The Magnitude of IFN-γ Responses Is Fine-Tuned by DNA Architecture and the Non-coding Transcript of Ifng-as1.

Interferon gamma (IFN-γ), critical for host defense and tumor surveillance, requires tight control of its expression. Multiple cis-regulatory elements exist around Ifng along with a non-coding transcript, Ifng-as1 (also termed NeST). Here, we describe two genetic models generated to dissect the molecular functions of this locus and its RNA product. DNA deletion within the Ifng-as1 locus disrupted chromatin organization of the extended Ifng locus, impaired Ifng response, and compromised host defense. Insertion of a polyA signal ablated the Ifng-as1 full-length transcript and impaired host defense, while allowing proper chromatin structure. Transient knockdown of Ifng-as1 also reduced IFN-γ production. In humans, discordant expression of IFNG and IFNG-AS1 was evident in memory T cells, with high expression of this long non-coding RNA (lncRNA) and low expression of the cytokine. These results establish Ifng-as1 as an important regulator of Ifng expression, as a DNA element and transcribed RNA, involved in dynamic and cell state-specific responses to infection.

Prediction of internalizing and externalizing symptoms in late childhood from attention-deficit/hyperactivity disorder symptoms in early childhood.

Limited analyses based on national samples have assessed whether early attention-deficit/hyperactivity disorder (ADHD) symptoms predict later internalizing and externalizing symptoms in youth and the influence of sex and pubertal timing on subsequent psychiatric symptoms. This study analyzed data (n = 2818) from the Environmental influences on Child Health Outcomes Program national cohort. Analyses used data from early childhood (mean age = 5.3 years) utilizing parent-reported ADHD symptoms to predict rates of internalizing and externalizing symptoms from late childhood/adolescence (mean age = 11.9 years). Within a subsample age at peak height velocity (APHV) acted as a proxy to assess pubertal timing from early childhood (mean age = 5.4 years) to adolescence (mean age = 12.3 years). Early-childhood ADHD symptoms predicted later psychiatric symptoms, including anxiety, depression, aggressive behavior, conduct problems, oppositional defiant disorder, and rule-breaking behavior. Earlier APHV was associated with increased Conduct Disorder symptoms from late childhood to adolescence for females only. A stronger relation between ADHD symptoms and later aggression was observed in females with earlier APHV, whereas this same pattern with aggression, conduct problems and depression was observed in males with later APHV. Clinicians should consider that both young girls and boys with elevated ADHD symptoms, particularly with off-set pubertal timing, may be at risk for later psychiatric symptoms.

Technological readiness and implementation of genomic-driven precision medicine for complex diseases.

The fields of human genetics and genomics have generated considerable knowledge about the mechanistic basis of many diseases. Genomic approaches to diagnosis, prognostication, prevention and treatment - genomic-driven precision medicine (GDPM) - may help optimize medical practice. Here, we provide a comprehensive review of GDPM of complex diseases across major medical specialties. We focus on technological readiness: how rapidly a test can be implemented into health care. Although these areas of medicine are diverse, key similarities exist across almost all areas. Many medical areas have, within their standards of care, at least one GDPM test for a genetic variant of strong effect that aids the identification/diagnosis of a more homogeneous subset within a larger disease group or identifies a subset with different therapeutic requirements. However, for almost all complex diseases, the majority of patients do not carry established single-gene mutations with large effects. Thus, research is underway that seeks to determine the polygenic basis of many complex diseases. Nevertheless, most complex diseases are caused by the interplay of genetic, behavioural and environmental risk factors, which will likely necessitate models for prediction and diagnosis that incorporate genetic and non-genetic data.

Asymmetric cryo-EM structure of the canonical Allolevivirus Qß reveals a single maturation protein and the genomic ssRNA in situ.

Single-stranded (ss) RNA viruses infect all domains of life. To date, for most ssRNA virions, only the structures of the capsids and their associated protein components have been resolved to high resolution. Qß, an ssRNA phage specific for the conjugative F-pilus, has a T = 3 icosahedral lattice of coat proteins assembled around its 4,217 nucleotides of genomic RNA (gRNA). In the mature virion, the maturation protein, A2, binds to the gRNA and is required for adsorption to the F-pilus. Here, we report the cryo-electron microscopy (cryo-EM) structures of Qß with and without symmetry applied. The icosahedral structure, at 3.7-Å resolution, resolves loops not previously seen in the published X-ray structure, whereas the asymmetric structure, at 7-Å resolution, reveals A2 and the gRNA. A2 contains a bundle of α-helices and replaces one dimer of coat proteins at a twofold axis. The helix bundle binds gRNA, causing denser packing of RNA in its proximity, which asymmetrically expands the surrounding coat protein shell to potentially facilitate RNA release during infection. We observe a fixed pattern of gRNA organization among all viral particles, with the major and minor grooves of RNA helices clearly visible. A single layer of RNA directly contacts every copy of the coat protein, with one-third of the interactions occurring at operator-like RNA hairpins. These RNA-coat interactions stabilize the tertiary structure of gRNA within the virion, which could further provide a roadmap for capsid assembly.

A Genetically Encoded, Phage-Displayed Cyclic-Peptide Library.

Superior to linear peptides in biological activities, cyclic peptides are considered to have great potential as therapeutic agents. To identify cyclic-peptide ligands for therapeutic targets, phage-displayed peptide libraries in which cyclization is achieved by the covalent conjugation of cysteines have been widely used. To resolve drawbacks related to cysteine conjugation, we have invented a phage-display technique in which its displayed peptides are cyclized through a proximity-driven Michael addition reaction between a cysteine and an amber-codon-encoded Nϵ -acryloyl-lysine (AcrK). Using a randomized 6-mer library in which peptides were cyclized at two ends through a cysteine-AcrK linker, we demonstrated the successful selection of potent ligands for TEV protease and HDAC8. All selected cyclic peptide ligands showed 4- to 6-fold stronger affinity to their protein targets than their linear counterparts. We believe this approach will find broad applications in drug discovery.

Signal Integration at Elongation Factor 2 Kinase: THE ROLES OF CALCIUM, CALMODULIN, AND SER-500 PHOSPHORYLATION.

Eukaryotic elongation factor 2 kinase (eEF-2K), the only calmodulin (CaM)-dependent member of the unique α-kinase family, impedes protein synthesis by phosphorylating eEF-2. We recently identified Thr-348 and Ser-500 as two key autophosphorylation sites within eEF-2K that regulate its activity. eEF-2K is regulated by Ca2+ ions and multiple upstream signaling pathways, but how it integrates these signals into a coherent output, i.e. phosphorylation of eEF-2, is unclear. This study focuses on understanding how the post-translational phosphorylation of Ser-500 integrates with Ca2+ and CaM to regulate eEF-2K. CaM is shown to be absolutely necessary for efficient activity of eEF-2K, and Ca2+ is shown to enhance the affinity of CaM toward eEF-2K. Ser-500 is found to undergo autophosphorylation in cells treated with ionomycin and is likely also targeted by PKA. In vitro, autophosphorylation of Ser-500 is found to require Ca2+ and CaM and is inhibited by mutations that compromise binding of phosphorylated Thr-348 to an allosteric binding pocket on the kinase domain. A phosphomimetic Ser-500 to aspartic acid mutation (eEF-2K S500D) enhances the rate of activation (Thr-348 autophosphorylation) by 6-fold and lowers the EC50 for Ca2+/CaM binding to activated eEF-2K (Thr-348 phosphorylated) by 20-fold. This is predicted to result in an elevation of the cellular fraction of active eEF-2K. In support of this mechanism, eEF-2K knock-out MCF10A cells reconstituted with eEF-2K S500D display relatively high levels of phospho-eEF-2 under basal conditions. This study reports how phosphorylation of a regulatory site (Ser-500) integrates with Ca2+ and CaM to influence eEF-2K activity.

Changing perceptions of protected area benefits and problems around Kibale National Park, Uganda.

Local residents' changing perceptions of benefits and problems from living next to a protected area in western Uganda are assessed by comparing household survey data from 2006, 2009, and 2012. Findings are contextualized and supported by long-term data sources for tourism, protected area-based employment, tourism revenue sharing, resource access agreements, and problem animal abundance. We found decreasing perceived benefit and increasing perceived problems associated with the protected area over time, with both trends dominated by increased human-wildlife conflict due to recovering elephant numbers. Proportions of households claiming benefit from specific conservation strategies were increasing, but not enough to offset crop raiding. Ecosystem services mitigated perceptions of problems. As human and animal populations rise, wildlife authorities in Sub-Saharan Africa will be challenged to balance perceptions and adapt policies to ensure the continued existence of protected areas. Understanding the dynamic nature of local people's perceptions provides a tool to adapt protected area management plans, prioritize conservation resources, and engage local communities to support protected areas.

Spatially explicit data: stewardship and ethical challenges in science.

Scholarly communication is at an unprecedented turning point created in part by the increasing saliency of data stewardship and data sharing. Formal data management plans represent a new emphasis in research, enabling access to data at higher volumes and more quickly, and the potential for replication and augmentation of existing research. Data sharing has recently transformed the practice, scope, content, and applicability of research in several disciplines, in particular in relation to spatially specific data. This lends exciting potentiality, but the most effective ways in which to implement such changes, particularly for disciplines involving human subjects and other sensitive information, demand consideration. Data management plans, stewardship, and sharing, impart distinctive technical, sociological, and ethical challenges that remain to be adequately identified and remedied. Here, we consider these and propose potential solutions for their amelioration.

Current State and Model for Development of Technology-Based Care for Attention Deficit Hyperactivity Disorder.

INTRODUCTION: Care (i.e., evaluation and intervention) delivered through technology is used in many areas of mental health services, including for persons with attention deficit hyperactivity disorder (ADHD). Technology can facilitate care for individuals with ADHD, their parents, and their care providers. The adoption of technological tools for ADHD care requires evidence-based studies to support the transition from development to integration into use in the home, school, or work for persons with the disorder. The initial phase, which is development of technological tools, has begun in earnest; however, the evidence base for many of these tools is lacking. In some instances, the uptake of a piece of technology into home use or clinical practice may be further along than the research to support its use. METHODS: In this study, we review the current evidence regarding technology for ADHD and also propose a model to evaluate the support for other tools that have yet to be tested. RESULTS: We propose using the Research Domain Criteria as a framework for evaluating the tools' relationships to dimensions related to ADHD. CONCLUSION: This article concludes with recommendations for testing new tools that may have promise in improving the evaluation or treatment of persons with ADHD.

Etanercept decreases synovial expression of tumour necrosis factor-α and lymphotoxin-α in rheumatoid arthritis.

OBJECTIVES: Etanercept is an effective tumour necrosis factor (TNF)-α inhibitor drug with the unique ability to block not only TNF-α but also lymphotoxin (LT)-α, at least in vitro. We aimed to investigate the in vivo effect of etanercept on synovial expression of TNF-α and LT-α. METHOD: Synovial biopsies from 12 rheumatoid arthritis (RA) patients started on etanercept and 11 RA patients started on infliximab were obtained at baseline and 8 weeks after treatment initiation. Synovial expression of TNF-α and LT-α was evaluated by immunohistochemistry followed by computer-assisted image analysis. Differences between paired samples were analysed by the Wilcoxon test and between groups by the Mann-Whitney test. A p-value < 0.05 was considered statistically significant. RESULTS: Six out of the 12 of the patients started on etanercept achieved an American College of Rheumatology (ACR)50 response. Macroscopic evaluation of the joints during arthroscopy revealed a significant decrease of local inflammation mainly in good ACR50 responders. Synovial expression of both LT-α and TNF-α decreased but the differences did not reach statistical significance at a group level. By contrast, a significant decrease in both LT-α and TNF-α was observed when only good ACR50 responders were analysed. Despite higher levels of baseline synovial TNF-α in the good responders, neither baseline LT-α nor TNF-α could predict clinical response after 8 weeks. A decreasing trend of the synovial levels of LT-α was also observed in good responders to infliximab, but the difference did not reach statistical significance. CONCLUSIONS: Etanercept treatment modulates the synovial expression of both TNF-α and LT-α in vivo, a mechanism that might partly explain its clinical efficacy in RA.

Use of single large or several small policies as strategies to manage people-park interactions.

Biodiversity conservation has been criticized for undermining or ignoring social well-being. Currently efforts to mutually promote social justice, rural development, and biodiversity conservation, which have been contentious and yielded mixed results, continue to spread despite a general dearth of effective management strategies. We contend that social and economic concerns should be integral to conservation planning and propose that the scale of these phenomena is also critical. To evaluate the merit of this proposal, we adopted and expanded a conservation management strategy framework developed by Joel Heinen and examined how population density, economic disparity, and ethnic heterogeneity vary spatially surrounding 2 contrasting protected areas in East Africa: Kibale National Park in Uganda and Tarangire National Park in Tanzania. Analyses of demographic, wealth, and ethnicity data from regional censuses and household surveys conducted in 2009 and 2010 indicated that choice of scale (landscape or community) changed the management strategies recommended by the model. Therefore, "several small" people-park management strategies varying around a given protected area may be more appropriate than a "single large" people-park strategy applied across an entire protected area. Correspondingly, scale adjusted Heinen recommendations offered new strategies for effective conservation management within these human landscapes not incorporated in current in situ management plans.

Synthesis and biological evaluation of pyrido[2,3-d]pyrimidine-2,4-dione derivatives as eEF-2K inhibitors.

A small molecule library of pyrido[2,3-d]pyrimidine-2,4-dione derivatives 6-16 was synthesized from 6-amino-1,3-disubstituted uracils 18, characterized, and screened for inhibitory activity against eukaryotic elongation factor-2 kinase (eEF-2K). To understand the binding pocket of eEF-2K, structural modifications of the pyrido[2,3-d]pyrimidine were made at three regions (R(1), R(2), and R(3)). A homology model of eEF-2K was created, and compound 6 (A-484954, Abbott laboratories) was docked in the catalytic domain of eEF-2K. Compounds 6 (IC50=420nM) and 9 (IC50=930nM) are found to be better molecules in this preliminary series of pyrido[2,3-d]pyrimidine analogs. eEF-2K activity in MDA-MB-231 breast cancer cells is significantly reduced by compound 6, to a lesser extent by compound 9, and is unaffected by compound 12. Similar inhibitory results are observed when eEF-2K activity is stimulated by 2-deoxy-d-glucose (2-DOG) treatment, suggesting that compounds 6 and 9 are able to inhibit AMPK-mediated activation of eEF-2K to a notable extent. The results of this work will shed light on the further design and optimization of novel pyrido[2,3-d]pyrimidine analogs as eEF-2K inhibitors.

Genetic variation in the serotonin receptor gene affects immune responses in rheumatoid arthritis.

Many genetic variants associate with the risk of developing rheumatoid arthritis (RA); however, their functional roles are largely unknown. Here, we aimed to investigate whether the RA-associated serotonin receptor 2A (HTR2A) haplotype affects T-cell and monocyte functions. Patients with established RA (n=379) were genotyped for two single-nucleotide polymorphisms (SNPs) in the HTR2A locus, rs6314 and rs1328674, to define presence of the risk haplotype for each individual. Patients with and without the RA-associated TC haplotype were selected and T-cell and monocyte function was monitored following in vitro stimulations with staphylococcal enterotoxin B and lipopolysaccharide (LPS) using multiparameter flow cytometry. Within the cohort, 44 patients were heterozygous for the TC haplotype (11.6%) while none were homozygous. Upon stimulation, T cells from TC-carrier patients produced more proinflammatory cytokines (tumor necrosis factor alpha (TNF-α), interleukin-17 (IL-17) and interferon gamma (IFN-γ)) and monocytes produced higher levels of TNF-α compared with patients carrying the non-TC haplotype (P<0.05 and 0.01, respectively). Such cytokine production could be inhibited in the presence of the selective 5-HT2 receptor agonist (2,5-Dimethoxy-4-iodoamphetamine, DOI); interestingly, this effect was more pronounced in TC carriers. Our data demonstrate that association of RA with a distinct serotonin receptor haplotype has functional impact by affecting the immunological phenotype of T cells and monocytes.

A(2) expression and assembly regulates lysis in Qß infections.

The capsids of ssRNA phages comprise a single copy of an ~45 kDa maturation protein that serves to recognize the conjugative pilus as receptor, to protect the ends of the viral RNA and also to escort the genomic RNA into the host cytoplasm. In the Alloleviviridae, represented by the canonical phage Qß, the maturation protein A(2) also causes lysis. This is achieved by inhibiting the activity of MurA, which catalyses the first committed step of murein biosynthesis. Previously, it was shown that Qß virions, with a single copy of A(2), inhibit MurA activity. This led to a model for lysis timing in which, during phage infection, A(2) is not active as a MurA inhibitor until assembled into virion particles, thus preventing premature lysis before a sufficient yield of viable progeny has accumulated. Here we report that MurA inactivates purified Qß particles, casting doubt on the notion that A(2) must assemble into particles prior to MurA inhibition. Furthermore, quantification of A(2) protein induced from a plasmid indicated that lysis is entrained when the amount of the lysis protein is approximately equimolar to that of cellular MurA. Qß por mutants, isolated as suppressors that overcome a murA(rat) mutation that reduces the affinity of MurA for A(2), were shown to be missense mutations in A(2) that increase the translation of the maturation protein. Because of the increased production of A(2), the por mutants have an attenuated infection cycle and reduced burst size, indicating that a delicate balance between assembled and unassembled A(2) levels regulates lysis timing.

Importance of tetrahedral intermediate formation in the catalytic mechanism of the serine proteases chymotrypsin and subtilisin.

Two new inhibitors in which the terminal α-carboxyl groups of Z-Ala-Ala-Phe-COOH and Z-Ala-Pro-Phe-COOH have been replaced with a proton to give Z-Ala-Ala-Phe-H and Z-Ala-Pro-Phe-H, respectively, have been synthesized. Using these inhibitors, we estimate that for α-chymotrypsin and subtilisin Carlsberg the terminal carboxylate group decreases the level of inhibitor binding 3-4-fold while a glyoxal group increases the level of binding by 500-2000-fold. We show that at pH 7.2 the effective molarities of the catalytic hydroxyl group of the active site serine are 41000-229000 and 101000-159000 for α-chymotrypsin and subtilisin Carlsberg, respectively. It is estimated that oxyanion stabilization and the increased effective molarity of the catalytic serine hydroxyl group can account for the catalytic efficiency of the reaction. We argue that substrate binding induces the formation of a strong hydrogen bond or low-barrier hydrogen bond between histidine-57 and aspartate-102 that increases the pK(a) of the active site histidine, allowing it to be an effective general base catalyst for the formation of the tetrahedral intermediate and increasing the effective molarity of the catalytic hydroxyl group of serine-195. A catalytic mechanism for acyl intermediate formation in the serine proteases is proposed.

Breastfed infants metabolize perchlorate.

Bifidobacteria are the dominant intestinal bacteria in breastfed infants. It is known that they can reduce nitrate. Although no direct experiments have been conducted until now, inferred pathways for Bifidobacterium bifidum include perchlorate reduction via perchlorate reductase. We show that when commercially available strains of bifidobacteria are cultured in milk, spiked with perchlorate, perchlorate is consumed. We studied 13 breastfed infant-mother pairs who provided 43 milk samples and 39 infant urine samples, and 5 formula-fed infant-mother pairs who provided 21 formula samples and 21 infant urine samples. Using iodine as a conservative tracer, we determined the average urinary iodine (UI) to milk iodine (MI) concentration ratio to be 2.87 for the breastfed infants. For the same samples, the corresponding perchlorate concentration ratio was 1.37 (difference significant, p < 0.001), indicating that perchlorate is lost. For the formula fed infant group the same ratios were 1.20 and 1.58; the difference was not significant (p = 0.68). However, the small number of subjects in the latter group makes it more difficult to conclude definitively whether perchlorate reduction does or does not occur.

Attention Control in Children With ADHD: An Investigation Using Functional Near Infrared Spectroscopy (fNIRS).

Attention problems are a predominant contributor to near- and far-term functional outcomes in attention-deficit/hyperactivity disorder (ADHD); however, most interventions focus on improving the alerting attentional network, which has failed to translate into improved learning for a majority of children with ADHD. Comparatively less is known regarding the executive attentional network and its overarching attention control process, which governs the ability to maintain relevant information in a highly active, interference-free state, and is intrinsic to a broad range of cognitive functions. This is the first study to compare attention control abilities in children with ADHD and typically developing (TD) children using the Visual Array Task (VAT) and to simultaneously measure hemodynamic functioning (oxyHb) using functional Near-Infrared Spectroscopy (fNIRS). Nineteen children with ADHD Combined type and 18 typically developing (TD) children aged 8 to 12 years were administered the VAT task while prefrontal activity was monitored using fNIRS. Results revealed that children with ADHD evinced large magnitude deficits in attention control and that oxyHb levels in the left dorsal lateral prefrontal cortex (dlPFC) were significantly greater in children with ADHD relative to TD children. These findings suggest that poor attention control abilities in children with ADHD may be related to increased left dlPFC activation in response to an underdeveloped and/or inefficient right dlPFC. The need to design interventions that target and strengthen attention control and its corresponding neural network is discussed based on the likelihood that attention control serves as the potential quaesitum for understanding a wide array of ADHD-related deficits.

Working Memory Training in Youth With Autism, Fragile X, and Intellectual Disability: A Pilot Study.

This pilot study sought to identify potential markers of improvement from pre-post treatment in response to computerized working memory (WM) training for youth (ages 8-18) with autism spectrum disorder (ASD) and comorbid intellectual disability (ID) in a single arm, pre-post design. Participants included 26 children with ASD and 18 with comorbid ASD and fragile X syndrome (ASD+FXS). Analyses were adjusted for age and IQ. The ASD group demonstrated greater improvement on WM training relative to the ASD+FXS group. Participants improved on WM and far transfer outcomes, however, there were no significant group differences in improvement except for repetitive behavior. Higher hyperactivity/impulsivity ratings predicted lower performance on visuospatial WM. Findings suggest cognitive training may be beneficial for youth with ASD and ID, warranting further exploration.

Fenton digestion of milk for iodinalysis.

Iodine is an essential micronutrient especially important in the neurodevelopment of infants. Spot samples of urinary iodine (UI) are used as an epidemiologic index of adult iodine nutrition. Individual infant iodine nutrition is of vital importance, but infant urine is difficult to collect, much less a 24 h sample. Monitoring the intake provides a pragmatic solution for determining infant iodine nutrition. Because of the high solids content of milk and the possible existence of iodine in an organically bound form, sample digestion is obligatory. The U.S. Food and Drug Administration, for example, uses wet ashing by HClO(4); special precautions and fume hoods are required. We present a method of Fenton digestion of human and bovine milk samples and infant formula. No specialized equipment or hazardous reagents are used; measurement is made by isotope dilution inductively coupled plasma mass spectrometry. In Fenton digestion, Fe(II) and H(2)O(2) oxidizes the sample. In an interlaboratory study, excellent agreement (r(2) = 0.9934) was observed with results obtained by HClO(4) digestion and Sandel-Kolthoff kinetic colorimetry. Average recoveries of iodide, triiodothyronine, and thyroxine ranged between 100% and 101%. Following digestion, iodine was found to exist entirely as iodide. Control of pH is imperative if loss cannot be corrected for by isotope dilution. Loss was below 20% for all samples when the pH was between 2.25 and 2.5.

Molecular characterization of an allelic series of mutations in the mouse Nox3 gene.

The inner ear consists of the cochlea (the organ of hearing) and the vestibular system (the organs of balance). Within the vestibular system, linear acceleration and gravity are detected by the saccule and utricle. Resting above the neurosensory epithelia of these organs are otoconia, minute proteinaceous and crystalline (calcite) inertial masses that shift under the physical forces imparted by linear movements and gravity. It is the transduction and sensation of these movements and their integration with vision and proprioceptive inputs that contribute to the sensation of balance. It has been proposed that a reactive oxygen species- (ROS-) generating NADPH oxidase comprising the gene products of the Nox3, Noxo1, and Cyba genes plays a critical and constructive role in the process of inner-ear development, specifically, the deposition of otoconia. Inactivation in mouse of any of the NADPH oxidase components encoded by the Nox3, Noxo1, or Cyba gene results in the complete congenital absence of otoconia and profound vestibular dysfunction. Here we describe our use of PCR, reverse transcription-PCR (RT-PCR), and rapid amplification of cDNA ends (RACE) with traditional and high-throughput (HTP) sequencing technologies to extend and complete the molecular characterization of an allelic series of seven mutations in the Nox3 gene. Collectively, the mutation spectrum includes an endogenous retrovirus insertion, two missense mutations, a splice donor mutation, a splice acceptor mutation, premature translational termination, and a small duplication. Together, these alleles provide tools to investigate the mechanisms of otoconial deposition over development, throughout aging, and in various disease states.