trials in premanifest HD with participants who have a medium or high probability of motor onset are calculated to be as resource-effective as those conducted in diagnosed HD and could interrupt disease 7–12years earlier. Methods and measures for preventive clinical trials in premanifest HD more than a dozen years from motor onset are also feasible. These findings represent the most thorough documentation of a clinical battery for experimental therapeutics in stages of premanifest HD, the time period for which effective intervention may provide the most positive possible outcome for patients and their families affected by this devastating disease

Genome-Wide Analysis of Fundamental Transcription Factors in Giardia lamblia

Giardia lamblia is a unicellular parasite of the mammalian intestinal tract and is the most common parasitic intestinal disease in the United States. Giardia is an early-diverging eukaryote characterized by a two-stage life cycle. Giardia lacks the canonical RNA polymerase II transcription apparatus of eukaryotes and Archaea; its genome lacks TFIIB and has a highly degenerate TBP, raising questions as to how Giardia initiates RNA polymerase II transcription. We hypothesize that giardial BRF (TFIIB-related factor) could be substituting for TFIIB by playing a dual role in RNAP II and III initiation. Gene expression data from three time points in the giardial life cycle were generated using RNA-seq. Only a small subset of genes showed significantly different expression. Comparison with recent proteomic studies suggests limited regulation at the transcriptional level, giving way to post-transcriptional regulation as the primary control of gene expression, though continued study is necessary to test this hypothesis. Investigating transcription in Giardia will provide insight into the evolution of complex transcription systems in eukaryotes

Global Survey of Water Quality Using Point-of-Use Water Filters

Waterborne illnesses continue to be a major global health concern. A leading strategy for providing clean drinking-water is the use of point-of-use water filters. Sawyer Products, Inc., a privately owned outdoor product company, launched Sawyer International to bring 0.1 micron hollow fiber membrane filters to people in need of safe, clean drinking-water. These filters remove harmful bacteria, protozoa, and cysts like Escherichia coli, Salmonella typhi, Vibrio cholerae, and Giardia. Additionally, Sawyer is providing polyurethane foam filters designed to remove metals known to be harmful in excess concentrations, including arsenic and cadmium. Hope College, in collaboration with Sawyer, is conducting a global water quality survey that will study drinking water sources from over 30 countries. We have partnered with NGO’s to deliver water filter kits to sites, collect and process water samples in the field, and return the filters to Hope College for analysis of microbial populations, classes of antibiotics, and chemicals found in the water. In addition, we will conduct an in-depth study of the introduction of filters to all households in 20 villages in Fiji. Samples will be obtained from 2 water sources per village in order to assess water quality and effective removal of potential pathogens from the water sources; surveys to assess the health status of members of the villages will be administered. Two more visits will be made to villages at 2-4 weeks and 8 weeks post filter introduction to obtain additional water samples and survey data. We anticipate that introduction of filters into villages without access to clean water will improve the health of residents. The data obtained will allow us to describe biological and chemical properties of global water sources that have adverse effects on the health and wellbeing of residents and give evidence for the efficacy of point of use water filters