bluuebunny/crossref_metadata_2025 huggingface dataset:
Biocontrol of Soft Rot: Confocal Microscopy Highlights Virulent Pectobacterial Communication and Its Jamming by Rhodococcal Quorum-Quenching
Authors: Chane Andrea , Barbey Corinne , Robert Magalie , Merieau Annabelle , Konto-Ghiorghi Yoan , Beury-Cirou Amélie , Feuilloley Marc , Pátek Miroslav , Gobert Virginie , Latour Xavier
Published: January 2019

Confocal laser-scanning microscopy was chosen to observe the colonization and damage caused by the soft rot Pectobacterium atrosepticum and the protection mediated by the biocontrol agent Rhodococcus erythropolis. We developed dual-color reporter strains suited for monitoring quorum-sensing and quorum-quenching activities leading to maceration or biocontrol, respectively. A constitutively expressed cyan or red fluorescent protein served as a cell tag for plant colonization, while an inducible expression reporter system based on the green fluorescent protein gene enabled the simultaneous recording of signaling molecule production, detection, or degradation. The dual-colored pathogen and biocontrol strains were used to coinoculate potato tubers. At cellular quorum, images revealed a strong pectobacterial quorum-sensing activity, especially at the plant cell walls, as well as a concomitant rhodococcal quorum-quenching response, at both the single-cell and microcolony levels. The generated biosensors appear to be promising and complementary tools useful for molecular and cellular studies of bacterial communication and interference.
Applications of Next-Generation Sequencing for Large-Scale Pathogen Diagnoses in Soybean
Authors: Díaz-Cruz Gustavo A. , Smith Charlotte M. , Wiebe Kiana F. , Villanueva Sachi M. , Klonowski Adam R. , Cassone Bryan J.
Published: January 2019

Soybean (Glycine max) has become an important crop in Manitoba, Canada, with a 10-fold increase in dedicated acreage over the past decade. Given the rapid increase in production, scarce information about foliar diseases present in the province has been recorded. In order to describe the foliar pathogens affecting this legume, we harnessed next-generation sequencing (NGS) to carry out a comprehensive survey across Manitoba in 2016. Fields were sampled during the V2/3 (33 fields) and R6 (70 fields) growth stages, with at least three symptomatic leaves per field collected and subjected to RNA sequencing. We successfully detected several bacteria, fungi, and viruses known to infect soybean, including Pseudomonas savastanoi pv. glycinea, Septoria glycines, and Peronospora manshurica, as well as pathogens not previously identified in the province (e.g., Pseudomonas syringae pv. tabaci, Cercospora sojina, and Bean yellow mosaic virus). For some microorganisms, we were able to disentangle the different pathovars present and/or assemble their genome sequence. Since NGS generates data on the entire flora and fauna occupying a leaf sample, we also identified residual pathogens (i.e., pathogens of crops other than soybean) and multiple species of arthropod pests. Finally, the sequence information produced by NGS allowed for the development of polymerase chain reaction-based diagnostics for some of the most widespread and important pathogens. Although there are many benefits of using NGS for large-scale plant pathogen diagnoses, we also discuss some of the limitations of this technology.
Persistence of Fusarium oxysporum f. sp. fragariae in Soil Through Asymptomatic Colonization of Rotation Crops
Authors: Henry Peter M. , Pastrana Ana M. , Leveau Johan H. J. , Gordon Thomas R.
Published: January 2019

Asymptomatic plant colonization is hypothesized to enhance persistence of pathogenic forms of Fusarium oxysporum. However, a correlation between pathogen populations on living, asymptomatic plant tissues and soilborne populations after tillage has not been demonstrated. Living and dead tissues of broccoli, lettuce, spinach, wheat, cilantro, raspberry, and strawberry plants grown in soil infested with F. oxysporum f. sp. fragariae (the cause of Fusarium wilt of strawberry) were assayed to quantify the incidence of infection and extent of colonization by this pathogen. All crops could be infected by F. oxysporum f. sp. fragariae but the extent of colonization varied between plant species. Pathogen population densities on nonliving crown tissues incorporated into the soil matrix were typically greater than those observed on living tissues. Crop-dependent differences in the inoculum density of F. oxysporum f. sp. fragariae in soil were only observed after decomposition of crop residue. Forty-four weeks after plants were incorporated into the soil, F. oxysporum f. sp. fragariae soil population densities were positively correlated with population densities on plant tissue fragments recovered at the same time point. Results indicate that asymptomatic colonization can have a significant, long-term impact on soilborne populations of Fusarium wilt pathogens. Cultural practices such as crop rotation should be leveraged to favor pathogen population decline by planting hosts that do not support extensive population growth on living or decomposing tissues.
Superficial and Deep Cutaneous Involvement by RAS-Associated Autoimmunne Leukoproliferative Disease (RALD Cutis): A Histologic Mimicker of Histiocytoid Sweet Syndrome
Authors: Tran Tien Anh N. , Grow William B. , Chang Chung-Che
Published: January 2019

RAS-associated autoimmune leukoproliferative disease (RALD) is a recently described noninfectious and nonmalignant clinical syndrome characterized by autoimmune disorders, massive splenomegaly, modest lymphadenopathy, and monocytosis. On the molecular level, RALD is defined by somatic mutations of either NRAS or KRAS gene in a subset of hematopoietic cells. To date, there is a dearth of well-documented histopathologic description of cutaneous involvement by RALD in the literature. In the current case report, a 43-year-old female patient with a history of RALD presented with clinical pictures of sepsis and an erythematous rash in the left lower extremity. Histologic examination revealed a dense perivascular and interstitial infiltrate of immature myeloid cells admixed with scattered neutrophils involving the dermis and subcutaneous adipose tissue, imparting a panniculitis-like histologic pictures. There was a strong angiocentric propensity of the immature hematopoietic cells as well as extensive extravasation of red blood cells, even in the subcutaneous adipose tissue. Immunohistochemically, the immature hematopoietic cells were positive for CD43, CD4, and CD68, but negative for CD34, CD117, and myeloperoxidase. Overall, the histologic and cytologic findings were highly reminiscent of histiocytoid Sweet syndrome. Review of the English literature revealed cutaneous involvements by RALD only in patients with KRAS mutation compared with none of its NRAS counterparts. However, larger clinicopathologic studies on cutaneous involvement by RALD are warranted. The term “RALD cutis” with its histologic and molecular features is suggested to serve as a potential groundwork for future studies of this rare phenomenon.
Mediators in Preterm Infants With Late‐onset Sepsis
Authors: Abdel‐Hady Hesham , Yahia Sohier , Megahed Ahmed , Mosbah Abeer , Seif Basma , Nageh Eman , Bhattacharjee Indrani , Aly Hany
Published: January 2019

Objective:

To evaluate biochemical and clinical effects of 2 different doses of vitamin D supplementation in preterm infants with late‐onset sepsis (LOS).

Study Design:

A double blinded randomized controlled stratified trial included preterm infants with gestational age (GA) ≥28 weeks with LOS. Subjects were randomly assigned to receive 400 or 800 IU/day of vitamin D3. Serum concentrations of 25(OH)D, TNF‐α, and IL‐6 were measured at enrollment, 7 days after vitamin D supplementation, and at 40 weeks of postmenstrual age (PMA). Short‐term outcomes and growth parameters were assessed.

Results:

A total of 50 infants were enrolled, 25 in each group. Seventy‐six percentage of enrolled infants were vitamin D‐deficient at enrollment in both groups whereas only one infant in the 400 IU and none in the 800 IU group remained deficient at 40 week's PMA; vitamin D concentrations at 40 weeks PMA were 54.8 ± 35.1 and 67.4 ± 37.1 ng/mL, respectively, P = 0.01). None of the infants enrolled in the study had signs of vitamin D toxicity. Serum pro‐inflammatory cytokines IL‐6 and TNF‐ α concentrations decreased at 1 week and at discharge in both groups without differences between groups. The 2 groups did not differ in anthropometric measurements, duration of oxygen and respiratory support, duration of antimicrobial use, length of hospital stay, and mortality.

Conclusions:

A dose of 400 IU of vitamin D was adequate to treat vitamin D deficiency in the majority of premature infants with LOS. The 2 dosing regimens did not differ in clinical or biochemical changes.
Transient Exocrine Pancreatic Insufficiency in Children
Authors: Garah Jamal , Rosen Irit , Shaoul Ron
Published: January 2019

Objectives:

Pancreatic insufficiency in children is usually associated with diseases such as cystic fibrosis, Shwachman‐Diamond syndrome, or chronic pancreatitis. Fecal elastase‐1 is a reliable laboratory test for the diagnosis of exocrine pancreatic insufficiency (EPI). Transient pancreatic insufficiency has been rarely described and data on this entity are lacking in the medical literature. In this retrospective study we report 17 cases of transient pancreatic insufficiency presented mainly with failure to thrive and/or diarrhea.

Methods:

We followed 43 children (age range 1 month–18 years) with low fecal elastase‐1 in our institution between the years 2009 and 2017. We followed growth and laboratory results (particularly, complete blood count, albumin, transaminases, celiac serology, sweat test, and fat‐soluble vitamins). Elastase levels <200 mg/g were considered as pancreatic insufficiency.

Results:

Twenty‐six were excluded due to missing data, a comorbidity or being syndromatic. Enrolled children (17) were all otherwise healthy.

The median age at diagnosis was 3 years (range 0.2–15 years), 11 girls and 6 boys. Their main presenting symptoms were failure to thrive and/or diarrhea. Median fecal elastase‐1 levels were 71 mg/g (range 18–160). Median time for normalization was 6 months (range 1–48 months). Abdominal sonography, celiac serology, and sweat test were normal for all patients. Most patients were treated with pancreatic enzymes until resolution.

Conclusions:

Transient EPI without clear etiology should be in the differential diagnosis of EPI after ruling out known etiologies. The resolving course pattern may be attributed to an unidentified infectious agent. Further studies to assess the etiology are mandated.
Does Changing Antiretroviral Therapy in the First Trimester of Pregnancy for Safety Concerns Have an Impact on Viral Suppression?
Authors: Peyronnet Violaine , Warszawski Josiane , Sibiude Jeanne , Dialla Olivia , Bourgeois-Moine Agnès , Bui Eida , Toulza Caroline Simon , Peretti Delphine , Brunet-Cartier Cécile , Avettand-Fenoel Véronique , Chenadec Jérôme L. , Faye Albert , Tubiana Roland , Mandelbrot Laurent ,   for the ANRS EPF-French Perinatal Cohort Study
Published: January 2019

Objective:

To determine whether changing antiretroviral therapy (ART) during pregnancy because of concern about fetal risks led to poorer virological outcomes.

Methods:

All pregnancies in women with HIV-1 infection enrolled in the national multicenter prospective French Perinatal cohort at 14 week gestation or more were included between January 2005 and December 2015, if the mother was on ART at conception with a plasma viral load <50 copies/mL. The reasons for a change in the ART were analyzed according to treatment guidelines at the time of the pregnancy and defined as for safety concerns in the absence of reported maternal intolerance. Virological and pregnancy outcomes were studied by survival analysis and logistic regression adjusted for a propensity score established for each patient according to baseline characteristics.

Results:

Of 7079 pregnancies in the overall cohort, 1797 had ART at conception with a viral load <50 copies/mL before 14 week gestation. Of these, 22 changed regimens in the first trimester for intolerance, and 411 of the remaining 1775 (23%) solely for safety concerns. The proportion of change was higher when the initial treatment was not recommended in the national guidelines (OR adjusted: 23.1 [14.0–38.2]), than when it was an alternative option (ORa: 2.2 [1.3–3.7]), as compared to recommended first-line regimens. Treatment changes for safety concerns did not lead to poorer virological control, compared with pregnancies without such changes (19.3% vs. 15.6%, HRa: 1.0 [0.7–1.4]).

Conclusions:

Changing ART early in pregnancy to regimens considered safer for pregnancy, and neonatal health did not have a destabilizing effect on viral suppression.
Identification of Physiological Response Functions to Correct for Fluctuations in Resting-State fMRI related to Heart Rate and Respiration
Authors: Kassinopoulos Michalis , Mitsis Georgios D.
Published: January 2019

Functional magnetic resonance imaging (fMRI) is widely viewed as the gold standard for studying brain function due to its high spatial resolution and non-invasive nature. However, it is well established that changes in breathing patterns and heart rate strongly influence the blood oxygen-level dependent (BOLD) fMRI signal and this, in turn, can have considerable effects on fMRI studies, particularly resting-state studies. The dynamic effects of physiological processes are often quantified by using convolution models along with simultaneously recorded physiological data. In this context, physiological response function (PRF) curves (cardiac and respiratory response functions), which are convolved with the corresponding physiological fluctuations, are commonly employed. While it has often been suggested that the PRF curves may be region- or subject- specific, it is still an open question whether this is the case. In the present study, we propose a novel framework for the robust estimation of PRF curves and use this framework to rigorously examine the implications of using population-, subject-, session- and scan-specific PRF curves. The proposed framework was tested on resting-state fMRI and physiological data from the Human Connectome Project. Our results suggest that PRF curves vary significantly across subjects and, to a lesser extent, across sessions from the same subject. These differences can be partly attributed to physiological variables such as the mean and variance of the heart rate during the scan. The proposed methodological framework can be used to obtain robust scan-specific PRF curves from data records with duration longer than 5 minutes, exhibiting significantly improved performance compared to previously defined canonical cardiac and respiration response functions. Besides removing physiological confounds from the BOLD signal, accurate modeling of subject- (or session-/scan-) specific PRF curves is of importance in studies that involve populations with altered vascular responses, such as aging subjects.

Highlights

Physiological response functions (PRF) vary considerably across subjects/sessions

Scan-specific PRF curves can be obtained from data records longer than 5 minutes

The shape of the cardiac response function is linked to the mean heart rate (HR)

Brain regions affected by HR and breathing patterns exhibit substantial overlap

HR and breathing patterns affect distinct regions as compared to cardiac pulsatility
Integrating Quality of Life and Survival Outcomes Cardiovascular Clinical Trials: Results from the PARTNER Trial
Authors: Spertus Jacob V. , Hatfield Laura A. , Cohen David J. , Arnold Suzanne V. , Ho Martin , Jones Philip G. , Leon Martin , Zuckerman Bram , Spertus John A.
Published: January 2019

Background

Survival and health status (e.g., symptoms and quality of life) are key outcomes in clinical trials of heart failure treatment. However, health status can only be recorded on survivors, potentially biasing treatment effect estimates when there is differential survival across treatment groups. Joint modeling of survival and health status can address this bias.

Methods and Results

We analyzed patient-level data from the PARTNER 1B trial of transcatheter aortic valve replacement (TAVR) versus standard care. Health status was quantified with the Kansas City Cardiomyopathy Questionnaire (KCCQ) at randomization, 1, 6, and 12 months. We compared hazard ratios for survival and mean differences in KCCQ scores at 12 months using several models: the original growth curve model for KCCQ scores (ignoring death), separate Bayesian models for survival and KCCQ scores, and a Bayesian joint longitudinal-survival model fit to either 12 or 30 months of survival follow-up. The benefit of TAVR on 12-month KCCQ scores was greatest in the joint model fit to all survival data (mean difference = 33.7 points; 95% CrI: 24.2, 42.4), followed by the joint model fit to 12 months of survival follow-up (32.3 points; 95% CrI: 22.5, 41.5), a Bayesian model without integrating death (30.4 points; 95% CrI: 21.4, 39.3), and the original growth curve model (26.0 points; 95% CI: 18.7, 33.3). At 12 months, the survival benefit of TAVR was also greater in the joint model (hazard ratio = 0.50; 95% CrI: 0.32, 0.73) than in the non-joint Bayesian model (0.54; 95% CrI: 0.37, 0.75) or the original Kaplan-Meier estimate (0.55; 95% CI: 0.40, 0.74).

Conclusions

In patients with severe symptomatic aortic stenosis and prohibitive surgical risk, the estimated benefits of TAVR on survival and health status compared with standard care were greater in joint Bayesian models than other approaches.
Comparing alternative cholera vaccination strategies in Maela refugee camp using a transmission model
Authors: Havumaki Joshua , Meza Rafael , Phares Christina R , Date Kashmira , Eisenberg Marisa C
Published: January 2019

Background

Cholera remains a major public health concern, particularly in refugee camps, which may contend with overcrowding and scarcity of resources. Maela, the largest long-standing refugee camp in Thailand, experienced four cholera outbreaks between 2005 and 2010. In 2013, a cholera vaccine campaign was implemented in the camp. To assist in the evaluation of the campaign and planning for subsequent campaigns, we developed a mathematical model of cholera in Maela.

Methods

We formulated a Susceptible-Infectious-Water-Recovered-based cholera transmission model and estimated parameters using incidence data from 2010. We next evaluated the reduction in cases conferred by several immunization strategies, varying timing, effectiveness, and resources (i.e., vaccine availability). Finally, we generated post-campaign case forecasts, to determine whether a booster campaign was needed.

Results

We found that preexposure vaccination can substantially reduce the risk of cholera even when the < 50% of the population is given the full two-dose series. Additionally, the preferred number of doses per person should be considered in the context of one vs. two dose effectiveness and vaccine availability. For reactive vaccination, a trade-off between timing and effectiveness was revealed, indicating that it may be beneficial to give one dose to more people rather than two doses to fewer people, given that a two-dose schedule would incur a delay in administration of the second dose. Forecasting using realistic coverage levels predicted that there was no need for a booster campaign in 2014 (consistent with our predictions, there was not a cholera epidemic in the 2014 season).

Conclusions

Our analyses suggest that vaccination in conjunction with ongoing water sanitation and hygiene efforts provides an effective strategy for cholera outbreaks in refugee camps. Effective preexposure vaccination depends on timing and effectiveness. If a camp is facing an outbreak, delayed distribution of vaccines can substantially alter the effectiveness of reactive vaccination, suggesting that quick distribution of vaccines may be more important than ensuring every individual receives both vaccine doses.
Heparan sulfate expression on B cells modulates IgM expression in aged mice and steady-state plasma cell numbers
Authors: Trujillo Damian L. , Jarousse Nadine , Coscoy Laurent
Published: January 2019

Heparan sulfate (HS) modulates many cellular processes including adhesion, motility, ligand-receptor interaction, and proliferation. We have previously reported that murine B cells strongly upregulate cell surface HS upon exposure to type I interferon, TLR-ligands, or B cell receptor stimulation. To investigate the role of HS on B cellsin vivo, we utilized EXT1lox/loxCD19-Cre conditional KO mice, which are incapable of synthesizing HS in B cells. We found that suppressing HS expression on B cells has no overt effect in B cell development, localization, or motility. However, we did observe that EXT1 conditional KO mice have decreased poly-reactive IgM in naïve aged mice relative to littermate control mice. Despite this decrease in poly-reactive IgM, EXT1 conditional KO mice mounted a normal B cell response to both model antigens and influenza infection. We also observed decreased plasma cells in EXT1 conditional KO mice after influenza infection. Although EXT1 conditional KO mice have decreased plasma cells, these mice still had comparable numbers of influenza-specific antibody secreting cells to littermate control mice. The findings presented here suggest that HS expression on B cells does not play a major role in B cell development or overall B cell function but instead might be involved in fine-tuning B-cell responses.
Plasmodium capraeinfection is negatively correlated with infection ofTheileria ovisandAnaplasma ovisin goats
Authors: Hakimi Hassan , Sarani Ali , Takeda Mika , Kaneko Osamu , Asada Masahito
Published: January 2019

Theileria, Babesia, andAnaplasmaare tick-borne pathogens affecting livestock industries worldwide. In this study, we surveyed the presence ofBabesia ovis, Theileria ovis, Theileria lestoquardi, Anaplasma ovis, Anaplasma phagocytophilum, andAnaplasma marginalein 200 goats from 3 different districts in Sistan and Baluchestan province, Iran. Species-specific diagnostic PCR and sequence analysis revealed that 1.5%, 12.5%, and 80% of samples were positive forT. lestoquardi, T. ovis, andA. ovis, respectively. Co-infections of goats with up to 3 pathogens were seen in 22% of the samples. We observed a positive correlation betweenA. ovisandT. ovisinfection. In addition, by analyzing the data with respect toPlasmodium capraeinfection in these goats, a negative correlation was found betweenP. capraeandA. ovisand betweenP. capraeandT. ovis. This study contributes to understanding the epidemiology of vector-borne pathogens and their interplay in goats.

Importance

Tick-borne pathogens include economically important pathogens restricting livestock farming worldwide. In endemic areas livestock are exposed to different tick species carrying various pathogens which could result in co-infection with several tick-borne pathogens in a single host. The co-infection and interaction among pathogens are important in determining the outcome of disease. Little is known about pathogen interactions in the vector and the host. In this study, we show for the first time that co-infection ofP. caprae, a mosquito transmitted pathogen, withT. ovisandA. ovis. Analysis of goat blood samples revealed a positive correlation betweenA. ovisandT. ovis. Moreover, a negative correlation was seen betweenP. caprae, a mosquito transmitted pathogen, and the tick-borne pathogensT. ovisorA. ovis.
Does testosterone impair men’s cognitive empathy? Evidence from two large-scale randomized controlled trials
Authors: Nadler Amos , Camerer Colin F. , Zava David T. , Ortiz Triana L. , Watson Neil V. , Carré Justin M. , Nave Gideon
Published: January 2019

The capacity to infer others’ mental states (known as “mind reading” and “cognitive empathy”) is essential for social interactions across species, and its impairment characterizes psychopathological conditions such as autism spectrum disorder and schizophrenia. Previous studies reported that testosterone administration impaired cognitive empathy in healthy humans, and that a putative biomarker of prenatal testosterone exposure (finger digit ratios) moderated the effect. However, empirical support for the relationship has relied on small-sample studies with mixed evidence. We investigate the reliability and generalizability of the relationship in two large-scale double-blind placebo-controlled experiments in young men (N=243 and N=400), using two different testosterone administration protocols. We find no evidence that cognitive empathy is impaired by testosterone administration or associated with digit ratios. With an unprecedented combined sample size, these results counter current theories and previous high-profile reports, and demonstrate that previous investigations of this topic have been statistically underpowered.
Expression of glucocorticoid and mineralocorticoid receptor genes co-vary with a stress-related colour signal in barn owls
Authors: Béziers Paul , Ducrest Anne-Lyse , San-Jose Luis M. , Simon Céline , Roulin Alexandre
Published: January 2019

Glucocorticoid hormones are important intermediates between an organism and its environment. They enable an organism to adjust its behavioural and physiological processes in response to environmental changes by binding to mineralocorticoid receptors (MR) and glucocorticoid receptors (GR) expressed in many tissues, including the integument. The regulation of glucocorticoids covaries with melanin-based colouration in numerous species, an association that might result from the melanocortin system and evolve within a signalling context. Most studies have focused on the circulating levels of glucocorticoids disregarding the receptors that mediate their action and could partly account for the covariation between the regulation of stress and melanin-based coloration. We investigated the association between melanin-based coloration and the gene expression levels of GR and MR but also of the melanocortin system and melanogenesis in the growing feathers of nestling barn owls (Tyto alba). We also considered the expression of genes related to the melanocortin system and melanogenesis to better understand the origin of the link between the expression of receptors to which corticosterone binds and melanin-based coloration. Nestling barn owls displaying larger black feather spots expressed GR and MR at lower levels than did smaller-spotted individuals. Because the expression of the GR and MR genes was positively, rather than negatively, correlated with the expression of melanogenic genes, we suggest that the link between melanin-based coloration, GR and MR is not directly associated to melanogenesis. The finding that the expression of GR and MR was positively associated with the expression of the PCSK2 gene (encoding the protein convertase responsible for post-translational modification of the proopiomelanocortin hormone) suggests that the melanocortin system may be implicated in the establishment of the covariation between melanism and the expression of receptors to which glucocorticoids bind. Together with previous studies, our results suggest that coloration is not only related to the production of glucocorticoids but also to the sensitivity of the integument to glucocorticoids.
Novel signaling hub of insulin receptor, dystrophin glycoprotein complex and plakoglobin regulates muscle size
Authors: Mutlak Yara Eid , Aweida Dina , Volodin Alexandra , Ayalon Bar , Dahan Nitsan , Parnis Anna , Cohen Shenhav
Published: January 2019

Signaling through the insulin receptor governs central physiological functions related to cell growth and metabolism. Here we show by tandem native protein complex purification approach and super-resolution STED microscopy that insulin receptor activity requires association with the fundamental structural module in muscle, the dystrophin glycoprotein complex (DGC), and the desmosomal component plakoglobin (γ-catenin). The integrity of this high-molecular-mass assembly renders skeletal muscle susceptibility to insulin because DGC-insulin receptor dissociation by plakoglobin downregulation reduced insulin signaling and caused atrophy. Furthermore, impaired insulin receptor function in muscles from diabetic mice reduced plakoglobin-DGC-insulin receptor content on the plasma membrane; however, plakoglobin overexpression alone restored DGC association with the insulin receptor, and stimulated glucose uptake. Our findings establish DGC as a signaling hub, containing plakoglobin as an auxiliary subunit, and provide a possible mechanism for the insulin resistance in Duchenne Muscular Dystrophy, and for the cardiomyopathies seen with plakoglobin mutations.
Molecular framework for TIR1/AFB-Aux/IAA-dependent auxin sensing controlling adventitious rooting in Arabidopsis
Authors: Lakehal Abdellah , Chaabouni Salma , Cavel Emilie , Le Hir Rozenn , Ranjan Alok , Raneshan Zahra , Novák Ondřej , Păcurar Daniel I. , Perrone Irene , Jobert François , Gutierrez Laurent , Bakò Laszlo , Bellini Catherine
Published: January 2019

In Arabidopsis thaliana, canonical auxin-dependent gene regulation is mediated by 23 transcription factors from the AUXIN RESPONSE FACTOR (ARF) family interacting with 29 auxin/indole acetic acid repressors (Aux/IAA), themselves forming coreceptor complexes with one of six TRANSPORT INHIBITOR1/AUXIN-SIGNALLING F-BOX (TIR1/AFB) PROTEINS. Different combinations of co-receptors drive specific sensing outputs, allowing auxin to control a myriad of processes. Considerable efforts have been made to discern the specificity of auxin action. However, owing to a lack of obvious phenotype in single loss-of-function mutants in Aux/IAA genes, most genetic studies have relied on gain-of-function mutants, which are highly pleiotropic. Using loss-of-function mutants, we show that three Aux/IAA proteins interact with ARF6 and/or ARF8, which we have previously shown to be positive regulators of AR formation upstream of jasmonate, and likely repress their activity. We also demonstrate that TIR1 and AFB2 are positive regulators of adventitious root formation and suggest a dual role for TIR1 in the control of JA biosynthesis and conjugation, as revealed by upregulation of several JA biosynthesis genes in the tir1-1 mutant. We propose that in the presence of auxin, TIR1 and AFB2 form specific sensing complexes with IAA6, IAA9 and/or IAA17 that modulate JA homeostasis to control AR initiation.
Tackling the research capacity challenge in Africa: An overview of African-led approaches to strengthen research capacity
Authors: Ngongalah Lem , Rawlings Ngwa Niba , Wepngong Emerson , Musisi James , Ngwayu Claude , Mumah Sharon
Published: January 2019

Background

Improved capacity for research is a valuable and sustainable means of advancing health and development in Africa. Local leadership in research capacity strengthening is important for developing contextually appropriate programs that increase locally-driven research, and improve Africa’s ability to adapt and use scientific knowledge. This study provides an overview of African organisations that aim to strengthen research capacity in Africa, and the major initiatives or approaches being used for this purpose.

Methods

A desk review of grey and published literature on research capacity strengthening in Africa was conducted, in addition to panel discussions on the determinants of research capacity in Africa. Data was analysed through thematic analysis and a framework developed by the Collaboration for Research Excellence in Africa (CORE Africa).

Results

11 organisations were identified, spread across South, Central, East and West Africa. The main approaches to improving research capacity were: providing opportunities for academic research and research training. Initiatives to provide research equipment, funding and facilitate research use for policy-making were limited; while strategies to increase research awareness, promote collaboration, and provide guidance and incentives for research were lacking. Most organisations had programs for researchers and academics, with none targeting funders or the general public.

Conclusion

Local leadership is essential for improving research capacity in Africa. In addition to providing adequate support to academics and researchers, initiatives that help revitalize the education system in Africa, promote collaboration and engage funders and the general public will be helpful for strengthening research capacity in Africa.
Do Synthesis Centers Synthesize? A semantic analysis of diversity and performance
Authors: Hackett Edward J. , Leahey Erin , Parker John N. , Rafols Ismael , Hampton Stephanie , Corte Ugo , Drake John M. , Penders Bart , Sheble Laura , Vermeulen Niki , Vision Todd
Published: January 2019

Synthesis centers are a recently-developed form of scientific organization that catalyzes and supports a form of interdisciplinary research that integrates diverse theories, methods and data across spatial or temporal scales, scientific phenomena, and forms of expertise to increase the generality, parsimony, applicability, or empirical soundness of scientific explanations. Research has shown the synthesis working group to be a distinctive form of scientific collaboration that reliably produces consequential, high-impact publications, but no one has asked: do synthesis working groups produce publications that are substantially more diverse than those produced outside of synthesis centers, and if so, how and with what effects? We have investigated these questions through a novel textual analysis. We found that if diversity is measured solely by mean difference in the Rao-Stirling (aggregate) measure of diversity, then the answer is no. But synthesis center papers have significantly greater variety and balance, but significantly lower disparity, than papers in the reference corpus. Synthesis center influence is mediated by the greater size of synthesis center collaborations (numbers of authors, distinct institutions, and references) but even when taking size into account, there is a persistent direct effect: synthesis center papers have significantly greater variety and balance, but less disparity, than papers in the reference corpus. We conclude by inviting further exploration of what this novel textual analysis approach might reveal about interdisciplinary research and by offering some practical implications of our results.
Skeletal descriptions of shape provide unique perceptual information for object recognition
Authors: Ayzenberg Vladislav , Lourenco Stella F.
Published: January 2019

With seemingly little effort, humans can both identify an object across large changes in orientation and extend category membership to novel exemplars. Although researchers argue that object shape is crucial in these cases, there are open questions as to how shape is represented for object recognition. Here we tested whether the human visual system incorporates a three-dimensional skeletal descriptor of shape to determine an object’s identity. Skeletal models not only provide a compact description of an object’s global shape structure, but also provide a quantitative metric by which to compare the visual similarity between shapes. Our results showed that a model of skeletal similarity explained the greatest amount of variance in participants’ object dissimilarity judgments when compared with other computational models of visual similarity (Experiment 1). Moreover, parametric changes to an object’s skeleton led to proportional changes in perceived similarity, even when controlling for another model of structure (Experiment 2). Importantly, participants preferentially categorized objects by their skeletons across changes to local shape contours and non-accidental properties (Experiment 3). Our findings highlight the importance of skeletal structure in vision, not only as a shape descriptor, but also as a diagnostic cue of object identity.
Genomic evidence of genetic variation with pleiotropic effects on caterpillar fitness and plant traits in a model legume
Authors: Gompert Zachariah , Brady Megan , Chalyavi Farzaneh , Saley Tara C. , Philbin Casey S. , Tucker Matthew J. , Forister Matt L. , Lucas Lauren K.
Published: January 2019

Plant-insect interactions are ubiquitous, and have been studied intensely because of their relevance to damage and pollination in agricultural plants, and to the ecology and evolution of biodiversity. Variation within species can affect the outcome of these interactions, such as whether an insect successfully develops on a plant species. Whereas specific genes and chemicals that mediate these interactions have been identified, studies of genome-or metabolome-wide intraspecific variation might be necessary to better explain patterns of host-plant use and adaptation often observed in the wild. Here, we present such a study. Specifically, we assess the consequences of genome-wide genetic variation in the model plantMedicago truncatulaforLycaeides melissacaterpillar growth and survival (i.e., larval performance). Using a rearing experiment and a whole-genome SNP data set (>5 million SNPs), we show that polygenic variation inM. truncatulaexplains 9–41% of the observed variation in caterpillar growth and survival. We detect genetic correlations among caterpillar performance and other plant traits, such as structural defenses and some anonymous chemical features; these genetic correlations demonstrate that multipleM. truncatulaalleles have pleiotropic effects on plant traits and caterpillar growth or survival (or that there is substantial linkage disequilibrium among loci affecting these traits). We further show that a moderate proportion of the genetic effect ofM. truncatulaalleles onL. melissaperformance can be explained by the effect of these alleles on the plant traits we measured, especially leaf toughness. Taken together, our results show that intraspecific genetic variation inM. truncatulahas a substantial effect on the successful development ofL. melissacaterpillars (i.e., on a plant-insect interaction), and further point toward traits mediating this genetic effect.
Acoustic community structure and seasonal turnover in tropical South Asian birds
Authors: Krishnan Anand
Published: January 2019

Birds produce diverse acoustic signals, with coexisting species occupying distinct ‘acoustic niches’ to minimize masking, resulting in overdispersion within acoustic space. In tropical regions of the world, an influx of migrants from temperate regions occurs during winter. The effects of these migrants on acoustic community structure and dynamics remain unstudied. Here, I show that in a tropical urban bird community, the influx of winter migrants is accompanied by a turnover of the acoustic community. However, in spite of this turnover, the acoustic community remains overdispersed in acoustic niche space. The winter acoustic community additionally exhibits lower frequency-band diversity, consistent with species singing less continuously, as well as lower phylogenetic diversity. My data thus suggests that acoustic niches and community structure are stable across seasons in spite of species turnover. Migrants occupy similar regions of acoustic space as residents, and are relatively closely related to some of these species. Their arrival therefore leads to greater phylogenetic clustering in the winter, and thus lower phylogenetic diversity, although the acoustic community remains overdispersed. Studying seasonal dynamics of acoustic communities thus provides valuable insight into assembly processes, as well as a potential framework for long-term monitoring of urban ecosystems.
Physiological Growth Indices of Maize (Zea mays L.) Genotypes in Sylhet
Authors: Islam M. Tazul , Islam A.F.M. Saiful , Sharaf Uddin M.
Published: January 2019

Maize (Zea mays L.) is an important food and feed crop in Bangladesh as well as in the world. But its cultivation is limited in the soils of Sylhet, Bangladesh. To study the physiological growth indices of maize genotypes an experiment was carried out at the experimental field of Sylhet Agricultural University (SAU), Bangladesh during December 2014 to May 2015. The maize genotypes as the experimental materials were ZM 0001, ZM 0002, ZM 0003, ZM 0004, ZM 0005, ZM 0006 ZM 0007 and BARI Maize 6. The experiment was laid out in a Randomized Complete Block Design (RCBD) with three replications. Seeds were sown on 26 December 2014. Proper cultural management practices were followed as and when necessary during the growing period of the crop. Data were recorded on dry matter partitioning, different growth rate parameters and dry matter production of different plant parts at 30 days interval. The results indicated significant variations in almost all of the growth indices. Dry matter accumulation continued to increase from seedling to harvesting. The highest root dry matter was found in ZM 0007 (36.03 g) whereas the highest shoot and leaf dry matter was found in BARI Maize 6 (254.6 and 45.99 g, respectively) at harvest. The highest total dry matter (TDM) was produced in BARI Maize 6 at harvest (287.5 g) and AGR and CGR value was also highest in BARI Maize 6 (5.686 g day-1 and 45.48 g m-2 day-1) but at 60-90 days after germination (DAG). The highest RGR value was in ZM 0001 at seedling stage (114.1 mg g-1 day-1). A zigzag pattern graph was observed in all genotypes for RSR, RWR and SWR at different growth stages but a declining trend from seedling to harvesting was observed for LWR. Correlation between the growth rate parameters and kernel yield showed that shoot, leaf, total dry weight, AGR, CGR, RGR and SWR had significant positive correlation with yield.
Topographic organization of the “third tier” dorsomedial visual cortex in the macaque
Authors: Hadjidimitrakis Kostas , Bakola Sophia , Chaplin Tristan A. , Yu Hsin-Hao , Alanazi Omar , Chan Jonathan M. , Worthy Katrina H. , Rosa Marcello G.P.
Published: January 2019

The boundaries of the visual areas located anterior to V2 in the dorsomedial region of the macaque cortex remain contentious. This region is usually conceptualized as including two functional subdivisions: the dorsal component of area V3 (V3d), laterally, and another area, named the parietooccipital area (PO) or V6, medially. However, the nature of the putative border between V3d and PO/V6 has remained undefined. We recorded the receptive fields of multiunit clusters in adult male macaques, and reconstructed the locations of recording sites using histological sections and “unfolded” cortical maps. Immediately adjacent to dorsomedial V2 we observed a representation of the lower contralateral quadrant, which represented the vertical meridian at its rostral border. This region, corresponding to V3d of previous studies, formed a simple eccentricity gradient, from approximately <5° in the annectant gyrus, to >60° in the parietooccipital sulcus. However, there was no topographic reversal where one would expect to find the border between V3d and PO/V6. Rather, near the midline, this lower quadrant map continued directly into a representation of the peripheral upper visual field, without an intervening lower quadrant representation that could be unambiguously assigned to PO/V6. Thus, V3d and PO/V6 form a continuous topographic map, which includes parts of both quadrants. Together with previous observations that V3d and PO/V6 are both densely myelinated relative to adjacent cortex, and share similar input from V1, these results suggest that they are parts of a single area, which is distinct from the one forming the ventral component of the third tier complex.

Significance statement

The primate visual cortex has a large number of areas. Knowing the extent of each visual area, and how they can be distinguished from each other, are essential for the interpretation of experiments aimed at understanding visual processing. Currently, there are conflicting models of the organization of the dorsomedial visual cortex rostral to area V2 (one of the earliest stages of cortical processing of vision). By conducting large-scale electrophysiological recordings, we found that what were originally thought to be distinct areas in this region (dorsal V3, and the parietooccipital area [PO/V6]), together form a single map the visual field. These results will help guide future functional studies, and the interpretation of the outcomes of lesions involving the dorsal visual cortex.
Benchmarking Database Systems for Genomic Selection Implementation
Authors: Nti-Addae Yaw , Matthews Dave , Ulat Victor Jun , Syed Raza , Sempéré Guil-hem , Pétel Adrien , Renner Jon , Larmande Pierre , Guignon Valentin , Jones Elizabeth , Robbins Kelly
Published: January 2019

Motivation

With high-throughput genotyping systems now available, it has become feasible to fully integration genotyping information into breeding programs [22]. To make use of this information effectively requires DNA extraction facilities and marker production facilities that can efficiently deploy the desired set of markers across samples with a rapid turnaround time that allows for selection before crosses needed to be made. In reality, breeders often have a short window of time to make decisions by the time they are able collect all their phenotyping data and receive corresponding genotyping data. This presents a challenge to organize information and utilize them in downstream analyses to support decisions made by breeders. In order to implement genomic selection routinely as part of breeding programs one would need an efficient genotype data storage system. We selected and benchmarked six popular open-source data storage systems, including relational database management and columnar storage systems.

Results

We found that data extract times are greatly influenced by the orientation in which genotype data is stored in a system. HDF5 consistently performed best, in part because it can more efficiently work with both orientations of the allele matrix.

Availability

http://gobiinx1.bti.cornell.edu:6083/projects/GBM/repos/benchmarking/browse

Contact

yn259@cornell.edu
Highly-accurate long-read sequencing improves variant detection and assembly of a human genome
Authors: Wenger Aaron M. , Peluso Paul , Rowell William J. , Chang Pi-Chuan , Hall Richard J. , Concepcion Gregory T. , Ebler Jana , Fungtammasan Arkarachai , Kolesnikov Alexey , Olson Nathan D. , Töpfer Armin , Alonge Michael , Mahmoud Medhat , Qian Yufeng , Chin Chen-Shan , Phillippy Adam M. , Schatz Michael C. , Myers Gene , DePristo Mark A. , Ruan Jue , Marschall Tobias , Sedlazeck Fritz J. , Zook Justin M. , Li Heng , Koren Sergey , Carroll Andrew , Rank David R. , Hunkapiller Michael W.
Published: January 2019

The major DNA sequencing technologies in use today produce either highly-accurate short reads or noisy long reads. We developed a protocol based on single-molecule, circular consensus sequencing (CCS) to generate highly-accurate (99.8%) long reads averaging 13.5 kb and applied it to sequence the well-characterized human HG002/NA24385. We optimized existing tools to comprehensively detect variants, achieving precision and recall above 99.91% for SNVs, 95.98% for indels, and 95.99% for structural variants. We estimate that 2,434 discordances are correctable mistakes in the high-quality Genome in a Bottle benchmark. Nearly all (99.64%) variants are phased into haplotypes, which further improves variant detection. De novo assembly produces a highly contiguous and accurate genome with contig N50 above 15 Mb and concordance of 99.998%. CCS reads match short reads for small variant detection, while enabling structural variant detection and de novo assembly at similar contiguity and markedly higher concordance than noisy long reads.
Fire ! The spread of the Caribbean fire coral Millepora alcicornis in the Eastern Atlantic
Authors: Wirtz Peter , Zilberberg Carla
Published: January 2019

The Western Atlantic fire coral Millepora alcicornis is recorded from Madeira Island in the Eastern Atlantic for the first time. A large colony of this species has apparently been present at a very exposed site at the northern shore of Madeira Island for more than 15 years. Genetic analyses suggest that the colonies of this tropical fire coral at a mid-Atlantic location (Ascension Island) and at each of three Eastern Atlantic locations (Cape Verde Islands, Canary Islands, Madeira Island) originated from independent long-distance dispersal events from the Caribbean area.