bluuebunny/crossref_metadata_2025 huggingface dataset:
A 3-Protein Expression Signature of Neuroblastoma for Outcome Prediction
Authors: Xie Yi , Xu Hua , Fang Fang , Li Zhiheng , Zhou Huiting , Pan Jian , Guo Wanliang , Zhu Xueming , Wang Jian , Wu Yi
Published: May 2018

Neuroblastoma (NB) is the most common extracranial solid tumor in children with contrasting outcomes. Precise risk assessment contributes to prognosis prediction, which is critical for treatment strategy decisions. In this study, we developed a 3-protein predictor model, including the neural stem cell marker Msi1, neural differentiation marker ID1, and proliferation marker proliferating cell nuclear antigen (PCNA), to improve clinical risk assessment of patients with NB. Kaplan-Meier analysis in the microarray data (GSE16476) revealed that low expression of ID1 and high expression of Msi1 and PCNA were associated with poor prognosis in NB patients. Combined application of these 3 markers to constitute a signature further stratified NB patients into different risk subgroups can help obtain more accurate prediction performance. Survival prognostic power of age and Msi1_ID1_PCNA signature by receiver operating characteristics analysis showed that this signature predicted more effectively and sensitively compared with classic risk stratification system, compensating for the deficiency of the prediction function of the age. Furthermore, we validated the expressions of these 3 proteins in neuroblastic tumor spectrum tissues by immunohistochemistry revealed that Msi1 and PCNA exhibited increased expression in NB compared with intermedial ganglioneuroblastoma and benign ganglioneuroma, whereas ID1 levels were reduced in NB. In conclusion, we established a robust risk assessment predictor model based on simple immunohistochemistry for therapeutic decisions of NB patients.
Herpes Simplex Virus Pneumonia in an Immunocompetent Child on Corticosteroids for Acute Wheezing
Authors: Pines Naama , Tsabari Reuven , Kerem Eitan , Reiter Joel
Published: May 2018

Herpes simplex virus (HSV) is rarely the cause of pneumonia in immunocompetent patients. We describe a previously healthy child, with no evidence of an immunodeficiency, who presented to the emergency department with severe pneumonia, wheezing, and pleural effusions with a history of orolabial HSV infection. On admission, he was started on antibiotics and systemic corticosteroids but continued to deteriorate. Oral lesions, blood, and pleural fluid tested positive for HSV, and improvement was achieved only after the addition of acyclovir and discontinuation of steroids. We suggest that steroids should be used with caution in patients presenting with lower respiratory tract symptoms and herpetic oral lesions.
Early Functional Treatment of Proximal Phalanx Fractures in Children
Authors: Bohr Stefan , Mammadli Toghrul
Published: May 2018

Objectives

The objective of this study was to assess proper indications a nonsurgical treatment regime for pediatric fractures of the proximal phalanx based on principles of early functional treatment.

Methods

A case series (evidence level 4) of 30 pediatric patients with fractures of the proximal phalanx were treated nonsurgically using protective dynamic splinting techniques and fiberglass casting material. Assessments were performed clinically and by x-ray within 4 to 8 weeks of commencement of treatment. Outcome measures included Disabilities of the Arm, Shoulder, and Hand score questionnaire as well as fingertip palm distance (cm) and dynamic pain interval assessments.

Results

All fractures healed without any clinically apparent bony deformities. Disabilities of the Arm, Shoulder, and Hand scores were of 25.17 ± 5.29 (mean ± SD), which indicated good functional results usually within 2 weeks of removal of dynamic splints. Fingertip palm distance measurements at endpoints were of 0.17 ± 0.27 cm (mean ± SD), which indicated an almost free range of finger motion. Absence of pain perception under active finger motion (dynamic pain interval) was noted at 14.10 ± 6.79 days (mean ± SD).

Conclusions

Well-established criteria for surgical treatment of phalangeal fractures exist. However, in our experience, a majority of pediatric fractures of the proximal phalanx can be safely treated nonsurgically with dynamic splinting along with shorter intervals of immobilization of the affected fingers and faster restoration of overall hand function compared to surgical treatment.
Quantification of Pain and Distress Associated With Intranasal Midazolam Administration in Children and Evaluation of Validity of Four Observational Measures
Authors: Tsze Daniel S. , Ieni Maria , Flores-Sanchez Pamela L. , Shen Sripriya T. , Bregstein Joan S. , O'Connell Nicole C. , Dayan Peter S.
Published: May 2018

Objectives

The aims of this study were to quantify the pain and distress associated with the administration of intranasal (IN) midazolam in young children using 4 observational measures and to evaluate the degree of validity of these measures.

Methods

We conducted a prospective observational pilot study. Children aged 1 to 7 years requiring IN midazolam were enrolled. Children were videotaped, and scores were assigned to baseline and administration phases using the Observational Scale of Behavioral Distress–Revised (OSBD-R), Children's Hospital of Eastern Ontario Pain Scale (CHEOPS), and the Faces-Legs-Activity-Cry-Consolability (FLACC) scale. The cry duration following administration was assessed. Interrater reliability and convergent validity were determined for all 4 measures. Internal consistency and responsivity for the OSBD-R, CHEOPS, and FLACC scales were determined.

Results

We enrolled 20 children. The mean OSBD-R, CHEOPS, and FLACC scores associated with administration of IN midazolam were 27.1 (SD, 13.5), 11.5 (SD, 1.2), and 8.9 (SD, 2.7), respectively. The mean cry duration was 105.5 (SD, 68.8) seconds. The intraclass correlation coefficients for all measures ranged from 0.82 to 0.99. The Cronbach α's for the OSBD-R, CHEOPS, and FLACC were between 0.71 and 0.97. Pearson correlation coefficients for comparisons between OSBD-R, CHEOPS, and FLACC were between 0.82 and 0.96 but were between 0.32 and 0.51 for comparisons involving cry duration.

Conclusions

We have identified estimates of pain and distress associated with administration of IN midazolam in young children that can be used to determine desired effect sizes for trials that study interventions to treat this pain and distress. The OSBD-R, CHEOPS, and FLACC scales are suitable choices for outcome measures.
BRCA Mutations in the Young, High-Risk Female Population: Genetic Testing, Management of Prophylactic Therapies, and Implications for Plastic Surgeons
Authors: Salibian Ara A. , Frey Jordan D. , Choi Mihye , Karp Nolan S.
Published: May 2018

Growing public awareness of hereditary breast cancers, notably BRCA1 and BRCA2, and increasing popularity of personalized medicine have led to a greater number of young adult patients presenting for risk-reduction mastectomies and breast reconstruction. Plastic surgeons must be familiar with treatment guidelines, necessary referral patterns, and particular needs of these patients to appropriately manage their care. Genetic testing for BRCA1 and BRCA2 is most often reserved for patients older than the age of consent, and can be performed in the young adult population (aged 18 to 25 years) with the appropriate preemptive genetic counseling. Subsequent risk-reduction procedures are usually delayed until at least the latter end of the young adult age range, and must be considered on an individualized basis with regard for a patient’s level of maturity and autonomy. Prophylactic mastectomies in young adults also can serve to aid the unique psychosocial needs of this population, although the long-term psychological and physical ramifications must be considered carefully. With the development of nipple-sparing mastectomy and improvement in reconstructive techniques, risk-reducing surgery has become more accepted in the younger population. Immediate, implant-based reconstruction is a common reconstructive technique in these patients but requires extensive discussion regarding reconstructive goals, the risk of possible complications, and long-term implications of these procedures. Comprehensive, continuous support with multispecialty counseling is necessary throughout the spectrum of care for the high-risk, young adult patient.
Brief Report: Circulating Markers of Immunologic Activity Reflect Adiposity in Persons With HIV on Antiretroviral Therapy
Authors: Koethe John R. , Jenkins Cathy A. , Furch Briana D. , Lake Jordan E. , Barnett Louise , Hager Cindy C. , Smith Rita , Hulgan Todd , Shepherd Bryan E. , Kalams Spyros A.
Published: May 2018

Background:

Obesity alters adipose tissue immunology, and these changes may be reflected in circulating soluble inflammatory biomarker and T-cell subset profiles measured in HIV research studies.

Methods:

We recruited 70 adults with HIV (50% obese) on efavirenz, tenofovir, and emtricitabine, virologic suppression for >2 years, and no rheumatologic or other known inflammatory conditions. We measured fasting plasma levels of several markers of innate immunity and major CD4+ and CD8+ T-cell subsets. We assessed relationships between measurements of total adiposity [body mass index (BMI), dual-energy X-ray absorptiometry-quantified fat mass index (FMI), and plasma leptin] and the immunologic parameters using covariate-adjusted Spearman's rank correlations.

Results:

The cohort was 43% women, 54% nonwhite, and median age was 45 years. Higher BMI, FMI, and plasma leptin were consistently associated with higher C-reactive protein, serum amyloid A, and interleukin-6 (P < 0.01 for all), but lower interleukin-10 (P ≤ 0.02 for all). BMI and FMI were positively associated with soluble tumor necrosis factor-α receptor 1 levels (P ≤ 0.02 for both), and a positive correlation approached significance for all 3 body composition measurements with soluble CD163 (P ≤ 0.09 for all). Higher BMI and FMI were associated with lower CD38 expression on CD4+ T cells (P ≤ 0.04 for both), but higher CD69 expression (P ≤ 0.01 for BMI and FMI, P = 0.07 for leptin).

Conclusions:

Greater adiposity is associated with alterations in a limited set of circulating immune markers, potentially reflecting changes known to occur in adipose tissue with treated HIV infection. Measuring total fat mass radiographically did not yield substantively different results compared with BMI.
Preventing healthcare-associated infections through human factors engineering
Authors: Jacob Jesse T. , Herwaldt Loreen A. , Durso Francis T.
Published: May 2018

Purpose of review

Human factors engineering (HFE) approaches are increasingly being used in healthcare, but have been applied in relatively limited ways to infection prevention and control (IPC). Previous studies have focused on using selected HFE tools, but newer literature supports a system-based HFE approach to IPC.

Recent findings

Cross-contamination and the existence of workarounds suggest that healthcare workers need better support to reduce and simplify steps in delivering care. Simplifying workflow can lead to better understanding of why a process fails and allow for improvements to reduce errors and increase efficiency. Hand hygiene can be improved using visual cues and nudges based on room layout. Using personal protective equipment appropriately appears simple, but exists in a complex interaction with workload, behavior, emotion, and environmental variables including product placement. HFE can help prevent the pathogen transmission through improving environmental cleaning and appropriate use of medical devices.

Emerging evidence suggests that HFE can be applied in IPC to reduce healthcare-associated infections. HFE and IPC collaboration can help improve many of the basic best practices including use of hand hygiene and personal protective equipment by healthcare workers during patient care.
Evaluation of Simplified Lymphatic Microsurgical Preventing Healing Approach (S-LYMPHA) for the Prevention of Breast Cancer–Related Clinical Lymphedema After Axillary Lymph Node Dissection
Authors: Ozmen Tolga , Lazaro Mesa , Zhou Yan , Vinyard Alicia , Avisar Eli
Published: May 2018

Objective:

To assess the efficiency of Simplified Lymphatic Microsurgical Preventing Healing Approach (S-LYMPHA) in preventing lymphedema (LE) in a prospective cohort of patients.

Background:

LE is a serious complication of axillary lymph node dissection (ALND) with an incidence rate of 25%. LYMPHA has been proposed as an effective adjunct to ALND for the prevention of LE. This procedure, however, requires microsurgical techniques and significant coordination between services.

Methods:

All patients, undergoing ALND with or without S-LYMPHA between January 2014 and December 2016 were included in the study. During follow-up visits, tape-measuring limb circumference method was used to detect LE. The incidence of LE was compared between ALND with and without S-LYMPHA.

Results:

A total of 380 patients were included in the analysis. Median follow-up time was 15 (1–32) months. Patients, who underwent S-LYMPHA, had a significantly lower rate of LE both in univariate and multivariate analysis [3% vs 19%; P = 0.001; odds ratio 0.12 (0.03–0.5)]. Excising more than 22 lymph nodes and a co-diagnosis of diabetes mellitus were also correlated with higher clinical LE rates on univariate analysis, but only excising more than 22 lymph nodes remained to be significant on multivariate analysis.

Conclusions:

S-LYMPHA is a simple method, which decreases incidence of LE dramatically. It should be considered as an adjunct procedure to ALND for all patients during initial surgery.
The Impact of an ICU “Bed Ahead” Policy on ED Length of Stay and Patient Outcomes
Authors: DiGiacomo Jody C. , Angus L. D. George , Wallace Raina , Cardozo-Stolberg Sara , Gerber Noam , Munnangi Swapna , Sookraj Kelley , Skarka Kathy
Published: May 2018

Objective:

To assess the impact of preassigning a single bed in the surgical intensive care unit (SICU) for the next trauma admission.

Background:

Prolonged emergency department (ED) dwell time before admission to a critical care unit has an adverse effect on patient outcomes and is often due to the lack of an available bed in the intensive care unit (ICU).

Methods:

A “Bed Ahead” policy was instituted at an urban level 1 Trauma Public Safety Net Teaching Hospital to preassign 1 SICU bed for the next trauma patient who warrants a critical care admission. A retrospective review of all trauma patients admitted to the SICU before and after implementation of this policy was performed to assess the impact on ED dwell time, ICU and hospital lengths of stay, complications, and in-hospital mortality.

Results:

ED length of stay (ED-LOS); ICU length of stay (ICU-LOS); hospital length of stay (HLOS); complications; and in-hospital mortality were compared before (PRE) and after (POST)implementation of the Bed Ahead policy. Statistically significant improvements were seen in the POST period for ED-LOS, HLOS, complications, and in-hospital mortality.

Conclusions:

Preassigning 1 ICU for the yet to arrive next injured patient decreases ED dwell times, complications, HLOS, and in-hospital mortality.
De novo mutations drive the spread of macrolide-resistant Mycoplasma genitalium: a mathematical modelling study
Authors: Cadosch Dominique , Garcia Victor , Althaus Christian L. , Jensen Jørgen Skov , Low Nicola
Published: May 2018

Background

The rapid spread of azithromycin resistance in sexually transmitted Mycoplasma genitalium infections is a growing concern. It is not yet clear to what degree macrolide resistance in M. genitalium results from the emergence of de novo mutations or the transmission of resistant strains.

Methods

We analyzed epidemiological data and developed a compartmental model to investigate the contribution of de novo macrolide resistance mutations to the spread of antimicrobial-resistant M. genitalium. We fitted the model to data from France, Denmark and Sweden and estimated treatment rates of infected individuals and the time point of azithromycin introduction.

Results

We found a high probability of de novo resistance (12%, 95% CI 8–17%), which is responsible for the observed rapid spread of antimicrobial resistant M. genitalium. The estimated per capita treatment rate in France was lower than in Denmark and Sweden but confidence intervals for the three estimates overlap. The estimated dates of introduction of azithromycin in each country are consistent with published reports.

Conclusions

Since de novo resistance is the main driver of macrolide resistance in M. genitalium, blind treatment of urethritis with azithromycin is not recommended. Clinical management strategies for M. genitalium should limit the unnecessary use of macrolides.
Stochastic rank aggregation for the identification of functional neuromarkers
Authors: Galdi Paola , Fratello Michele , Trojsi Francesca , Russo Antonio , Tedeschi Gioacchino , Tagliaferri Roberto , Esposito Fabrizio
Published: May 2018

Background and aims

The main challenge in analysing functional magnetic resonance imaging (fMRI) data from extended samples of subject (N>100) is to extract as much relevant information as possible from big amounts of noisy data. When studying neurodegenerative diseases with resting-state fMRI, one of the objectives is to determine regions with abnormal background activity with respect to a healthy brain and this is often attained with comparative statistical models applied to single voxels or brain parcels within one or several functional networks. In this work, we propose a novel approach based on clustering and stochastic rank aggregation to identify parcels that exhibit a coherent behaviour in groups of subjects affected by the same disorder and apply it to default-mode network independent component maps from resting-state fMRI data sets.

Methods

Brain voxels are partitioned into parcels through k-means clustering, then solutions are enhanced by means of consensus techniques. For each subject, clusters are ranked according to their median value and a stochastic rank aggregation method, TopKLists, is applied to combine the individual rankings within each class of subjects. For comparison, the same approach was tested on an anatomical parcellation.

Results

We found parcels for which the rankings were different among control subjects and subjects affected by Parkinson’s disease and amyotrophic lateral sclerosis and found evidence in literature for the relevance of top ranked regions in default-mode brain activity.

Conclusions

The proposed framework represents a valid method for the identification of functional neuromarkers from resting-state fMRI data, and it might therefore constitute a step forward in the development of fully automated data-driven techniques to support early diagnoses of neurodegenerative diseases.
Auditory evoked potentials to changes in speech sound duration in anesthetized mice
Authors: Lipponen A. , Kurkela J.L.O. , I. Kyläheiko , S. Hölttä , Ruusuvirta T. , Astikainen P.
Published: May 2018

Electrophysiological response termed mismatch negativity (MMN) indexes auditory change detection in humans. An analogous response, called the mismatch response (MMR), is also elicited in animals. Mismatch response has been widely utilized in investigations of change detection in human speech sounds in rats and guinea pigs, but not in mice. Since e.g. transgenic mouse models provide important advantages for further studies, we studied processing of speech sounds in anesthetized mice. Auditory evoked potentials were recorded from the dura above the auditory cortex to changes in duration of a human speech sound /a/. In oddball stimulus condition, the MMR was elicited at 53-259 ms latency in response to the changes. The MMR was found to the large (from 200 ms to 110 ms) but not to smaller (from 200 ms to 120-180 ms) changes in duration. The results suggest that mice can represent human speech sounds in order to detect changes in their duration. The findings can be utilized in future investigations applying mouse models for speech perception.
Genome Wide Interaction Studies Identify Sex-Specific Risk Alleles for Nonsyndromic Orofacial Clefts
Authors: Carlson Jenna C. , Nidey Nichole L. , Butali Azeez , Buxo Carmen J. , Christensen Kaare , Deleyiannis Frederic W-D , Hecht Jacqueline T. , Field L. Leigh , Moreno-Uribe Lina M. , Orioli Ieda M. , Poletta Fernando A. , Padilla Carmencita , Vieira Alexandre R. , Weinberg Seth M. , Wehby George L. , Feingold Eleanor , Murray Jeffrey C. , Marazita Mary L. , Leslie Elizabeth J.
Published: May 2018

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is the most common craniofacial birth defect in humans and is notable for its apparent sexual dimorphism where approximately twice as many males are affected as females. The sources of this disparity are largely unknown, but interactions between genetic and sex effects are likely contributors. We examined gene-by-sex (G x S) interactions in a worldwide sample of 2,142 NSCL/P cases and 1,700 controls recruited from 13 countries. First, we performed genome-wide joint tests of the genetic (G) and G x S effects genome-wide using logistic regression assuming an additive genetic model and adjusting for 18 principal components of ancestry. We further interrogated loci with suggestive results from the joint test (p < 1.00 × 10−5) by examining the G x S effects from the same model. Out of the 133 loci with suggestive results (p < 1.00 × 10−5) for the joint test, we observed one genome-wide significant G x S effect in the 10q21 locus (rs72804706; p = 6.69 × 10−9; OR = 2.62 [1.89, 3.62]) and 16 suggestive G x S effects. At the intergenic 10q21 locus, the risk of NSCL/P is estimated to increase with additional copies of the minor allele for females, but the opposite effect for males. Our observation that the impact of genetic variants on NSCL/P risk differs for males and females may further our understanding of the genetic architecture of NSCL/P and the sex differences underlying clefts and other birth defects.
A genome-scale metabolic model forMethylococcus capsulatuspredicts reduced efficiency uphill electron transfer to pMMO
Authors: Lieven Christian , Petersen Leander A. H. , Jørgensen Sten Bay , Gernaey Krist V. , Herrgard Markus J. , Sonnenschein Nikolaus
Published: May 2018

Background

Genome-scale metabolic models allow researchers to calculate yields, to predict consumption and production rates, and to study the effect of genetic modificationsin silico, without running resource-intensive experiments. While these models have become an invaluable tool for optimizing industrial production hosts likeE. coliandS. cerevisiae, few such models exist for one-carbon (C1) metabolizers.

Results

Here we present a genome-scale metabolic model forMethylococcus capsulatus, a well-studied obligate methanotroph, which has been used as a production strain of single cell protein (SCP). The model was manually curated, and spans a total of 877 metabolites connected via 898 reactions. The inclusion of 730 genes and comprehensive annotations, make this model not only a useful tool for modeling metabolic physiology, but also a centralized knowledge base forM. capsulatus. With it, we determined that oxidation of methane by the particulate methane monooxygenase is most likely driven through uphill electron transfer operating at reduced efficiency as this scenario matches best with experimental data from literature.

Conclusions

The metabolic model will serve the ongoing fundamental research of C1 metabolism, and pave the way for rational strain design strategies towards improved SCP production processes inM. capsulatus.
The high turnover of ribosome-associated transcripts fromde novoORFs produces gene-like characteristics available forde novogene emergence in wild yeast populations
Authors: Durand Éléonore , Gagnon-Arsenault Isabelle , Hallin Johan , Hatin Isabelle , Dubé Alexandre K , Nielly-Thibaut Lou , Namy Olivier , Landry Christian R
Published: May 2018

Little is known about the rate of emergence of genesde novo, how they spread in populations and what their initial properties are. We examined wild yeast (Saccharomyces paradoxus) populations to characterize the diversity and turnover of intergenic ORFs over short evolutionary time-scales. With ~34,000 intergenic ORFs per individual genome for a total of ~64,000 orthogroups identified, we foundde novoORF formation to have a lower estimated turnover rate than gene duplication. Hundreds of intergenic ORFs show translation signatures similar to canonical genes. However, they have lower translation efficiency, which could reflect a mechanism to reduce their production cost or simply a lack of optimization. We experimentally confirmed the translation of many of these ORFs in laboratory conditions using a reporter assay. Translated intergenic ORFs tend to display low expression levels with sequence properties that generally are close to expectations based on intergenic sequences. However, some of the very recent translated intergenic ORFs, which appeared less than 110 Kya ago, already show gene- like characteristics, suggesting that the raw material for functional innovations could appear over short evolutionary time-scales.
Interactive single cell RNA-Seq analysis with the Single Cell Toolkit (SCTK)
Authors: Jenkins David F. , Faits Tyler , Briars Emma , Carrasco Pro Sebastian , Cunningham Steve , Campbell Joshua D. , Yajima Masanao , Evan Johnson W.
Published: May 2018

Single cell RNA-sequencing (scRNA-Seq) allows researchers to profile transcriptional activity in individual cells. However, the complex nature of these data and variability in study design and data generation requires sophisticated computational tools and informed analytical decisions. Here, we present the Single Cell Toolkit (SCTK), an interactive scRNA-Seq analysis package that enables users to perform scRNA-Seq analysis interactively using a command-line workflow or a graphical user interface (GUI) written in R/Shiny.
Joint precursor elution profile inference via regression for peptide detection in data-independent acquisition mass spectra
Authors: Hu Alex , Lu Yang Young , Bilmes Jeff , Noble William Stafford
Published: May 2018

In data independent acquisition (DIA) mass spectrometry, precursor scans are interleaved with wide-window fragmentation scans, resulting in complex fragmentation spectra containing multiple co-eluting peptide species. In this setting, detecting the isotope distribution profiles of intact peptides in the precursor scans can be a critical initial step in accurate peptide detection and quantification. This peak detection step is particularly challenging when the isotope peaks associated with two different peptide species overlap—orinterfere—with one another. We propose a regression model, called Siren, to detect isotopic peaks in precursor DIA data that can explicitly account for interference. We validate Siren’s peak-calling performance on a variety of data sets by counting how many of the peaks Siren identifies are associated with confidently detected peptides. In particular, we demonstrate that substituting the Siren regression model in place of the existing peak-calling step in DIA-Umpire leads to improved overall rates of peptide detection.
Improved G-AgarTrap: A highly efficient transformation method for intact gemmalings of the liverwortMarchantia polymorpha
Authors: Tsuboyama Shoko , Nonaka Satoko , Ezura Hiroshi , Kodama Yutaka
Published: May 2018

Liverworts are key species for studies of plant evolution, occupying a basal position among the land plants.Marchantia polymorphahas emerged as a highly studied model liverwort, and many relevant techniques, including genetic transformation, have been established for this species.Agrobacterium-mediated transformation is widely used in many plant species because of its low cost. Recently, we developed a simplifiedAgrobacterium-mediated method for transformingM. polymorpha, known as AgarTrap (agar-utilized transformation with pouring solutions). The AgarTrap procedure, which involves culturing the liverwort tissue in various solutions on a single solid medium, yields up to a hundred independent transformants. AgarTrap is a simple procedure, requiring minimal expertise, cost, and time.

Here, we investigated four factors that influence AgarTrap transformation efficiency: (1) humidity, (2) surfactant in the transformation buffer, (3)Agrobacteriumstrain, and (4) light/dark condition. We adapted the AgarTrap protocol for transforming intact gemmalings, achieving an exceptionally high transformation efficiency of 97%. The improved AgarTrap method will enhance the molecular biological study ofM. polymorpha. The present study also provides new possibilities for improving transformation techniques for a variety of plant species.
Long noncoding RNA ANRIL supports proliferation of adult T-cell leukemia cells through cooperation with EZH2
Authors: Song Zaowen , Wu Wencai , Chen Mengyun , Cheng Wenzhao , Yu Juntao , Fang Jinyong , Xu Lingling , Yasunaga Jun-ichirou , Matsuoka Masao , Zhao Tiejun
Published: May 2018

Adult T-cell leukemia (ATL) is a highly aggressive T-cell malignancy induced by human T-cell leukemia virus type 1 (HTLV-1) infection. Long noncoding RNA (lncRNA) plays a critical role in the development and progression of multiple human cancers. However, the function of lncRNA on HTLV-1-induced oncogenesis has not been elucidated. In the present study, we show that the expression of the lncRNA ANRIL was elevated in HTLV-1 infected cell lines and clinical ATL samples. E2F1 induced ANRIL transcription by enhancing its promoter activity. Knocking down of ANRIL in ATL cells repressed cellular proliferation and increased apoptosis in vitro and in vivo. As a mechanism for these actions, we found that ANRIL targeted EZH2, and activated the NF-κB pathway in ATL cells. This activation was independent of the histone methyltransferase (HMT) activity of EZH2, but required the formation of an ANRIL/EZH2/p65 ternary complex. Chromatin immunoprecipitation assay revealed that ANRIL/EZH2 enhanced p65 DNA binding capability. In addition, we observed that ANRIL/EZH2 complex repressed p21/CDKN1A transcription through H3K27 trimethylation of the p21/CDKN1A promoter. Taken together, our results implicate that lncRNA ANRIL, by cooperating with EZH2, supports the proliferation of HTLV-1 infected cells, which is thought to be critical for oncogenesis.

IMPORTANCE

Human T-cell leukemia virus type 1 (HTLV-1) is the pathogen that causes adult T-cell leukemia (ATL), which is a unique malignancy of CD4+ T cells. A role for long noncoding RNA (lncRNA) in HTLV-1-mediated cellular transformation has not been described. In this study, we demonstrated that lncRNA ANRIL was important for maintaining proliferation of ATL cells in vitro and in vivo. ANRIL was shown to activate NF-κB signaling through forming a ternary complex with EZH2 and p65. Further, epigenetic inactivation of p21/CDKN1A was involved in the oncogenic function of ANRIL. To the best of our knowledge, this is the first study to address the regulatory role of the lncRNA ANRIL in ATL and provides an important clue to prevent or treat HTLV-1 associated human diseases.
Olive mild mosaic virus coat protein and p6 are suppressors of RNA silencing and their silencing confers resistance against OMMV
Authors: Varanda CMR , Materatski P , Campos MD , Clara MIE , Nolasco G , Félix MR
Published: May 2018

RNA silencing is an important defense mechanism in plants, yet several plant viruses encode proteins that suppress it. Here the genome of Olive mild mosaic virus (OMMV) was screened for silencing suppressors using a green fluorescent based transient suppression assay. The full OMMV cDNA and 5 different OMMV open reading frames (ORFs) were cloned into Gateway binary destination vector pK7WG2, transformed into Agrobacterium tumefaciens C58C1 and agroinfiltrated into Nicotiana benthamiana 16C plants. Among all ORFs tested, CP and p6 showed suppressor activity, with CP showing a significant higher activity when compared to p6, yet lower than that of the full OMMV. This suggests that OMMV silencing suppression results from a complementary action of both CP and p6.

Such discovery led to the use of those viral suppressors in the development of OMMV resistant plants through pathogen-derived resistance (PDR) based on RNA silencing. Two hairpin constructs targeting each suppressor were agroinfiltrated in N. benthamiana plants which were then inoculated with OMMV RNA. When silencing of both suppressors was achieved, a highly significant reduction in viral accumulation and symptom attenuation was observed as compared to that seen when each construct was used alone, and to the respective controls, thus showing clear effectiveness against OMMV infection. Data here obtained indicate that the use of both OMMV viral suppressors as transgenes is a very efficient and promising approach to obtain plants resistant to OMMV.

Importance

OMMV silencing suppressors were determined. Among all ORFs tested, CP and p6 showed suppressor activity, with CP showing a significant higher activity when compared to p6, yet lower than that of the full OMMV, suggesting a complementary action of both CP and p6 in silencing suppression.

This is the first time that a silencing suppressor was found in a necrovirus and that two independent proteins act as silencing suppressors in a member of the Tombusviridae family.

When silencing of both suppressors was achieved, a highly significant reduction in viral accumulation and symptom attenuation was observed as compared to that seen when each was used alone, thus showing clear effectiveness against OMMV infection. A high percentage of resistant plants was obtained (60%), indicating that the use of both OMMV viral suppressors as transgenes is a very efficient and promising approach to obtain plants resistant to OMMV.
In vitro and In vivo characterization of NOSO-502, a novel inhibitor of bacterial translation
Authors: Racine Emilie , Nordmann Patrice , Pantel Lucile , Sarciaux Matthieu , Serri Marine , Houard Jessica , Villain-Guillot Philippe , Demord Anthony , Lundberg Carina Vingsbo , Gualtieri Maxime
Published: May 2018

Antibacterial activity screening of a collection of Xenorhabdus strains led to the discovery of the Odilorhabdins, a novel antibiotic class with broad-spectrum activity against Gram-positive and Gram-negative pathogens. Odilorhabdins inhibit bacterial translation by a novel mechanism of action on ribosomes. A lead-optimization program identified NOSO-502 as a promising candidate. NOSO-502 has MIC values ranging from 0.5 to 4 μg/ml against standard Enterobacteriaceae strains and carbapenem-resistant Enterobacteriaceae (CRE) isolates that produce KPC, AmpC, or OXA enzymes and metallo-β-lactamases. In addition, this compound overcomes multiple chromosome-encoded or plasmid-mediated resistance mechanisms of acquired resistance to colistin. It is effective in mouse systemic infection models against E. coli EN122 (ESBL) or E. coli ATCC BAA-2469 (NDM-1), achieving an ED50 of 3.5 mg/kg and 1-, 2- and 3-log reductions in blood burden at 2.6, 3.8, and 5.9 mg/kg, respectively, in the first model and 100% survival in the second, starting with a dose as low as 4 mg/kg. In a UTI model of E. coli UTI89, urine, bladder and kidney burdens were reduced by 2.39, 1.96, and 1.36 log10 CFU/ml, respectively, after injecting 24 mg/kg. There was no cytotoxicity against HepG2, HK-2, or HRPT cells, no inhibition of hERG-CHO or Nav 1.5 -HEK current, and no increase of micronuclei at 512 μM. NOSO-502, a compound with a novel mechanism of action, is active against Enterobacteriaceae, including all classes of CRE, has a low potential for resistance development, shows efficacy in several mouse models, and has a favorable in vitro safety profile.
When is a fish stock collapsed?
Authors: Yletyinen J , Butler WE , Ottersen G , Andersen KH , Bonanomi S , Diekert FK , Folke C , Lindegren M , Nordström MC , Richter A , Rogers L , Romagnoni G , Weigel B , Whittington JD , Blenckner T , Stenseth NC
Published: May 2018

Marine fish stock collapses are a major concern for scientists and society due to the potentially severe impacts on ecosystem resilience, food security and livelihoods. Yet the general state of harvested fish populations has proven difficult to summarize, and the actual occurrence rate of stock collapses remains unclear. We have carried out a literature review and multi-stock analysis to show that numerous definitions exist for classifying stocks as collapsed, and that the classification of a stock’s status is sensitive to changes in the collapse definition’s formulation. We suggest that the lack of a unified definition has contributed to contrasting perceptions on the state of fish stocks. Therefore, we comprehensively define what constitutes a fish stock collapse and provide a time-series based method for collapse detection. Unlike existing definitions, our definition is process-based, because it links together three important phases of collapse events: the abrupt decline, an ensuing period of prolonged depletion, and potential recovery. Furthermore, these phases are specified in terms of population turnover. Through systematic evaluation, our definition can accurately distinguish collapses from less severe depletions or natural fluctuations for stocks with diverse life histories, helping identify the stocks in greatest need of reparatory measures. Our study advocates the consistent use of definitions to limit both alarmist and conservative narratives on the state of fish stocks, and to promote cooperation between conservation and fisheries scientists. This will facilitate clear and accurate communication of science to both the public and to policy-makers to ensure healthy fish stocks in the future.
ATM orchestrates the DNA-damage response to counter toxic non-homologous end-joining at broken replication forks
Authors: Balmus Gabriel , Pilger Domenic , Coates Julia , Demir Mukerrem , Sczaniecka-Clift Matylda , Barros Ana , Woods Michael , Fu Beiyuan , Yang Fengtang , Chen Elisabeth , Ostermaier Matthias , Stankovic Tatjana , Ponstingl Hannes , Herzog Mareike , Yusa Kosuke , Munoz Martinez Francisco , Durant Stephen T. , Galanty Yaron , Beli Petra , Adams David J. , Bradley Allan , Metzakopian Emmanouil , Forment Josep V. , Jackson Stephen P.
Published: May 2018

Mutations in the ATM tumor suppressor confer hypersensitivity to DNA-damaging agents. To explore genetic resistance mechanisms, we performed genome-wide CRISPR-Cas9 screens in cells treated with the DNA topoisomerase poison topotecan. Thus, we establish that loss of terminal components of the non-homologous end-joining (NHEJ) machinery or the BRCA1-A complex specifically confers topotecan resistance to ATM-deficient cells. We show that hypersensitivity of ATM-mutant cells to topotecan or the poly-(ADP-ribose) polymerase inhibitor olaparib is due to delayed homologous recombination repair at DNA-replication-fork-associated double-strand breaks (DSBs), resulting in toxic NHEJ-mediated chromosome fusions. Accordingly, restoring legitimate repair in ATM-deficient cells, either by preventing NHEJ DNA ligation or by enhancing DSB-resection by BRCA1-A complex inactivation, markedly suppresses this toxicity. Our work suggests opportunities for patient stratification in ATM-deficient cancers and when using ATM inhibitors in the clinic, and identifies additional therapeutic vulnerabilities that might be exploited when such cancers evolve drug resistance.

One Sentence Summary

ATM counteracts toxic NHEJ at broken replication forks
Critical role for Piccolo in Synaptic Vesicle Retrieval
Authors: Ackermann Frauke , Schink Kay O. , Bruns Christine , Izsvák Zsuzsanna , Hamra F. Kent , Rosenmund Christian , Garner Craig C.
Published: May 2018

Loss of function of the presynaptic active zone protein Piccolo has recently been linked to a devastating disease causing brain atrophy. Here, we address how Piccolo inactivation adversely affects synaptic function and thus may contributes to neuronal loss. Our analysis shows that Piccolo is critical for the activity dependent recycling and maintenance of synaptic vesicles (SVs). Specifically, we find that boutons lacking Piccolo have deficits in the Rab5/EEA1 dependent formation of early endosomes and thus the recycling of SVs. Mechanistically, impaired Rab5 function was caused by the reduced synaptic recruitment of Pra1, known to interact selectively with the zinc fingers of Piccolo. Importantly, over-expression of GTPase deficient Rab5 or the Znf1 domain of Piccolo restores the size and recycling of SV pools. These data provide a molecular link between the active zone and endosome sorting at synapses providing hints to how Piccolo contributes to both developmental and psychiatric disorders.

Impact Statement

The efficient recycling of synaptic vesicle proteins is critical for the integrity and reliability of synaptic transmission. Increasingly genetic and environmental insults have been shown to affect this recycling pathway, resulting in both cognitive impairment in humans and neurodegenerative diseases, yet the underlying mechanisms are poorly understood. Here we could show that the presynaptic active zone protein Piccolo regulates efficient recycling of synaptic vesicles via Pra1 and Rab5, perhaps explaining why Piccolo loss of function contributes to Pontocerebellar Hypoplasia and major depressive disorders.
mitoNEET Regulates Mitochondrial Iron Homeostasis Interacting with Transferrin Receptor
Authors: Furihata Takaaki , Takada Shingo , Maekawa Satoshi , Mizushima Wataru , Watanabe Masashi , Takahashi Hidehisa , Fukushima Arata , Tsuda Masaya , Matsumoto Junichi , Kakutani Naoya , Yokota Takashi , Matsushima Shouji , Otsuka Yutaro , Matsumoto Masaki , Nakayama Keiichi I. , Nio-Kobayashi Junko , Iwanaga Toshihoko , Sabe Hisataka , Hatakeyama Shigetsugu , Tsutsui Hiroyuki , Kinugawa Shintaro
Published: May 2018

Iron is an essential trace element for regulation of redox and mitochondrial function, and then mitochondrial iron content is tightly regulated in mammals. We focused on a novel protein localized at the outer mitochondrial membrane. Immunoelectron microscopy revealed transferrin receptor (TfR) displayed an intimate relationship with the mitochondria, and mass spectrometry analysis also revealed mitoNEET interacted with TfR in vitro. Moreover, mitoNEET was endogenously coprecipitated with TfR in the heart, which indicates that mitoNEET also interacts with TfR in vivo. We generated mice with cardiac-specific deletion of mitoNEET (mitoNEET-knockout). Iron contents in isolated mitochondria were significantly increased in mitoNEET-knockout mice compared to control mice. Mitochondrial reactive oxygen species (ROS) were higher, and mitochondrial maximal capacity and reserve capacity were significantly decreased in mitoNEET-knockout mice, which was consistent with cardiac dysfunction evaluated by echocardiography. The complex formation of mitoNEET with TfR may regulate mitochondrial iron contents via an influx of iron. A disruption of mitoNEET could thus be involved in mitochondrial ROS production by iron overload in the heart.
Transcranial alternating current stimulation at 10 Hz modulates response bias in the Somatic Signal Detection Task
Authors: Craddock Matt , Klepousniotou Ekaterini , el-Deredy Wael , Poliakoff Ellen , Lloyd Donna
Published: May 2018

Background

Ongoing, pre-stimulus oscillatory activity in the 8-13 Hz alpha range has been shown to correlate with both true and false reports of peri-threshold somatosensory stimuli. However, to directly test the role of such oscillatory activity in behaviour, it is necessary to manipulate it. Transcranial alternating current stimulation (tACS) offers a method of directly manipulating oscillatory brain activity using a sinusoidal current passed to the scalp.

Objective

We tested whether alpha tACS would change somatosensory sensitivity or response bias in a signal detection task in order to test whether alpha oscillations have a causal role in behaviour.

Methods

Active 10 Hz tACS or sham stimulation was applied using electrodes placed bilaterally at positions CP3 and CP4 of the 10-20 electrode placement system. Participants performed the Somatic Signal Detection Task (SSDT), in which they must detect brief somatosensory targets delivered at their detection threshold. These targets are sometimes accompanied by a light flash, which could also occur alone.

Results

Active tACS did not modulate sensitivity to targets but did modulate response criterion. Specifically, we found that active stimulation generally increased touch reporting rates, but particularly increased responding on light trials. Stimulation did not interact with the presence of touch, and thus increased both hits and false alarms.

Conclusions

tACS stimulation increased reports of touch in a manner consistent with our observational reports, changing response bias, and consistent with a role for alpha activity in somatosensory detection.
Gene function contributes to gene expression levels inS. cerevisiae
Authors: Hickman Mark J. , Jackson Andrea , Smith Abigail , Thornton Julianne , Tursi Amanda
Published: May 2018

It is not understood what evolutionary factors drive some genes to be expressed at a higher level than others. Here, we hypothesized that a gene’s function plays an important role in setting expression level. First, we established that eachS. cerevisiaegene is maintained at a specific expression level by analyzing RNA-seq data from multiple studies. Next, we found that mRNA and protein levels were maintained for the orthologous genes inS. pombe, showing that gene function, conserved in orthologs, is important in setting expression level. To further explore the role of gene function in setting expression level, we analyzed mRNA and protein levels ofS. cerevisiaegenes within gene ontology (GO) categories. The GO framework systematically defines gene function based on experimental evidence. We found that several GO categories contain genes with statistically significant expression extremes; for example, genes involved in translation or energy production are highly expressed while genes involved in chromosomal activities, such as replication and transcription, are weakly expressed. Finally, we were able to predict expression levels using GO information alone. We created and optimized a linear equation that predicted a gene’s expression based on the gene’s membership in 161 GO categories. The greater number of GO categories with which a gene is associated, the more accurately expression could be predicted. Taken together, our analysis systematically demonstrates that gene function is an important determinant of expression level.
Examining the Role of the Surfactant Family Member SFTA3 in Interneuron Specification
Authors: Chen Christopher Y. , Anderson Nickesha C. , Becker Sandy , Schicht Martin , Stoddard Christopher , Bräuer Lars , Paulsen Friedrich , Grabel Laura
Published: May 2018

The transcription factorNKX2.1, expressed at high levels in the medial ganglionic eminence (MGE), is a master regulator of cortical interneuron progenitor development. To identify gene candidates with expression profiles similar toNKX2.1, previous transcriptome analysis of human embryonic stem cell (hESC)-derived MGE-like progenitors revealedSFTA3as the strongest candidate. Quantitative real-time PCR analysis of hESC-derived NKX2.1-positive progenitors and transcriptome data available from the Allen Institute for Brain Science revealed comparable expression patterns forNKX2.1andSFTA3during interneuron differentiationin vitroand demonstrated highSFTA3expression in the human MGE. AlthoughSFTA3has been well studied in the lung, the possible role of this surfactant protein in the MGE during embryonic development remains unexamined. To determine ifSFTA3plays a role in MGE specification,SFTA3-/- andNKX2.1 -/-hESC lines were generated using custom designed CRISPRs. We show thatNKX2.1KOs have a significantly diminished capacity to differentiate into MGE interneuron subtypes.SFTA3KOs also demonstrated a somewhat reduced ability to differentiate down the MGE-like lineage, although not as severe relative toNKX2.1deficiency. These results suggestNKX2.1andSFTA3are co-regulated genes, and that deletion ofSFTA3does not lead to a major change in the specification of MGE derivatives.