bluuebunny/crossref_metadata_2025 huggingface dataset:
The Phenylalanine Ammonia Lyase Gene LjPAL1 Is Involved in Plant Defense Responses to Pathogens and Plays Diverse Roles in Lotus japonicus-Rhizobium Symbioses
Authors: Chen Yaping , Li Fengjiao , Tian Lu , Huang Mingchao , Deng Rufang , Li Xueliu , Chen Wei , Wu Pingzhi , Li Meiru , Jiang Huawu , Wu Guojiang
Published: June 2017

Phenylalanine ammonia lyase (PAL) is important in the biosynthesis of plant secondary metabolites that regulate growth responses. Although its function is well-established in various plants, the functional significance of PAL genes in nodulation is poorly understood. Here, we demonstrate that the Lotus japonicus PAL (LjPAL1) gene is induced by Mesorhizobium loti infection and methyl-jasmonate (Me-JA) treatment in roots. LjPAL1 altered PAL activity, leading to changes in lignin contents and thicknesses of cell walls in roots and nodules of transgenic plants and, hence, to structural changes in roots and nodules. LjPAL1-knockdown plants (LjPAL1i) exhibited increased infection thread and nodule numbers and the induced upregulation of nodulin gene expression after M. loti infection. Conversely, LjPAL1 overexpression delayed the infection process and reduced infection thread and nodule numbers after M. loti inoculation. LjPAL1i plants also exhibited reduced endogenous salicylic acid (SA) accumulation and expression of the SA-dependent marker gene. Their infection phenotype could be partially restored by exogenous SA or Me-JA application. Our data demonstrate that LjPAL1 plays diverse roles in L. japonicus–rhizobium symbiosis, affecting rhizobial infection progress and nodule structure, likely by inducing lignin modification, regulating endogenous SA biosynthesis, and modulating SA signaling.
Dive into deep brain stimulation
Authors: Murphy Kathryn
Published: June 2017

This technique provides new hope for patients with movement disorders.
Using Qualitative Research to Inform Development of Professional Guidelines: A Case Study of the Society of Critical Care Medicine Family-Centered Care Guidelines
Authors: Coombs Maureen A. , Davidson Judy E. , Nunnally Mark E. , Wickline Mary A. , Curtis J. Randall
Published: June 2017

Objectives:

To explore the importance, challenges, and opportunities using qualitative research to enhance development of clinical practice guidelines, using recent guidelines for family-centered care in the ICU as an example.

Methods:

In developing the Society of Critical Care Medicine guidelines for family-centered care in the neonatal ICU, PICU, and adult ICU, we developed an innovative adaptation of the Grading of Recommendations, Assessments, Development and Evaluations approach to explicitly incorporate qualitative research. Using Grading of Recommendations, Assessments, Development and Evaluations and the Council of Medical Specialty Societies principles, we conducted a systematic review of qualitative research to establish family-centered domains and outcomes. Thematic analyses were undertaken on study findings and used to support Population, Intervention, Comparison, Outcome question development.

Results:

We identified and employed three approaches using qualitative research in these guidelines. First, previously published qualitative research was used to identify important domains for the Population, Intervention, Comparison, Outcome questions. Second, this qualitative research was used to identify and prioritize key outcomes to be evaluated. Finally, we used qualitative methods, member checking with patients and families, to validate the process and outcome of the guideline development.

Conclusions:

In this, a novel report, we provide direction for standardizing the use of qualitative evidence in future guidelines. Recommendations are made to incorporate qualitative literature review and appraisal, include qualitative methodologists in guideline taskforce teams, and develop training for evaluation of qualitative research into guideline development procedures. Effective methods of involving patients and families as members of guideline development represent opportunities for future work.
Value and Meaning of Faith Community Nursing
Authors: Mock Gabrielle Sheridan
Published: June 2017

The literature that supports and describes faith community nursing (FCN) practice is extensive, but limited in describing the value and meaning of FCN to the community. A qualitative investigation of one FCN program led to emergence of five themes that illustrate the perceived importance of FCN to this community: tasks and services offered, nursing expertise, spirituality, familiarity, and community support. This exploration reveals the deeper value and meaning of FCN to the communities these nurses support.
The role of nonpharmacologic therapies in management of chronic pelvic pain: what to do when surgery fails
Authors: Till Sara R. , Wahl Heather N. , As-Sanie Sawsan
Published: June 2017

Purpose of review

To provide an update on nonsurgical and nonpharmacologic strategies for the management of chronic pelvic pain (CPP).

Recent findings

Effective treatment of patients with CPP requires a multifaceted approach, with thoughtful consideration of surgical, pharmacologic, and nonpharmacologic strategies. Evidence for physical therapy and trigger point injections for treatment of myofascial components of CPP is increasing. Neuromodulation techniques, such as percutaneous tibial nerve stimulation and transcutaneous electrical stimulation, have limited but favorable preliminary data in patients with CPP. Behavioral strategies, such as exercise, cognitive behavioral therapy, and mindfulness, have demonstrated significant improvements in pain, function and quality of life in patients with a variety of chronic pain conditions and are promising avenues for future research in CPP.

Nonpharmacologic therapies are important adjuncts to surgical and pharmacologic treatment for CPP and should be considered integral to a comprehensive treatment approach.
Safety and Efficacy of the Push Endoscopic Technique in the Management of Esophageal Food Bolus Impactions in Children
Authors: Kriem Jamal , Rahhal Riad
Published: June 2017

Objectives:

Adult‐based guidelines support the use of the pull (extraction) endoscopic technique in managing esophageal food bolus impactions (FBIs) but allow the consideration of the push (advancement) technique with caution based on available published literature. The North American Society for Pediatric Gastroenterology, Hepatology and Nutrition guidelines mention the use of gentle endoscopic pushing for disimpaction but elaborate that this technique has not been studied in children. Our study aimed at assessing the safety and efficacy of the push technique in managing pediatric esophageal FBIs.

Methods:

This was a retrospective cohort study of all pediatric patients presenting with esophageal FBIs to a pediatric tertiary care center from 2003 to 2016.

Results:

Two hundred forty‐two procedures for esophageal foreign body removal were reviewed. Thirty‐nine procedures for managing esophageal FBIs were included in a total of 23 patients (1–4 procedures per patient). The most common underlying diagnoses were eosinophilic esophagitis and repaired tracheoesophageal fistula. The cohort had a median age of 8 years and median weight of 34.4 kg. Initial endoscopic disimpaction methods included 20 push and 19 pull technique attempts with success rates of 65% and 68%, respectively (P = 1.0). Unsuccessful attempts using 1 technique were successfully accomplished using the other technique. Patients initially managed by either of the 2 disimpaction techniques did not differ in age, weight, sex, or underlying diagnoses. No procedure‐related complications were reported at our center.

Conclusion:

The present study shows that the push technique is as safe and effective as the pull technique in managing esophageal FBIs in pediatric patients.
Reductions in HIV Diagnoses Among African American Women: A Search for Explanations
Authors: Ivy Wade , Nwangwu-Ike Ndidi , Paz-Bailey Gabriela ,   for the NHBS Study Group
Published: June 2017

Background:

African American women experienced a 46% reduction in the rate of HIV diagnoses from 56.0 in 2008, to 30.0 in 2014 (per 100,000). The reasons for this decrease are unknown; however, we hypothesize that improvements in socioeconomic status, health care access, and risk behaviors may have contributed to this reduction.

Methods:

We analyzed data from 2006, 2010, and 2013 of the National HIV Behavioral Surveillance system. African American women living at or below poverty were surveyed from 19 United States cities using respondent-driven and venue-based sampling, and tested for HIV infection. We used generalized estimating equations to determine differences for selected outcomes regarding health care and risk behaviors over time.

Results:

Among 11,065 women, we found increases in the percentage of women who reported having a recent HIV test (P value = 0.0002); having health insurance (P < 0.0001); and recently visiting a health care provider (P < 0.0001). Being unemployed declined significantly (P = 0.0057), as did reporting recent injection drug use (P < 0.0001). Crack use declined among women aged 25–44 years (P < 0.0001). However, reporting condomless vaginal sex at last sex (P = 0.0268), condomless anal sex at last sex (P = 0.6462), or 3 or more sex partners in the past 12 months (P = 0.5449) remained stable.

Discussion:

Enhanced health care access and socioeconomic status and reductions in drug use may have contributed to the declines in HIV diagnoses among African American women in the United States.
Awareness, Willingness, and Use of Pre-exposure Prophylaxis Among Men Who Have Sex With Men in Washington, DC and Miami-Dade County, FL: National HIV Behavioral Surveillance, 2011 and 2014
Authors: Patrick Rudy , Forrest David , Cardenas Gabriel , Opoku Jenevieve , Magnus Manya , Phillips Gregory , Greenberg Alan , Metsch Lisa , Kharfen Michael , LaLota Marlene , Kuo Irene
Published: June 2017

Introduction:

Despite the effectiveness of oral pre-exposure prophylaxis (PrEP) for HIV prevention, knowledge, and uptake of this new prevention intervention over time has not been fully studied. Using NHBS data from 2 urban areas highly impacted by HIV, we examined awareness, use, and willingness to use daily oral PrEP and factors associated with willingness to take oral PrEP among men who have sex with men (MSM) over time.

Methods:

MSM from Washington, DC and Miami, FL were recruited in 2011 and 2014 using venue-based sampling. Participants completed behavioral surveys and HIV testing. Awareness, use, and willingness to use oral PrEP were examined. Demographic and behavioral correlates of being “very likely” to use PrEP in 2011 and 2014 were assessed.

Results:

PrEP awareness increased from 2011 to 2014 in both cities (DC: 39.1%–73.8% and Miami: 19.4%–41.2%), but use remained low in 2014 (DC: 7.7%; Miami: 1.4%). Being very likely to use PrEP decreased over time in DC (61%–48%), but increased in Miami (48%–60%). In DC, minority race was associated with increased odds of being very likely to use PrEP, whereas reduced odds of being very likely to use PrEP was observed for MSM with 1 or 2–5 partners versus having 6+ partners. In Miami, a higher proportion of white versus Hispanic MSM reported being very likely to use PrEP in 2011, but this observation was reversed in 2014.

Conclusion:

Geographic differences in awareness, use, and willingness to use PrEP indicate that innovative strategies are needed to educate MSM about this effective prevention strategy.
Antiretroviral Therapy Use Among HIV-Infected People Who Inject Drugs—20 Cities, United States, 2009–2015
Authors: Hoots Brooke E. , Finlayson Teresa J. , Broz Dita , Paz-Bailey Gabriela ,   for the NHBS Study Group
Published: June 2017

Background:

Approximately 16% of infections among those living with diagnosed HIV infection in the United States are attributable to injection drug use. Antiretrovirals (ARVs) are recommended for all infected persons to improve health and prevent transmission. Using data from National HIV Behavioral Surveillance, we evaluated changes in ARV use from 2009 to 2015 among HIV-positive people who inject drugs (PWID).

Methods:

PWID were recruited by respondent-driven sampling in 20 cities. ARV use was defined as self-reported use at the time of interview. Prevalence ratios measuring change in ARV use per 3-year increase in year were estimated using log-linked Poisson regression models with generalized estimating equations.

Results:

ARV use was 58% (319/548) in 2009, 67% (410/608) in 2012, and 71% (386/545) in 2015. In all 3 cycle years, a higher percentage of ARV treatment was observed among males, PWID of older age (≥50), and PWID with current health insurance. ARV use increased overall, with an adjusted relative increase of 8% per every 3-year increase in year (adjusted prevalence ratio 1.08, 95% confidence interval: 1.03 to 1.12). ARV use also increased among most subgroups.

Conclusions:

These findings show progress in ARV treatment, although ARV coverage remains low compared with other populations at risk for HIV. Efforts to improve ARV coverage among PWIDs are needed.
Achieving Greater HIV Prevention Impact Through CDC's National HIV Behavioral Surveillance System
Authors: Wejnert Cyprian , Raymond Henry Fisher , Robbins Taylor , Prejean Joseph , Hall H. Irene , McCray Eugene , Paz-Bailey Gabriela ,   for the NHBS study group
Published: June 2017

The National HIV Behavioral Surveillance system was designed to monitor risk factors for HIV infection and HIV prevalence among individuals at higher risk for HIV infection, that is, sexually active men who have sex with men who attend venues, persons who recently injected drugs, and heterosexuals of low socioeconomic status living in urban areas. These groups were selected as priorities for behavioral surveillance because they represent the major HIV transmission routes and the populations with the highest HIV burden. Accurate data on the behaviors in these populations are critical for understanding trends in HIV infections and planning and evaluating effective HIV prevention activities. The articles in this supplement illustrate how National HIV Behavioral Surveillance data can be used to assess HIV risk behaviors, prevalence, and service utilization of the populations most affected by HIV in the United States and guide local and national high-impact prevention strategies to meet national HIV prevention goals.
Multicountry Validation of SAMBA - A Novel Molecular Point-of-Care Test for HIV-1 Detection in Resource-Limited Setting
Authors: Ondiek Johnson , Namukaya Zikulah , Mtapuri-Zinyowera Sekesai , Balkan Suna , Elbireer Ali , Ushiro Lumb Ines , Kiyaga Charles , Goel Neha , Ritchie Allyson , Ncube Patience , Omuomu Kenneth , Ndiege Kenneth , Kekitiinwa Adeodata , Mangwanya Douglas , Fowler Mary G. , Nadala Lou , Lee Helen
Published: June 2017

Introduction:

Early diagnosis of HIV-1 infection and the prompt initiation of antiretroviral therapy are critical to achieving a reduction in the morbidity and mortality of infected infants. The Simple AMplification-Based Assay (SAMBA) HIV-1 Qual Whole Blood Test was developed specifically for early infant diagnosis and prevention of mother-to-child transmission programs implemented at the point-of-care in resource-limited settings.

Methods:

We have evaluated the performance of this test run on the SAMBA I semiautomated platform with fresh whole blood specimens collected from 202 adults and 745 infants in Kenya, Uganda, and Zimbabwe. Results were compared with those obtained with the Roche COBAS AmpliPrep/COBAS TaqMan (CAP/CTM) HIV-1 assay as performed with fresh whole blood or dried blood spots of the same subjects, and discrepancies were resolved with alternative assays.

Results:

The performance of the SAMBA and CAP/CTM assays evaluated at 5 laboratories in the 3 countries was similar for both adult and infant samples. The clinical sensitivity, specificity, positive predictive value, and negative predictive value for the SAMBA test were 100%, 99.2%, 98.7%, and 100%, respectively, with adult samples, and 98.5%, 99.8%, 99.7%, and 98.8%, respectively, with infant samples.

Discussion:

Our data suggest that the SAMBA HIV-1 Qual Whole Blood Test would be effective for early diagnosis of HIV-1 infection in infants at point-of-care settings in sub-Saharan Africa.
Meta-analysis of Cytometry Data Reveals Racial Differences in Immune Cells
Authors: Hu Zicheng , Jujjavarapu Chethan , Hughey Jacob J. , Andorf Sandra , Lee Hao-Chih , Gherardini Pier Federico , Spitzer Matthew H. , Dunn Patrick , Thomas Cristel G. , Campbell John , Wiser Jeff , Kidd Brian A. , Dudley Joel T. , Nolan Garry P. , Bhattacharya Sanchita , Butte Atul J.
Published: June 2017

While meta-analysis has demonstrated increased statistical power and more robust estimations in studies, the application of this commonly accepted methodology to cytometry data has been challenging. Different cytometry studies often involve diverse sets of markers. Moreover, the detected values of the same marker are inconsistent between studies due to different experimental designs and cytometer configurations. As a result, the cell subsets identified by existing auto-gating methods cannot be directly compared across studies. We developed MetaCyto for automated meta-analysis of both flow and mass cytometry (CyTOF) data. By combining clustering methods with a silhouette scanning method, MetaCyto is able to identify commonly labeled cell subsets across studies, thus enabling meta-analysis. Applying MetaCyto across a set of 10 heterogeneous cytometry studies totaling 2926 samples enabled us to identify multiple cell populations exhibiting differences in abundance between White and Asian adults. Software is released to the public through GitHub (github.com/hzc363/MetaCyto).
Measuring Protein Binding to Lipid Vesicles by Fluorescence Cross-Correlation Spectroscopy
Authors: Krüger Daniela , Ebenhan Jan , Bacia Kirsten
Published: June 2017

Fluorescence Correlation Spectroscopy (FCS) has been previously used to investigate peptide and protein binding to lipid membranes, as it allows for very low amounts of sample, short measurement times and equilibrium binding conditions. Labeling only one of the binding partners however comes with certain drawbacks, as it relies on identifying binding events by a change in diffusion coefficient. Since peptide and protein aggregation can obscure specific binding and since non-stoichiometric binding necessitates the explicit choice of a statistical distribution for the number of bound ligands, we additionally label the liposomes and perform dual-color Fluorescence Cross-Correlation Spectroscopy (dcFCCS). We develop a theoretical framework showing that dcFCCS amplitudes allow calculation of the degree of ligand binding and the concentration of unbound ligand, leading to a binding model-independent binding curve. As the degree of labeling of the ligands does not factor into the measured quantities, it is permissible to mix labeled and unlabeled ligand, thereby extending the range of usable protein concentrations and accessible dissociation constantsKD. The total protein concentration, but not the fraction of labeled protein needs to be known. In this work, we apply our dcFCCS analysis scheme to Sar1p, a protein of the COPII complex, which binds ‘major-minor-mix’ liposomes. A Langmuir isotherm model yieldsKD= (2.1±1.1)μMas the single site dissociation constant. The dual-color FCCS framework presented here is highly versatile for biophysical analysis of binding interactions. It may be applied to many types of fluorescently labeled ligands and small diffusing particles, including nanodiscs and liposomes containing membrane protein receptors.
Segway 2.0: Gaussian mixture models and minibatch training
Authors: Chan Rachel C.W. , Libbrecht Maxwell W. , Roberts Eric G. , Noble William Stafford , Hoffman Michael M.
Published: June 2017

Segway performs semi-automated genome annotation, discovering joint patterns across multiple genomic signal datasets. We discuss a major new version of Segway and highlight its ability to model data with substantially greater accuracy. Major enhancements in Segway 2.0 include the ability to model data with a mixture of Gaussians, enabling capture of arbitrarily complex signal distributions, and minibatch training, leading to better learned parameters.

Availability and Implementation

Segway and its source code are freely available for download athttps://segway.hoffmanlab.org. We have made available scripts (https://doi.org/10.5281/zenodo.802940) and datasets (https://doi.org/10.5281/zenodo.802907) for this paper’s analysis.

Contact

michael.hoffman@utoronto.ca
Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map
Authors: Smith Ian , Greenside Peyton G , Wadden David , Tirosh Itay , Natoli Ted , Narayan Rajiv , Root David E , Golub Todd R , Subramanian Aravind , Doench John G
Published: June 2017

The application of RNA interference (RNAi) to mammalian cells has provided the means to perform phenotypic screens to determine the functions of genes. Although RNAi has revolutionized loss of function genetic experiments, it has been difficult to systematically assess the prevalence and consequences of off-target effects. The Connectivity Map (CMAP) represents an unprecedented resource to study the gene expression consequences of expressing short hairpin RNAs (shRNAs). Analysis of signatures for over 13,000 shRNAs applied in 9 cell lines revealed that miRNA-like off-target effects of RNAi are far stronger and more pervasive than generally appreciated. We show that mitigating off-target effects is feasible in these datasets via computational methodologies to produce a Consensus Gene Signature (CGS). In addition, we compared RNAi technology to clustered regularly interspaced short palindromic repeat (CRISPR)-based knockout by analysis of 373 sgRNAs in 6 cells lines, and show that the on-target efficacies are comparable, but CRISPR technology is far less susceptible to systematic off-target effects. These results will help guide the proper use and analysis of loss-of-function reagents for the determination of gene function.
ESCRT-III acts in scissioning new peroxisomes from the ER
Authors: Mast Fred D. , Herricks Thurston , Strehler Kathleen M. , Miller Leslie R. , Saleem Ramsey A. , Rachubinski Richard A. , Aitchison John D.
Published: June 2017

Dynamic control of peroxisome proliferation is integral to the peroxisome’s many functions. A breakdown in the ability of cells to form peroxisomes is linked to many human health issues, including defense against infectious agents, cancer, aging, heart disease, obesity and diabetes, and forms the basis of a spectrum of peroxisomal genetic disorders that cause severe neuropathologies. The ER serves as a source for preperoxisomal vesicles (PPVs) that mature into peroxisomes during de novo peroxisome biogenesis and to support growth and division of existing peroxisomes. However, the mechanism of PPV formation and release from the ER remains poorly understood. Here we show that the evolutionarily ancient endosomal sorting complexes required for transport (ESCRT)-III are peroxisome biogenesis factors that function to cleave PPVs budding from the ER into the cytosol. Using comprehensive morphological and genetic assays of peroxisome formation and function we find that absence of ESCRT-III proteins impedes de novo peroxisome formation and results in an aberrant peroxisome population in vivo. Using a cell-free PPV budding assay we show that ESCRT-III proteins Vps20 and Snf7 are required to release PPVs from the ER. ESCRT-III is therefore a positive effector of membrane scission for vesicles budding both away from and towards the cytosol, a finding that has important implications for the evolutionary timing of emergence of peroxisomes and the rest of the internal membrane architecture of the eukaryotic cell.
Combining global tree cover loss data with historical national forest-cover maps to look at six decades of deforestation and forest fragmentation in Madagascar
Authors: Vieilledent Ghislain , Grinand Clovis , Rakotomalala Fety A. , Ranaivosoa Rija , Rakotoarijaona Jean-Roger , Allnutt Thomas F. , Achard Frédéric
Published: June 2017

The island of Madagascar has a unique biodiversity, mainly located in the tropical forests of the island. This biodiversity is highly threatened by anthropogenic deforestation. Existing historical forest maps at national level are scattered and have substantial gaps which prevent an exhaustive assessment of long-term deforestation trends in Madagascar. In this study, we combined historical national forest cover maps (covering the period 1953-2000) with a recent global annual tree cover loss dataset (2001-2014) to look at six decades of deforestation and forest fragmentation in Madagascar (from 1953 to 2014). We produced new forest cover maps at 30 m resolution for the year 1990 and annually from 2000 to 2014 over the full territory of Madagascar. We estimated that Madagascar has lost 44% of its natural forest cover over the period 1953-2014 (including 37% over the period 1973-2014). Natural forests cover 8.9 Mha in 2014 (15% of the national territory) and include 4.4 Mha (50%) of moist forests, 2.6 Mha (29%) of dry forests, 1.7 Mha of spiny forests (19%) and 177,000 ha (2%) of mangroves. Since 2005, the annual deforestation rate has progressively increased in Madagascar to reach 99,000 ha/yr during 2010-2014 (corresponding to a rate of 1.1%/yr). Around half of the forest (46%) is now located at less than 100 m from the forest edge. Our approach could be replicated to other developing countries with tropical forest. Accurate forest cover change maps can be used to assess the effectiveness of past and current conservation programs and implement new strategies for the future. In particular, forest maps and estimates can be used in the REDD+ framework which aims at “Reducing Emissions from Deforestation and forest Degradation” and for optimizing the current protected area network.
Decoding the orientation of contrast edges from MEG evoked and induced responses
Authors: Pantazis Dimitrios , Fang Mingtong , Qin Sheng , Mohsenzadeh Yalda , Li Quanzheng , Cichy Radoslaw Martin
Published: June 2017

1

Visual gamma oscillations have been proposed to subserve perceptual binding, but their strong modulation by diverse stimulus features confounds interpretations of their precise functional role. Overcoming this challenge necessitates a comprehensive account of the relationship between gamma responses and stimulus features. Here we used multivariate pattern analyses on human MEG data to characterize the relationships between gamma responses and one basic stimulus feature, the orientation of contrast edges. Our findings confirmed we could decode orientation information from induced responses in two dominant frequency bands at 24-32 Hz and 50-58 Hz. Decoding was higher for cardinal than oblique orientations, with similar results also obtained for evoked MEG responses. In contrast to multivariate analyses, orientation information was mostly absent in univariate signals: evoked and induced responses in early visual cortex were similar in all orientations, with only exception an inverse oblique effect observed in induced responses, such that cardinal orientations produced weaker oscillatory signals than oblique orientations. Taken together, our results showed multivariate methods are well suited for the analysis of gamma oscillations, with multivariate patterns robustly encoding orientation information and predominantly discriminating cardinal from oblique stimuli.
Principles that govern competition or co-existence in Rho-GTPase driven polarization
Authors: Chiou Jian-geng , Elston Timothy C. , Witelski Thomas P. , Schaeffer David G. , Lew Daniel J.
Published: June 2017

Rho-GTPases are master regulators of polarity establishment and cell morphology. Positive feedback enables concentration of Rho-GTPases into clusters at the cell cortex, from where they regulate the cytoskeleton. Different cell types reproducibly generate either one (e.g. the front of a migrating cell) or several clusters (e.g. the multiple dendrites of a neuron), but the mechanistic basis for uni-polar or multi-polar outcomes is unclear. The design principles of Rho-GTPase circuits are captured by reaction-diffusion models based on conserved aspects of Rho-GTPase biochemistry. Some such models display rapid winner-takes-all competition between clusters, yielding a unipolar outcome. Other models allow prolonged co-existence of clusters. We derive a “saturation rule” general to all relevant models that governs the timescale of competition, and thereby predicts whether the system will generate uni-polar or multi-polar outcomes. We suggest that the saturation rule is a fundamental property of the Rho-GTPase polarity machinery, regardless of the specific feedback mechanism.
Multi-dimensional genomic analysis of myoepithelial carcinoma identifies prevalent oncogenic gene fusions
Authors: Dalin Martin G. , Katabi Nora , Persson Marta , Lee Ken-Wing , Makarov Vladimir , Desrichard Alexis , Walsh Logan A. , West Lyndsay , Nadeem Zaineb , Ramaswami Deepa , Havel Jonathan J. , Kuo Fengshen , Chadalavada Kalyani , Nanjangud Gouri J. , Riaz Nadeem , Ho Alan L , Antonescu Cristina R. , Ghossein Ronald , Stenman Göran , Chan Timothy A. , Morris Luc G.T.
Published: June 2017

Myoepithelial carcinoma (MECA) is an aggressive type of salivary gland cancer with largely unknown molecular features. MECA may arise de novo or result from oncogenic transformation of a pre-existing pleomorphic adenoma (MECA ex-PA). We comprehensively analyzed the molecular alterations in MECA with integrated genomic analyses. We identified a low mutational load (0.5/MB), but a high prevalence of fusion oncogenes (28/40 tumors; 70%). We foundFGFR1-PLAG1in 7 (18%) cases, and the novelTGFBR3-PLAG1fusion in 6 (15%) cases.TGFBR3-PLAG1was specific for MECA de novo tumors or the malignant component of MECA ex-PA, was absent in 723 other salivary gland tumors, and promoted a tumorigenic phenotype in vitro. We discovered other novelPLAG1fusions, includingND4-PLAG1,which is an oncogenic fusion between mitochondrial and nuclear DNA. One tumor harbored anMSN-ALKfusion, which was tumorigenic in vitro, and targetable with ALK inhibitors. Certain gene fusions were predicted to result in neoantigens with high MHC binding affinity. A high number of copy number alterations was associated with poorer prognosis. Our findings indicate that MECA is a fusion-driven disease, nominateTGFBR3-PLAG1as a hallmark of MECA, and provide a framework for future steps of diagnostic and therapeutic research in this lethal cancer.
Multiple conserved cell adhesion protein interactions mediate neural wiring of a sensory circuit inC. elegans
Authors: Kim Byunghyuk , Emmons Scott W.
Published: June 2017

Nervous system function relies on precise synaptic connections. A number of widely-conserved cell adhesion proteins are implicated in cell recognition between synaptic partners, but how these proteins act as a group to specify a complex neural network is poorly understood. Taking advantage of known connectivity inC. elegans, we identified and studied cell adhesion genes expressed in three interacting neurons in the mating circuits of the adult male. Two interacting pairs of cell surface proteins independently promote fasciculation between sensory neuron HOA and its postsynaptic target interneuron AVG: BAM-2/neurexin-related in HOA binds to CASY-1/calsyntenin in AVG; SAX-7/L1CAM in sensory neuron PHC binds to RIG-6/contactin in AVG. A third, basal pathway results in considerable HOA-AVG fasciculation and synapse formation in the absence of the other two. The features of this multiplexed mechanism help to explain how complex connectivity is encoded and robustly established during nervous system development.
Warm and wet: robust lipase-producing bacteria from the indoor environment
Authors: Tanner Kristie , Abendrotht Christian , Porcar Manuel
Published: June 2017

Lipases are key biocatalysts with important biotechnological applications. With the aim of isolating robust lipolytic microbial strains, we have analyzed the bacterial communities inhabiting two domestic extreme environments: a thermophilic sauna and a dishwasher filter. Scanning electron microscopy revealed biofilm-forming and scattered microorganisms in the sauna and dishwasher sample, respectively. A culture-independent approach based on 16S rRNA analysis indicated a high abundance of Proteobacteria in the sauna sample; and, a large amount of Proteobacteria, Firmicutes, Cyanobacteria and Actinobacteria in the dishwasher filter. With a culture-dependent approach, we isolated 48 bacterial strains, screened their lipolytic activities on media with tributyrin as the main carbon source, and finally selected five isolates for further characterization. These strains, all of them identified as members of the genusBacillus,displayed optimum lipolytic peaks at pH 6.5 and with 1-2% NaCl, and the activity proved very robust at a wide range of pH (up to 11.5) and added NaCl concentrations (up to 4%). The thermal, pH and salt robustness of the selected isolates is a valuable attribute for these strains, which are promising as highly tolerant biodetergents. To our knowledge, this is the first report regarding the isolation from an indoor environment ofBacillusstrains with a high potential for industry.
Renewed diversification following Miocene landscape turnover in a Neotropical butterfly radiation
Authors: Chazot Nicolas , Willmott Keith R. , Lamas Gerardo , Freitas André V. L. , Piron-Prunier Florence , Arias Carlos F. , Mallet Jim , De-Silva Donna Lisa , Elias Marianne
Published: June 2017

“This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100032)”

The Neotropical region has experienced a dynamic landscape evolution throughout the Miocene, with the large wetland Pebas occupying western Amazonia until 11-8 my ago and continuous uplift of the Andes mountains along the western edge of South America. Although the complex dynamics between the Andes and Amazonia may have strongly affected the trajectory of Neotropical biodiversity, there is little evidence for such an influence from time-calibrated phylogenies of groups that diversified during this period. Here, we generate one of the most comprehensive time-calibrated molecular phylogenies of a group of Neotropical insects: the butterfly tribe Ithomiini. Our tree includes 340 species (87% of extant species), spanning 26 million years of diversification in the Neotropics. We investigate temporal and spatial patterns of diversification, focusing on the influence of Miocene landscape tranformations on the dynamics of speciation, extinction and biotic interchanges at the Amazonia/Andes interface. We find that Ithomiini likely began diversifying at the interface between the Andes and the Amazonia around 26.4 my ago. Five subtribes with a very low extant diversity started diversifying early in western Amazonia, but a rapid decrease in diversification rate due to increased extinction rate between 20 and 10 my ago suggests a negative impact of the Pebas wetland system on these early lineages. By contrast, the clade containing the five most species-rich subtribes (85% of extant species) was characterized by a high, positive net diversification rate. This clade diversified exclusively in the Central Andes from 20 to 10 my ago. After the demise of the Pebas system (11-8 my ago), we found a sudden increase of interchanges with the Northern Andes and Amazonia, followed by local diversification, which led to a substantial renewal of diversification. In general, ecological turnovers throughout the Miocene strongly determined the dynamics of speciation, and extinction and interchanges, and appear as a key driving force shaping the region’s current extraordinary biodiversity.
aPKC-mediated displacement and actomyosin-mediated retention polarize Miranda inDrosophilaneuroblasts
Authors: Hannaford Matthew , Ramat Anne , Loyer Nicolas , Januschke Jens
Published: June 2017

Cell fate generation can rely on the unequal distribution of molecules during progenitor cell division in the nervous system of vertebrates and invertebrates. Here we address asymmetric fate determinant localization in the developingDrosophilanervous system, focussing on the control of asymmetric Miranda distribution in larval neuroblasts. We used live imaging of neuroblast polarity reporters at endogenous levels of expression to address Miranda localization during the cell cycle. We reveal that the regulation and dynamics of cortical association of Miranda in interphase and mitosis are different. In interphase Miranda binds directly to the plasma membrane. At the onset of mitosis, Miranda is phosphorylated by aPKC and displaced from the PM. After nuclear envelope breakdown asymmetric localization of Miranda requires actomyosin activity. Therefore, Miranda phosphorylation by aPKC and differential binding to the actomyosin network are required at distinct phases of the cell cycle to polarize fate determinant localization.
Development of an HPTLC method for determination of hypoglycin A in aqueous extracts of seedlings and samaras ofAcerspecies
Authors: Habyarimana J.A. , Baise E. , Douny C. , Weber M. , Boemer F. , De Tullio P. , Franck T. , Marcillaud-Pitel C. , Frederich M. , Mouithys-Mickalad A. , Richard E. , Scippo M.-L. , Votion D. , Gustin P.
Published: June 2017

Hypoglycin A (HGA) is a toxin contained in seeds of the sycamore maple tree (Acer pseudoplatanus). Ingestion of this amino acid causes equine atypical myopathy (AM) in Europe. Another variety,A. negundo,is claimed to be present where AM cases were reported in the US. For unknown reasons, occurrence of this disease has increased. It is important to define environmental key factors that may influence toxicity of samaras fromAcerspecies. In addition, the content of HGA in seedlings needs to be determined since AM outbreaks, during autumn period when the seeds fall but also during spring when seeds are germinating. The present study aims to validate a reliable method using high performance thin layer chromatography for determination and comparison of HGA in samaras and seedlings.

The working range of the method was between 20 μg HGA to 408 μg HGA per ml water, corresponding to 12 - 244 mg/kg fresh weight or 40 - 816 mg/kg dry weight, taking into account of an arbitrary average dry matter content of 30%. Instrumental limit of detection and limit of quantification were of 10 μg HGA/ml and 20 μg HGA/ml water, respectively. Instrumental precision was 4% (RSD on 20 repeated measurements) while instrumental accuracy ranged between 86% and 121% of expected value. The HGA recovery of the analytical method estimated from spiked samaras and seedlings samples ranged between 63 and 103%. The method was applied to 9 samples of samaras fromAcer pseudoplatanus, A. platanoidesandA. campestreand 5 seedlings samples fromA. pseudoplatanus.The results confirm detection of HGA in samaras fromA. pseudoplatanusand the absence of detection in samaras of other tested species. They also suggest that detected levels of HGA are highly variable. This confirmed the suitability of the method for HGA detection in samaras or seedling.
Indexcov: fast coverage quality control for whole-genome sequencing
Authors: Pedersen Brent S. , Collins Ryan L. , Talkowski Michael E. , Quinlan Aaron R.
Published: June 2017

The BAM1and CRAM2formats provide a supplementary linear index that facilitates rapid access to sequence alignments in arbitrary genomic regions. Comparing consecutive entries in a BAM or CRAM index allows one to infer the number of alignment records per genomic region for use as an effective proxy of sequence depth in each genomic region. Based on these properties, we have developedindexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample.Indexcovis available at:https://github.com/brentp/goleftunder the MIT license.
Phytoplankton traits from long-term oceanographic time-series
Authors: Mutshinda Crispin M , Finkel Zoe V , Widdicombe Claire E , Irwin Andrew J
Published: June 2017

Trait values are usually extracted from laboratory studies of single phytoplankton species, which presents challenges for understanding the immense diversity of phytoplankton species and the wide range of dynamic ocean environments. Here we use a Bayesian approach and a trait-based model to extract trait values for four functional types and ten diatom species from field data collected at Station L4 in the Western Channel Observatory. We find differences in maximum net growth rate, temperature optimum and sensitivity, half-saturation constants for light and nitrogen, and density-dependent loss terms across the functional types. We find evidence of very high linear loss rates, suggesting that grazing may be even more important than commonly assumed and differences in density-dependent loss rates across functional types, indicating the presence of strong niche differentiation among functional types. Low half-saturation constants for nitrogen at the functional type level may indicate widespread mixotrophy. At the species level, we find a wide range of density-dependent effects, which may be a signal of diversity in grazing susceptibility or biotic interactions. This approach may be a way to obtain more realistic and better-constrained trait-values for functional types to be used in ecosystem modeling.
Intercellular Communication via thecomX-Inducing Peptide (XIP) ofStreptococcus Mutans
Authors: Kaspar Justin , Underhill Simon A. M. , Shields Robert C. , Reyes Adrian , Rosenzweig Suzanne , Hagen Stephen J. , Burne Robert A.
Published: June 2017

Gram-positive bacteria utilize exported peptides to coordinate genetic and physiological processes required for biofilm formation, stress responses and ecological competitiveness. One example is activation of natural genetic competence by ComR and thecomX-inducing peptide (XIP) inStreptococcus mutans. Although the competence pathway can be activated by addition of synthetic XIP in defined medium, the hypothesis that XIP is able to function as an intercellular signal molecule has not been rigorously tested. Co-culture model systems were developed that included a “sender” strain that overexpressed the XIP precursor (ComS) and a “responder” strain harboring a GFP reporter fusion to a ComR-activated gene (comX) promoter. The ability of the sender strain to provide a signal to activate GFP expression was monitored at the individual cell and population levels using i) planktonic culture systems, ii) cells suspended in an agarose matrix or iii) cells growing in biofilms. XIP was shown to be freely diffusible and XIP signaling between theS. mutanssender and responder strains did not require cell-to-cell contact. The presence of a sucrose-derived exopolysaccharide matrix diminished the efficiency of XIP signaling in biofilms, possibly by affecting spatial distribution of XIP senders and potential responders. Intercellular signaling was greatly impaired in a strain lacking the primary autolysin, AtlA, and was substantially greater when the sender strain underwent lysis. Collectively, these data provide evidence thatS. mutansXIP can indeed function as a peptide signal between cells and highlight the importance of studying signaling with endogenously-produced peptide(s) in populations in various environments and physiologic states.

IMPORTANCE

ThecomX-inducing peptide (XIP) ofStreptococcus mutansis a key regulatory element in the activation of genetic competence, which allows cells to take up extracellular DNA. XIP has been found in cell culture fluids and addition of synthetic XIP to physiologically receptive cells can robustly induce competence gene expression. However, there is a lack of consensus as to whether XIP can function as an intercellular communication signal. Here, we show that XIP indeed signals between cells inS. mutans, but that cell lysis may be a critical factor, as opposed to a dedicated secretion/processing system, in allowing for release of XIP into the environment. The results have important implications in the context of the ecology, virulence and evolution of a ubiquitous human pathogen and related organisms.
A First Order Phase Transition Underlies the Formation of Sub-Diffractive Protein Aggregates in Mammalian Cells
Authors: Narayanan Arjun , Meriin Anatoli B. , Sherman Michael Y. , Cissé Ibrahim I.
Published: June 2017

Failure in protein quality control can often lead to protein aggregation, yet in neuro-degenerative diseases, by the time aggregates can be seen, the cells have advanced well into the disease pathology. Here, we develop a quantitative imaging approach to study the protein aggregation process in living mammalian cells with unprecedented spatio-temporal resolution. We find that sub-diffractive precursor aggregates may form even in untreated cells, and their size distribution is exactly as predicted for a system undergoing a first order phase transition. Practically, this implies that as soon as aggregates reach a critical size (Rc= 162 ± 4 nm untreated cells), they will spontaneously grow into large inclusions. Our data suggest that a previously uncharacterized, RuvBL1 dependent mechanism clears aggregates above the critical size. Our study unveils the existence of sub-diffractive aggregates in living cells; and the strong agreement between cellular data and a nucleation theory, based on first order phase transition, provides insight into regulatory steps in the early stages of aggregate formation in vivo.
Graphtyper: Population-scale genotyping using pangenome graphs
Authors: Eggertsson Hannes P. , Jonsson Hakon , Kristmundsdottir Snaedis , Hjartarson Eirikur , Kehr Birte , Masson Gisli , Zink Florian , Jonasdottir Aslaug , Jonasdottir Adalbjorg , Jonsdottir Ingileif , Gudbjartsson Daniel F. , Melsted Pall , Stefansson Kari , Halldorsson Bjarni V.
Published: June 2017

A fundamental requisite for genetic studies is an accurate determination of sequence variation. While human genome sequence diversity is increasingly well characterized, there is a need for efficient ways to utilize this knowledge in sequence analysis. Here we present Graphtyper, a publicly available novel algorithm and software for discovering and genotyping sequence variants. Graphtyper realigns short-read sequence data to a pangenome, a variation-aware graph structure that encodes sequence variation within a population by representing possible haplotypes as graph paths. Our results show that Graphtyper is fast, highly scalable, and provides sensitive and accurate genotype calls. Graphtyper genotyped 89.4 million sequence variants in whole-genomes of 28,075 Icelanders using less than 100,000 CPU days, including detailed genotyping of six human leukocyte antigen (HLA) genes. We show that Graphtyper is a valuable tool in characterizing sequence variation in population-scale sequencing studies.
Intracellular BH3 profiling reveals shifts in anti-apoptotic dependency in B-cell maturation and activation
Authors: Dai Joanne , Luftig Micah A.
Published: June 2017

Apoptosis is critical to B-cell maturation, but studies of apoptotic regulation in primary human B cells is lacking. Previously, we found that infecting human B cells with Epstein-Barr virus induces two different survival strategies (Priceet al., 2017). Here, we sought to better understand the mechanisms of apoptotic regulation in normal and activated B cells. Using intracellular BH3 profiling (iBH3), we defined the Bcl2-dependency of B-cell subsets from human peripheral blood and tonsillar lymphoid tissue as well as mitogen-activated B cells. We found that naïve and memory B cells were BCL-2 dependent, while germinal center B cells were MCL-1 dependent and plasma cells were BCL-XL dependent. Proliferating B cells activated by CpG or CD40L/IL-4 became more dependent upon MCL-1 and BCL-XL. As B-cell lymphomas often rely on survival mechanisms derived from normal and activated B cells, these findings offer new insight into potential therapeutic strategies for lymphomas.