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1.  Ebola Virus Disease: Experience and Decision Making for the First Patients outside of Africa 
PLoS Medicine  2015;12(7):e1001857.
David Stephens and colleagues describe their experience of treating patients with Ebola virus disease at Emory University in the United States.
doi:10.1371/journal.pmed.1001857
PMCID: PMC4517924  PMID: 26218574
2.  Linear growth faltering in infants is associated with Acidaminococcus sp. and community-level changes in the gut microbiota 
Microbiome  2015;3:24.
Background
Chronic malnutrition, termed stunting, is defined as suboptimal linear growth, affects one third of children in developing countries, and leads to increased mortality and poor developmental outcomes. The causes of childhood stunting are unknown, and strategies to improve growth and related outcomes in children have only had modest impacts. Recent studies have shown that the ecosystem of microbes in the human gut, termed the microbiota, can induce changes in weight. However, the specific changes in the gut microbiota that contribute to growth remain unknown, and no studies have investigated the gut microbiota as a determinant of chronic malnutrition.
Results
We performed secondary analyses of data from two well-characterized twin cohorts of children from Malawi and Bangladesh to identify bacterial genera associated with linear growth. In a case-control analysis, we used the graphical lasso to estimate covariance network models of gut microbial interactions from relative genus abundances and used network analysis methods to select genera associated with stunting severity. In longitudinal analyses, we determined associations between these selected microbes and linear growth using between-within twin regression models to adjust for confounding and introduce temporality. Reduced microbiota diversity and increased covariance network density were associated with stunting severity, while increased relative abundance of Acidaminococcus sp. was associated with future linear growth deficits.
Conclusions
We show that length growth in children is associated with community-wide changes in the gut microbiota and with the abundance of the bacterial genus, Acidaminococcus. Larger cohorts are needed to confirm these findings and to clarify the mechanisms involved.
Electronic supplementary material
The online version of this article (doi:10.1186/s40168-015-0089-2) contains supplementary material, which is available to authorized users.
doi:10.1186/s40168-015-0089-2
PMCID: PMC4477476  PMID: 26106478
Microbiota; Microbiome; Intestinal; Stunting; Growth; Statistical learning; Networks
3.  Straightforward Access to Hexahydropyrrolo[2,3-b]indole Core by a Regioselective C3-Azo Coupling Reaction of Arenediazonium Compounds with Tryptamines 
European journal of organic chemistry  2014;2014(17):3662-3670.
A base-mediated regioselective electrophilic addition of arenediazonium salts at the C3-position of tryptamines followed by cyclization provides an efficient entry to C3-nitrogenated hexahydropyrrolo[2,3-b]indoles (HPIs) that can subsequently be transformed into 3-arylhexahydropyrrolo[2,3-b]indoles and other HPI derivatives. The reaction is the first example of a 1,2-diamination that utilizes easily accessible arenediazonium salts as nitrogenous electrophiles.
doi:10.1002/ejoc.201402088
PMCID: PMC4233011  PMID: 25408620
Diazonium compounds; Electrophilic addition; Hydrazines; Pyrroloindolines; Synthetic methods
4.  Insights into the mechanistic and synthetic aspects of the Mo/P-catalyzed oxidation of N-heterocycles† 
Organic & biomolecular chemistry  2014;12(19):3026-3036.
A Mo/P catalytic system for an efficient gram-scale oxidation of a variety of nitrogen heterocycles to N-oxides with hydrogen peroxide as terminal oxidant has been investigated. Combined spectroscopic and crystallographic studies point to the tetranuclear Mo4P peroxo complex as one of the active catalytic species present in the solution. Based on this finding an optimized catalytic system has been developed. The utility and chemoselectivity of the catalytic system has been demonstrated by the synthesis of over 20 heterocyclic N-oxides.
doi:10.1039/c4ob00115j
PMCID: PMC4134924  PMID: 24643619
5.  Personalized versus standardized dosing strategies for the treatment of childhood amblyopia: study protocol for a randomized controlled trial 
Trials  2015;16:189.
Background
Amblyopia is the commonest visual disorder of childhood in Western societies, affecting, predominantly, spatial visual function. Treatment typically requires a period of refractive correction (‘optical treatment’) followed by occlusion: covering the nonamblyopic eye with a fabric patch for varying daily durations. Recent studies have provided insight into the optimal amount of patching (‘dose’), leading to the adoption of standardized dosing strategies, which, though an advance on previous ad-hoc regimens, take little account of individual patient characteristics. This trial compares the effectiveness of a standardized dosing strategy (that is, a fixed daily occlusion dose based on disease severity) with a personalized dosing strategy (derived from known treatment dose-response functions), in which an initially prescribed occlusion dose is modulated, in a systematic manner, dependent on treatment compliance.
Methods/design
A total of 120 children aged between 3 and 8 years of age diagnosed with amblyopia in association with either anisometropia or strabismus, or both, will be randomized to receive either a standardized or a personalized occlusion dose regimen. To avoid confounding by the known benefits of refractive correction, participants will not be randomized until they have completed an optical treatment phase. The primary study objective is to determine whether, at trial endpoint, participants receiving a personalized dosing strategy require fewer hours of occlusion than those in receipt of a standardized dosing strategy. Secondary objectives are to quantify the relationship between observed changes in visual acuity (logMAR, logarithm of the Minimum Angle of Resolution) with age, amblyopia type, and severity of amblyopic visual acuity deficit.
Discussion
This is the first randomized controlled trial of occlusion therapy for amblyopia to compare a treatment arm representative of current best practice with an arm representative of an entirely novel treatment regimen based on statistical modelling of previous trial outcome data. Should the personalized dosing strategy demonstrate superiority over the standardized dosing strategy, then its adoption into routine practice could bring practical benefits in reducing the duration of treatment needed to achieve an optimal outcome.
Trial registration
ISRCTN ISRCTN12292232.
doi:10.1186/s13063-015-0711-4
PMCID: PMC4414426  PMID: 25906974
amblyopia; child; occlusion therapy; personalized dosing strategy; randomized clinical trial; standardized dosing strategy; total effective dose; visual acuity
6.  New quantitative approaches reveal the spatial preference of nuclear compartments in mammalian fibroblasts 
Journal of the Royal Society Interface  2015;12(104):20140894.
The nuclei of higher eukaryotic cells display compartmentalization and certain nuclear compartments have been shown to follow a degree of spatial organization. To date, the study of nuclear organization has often involved simple quantitative procedures that struggle with both the irregularity of the nuclear boundary and the problem of handling replicate images. Such studies typically focus on inter-object distance, rather than spatial location within the nucleus. The concern of this paper is the spatial preference of nuclear compartments, for which we have developed statistical tools to quantitatively study and explore nuclear organization. These tools combine replicate images to generate ‘aggregate maps' which represent the spatial preferences of nuclear compartments. We present two examples of different compartments in mammalian fibroblasts (WI-38 and MRC-5) that demonstrate new knowledge of spatial preference within the cell nucleus. Specifically, the spatial preference of RNA polymerase II is preserved across normal and immortalized cells, whereas PML nuclear bodies exhibit a change in spatial preference from avoiding the centre in normal cells to exhibiting a preference for the centre in immortalized cells. In addition, we show that SC35 splicing speckles are excluded from the nuclear boundary and localize throughout the nucleoplasm and in the interchromatin space in non-transformed WI-38 cells. This new methodology is thus able to reveal the effect of large-scale perturbation on spatial architecture and preferences that would not be obvious from single cell imaging.
doi:10.1098/rsif.2014.0894
PMCID: PMC4345468  PMID: 25631564
spatial point pattern analysis; nuclear compartments; spatial preference; thin-plate spline; intensity estimation; mammalian fibroblasts
7.  Neisseria meningitidis: Biology, Microbiology, and Epidemiology 
Neisseria meningitidis (the meningococcus) causes significant morbidity and mortality in children and young adults worldwide through epidemic or sporadic meningitis and/or septicemia. In this review, we describe the biology, microbiology, and epidemiology of this exclusive human pathogen. N. meningitidis is a fastidious, encapsulated, aerobic gram-negative diplococcus. Colonies are positive by the oxidase test and most strains utilize maltose. The phenotypic classification of meningococci, based on structural differences in capsular polysaccharide, lipooligosaccharide (LOS) and outer membrane proteins, is now complemented by genome sequence typing (ST). The epidemiological profile of N. meningitidis is variable in different populations and over time and virulence of the meningococcus is based on a transformable/plastic genome and expression of certain capsular polysaccharides (serogroups A, B, C, W-135, Y and X) and non-capsular antigens. N. meningitidis colonizes mucosal surfaces using a multifactorial process involving pili, twitching motility, LOS, opacity associated, and other surface proteins. Certain clonal groups have an increased capacity to gain access to the blood, evade innate immune responses, multiply, and cause systemic disease. Although new vaccines hold great promise, meningococcal infection continues to be reported in both developed and developing countries, where universal vaccine coverage is absent and antibiotic resistance increasingly more common.
doi:10.1007/978-1-61779-346-2_1
PMCID: PMC4349422  PMID: 21993636
Neisseria meningitidis; Pathogenesis; Bacterial infections; Microbiology; Epidemiology
8.  Long-term treatment with responsive brain stimulation in adults with refractory partial seizures 
Neurology  2015;84(8):810-817.
Objective:
The long-term efficacy and safety of responsive direct neurostimulation was assessed in adults with medically refractory partial onset seizures.
Methods:
All participants were treated with a cranially implanted responsive neurostimulator that delivers stimulation to 1 or 2 seizure foci via chronically implanted electrodes when specific electrocorticographic patterns are detected (RNS System). Participants had completed a 2-year primarily open-label safety study (n = 65) or a 2-year randomized blinded controlled safety and efficacy study (n = 191); 230 participants transitioned into an ongoing 7-year study to assess safety and efficacy.
Results:
The average participant was 34 (±11.4) years old with epilepsy for 19.6 (±11.4) years. The median preimplant frequency of disabling partial or generalized tonic-clonic seizures was 10.2 seizures a month. The median percent seizure reduction in the randomized blinded controlled trial was 44% at 1 year and 53% at 2 years (p < 0.0001, generalized estimating equation) and ranged from 48% to 66% over postimplant years 3 through 6 in the long-term study. Improvements in quality of life were maintained (p < 0.05). The most common serious device-related adverse events over the mean 5.4 years of follow-up were implant site infection (9.0%) involving soft tissue and neurostimulator explantation (4.7%).
Conclusions:
The RNS System is the first direct brain responsive neurostimulator. Acute and sustained efficacy and safety were demonstrated in adults with medically refractory partial onset seizures arising from 1 or 2 foci over a mean follow-up of 5.4 years. This experience supports the RNS System as a treatment option for refractory partial seizures.
Classification of evidence:
This study provides Class IV evidence that for adults with medically refractory partial onset seizures, responsive direct cortical stimulation reduces seizures and improves quality of life over a mean follow-up of 5.4 years.
doi:10.1212/WNL.0000000000001280
PMCID: PMC4339127  PMID: 25616485
9.  Transcriptional Attenuation Controls Macrolide Inducible Efflux and Resistance in Streptococcus pneumoniae and in Other Gram-Positive Bacteria Containing mef/mel(msr(D)) Elements 
PLoS ONE  2015;10(2):e0116254.
Macrolide resistance, emerging in Streptococcus pneumoniae and other Gram-positive bacteria, is increasingly due to efflux pumps encoded by mef/mel(msr) operons found on discrete mobile genetic elements. The regulation of mef/mel(msr) in these elements is not well understood. We identified the mef(E)/mel transcriptional start, localized the mef(E)/mel promoter, and demonstrated attenuation of transcription as a mechanism of regulation of macrolide-inducible mef-mediated macrolide resistance in S. pneumoniae. The mef(E)/mel transcriptional start site was a guanine 327 bp upstream of mef(E). Consensus pneumococcal promoter -10 (5′-TATACT-3′) and -35 (5′-TTGAAC-3′) boxes separated by 17 bp were identified 7 bp upstream of the start site. Analysis of the predicted secondary structure of the 327 5’ region identified four pairs of inverted repeats R1-R8 predicted to fold into stem-loops, a small leader peptide [MTASMRLR, (Mef(E)L)] required for macrolide induction and a Rho-independent transcription terminator. RNA-seq analyses provided confirmation of transcriptional attenuation. In addition, expression of mef(E)L was also influenced by mef(E)L-dependent mRNA stability. The regulatory region 5’ of mef(E) was highly conserved in other mef/mel(msr)-containing elements including Tn1207.1 and the 5612IQ complex in pneumococci and Tn1207.3 in Group A streptococci, indicating a regulatory mechanism common to a wide variety of Gram-positive bacteria containing mef/mel(msr) elements.
doi:10.1371/journal.pone.0116254
PMCID: PMC4335068  PMID: 25695510
10.  Composite mobile genetic elements disseminating macrolide resistance in Streptococcus pneumoniae 
Macrolide resistance in Streptococcus pneumoniae emerged in the U.S. and globally during the early 1990's. The RNA methylase encoded by erm(B) and the macrolide efflux genes mef(E) and mel were identified as the resistance determining factors. These genes are disseminated in the pneumococcus on mobile, often chimeric elements consisting of multiple smaller elements. To better understand the variety of elements encoding macrolide resistance and how they have evolved in the pre- and post-conjugate vaccine eras, the genomes of 121 invasive and ten carriage isolates from Atlanta from 1994 to 2011 were analyzed for mobile elements involved in the dissemination of macrolide resistance. The isolates were selected to provide broad coverage of the genetic variability of antibiotic resistant pneumococci and included 100 invasive isolates resistant to macrolides. Tn916-like elements carrying mef(E) and mel on the Macrolide Genetic Assembly (Mega) and erm(B) on the erm(B) element and Tn917 were integrated into the pneumococcal chromosome backbone and into larger Tn5253-like composite elements. The results reported here include identification of novel insertion sites for Mega and characterization of the insertion sites of Tn916-like elements in the pneumococcal chromosome and in larger composite elements. The data indicate that integration of elements by conjugation was infrequent compared to recombination. Thus, it appears that conjugative mobile elements allow the pneumococcus to acquire DNA from distantly related bacteria, but once integrated into a pneumococcal genome, transformation and recombination is the primary mechanism for transmission of novel DNA throughout the pneumococcal population.
doi:10.3389/fmicb.2015.00026
PMCID: PMC4321634  PMID: 25709602
mobile genetic elements; transposons; integrative and conjugative elements; macrolides; antibiotic resistance; Streptococcus pneumoniae
11.  Direct, Catalytic and Regioselective Synthesis of 2-Alkyl, Aryl, and Alkenyl-Substituted N-Heterocycles from N-Oxides 
Organic letters  2014;16(3):864-867.
A one-step transformation of heterocyclic N-oxides to 2-alkyl, aryl, and alkenyl-substituted N-heterocycles is described. The success of this broad-scope methodology hinges on the combination of copper catalysis and activation by lithium fluoride or magnesium chloride. The utility of this method for the late-stage modification of complex N-heterocycles is exemplified by facile syntheses of new structural analogs of several antimalarial, antimicrobial and fungicidal agents.
doi:10.1021/ol403631k
PMCID: PMC4134923  PMID: 24410049
12.  Why not lie? Costs enforce honesty in an experimental signalling game 
Communication depends on reliability. Yet, the existence of stable honest signalling presents an evolutionary puzzle. Why should animals signal honestly in the face of a conflict of interest? While students of animal signalling have offered several theoretical answers to this puzzle, the most widely studied model, commonly called the ‘handicap principle’, postulates that the costs of signals stabilize honesty. This model is the motivating force behind an enormous research enterprise that explores signal costs—whether they are physiological, immunological, neural, developmental or caloric. While there can be no question that many signals are costly, we lack definitive experimental evidence demonstrating that costs stabilize honesty. This study presents a laboratory signalling game using blue jays (Cyanocitta cristata) that provides, to our knowledge, the first experimental evidence showing honesty persists when costs are high and disappears when costs are low.
doi:10.1098/rspb.2013.2457
PMCID: PMC3843836  PMID: 24225460
communication; honesty; signal costs; handicap principle; game theory
13.  Propensity Score Estimation in the Presence of Length-biased Sampling: A Nonparametric Adjustment Approach 
Stat  2014;3(1):83-94.
The pervasive use of prevalent cohort studies on disease duration increasingly calls for an appropriate methodology to account for the biases that invariably accompany samples formed by such data. It is well-known, for example, that subjects with shorter lifetime are less likely to be present in such studies. Moreover, certain covariate values could be preferentially selected into the sample, being linked to the long-term survivors. The existing methodology for estimating the propensity score using data collected on prevalent cases requires the correct conditional survival/hazard function given the treatment and covariates. This requirement can be alleviated if the disease under study has stationary incidence, the so-called stationarity assumption. We propose a nonparametric adjustment technique based on a weighted estimating equation for estimating the propensity score which does not require modeling the conditional survival/hazard function when the stationarity assumption holds. The estimator’s large-sample properties are established and its small-sample behavior is studied via simulation. The estimated propensity score is utilized to estimate the survival curves.
doi:10.1002/sta4.46
PMCID: PMC4142657  PMID: 25170178
Propensity score; Length-biased sampling; Causal inference; Survival curve
14.  Two-year seizure reduction in adults with medically intractable partial onset epilepsy treated with responsive neurostimulation: Final results of the RNS System Pivotal trial 
Epilepsia  2014;55(3):432-441.
Objective
To demonstrate the safety and effectiveness of responsive stimulation at the seizure focus as an adjunctive therapy to reduce the frequency of seizures in adults with medically intractable partial onset seizures arising from one or two seizure foci.
Methods
Randomized multicenter double-blinded controlled trial of responsive focal cortical stimulation (RNS System). Subjects with medically intractable partial onset seizures from one or two foci were implanted, and 1 month postimplant were randomized 1:1 to active or sham stimulation. After the fifth postimplant month, all subjects received responsive stimulation in an open label period (OLP) to complete 2 years of postimplant follow-up.
Results
All 191 subjects were randomized. The percent change in seizures at the end of the blinded period was −37.9% in the active and −17.3% in the sham stimulation group (p = 0.012, Generalized Estimating Equations). The median percent reduction in seizures in the OLP was 44% at 1 year and 53% at 2 years, which represents a progressive and significant improvement with time (p < 0.0001). The serious adverse event rate was not different between subjects receiving active and sham stimulation. Adverse events were consistent with the known risks of an implanted medical device, seizures, and of other epilepsy treatments. There were no adverse effects on neuropsychological function or mood.
Significance
Responsive stimulation to the seizure focus reduced the frequency of partial-onset seizures acutely, showed improving seizure reduction over time, was well tolerated, and was acceptably safe. The RNS System provides an additional treatment option for patients with medically intractable partial-onset seizures.
doi:10.1111/epi.12534
PMCID: PMC4233950  PMID: 24621228
Cortical stimulation; Partial seizures; Focal seizures; Responsive stimulation; Neurostimulator
15.  Subunit composition of the human cytoplasmic dynein-2 complex 
Journal of Cell Science  2014;127(21):4774-4787.
ABSTRACT
Cytoplasmic dynein-2 is the motor for retrograde intraflagellar transport (IFT), and mutations in dynein-2 are known to cause skeletal ciliopathies. Here, we define for the first time the composition of the human cytoplasmic dynein-2 complex. We show that the proteins encoded by the ciliopathy genes WDR34 and WDR60 are bona fide dynein-2 intermediate chains and are both required for dynein-2 function. In addition, we identify TCTEX1D2 as a unique dynein-2 light chain that is itself required for cilia function. We define several subunits common to both dynein-1 and dynein-2, including TCTEX-1 (also known as DYNLT1) and TCTEX-3 (also known as DYNLT3), roadblock-1 (also known as DYNLRB1) and roadblock-2 (also known as DYNLRB2), and LC8-1 and LC8-2 light chains (DYNLL1 and DYNLL2, respectively). We also find that NudCD3 associates with dynein-2 as it does with dynein-1. By contrast, the common dynein-1 regulators dynactin, LIS1 (also known as PAFAH1B1) and BICD2 are not found in association with dynein-2. These data explain why mutations in either WDR34 or WDR60 cause disease, as well as identifying TCTEX1D2 as a candidate ciliopathy gene.
doi:10.1242/jcs.159038
PMCID: PMC4215718  PMID: 25205765
Microtubule motor; Dynein; Cilia; Intraflagellar transport
16.  Molecular signatures of antibody responses derived from a systems biological study of 5 human vaccines 
Nature immunology  2013;15(2):195-204.
Many vaccines induce protective immunity via antibodies. Recent studies have used systems biological approaches to determine signatures that predict vaccine immunity in humans, but whether there is a ‘universal signature’ that can predict antibody responses to any vaccine, is unknown. Here we performed systems analyses of immune responses to the meningococcal polysaccharide and conjugate vaccines in healthy adults, in the broader context of our previous studies with the yellow fever and two influenza vaccines. To achieve this, we performed a large-scale network integration of public human blood transcriptomes, and systems-scale databases in specific biological contexts, and deduced a set of blood transcription modules. These modules revealed distinct transcriptional signatures of antibody responses to different classes of vaccines providing key insights into primary viral, protein recall and anti-polysaccharide responses. These results illuminate the early transcriptional programs orchestrating vaccine immunity in humans, and demonstrate the power of integrative network modeling.
doi:10.1038/ni.2789
PMCID: PMC3946932  PMID: 24336226
17.  Tonic Inhibition of Accumbal Spiny Neurons by Extrasynaptic α4βδ GABAA Receptors Modulates the Actions of Psychostimulants 
The Journal of Neuroscience  2014;34(3):823-838.
Within the nucleus accumbens (NAc), synaptic GABAA receptors (GABAARs) mediate phasic inhibition of medium spiny neurons (MSNs) and influence behavioral responses to cocaine. We demonstrate that both dopamine D1- and D2-receptor-expressing MSNs (D-MSNs) additionally harbor extrasynaptic GABAARs incorporating α4, β, and δ subunits that mediate tonic inhibition, thereby influencing neuronal excitability. Both the selective δ-GABAAR agonist THIP and DS2, a selective positive allosteric modulator, greatly increased the tonic current of all MSNs from wild-type (WT), but not from δ−/− or α4−/− mice. Coupling dopamine and tonic inhibition, the acute activation of D1 receptors (by a selective agonist or indirectly by amphetamine) greatly enhanced tonic inhibition in D1-MSNs but not D2-MSNs. In contrast, prolonged D2 receptor activation modestly reduced the tonic conductance of D2-MSNs. Behaviorally, WT and constitutive α4−/− mice did not differ in their expression of cocaine-conditioned place preference (CPP). Importantly, however, mice with the α4 deletion specific to D1-expressing neurons (α4D1−/−) showed increased CPP. Furthermore, THIP administered systemically or directly into the NAc of WT, but not α4−/− or α4D1−/− mice, blocked cocaine enhancement of CPP. In comparison, α4D2−/− mice exhibited normal CPP, but no cocaine enhancement. In conclusion, dopamine modulation of GABAergic tonic inhibition of D1- and D2-MSNs provides an intrinsic mechanism to differentially affect their excitability in response to psychostimulants and thereby influence their ability to potentiate conditioned reward. Therefore, α4βδ GABAARs may represent a viable target for the development of novel therapeutics to better understand and influence addictive behaviors.
doi:10.1523/JNEUROSCI.3232-13.2014
PMCID: PMC3891962  PMID: 24431441
addiction; GABAA receptors; gaboxadol; nucleus accumbens; THIP
18.  Tracking a changing environment: optimal sampling, adaptive memory and overnight effects 
Behavioural processes  2011;89(2):86-94.
Foraging in a variable environment presents a classic problem of decision making with incomplete information. Animals must track the changing environment, remember the best options and make choices accordingly. While several experimental studies have explored the idea that sampling behavior reflects the amount of environmental change, we take the next logical step in asking how change influences memory. We explore the hypothesis that memory length should be tied to the ecological relevance and the value of the information learned, and that environmental change is a key determinant of the value of memory. We use a dynamic programming model to confirm our predictions and then test memory length in a factorial experiment. In our experimental situation we manipulate rates of change in a simple foraging task for blue jays over a 36 hour period. After jays experienced an experimentally determined change regime, we tested them at a range of retention intervals, from 1 to 72 hours. Manipulated rates of change influenced learning and sampling rates: subjects sampled more and learned more quickly in the high change condition. Tests of retention revealed significant interactions between retention interval and the experienced rate of change. We observed a striking and surprising difference between the high and low change treatments at the 24 hour retention interval. In agreement with earlier work we find that a circadian retention interval is special, but we find that the extent of this ‘specialness’ depends on the subject’s prior experience of environmental change. Specifically, experienced rates of change seem to influence how subjects balance recent information against past experience in a way that interacts with the passage of time.
doi:10.1016/j.beproc.2011.10.005
PMCID: PMC4070854  PMID: 22024660
tracking; sampling; memory; environmental change; foraging; blue jays
19.  Models of Interinstitutional Partnerships between Research Intensive Universities and Minority Serving Institutions (MSI) across the Clinical Translational Science Award (CTSA) Consortium 
Health disparities are an immense challenge to American society. Clinical and Translational Science Awards (CTSAs) housed within the National Center for Advancing Translational Science (NCATS) are designed to accelerate the translation of experimental findings into clinically meaningful practices and bring new therapies to the doorsteps of all patients. Research Centers at Minority Institutions (RCMI) program at the National Institute on Minority Health and Health Disparities (NIMHD) are designed to build capacity for biomedical research and training at minority serving institutions. The CTSA created a mechanism fostering formal collaborations between research intensive universities and minority serving institutions (MSI) supported by the RCMI program. These consortium-level collaborations activate unique translational research approaches to reduce health disparities with credence to each academic institutions history and unique characteristics. Five formal partnerships between research intensive universities and MSI have formed as a result of the CTSA and RCMI programs. These partnerships present a multifocal approach; shifting cultural change and consciousness toward addressing health disparities, and training the next generation of minority scientists. This collaborative model is based on the respective strengths and contributions of the partnering institutions, allowing bidirectional interchange and leveraging NIH and institutional investments providing measurable benchmarks toward the elimination of health disparities.
doi:10.1111/cts.12118
PMCID: PMC4038384  PMID: 24119157
translational research; consortium; partnerships; minority serving institutions
20.  MUTATIONS IN THE GABRB1 GENE PROMOTE ALCOHOL CONSUMPTION THROUGH INCREASED TONIC INHIBITION 
Nature communications  2013;4:10.1038/ncomms3816.
Alcohol-dependence is a common, complex and debilitating disorder with genetic and environmental influences. Here we show that alcohol consumption increases following mutations to the γ-aminobutyric acidA receptor (GABAAR) β1 subunit gene (Gabrb1). Using N-ethyl-N-nitrosourea mutagenesis on an alcohol-averse background (F1 BALB/cAnN × C3H/HeH), we develop a mouse model exhibiting strong heritable preference for ethanol resulting from a dominant mutation (L285R) in Gabrb1. The mutation causes spontaneous GABA ion channel opening and increases GABA sensitivity of recombinant GABAARs, coupled to increased tonic currents in the nucleus accumbens, a region long-associated with alcohol reward. Mutant mice work harder to obtain ethanol, and are more sensitive to alcohol intoxication. Another spontaneous mutation (P228H) in Gabrb1 also causes high ethanol consumption accompanied by spontaneous GABA ion channel opening and increased accumbal tonic current. Our results provide a new and important link between GABAAR function and increased alcohol consumption that could underlie some forms of alcohol abuse.
doi:10.1038/ncomms3816
PMCID: PMC3843143  PMID: 24281383
21.  Opposing microtubule motors control motility, morphology and cargo segregation during ER-to-Golgi transport 
Biology Open  2014;3(5):307-313.
ABSTRACT
We recently demonstrated that dynein and kinesin motors drive multiple aspects of endosomal function in mammalian cells. These functions include driving motility, maintaining morphology (notably through providing longitudinal tension to support vesicle fission), and driving cargo sorting. Microtubule motors drive bidirectional motility during traffic between the endoplasmic reticulum (ER) and Golgi. Here, we have examined the role of microtubule motors in transport carrier motility, morphology, and domain organization during ER-to-Golgi transport. We show that, consistent with our findings for endosomal dynamics, microtubule motor function during ER-to-Golgi transport of secretory cargo is required for motility, morphology, and cargo sorting within vesicular tubular carriers en route to the Golgi. Our data are consistent with previous findings that defined roles for dynein-1, kinesin-1 (KIF5B) and kinesin-2 in this trafficking step. Our high resolution tracking data identify some intriguing aspects. Depletion of kinesin-1 reduces the number of motile structures seen, which is in line with other findings relating to the role of kinesin-1 in ER export. However, those transport carriers that were produced had a much greater run length suggesting that this motor can act as a brake on anterograde motility. Kinesin-2 depletion did not significantly reduce the number of motile transport carriers but did cause a similar increase in run length. These data suggest that kinesins act as negative regulators of ER-to-Golgi transport. Depletion of dynein not only reduced the number of motile carriers formed but also caused tubulation of carriers similar to that seen for sorting nexin-coated early endosomes. Our data indicated that the previously observed anterograde–retrograde polarity of transport carriers in transit to the Golgi from the ER is maintained by microtubule motor function.
doi:10.1242/bio.20147633
PMCID: PMC4021352  PMID: 24705013
Microtubule motor; Dynein; Kinesin; Endoplasmic reticulum; Golgi; Secretory cargo trafficking
22.  A Comparison of Supervised Classification Methods for the Prediction of Substrate Type Using Multibeam Acoustic and Legacy Grain-Size Data 
PLoS ONE  2014;9(4):e93950.
Detailed seabed substrate maps are increasingly in demand for effective planning and management of marine ecosystems and resources. It has become common to use remotely sensed multibeam echosounder data in the form of bathymetry and acoustic backscatter in conjunction with ground-truth sampling data to inform the mapping of seabed substrates. Whilst, until recently, such data sets have typically been classified by expert interpretation, it is now obvious that more objective, faster and repeatable methods of seabed classification are required. This study compares the performances of a range of supervised classification techniques for predicting substrate type from multibeam echosounder data. The study area is located in the North Sea, off the north-east coast of England. A total of 258 ground-truth samples were classified into four substrate classes. Multibeam bathymetry and backscatter data, and a range of secondary features derived from these datasets were used in this study. Six supervised classification techniques were tested: Classification Trees, Support Vector Machines, k-Nearest Neighbour, Neural Networks, Random Forest and Naive Bayes. Each classifier was trained multiple times using different input features, including i) the two primary features of bathymetry and backscatter, ii) a subset of the features chosen by a feature selection process and iii) all of the input features. The predictive performances of the models were validated using a separate test set of ground-truth samples. The statistical significance of model performances relative to a simple baseline model (Nearest Neighbour predictions on bathymetry and backscatter) were tested to assess the benefits of using more sophisticated approaches. The best performing models were tree based methods and Naive Bayes which achieved accuracies of around 0.8 and kappa coefficients of up to 0.5 on the test set. The models that used all input features didn't generally perform well, highlighting the need for some means of feature selection.
doi:10.1371/journal.pone.0093950
PMCID: PMC3974812  PMID: 24699553
23.  The Endoplasmic Reticulum Coat Protein II Transport Machinery Coordinates Cellular Lipid Secretion and Cholesterol Biosynthesis*  
The Journal of Biological Chemistry  2013;289(7):4244-4261.
Background: Sar1 mediates the onward transport of ER cargo.
Results: Sar1B promotes VLDL secretion, whereas Sar1A antagonizes this activity, and a deficit of both reduces cholesterol biosynthesis.
Conclusion: Sar1B independently of and through its lipoprotein secretion function promotes the expression of genes regulating cholesterol biosynthesis.
Significance: Sar1B-mediated transport activities contribute to both the functional integrity of the ER membrane and blood cholesterol levels.
Triglycerides and cholesterol are essential for life in most organisms. Triglycerides serve as the principal energy storage depot and, where vascular systems exist, as a means of energy transport. Cholesterol is essential for the functional integrity of all cellular membrane systems. The endoplasmic reticulum is the site of secretory lipoprotein production and de novo cholesterol synthesis, yet little is known about how these activities are coordinated with each other or with the activity of the COPII machinery, which transports endoplasmic reticulum cargo to the Golgi. The Sar1B component of this machinery is mutated in chylomicron retention disorder, indicating that this Sar1 isoform secures delivery of dietary lipids into the circulation. However, it is not known why some patients with chylomicron retention disorder develop hepatic steatosis, despite impaired intestinal fat malabsorption, and why very severe hypocholesterolemia develops in this condition. Here, we show that Sar1B also promotes hepatic apolipoprotein (apo) B lipoprotein secretion and that this promoting activity is coordinated with the processes regulating apoB expression and the transfer of triglycerides/cholesterol moieties onto this large lipid transport protein. We also show that although Sar1A antagonizes the lipoprotein secretion-promoting activity of Sar1B, both isoforms modulate the expression of genes encoding cholesterol biosynthetic enzymes and the synthesis of cholesterol de novo. These results not only establish that Sar1B promotes the secretion of hepatic lipids but also adds regulation of cholesterol synthesis to Sar1B's repertoire of transport functions.
doi:10.1074/jbc.M113.479980
PMCID: PMC3924288  PMID: 24338480
Apolipoproteins; Cholesterol Regulation; Endoplasmic Reticulum (ER); Lipoprotein Secretion; Transcriptomics
24.  A role for endoplasmic reticulum exit sites in foot-and-mouth disease virus infection 
The Journal of General Virology  2013;94(Pt 12):2636-2646.
Picornaviruses replicate their genomes in association with cellular membranes. While enteroviruses are believed to utilize membranes of the early secretory pathway, the origin of the membranes used by foot-and-mouth disease virus (FMDV) for replication are unknown. Secretory-vesicle traffic through the early secretory pathway is mediated by the sequential acquisition of two distinct membrane coat complexes, COPII and COPI, and requires the coordinated actions of Sar1, Arf1 and Rab proteins. Sar1 is essential for generating COPII vesicles at endoplasmic reticulum (ER) exit sites (ERESs), while Arf1 and Rab1 are required for subsequent vesicle transport by COPI vesicles. In the present study, we have provided evidence that FMDV requires pre-Golgi membranes of the early secretory pathway for infection. Small interfering RNA depletion of Sar1 or expression of a dominant-negative (DN) mutant of Sar1a inhibited FMDV infection. In contrast, a dominant-active mutant of Sar1a, which allowed COPII vesicle formation but inhibited the secretory pathway by stabilizing COPII coats, caused major disruption to the ER–Golgi intermediate compartment (ERGIC) but did not inhibit infection. Treatment of cells with brefeldin A, or expression of DN mutants of Arf1 and Rab1a, disrupted the Golgi and enhanced FMDV infection. These results show that reagents that block the early secretory pathway at ERESs have an inhibitory effect on FMDV infection, while reagents that block the early secretory pathway immediately after ER exit but before the ERGIC and Golgi make infection more favourable. Together, these observations argue for a role for Sar1 in FMDV infection and that initial virus replication takes place on membranes that are formed at ERESs.
doi:10.1099/vir.0.055442-0
PMCID: PMC3836498  PMID: 23963534
25.  Reductions in intestinal Clostridiales precede the development of nosocomial Clostridium difficile infection 
Microbiome  2013;1:18.
Background
Antimicrobial use is thought to suppress the intestinal microbiota, thereby impairing colonization resistance and allowing Clostridium difficile to infect the gut. Additional risk factors such as proton-pump inhibitors may also alter the intestinal microbiota and predispose patients to Clostridium difficile infection (CDI). This comparative metagenomic study investigates the relationship between epidemiologic exposures, intestinal bacterial populations and subsequent development of CDI in hospitalized patients. We performed a nested case–control study including 25 CDI cases and 25 matched controls. Fecal specimens collected prior to disease onset were evaluated by 16S rRNA gene amplification and pyrosequencing to determine the composition of the intestinal microbiota during the at-risk period.
Results
The diversity of the intestinal microbiota was significantly reduced prior to an episode of CDI. Sequences corresponding to the phylum Bacteroidetes and to the families Bacteroidaceae and Clostridiales Incertae Sedis XI were depleted in CDI patients compared to controls, whereas sequences corresponding to the family Enterococcaceae were enriched. In multivariable analyses, cephalosporin and fluoroquinolone use, as well as a decrease in the abundance of Clostridiales Incertae Sedis XI were significantly and independently associated with CDI development.
Conclusions
This study shows that a reduction in the abundance of a specific bacterial family - Clostridiales Incertae Sedis XI - is associated with risk of nosocomial CDI and may represent a target for novel strategies to prevent this life-threatening infection.
doi:10.1186/2049-2618-1-18
PMCID: PMC3971611  PMID: 24450844
Intestinal microbiota; Clostridium difficile infection; 16S rRNA gene sequencing; Clostridiales Incertae Sedis XI

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