bluuebunny/crossref_metadata_2025 huggingface dataset:
A Macaque Model for Rectal Lymphogranuloma Venereum and Non-Lymphogranuloma Venereum Chlamydia trachomatis: Impact on Rectal Simian/Human Immunodeficiency Virus Acquisition
Authors: Vishwanathan Sundaram Ajay , Aubert Rachael D. , Morris Monica R. , Zhao Chunxia , Philips Christi , Khalil George M. , Deyounks Frank , Kelley Kristen , Ritter Jana M. , Chen C.Y. , Kersh Ellen N. , McNicholl Janet M.
Published: June 2017

Background

Sustained genital tract inflammation caused by sexually transmitted infections (STIs) is known to increase risk of vaginal human immunodeficiency virus (HIV) infections but, to our knowledge, there are no nonhuman primate studies that have evaluated its link to rectal HIV acquisition.

Methods

Rhesus macaques inoculated with Chlamydia trachomatis (CT) (serovars LGV-L2 and CT-E; n = 7) or saline (n = 7) received up to 20 rectal challenges twice a week of simian/HIV immunodeficiency virus (SHIVSF162p3). SHIV viremia was determined by real-time PCR and Chlamydia infection by APTIMA Combo 2 testing. The rectal cytokine-chemokine levels were evaluated by multiplex bead assays.

Results

Rectal Chlamydia infection was maintained throughout the study. We did not observe significant differences (P = 1.0) in frequency of SHIV acquisition between the STI and control arms. It took fewer SHIV challenges to infect the STI animals although the difference was not significant (P = 0.59). There were no significant differences in peak plasma viremia between STI and control arms (P = 0.63). The association of plasma viremia with rectal shedding was significantly different by arm (P = 0.038).

Conclusions

In the first such study in a macaque model, we did not observe an increased risk of SHIV acquisition due to rectal Chlamydia coinfection. This macaque model can be further developed and expanded to better investigate the impact of different rectal STIs on HIV acquisition.
Recurrence of Human Papillomavirus External Genital Wart Infection Among High-Risk Adults in Montréal, Canada
Authors: Thomas Réjean , Steben Marc , Greenwald Zoë , Stutz Melissa , Rodier Caroline , DeAngelis Fern , Rampakakis Emmanouil
Published: June 2017

Objectives

The incidence of recurrent genital warts is not well characterized; this is especially true in a post-human papillomavirus (HPV) vaccination era. The objectives of this study were to assess the incidence of subsequent HPV-related external genital warts (EGW) episodes in high-risk male and female adults, as well as ascertain patient profile and disease characteristics, in a real-world Canadian sexual health clinical setting.

Methods

Retrospective chart review study conducted at Clinique médicale l’Actuel, a sexual health clinic in Montréal, Québec, Canada. Eligible patients were 18 to 45 years of age with a first diagnosis of EGW associated with a HPV infection between July 1, 2006, and June 30, 2012.

Results

A total of 400 first-episode EGW cases were identified. Up to 6 subsequent episodes were documented, with 194 (48.5%) patients reporting at least 1 subsequent EGW episode. Median time to first subsequent EGW episode was 3.97 years, and the incidence density rate for all subsequent episodes was 0.18/100 patient-years. Over 90% of patients reported clearance of the first subsequent episode, with median time to clearance of 0.30 years. Regardless of subsequent episode number, greater than 95% of patients received treatment, primarily cryotherapy, with high-risk sexual behavior reducing as number of episodes increased.

Conclusions

Overall, a high rate of subsequent EGW episodes was observed in this high-risk population, despite high treatment rates and improvement in high-risk sexual behavior. These data, assessed in a prevaccination Québec health care system, may be compared with future EGW rates to assess the impact of a governmentally-funded HPV vaccination program.
Laboratory Processes for Confirmation of Lymphogranuloma Venereum Infection During a 2015 Investigation of a Cluster of Cases in the United States
Authors: Kersh Ellen N. , Pillay Allan , de Voux Alex , Chen Cheng
Published: June 2017

In September 2015, the Centers for Disease Control and Prevention were notified of a suspected outbreak investigation of lymphogranuloma venereum (LGV) cases by the Michigan Department of Health and Human Services. The Centers for Disease Control and Prevention offered support with a laboratory-developed polymerase chain reaction test for LGV. This note describes the laboratory workflow and procedures used for the laboratory confirmation of LGV infection.
Clinical Profile, Etiology, and Outcome of Infantile Ocular Trauma
Authors: Shah Vedang D. , Uddaraju Madhu , Singh Amitabh , Das Rashmi Ranjan
Published: June 2017

Objective

The aim of this article was to study the clinical profile, etiology, and outcome of infantile ocular trauma in a developing country setting.

Methods

A retrospective study on corneal trauma in infants (≤12 months old) was undertaken in a tertiary care hospital during a 2-year period. An analysis of clinical profile, etiology, microbiological profile, clinical course, and outcome was studied.

Results

Seventy-six infants were included. Approximately 69% presented within 24 hours of injury. The common presentations were inability to open the eyelids, redness of eyes, and watering. Self-infliction by child's hand (49%) was found to be the main cause of corneal trauma. Corneal abrasion was seen in 34 cases (45%), isolated epithelial defects were seen in 30%, and infective keratitis was seen in 25%. Infection was found in 14 cases (fungal filaments in 7 and gram-positive cocci in 7). Only 36 infants followed up regularly in the hospital. All the infants following up in the hospital recovered in due course.

Conclusions

Infantile ocular trauma is a common morbidity that is underreported. Self-infliction by child's hand was found to be the main cause of corneal trauma. Cases presenting early and following up regularly till recovery have a favorable clinical course with good outcome. A high loss to follow-up indicates that awareness needs to be created among the caregivers.
Brief Report: Recovery of Bone Mineral Density After Discontinuation of Tenofovir-Based HIV Pre-exposure Prophylaxis
Authors: Glidden David V. , Mulligan Kathleen , McMahan Vanessa , Anderson Peter L. , Guanira Juan , Chariyalertsak Suwat , Buchbinder Susan P. , Bekker Linda Gail , Schechter Mauro , Grinsztejn Beatriz , Grant Robert M.
Published: June 2017

Background:

Oral tenofovir disoproxil fumarate (TDF) for HIV prevention and treatment is associated with decreases in bone mineral density (BMD). Previous reports suggest that these changes may be reversible after discontinuation of TDF.

Setting:

A metabolic substudy of 498 participants in a randomized, placebo-controlled HIV prevention trial of oral coformulated TDF with emtricitabine (TDF/FTC, Truvada) for HIV pre-exposure prophylaxis (PrEP) enrolling a global sample of men who have sex with men and trans women.

Methods:

Participants underwent dual X-ray absorptiometry to quantify bone mineral density (BMD) in the hip and spine during PrEP and at 2 visits after stopping (median of 23 and 79 weeks post-PrEP, respectively). Results are stratified by pharmacologic measure of TDF/FTC adherence.

Results:

There was no significant difference in change in hip/spine BMD at any time point between placebo and those with low adherence. Adherent participants had a mean (standard error) BMD change at TDF/FTC discontinuation of −1.02% (0.24) in the hip and −1.84% (0.36) in the spine. After stop, annualized BMD increases of 1.13% per year (0.27) in hip and 1.81% per year (0.36) in spine BMD were observed in adherent participants compared with 0.19% (0.16) and 0.74% (0.21) in the placebo group, respectively (P = 0.003, both comparisons). On average, BMD returned to baseline levels by 1 year after PrEP stop. Recovery was consistent across age, baseline BMD z-score, and treatment duration.

Conclusions:

Mean BMD returns to baseline levels within 12–18 months after TDF-based PrEP discontinuation in both hip and spine with consistency across participant subgroups.

Clinical Trials Registration:

clinicaltrials.gov NCT00458393.
Evaluation of a Nutritional Support Intervention in Malnourished HIV-Infected Children in Bamako, Mali
Authors: Jesson Julie , Coulibaly Aba , Sylla Mariam , N'Diaye Clémentine , Dicko Fatoumata , Masson David , Leroy Valériane
Published: June 2017

Background:

We assessed a nutritional support intervention in malnourished HIV-infected children in a HIV-care program of the University Hospital Gabriel Touré, Bamako, Mali.

Methods:

All HIV-infected children younger than 15 years were diagnosed for malnutrition between 07 and 12, 2014. Malnutrition was defined according to the WHO growth standards with Z-scores. Two types were studied: acute malnutrition (AM) and chronic malnutrition (CM). All participants were enrolled in a 6-month prospective interventional cohort, receiving Ready-To-Use Therapeutic Food, according to type of malnutrition. The nutritional intervention was offered until child growth reached −1.5 SD threshold. Six-month probability to catch up growth (>−2 SD) was assessed for AM using Kaplan-Meier curves and Cox model.

Results:

Among the 348 children screened, 198 (57%) were malnourished of whom 158 (80%) children were included: 97 (61%) for AM (35 with associated CM) and 61 (39%) with CM. Fifty-nine percent were boys, 97% were on antiretroviral therapy, median age was 9.5 years (Interquartile Range: 6.7–12.3). Among children with AM, 74% catch-up their growth at 6-month; probability to catch-up growth was greater for those without associated CM (adjusted Hazard Ratio = 1.97, CI 95%: 1.13 to 3.44). Anemia decreased significantly from 40% to 12% at the end of intervention (P < 0.001).

Conclusions:

This macronutrient intervention showed 6-month benefits for weight gain and reduced anemia among these children mainly on antiretroviral therapy for years and aged greater than 5 years at inclusion. Associated CM slows down AM recovery and needs longer support. Integration of nutritional screening and care in the pediatric HIV-care package is needed to optimize growth and prevent metabolic disorders.
Age is the Most Significantly Associated Risk Factor With the Development of Delirium in Patients Hospitalized for More Than Five Days in Surgical Wards
Authors: Kubota Keisuke , Suzuki Akihiro , Ohde Sachiko , Yamada Ui , Hosaka Takashi , Okuno Fumiko , Fujitani Ikumi , Koitabashi Aya , Shimada Gen , Kishida Akihiro
Published: June 2017

Objective:

The primary purpose of this study was to assess risk factors for delirium in patients staying in a surgical ward for more than 5 days. The secondary purpose was to assess outcomes in patients with delirium.

Background:

Delirium is a syndrome characterized by acute fluctuations in mental status. Patients with delirium are at increased risk of adverse inpatient events, higher mortality and morbidity rates, prolonged hospital stays, and increased health care costs.

Methods:

Participants in this study were 2168 patients who had been admitted to the surgical ward of St. Luke's International Hospital for 5 days or more between January 2011 and December 2014. Data on these patients were collected retrospectively from hospital medical records. Firstly, univariate and multivariate analyses were conducted to identify risk factors for delirium. Secondly, morbidity and mortality associated with delirium were analyzed.

Results:

Delirium occurred in 205 of 2168 patients (9.5%). Age, physical restraint, past history of a cerebrovascular disorder, malignancy, intensive care unit stay, pain, and high blood urea nitrogen value were significant risk factors for delirium in the multivariate analysis. Among these, age was the strongest factor, with an odds ratio for delirium of 12.953 in patients 75 years of age or older. The length of hospital stays and the mortality rates were higher in patients with delirium.

Conclusions:

Results showed that age, and also physical restraint, past history of cerebrovascular disorder, malignancy, intensive care unit stay, pain, and high serum blood urea nitrogen were important factors associated with delirium in patients hospitalized for more than 5 days in a surgical ward.
A cohort study of blunt cerebrovascular injury screening in children: Are they just little adults?
Authors: Cook Mackenzie R. , Witt Cordelie E. , Bonow Robert H. , Bulger Eileen M. , Linnau Ken F. , Arbabi Saman , Robinson Bryce R.H. , Cuschieri Joseph
Published: June 2017

BACKGROUND

Blunt cerebrovascular injuries (BCVIs) are rare with nonspecific predictors, making optimal screening critical. Radiation concerns magnify these issues in children. The Eastern Association for the Surgery of Trauma (EAST) criteria, the Utah score (US), and the Denver criteria (DC) have been advocated for pediatric BCVI screening, although direct comparison is lacking. We hypothesized that current screening guidelines inaccurately identify pediatric BCVI.

METHODS

This was a retrospective cohort study of pediatric trauma patients treated from 2005 to 2015 with radiographically confirmed BCVI. Our primary outcome was a false-negative screen, defined as a patient with a BCVI who would not have triggered screening.

RESULTS

We identified 7,440 pediatric trauma admissions, and 96 patients (1.3%) had 128 BCVIs. Median age was 16 years (13, 17 years). A cervical-spine fracture was present in 41%. There were 83 internal carotid injuries, of which 73% were Grade I or II, as well as 45 vertebral injuries, of which 76% were Grade I or II, p = 0.8. More than one vessel was injured in 28% of patients. A cerebrovascular accident (CVA) occurred in 17 patients (18%); eight patients were identified on admission, and nine patients were identified thereafter. The CVA incidence was similar in those with and without aspirin use. The EAST screening missed injuries in 17% of patients, US missed 36%, and DC missed 2%. Significantly fewer injuries would be missed using DC than either EAST or US, p < 0.01.

CONCLUSIONS

Blunt cerebrovascular injury does occur in pediatric patients, and a significant proportion of patients develop a CVA. The DC appear to have the lowest false-negative rate, supporting liberal screening of children for BCVI. Optimal pharmacotherapy for pediatric BCVI remains unclear despite a relative high incidence of CVA.

LEVEL OF EVIDENCE

Diagnostic study, level III.
Are Sex-Related Category-Specific Differences in Semantic Tasks Innate or Influenced by Social Roles? A Viewpoint
Authors: Gainotti Guido
Published: June 2017

In semantic tasks, sex-related categorical differences, in the form of better processing of fruits and vegetables by women and of artifacts (human-made objects) and animals by men, have been reported both in healthy participants and in brain-damaged patients. Researchers’ interpretation of these sex-related categorical asymmetries has, however, been controversial, being connected with the more general (innatist versus experience-dependent) interpretations that had been given of the mechanisms subsuming the categorical organization of the brain. I begin this review with a brief reminder of the debate between supporters of the innatist and the experience-related accounts of categorical brain organization. Then I summarize results that have documented a preference by women for fruits and vegetables and a preference by men for artifacts and animals, and I discuss the innatist and social role-related interpretations that have been given of these results. I conclude that sex-related categorical effects disappear in generations in which the traditional social roles have almost completely disappeared, and these differences are not seen in young individuals raised in societies that emphasize sex equality.
The Use of Lorazepam and Electroconvulsive Therapy in the Treatment of Catatonia
Authors: Unal Ahmet , Altindag Abdurrahman , Demir Bahadir , Aksoy Ihsan
Published: June 2017

Objectives

Lorazepam and electroconvulsive therapy (ECT) are effective treatments for catatonia. However, systematic data on these treatments in catatonia are limited. In the present study, we aimed to investigate the clinical and treatment-related characteristics of patients with catatonia who underwent lorazepam and/or ECT.

Methods

Between January 2012 and December 2016, we received 60 patients with catatonia hospitalized in the Gaziantep University Faculty of Medicine Clinic of Psychiatry. Lorazepam and/or ECT were used in the patients' treatment schedule. Treatment results were evaluated using the Bush-Francis Catatonia Rating Scale and Clinical Global Impression-Improvement.

Results

Thirty-five patients (58.3%) in the sample were in their first catatonic episode. The most common comorbidity was mood disorder (n = 34, 56.7%), whereas the most frequent catatonic sign was mutism (n = 43, 71.7%). Moreover, 31 patients (51.7%) had some form of medical comorbidity. Cerebral abnormalities were detected in computed tomography/magnetic resonance imaging in 22 patients (36.7%). Furthermore, 95% of the patients (n = 57) fully recovered after administration of the treatment.

Conclusions

Lorazepam is a reasonable initial choice in the treatment of catatonia, with rapid consideration for ECT if there is no rapid response to lorazepam.
Molecular mechanism of pore formation by aerolysin-like proteins
Authors: Podobnik Marjetka , Kisovec Matic , Anderluh Gregor
Published: June 2017

Aerolysin-like pore-forming proteins are an important family of proteins able to efficiently damage membranes of target cells by forming transmembrane pores. They are characterized by a unique domain organization and mechanism of action that involves extensive conformational rearrangements. Although structures of soluble forms of many different members of this family are well understood, the structures of pores and their mechanism of assembly have been described only recently. The pores are characterized by well-defined β-barrels, which are devoid of any vestibular regions commonly found in other protein pores. Many members of this family are bacterial toxins; therefore, structural details of their transmembrane pores, as well as the mechanism of pore formation, are an important base for future drug design. Stability of pores and other properties, such as specificity for some cell surface molecules, make this family of proteins a useful set of molecular tools for molecular recognition and sensing in cell biology.

This article is part of the themed issue ‘Membrane pores: from structure and assembly, to medicine and technology’.
Assembly mechanism of the α-pore–forming toxin cytolysin A from
Escherichia coli
Authors: Roderer Daniel , Glockshuber Rudi
Published: June 2017

The cytolytic toxin cytolysin A (ClyA) from
Escherichia coli
is probably one of the best-characterized examples of bacterial, α-pore–forming toxins (α-PFTs). Like other PFTs, ClyA exists in a soluble, monomeric form that assembles to an annular, homo-oligomeric pore complex upon contact with detergent or target membranes. Comparison of the three-dimensional structures of the 34 kDa monomer and the protomer in the context of the dodecameric pore complex revealed that ClyA undergoes one of the largest conformational transitions described for proteins so far, in which 55% of the residues change their position and 16% of the residues adopt a different secondary structure in the protomer. Studies on the assembly of ClyA revealed a unique mechanism that differs from the assembly mechanism of other PFTs. The rate-liming step of pore formation proved to be the unimolecular conversion of the monomer to an assembly-competent protomer, during which a molten globule-like off-pathway intermediate accumulates. The oligomerization of protomers to pore complexes is fast and follows a kinetic scheme in which mixtures of linear oligomers of different size are formed first, followed by very rapid and specific association of pairs of oligomers that can directly perform ring closure to the dodecameric pore complex.

This article is part of the themed issue ‘Membrane pores: from structure and assembly, to medicine and technology’.
Apoptotic foci at mitochondria: in and around Bax pores
Authors: Ugarte-Uribe Begoña , García-Sáez Ana J.
Published: June 2017

The permeabilization of the mitochondrial outer membrane by Bax and Bak during apoptosis is considered a key step and a point of no return in the signalling pathway. It is always closely related to the reorganization of mitochondrial cristae that frees cytochrome
c
to the intermembrane space and to massive mitochondrial fragmentation mediated by the dynamin-like protein Drp1. Despite multiple evidence in favour of a functional link between these processes, the molecular mechanisms that connect them and their relevance for efficient apoptosis signalling remain obscure. In this review, we discuss recent progress on our understanding of how Bax forms pores in the context of Drp1-stabilized signalling platforms at apoptotic foci in mitochondria.

This article is part of the themed issue ‘Membrane pores: from structure and assembly, to medicine and technology’.
The mystery behind membrane insertion: a review of the complement membrane attack complex
Authors: Bayly-Jones Charles , Bubeck Doryen , Dunstone Michelle A.
Published: June 2017

The membrane attack complex (MAC) is an important innate immune effector of the complement terminal pathway that forms cytotoxic pores on the surface of microbes. Despite many years of research, MAC structure and mechanism of action have remained elusive, relying heavily on modelling and inference from biochemical experiments. Recent advances in structural biology, specifically cryo-electron microscopy, have provided new insights into the molecular mechanism of MAC assembly. Its unique ‘split-washer’ shape, coupled with an irregular giant β-barrel architecture, enable an atypical mechanism of hole punching and represent a novel system for which to study pore formation. This review will introduce the complement terminal pathway that leads to formation of the MAC. Moreover, it will discuss how structures of the pore and component proteins underpin a mechanism for MAC function, modulation and inhibition.

This article is part of the themed issue ‘Membrane pores: from structure and assembly, to medicine and technology’.
Measuring the potential energy barrier to lipid bilayer electroporation
Authors: Sengel Jason T. , Wallace Mark I.
Published: June 2017

Electroporation is a common tool for gene transfection, tumour ablation, sterilization and drug delivery. Using experimental methods, we explore the temperature dependence of electropore formation in a model membrane system (droplet-interface bilayers), using optical single-channel recording to image the real-time gating of individual electropores. We investigate the influence of the agarose substrate on electropores formed in this system. Furthermore, by examining the temperature-dependent kinetics of pore opening and closure we are able to estimate a barrier to pore opening in 1,2-diphytanoyl-
sn
-glycero-3-phosphocholine (DPhPC) membranes to be 25.0 ± 8.3
k
B
T
, in agreement with previous predictions. Overall these measurements help support the toroidal model of membrane electroporation.

This article is part of the themed issue ‘Membrane pores: from structure and assembly, to medicine and technology’.
A dead gene walking: convergent degeneration of a clade of MADS-box genes in Brassicaceae
Authors: Hoffmeier Andrea , Gramzow Lydia , Bhide Amey S. , Kottenhagen Nina , Greifenstein Andreas , Schubert Olesia , Mummenhoff Klaus , Becker Annette , Theißen Günter
Published: June 2017

Genes are ‘born’, and eventually they ‘die’. In contrast to gene birth, however, gene death has found only limited scientific interest, even though it is of considerable evolutionary importance. Here we use Bsistergenes, a subfamily of MIKC-type MADS-box genes, as a model to investigate gene death in unprecedented detail. Typical MIKC-type genes encode conserved transcription factors controlling plant development. We show thatABS-like genes, a clade of Bsistergenes, are indeed highly conserved in Brassicaceae maintaining the ancestral function of Bsistergenes in ovule and seed development. In contrast, their closest paralogs, theGOA-like genes, have been undergoing convergent gene death in Brassicaceae. Intriguingly, erosion ofGOA-like genes occurred after millions of years of co-existence withABS-like genes. We thus describe Delayed Convergent Asymmetric Degeneration (DCAD), a so far neglected but possibly frequent pattern of duplicate gene evolution that does not fit classical scenarios. DCAD ofGOA-like genes may have been initiated by a reduction in the expression of an ancestralGOA-like gene in the stem group of Brassicaceae and driven by dosage subfunctionalization. Our findings have profound implications for gene annotations in genomics, interpreting patterns of gene evolution and using genes in phylogeny reconstructions of species.
The anticancer activity and immune modulating properties of combinatorial ensemble complementary (antisense) microRNA (fRNA) in combination with the immunomodulator - glycoproteid lectin fromB. subtilisB-7025
Authors: Martynov Artur , Didenko Gennady , Farber Boris , Farber Sophya , Cruts Olena
Published: June 2017

Background

Many adenocarcinomas have the ability to capture from an extracellular matrix the oligonucleotides and nanoparticles by pinocytosis, when the non-cancerous cells are not capable to capture the oligonucleotides and small liposomes. This provides selective accumulation of proposed protected oligonucleotides (fRNA) in cancer cells and also provides the absence toxicity in the fRNA.

Materials and methods

For the immunotherapy we used immunotropic 70 kDa lectinB. subtilis B-7025.In vivoexperiments were carried out in C57BL line mice in Lewis lung carcinoma. The cytotoxic activity, lymphocytes, macrophages was determinedin vitrousing the MTT assay.

Results and discussion

Animal survival rate in groups receiving either the fRNA or Vaccine was 70 and 40%, respectively. Combined use fRNA and Vaccine has the advantage compared with the use these drugs in monotherapy, as the anticancer efficacy of the scheme is much higher, which is manifested in the primary tumor node and metastasis inhibition.
Cell-to-cell heterogeneity in p38-mediated cross-inhibition of JNK causes stochastic cell death
Authors: Miura Haruko , Kondo Yohei , Matsuda Michiyuki , Aoki Kazuhiro
Published: June 2017

Abstract

The stress activated protein kinases (SAPKs), c-Jun N-terminal kinase (JNK) and p38, are important players in cell fate decisions in response to environmental stress signals. Crosstalk signaling between JNK and p38 is emerging as an important regulatory mechanism in the inflammatory and stress responses. However, it is still unknown how this crosstalk affects signaling dynamics, cell-to-cell variation, and cellular responses at the single-cell level. To address these questions, we established a multiplexed live-cell imaging system based on kinase translocation reporters to simultaneously monitor JNK and p38 activities with high specificity and sensitivity at single-cell resolution. Various stresses, such as anisomycin, osmotic stress, and UV irradiation, and pro-inflammatory cytokines activated JNK and p38 with various dynamics. In all cases, however, p38 suppressed JNK activity in a cross-inhibitory manner. We demonstrate that p38 antagonizes JNK through both transcriptional and post-translational mechanisms. This cross-inhibition of JNK appears to generate cellular heterogeneity in JNK activity after stress exposure. Our data indicate that this heterogeneity in JNK activity plays a role in fractional killing in response to UV stress. Our highly sensitive multiplexed imaging system enables detailed investigation into the p38-JNK interplay in single cells.

One Sentence Summary

Cross-inhibition by p38 generates cell-to-cell variability in JNK activity.
Developmental switching inPhysarum polycephalum: Petri net analysis of single cell trajectories of gene expression indicates responsiveness and genetic plasticity of the Waddington quasipotential landscape
Authors: Werthmann Britta , Marwan Wolfgang
Published: June 2017

The developmental switch to sporulation inPhysarum polycephalumis a phytochrome-mediated far-red light-induced cell fate decision that synchronously encompasses the entire multinucleate plasmodial cell and is associated with extensive reprogramming of the transcriptome. By repeatedly taking samples of single cells after delivery of a light stimulus pulse, we analysed differential gene expression in two mutant strains and in a heterokaryon of the two strains all of which display a different propensity for making the cell fate decision. Multidimensional scaling of the gene expression data revealed individually different single cell trajectories eventually leading to sporulation. Characterization of the trajectories as walks through states of gene expression discretized by hierarchical clustering allowed the reconstruction of Petri nets that model and predict the observed behavior. Structural analyses of the Petri nets indicated stimulus- and genotype-dependence of both, single cell trajectories and of the quasipotential landscape through which these trajectories are taken. The Petri net-based approach to the analysis and decomposition of complex cellular responses and of complex mutant phenotypes may provide a scaffold for the data-driven reconstruction of causal molecular mechanisms that shape the topology of the quasipotential landscape.
APRIL and BAFF increase breast cancer cell stemness
Authors: Pelekanou Vasiliki , Notas George , Athanasouli Paraskevi , Alexakis Konstantinos , Kiagiadaki Fotini , Peroulis Nikolaos , Kalyvianaki Konstantina , Kampouri Errika , Polioudaki Hara , Theodoropoulos Panayiotis , Tsapis Andreas , Castanas Elias , Kampa Marilena
Published: June 2017

Recent advances in cancer immunology revealed immune-related properties of cancer cells as novel promising therapeutic targets. The two TNF superfamily members, APRIL and BAFF even though were primarily studied in lymphocyte maturation, they have also been associated with tumor growth and aggressiveness in a number of solid tumors, including breast cancer. In the present work we studied the effect of APRIL and BAFF on epithelial to mesenchymal transition and migration of breast cancer cells, and their action on the sub-population of cancer stem cells identified by autofluorescence and ALDH activity. Their action on an number of pluripotency genes was examined and breast cancer stem cell ability to form mammospheres was also utilized. The receptor and the signaling pathway involved as well as the role of steroid hormones in their action were also investigated. Our findings show that both APRIL and BAFF increase epithelial to mesenchymal transition and migratory capacity of breast cancer cells, as well as cancer stem cell numbers, by inducing pluripotency genes such as KLF4 and NANOG. These effects are mediated by their common receptor BCMA and the JNK signaling pathway. Interestingly, androgens enhance APRIL transcription and subsequently its pluripotency effect. In conclusion, our data support the significant role of APRIL and BAFF in breast cancer disease progression and provide evidence for a new possible mechanism of therapy resistance, that could be particularly relevant in aromatase inhibitors-treated patients, were local androgen is increased.
Intrinsic adaptive value and early fate of gene duplication revealed by a bottom-up approach
Authors: Rodrigo Guillermo , Fares Mario A.
Published: June 2017

Gene duplication is a major source of functional innovations and genome complexity, albeit this evolutionary process requires the preservation of duplicates in the genomes for long time. However, the population genetic mechanisms governing this preservation, especially in the critical very initial phase, have remained largely unknown. Here, we demonstrate that gene duplication confersper sea weak selective advantage in scenarios of fitness trade-offs. Through a precise quantitative description of a model system, we show that a second gene copy enhances the information transfer from the environmental signal to the phenotypic response by reducing gene expression inaccuracies derived from pervasive molecular noise and suboptimal gene regulation. We then reveal that such a phenotypic accuracy yields a selective advantage in the order of 0.1% on average, which would allow the positive selection of gene duplication in populations with moderate or large sizes. This advantage is greater at higher noise levels and intermediate concentrations of the environmental molecule, when fitness trade-offs become more evident. Moreover, we show that the genome rearrangement rates greatly condition the eventual fixation of duplicated genes, either by natural selection or by random genetic drift. Overall, our theoretical results highlight an original adaptive value for cells carrying new-born duplicates, broadly analyze the selective conditions that determine their early fates in different organisms, and reconcile population genetics with evolution by gene duplication.

SIGNIFICANCE

Gene duplication is considered a major driver for the evolution of biological complexity. However, it is still enigmatic to what extent natural selection and genetic drift have governed this evolutionary process. This work uncovers a selective advantage for genotypes carrying duplicates, called phenotypic accuracy, widely characterized thanks to a multi-scale mathematical model coupling gene regulation with population genetics. Importantly, the integrative results presented here provide a detailed mechanistic description for the fixation of duplicates, which allows making predictions about the genome architectures, and which is relevant to understand the origins of complexity.
YASS: Yet Another Spike Sorter
Authors: Lee JinHyung , Carlson David , Shokri Hooshmand , Yao Weichi , Goetz Georges , Hagen Espen , Batty Eleanor , Chichilnisky EJ , Einevoll Gaute , Paninski Liam
Published: June 2017

Spike sorting is a critical first step in extracting neural signals from large-scale electrophysiological data. This manuscript describes an efficient, reliable pipeline for spike sorting on dense multi-electrode arrays (MEAs), where neural signals appear across many electrodes and spike sorting currently represents a major computational bottleneck. We present several new techniques that make dense MEA spike sorting more robust and scalable. Our pipeline is based on an efficient multi-stage “triage-then-cluster-then-pursuit” approach that initially extracts only clean, high-quality waveforms from the electrophysiological time series by temporarily skipping noisy or “collided” events (representing two neurons firing synchronously). This is accomplished by developing a neural network detection method followed by efficient outlier triaging. The clean waveforms are then used to infer the set of neural spike waveform templates through nonparametric Bayesian clustering. Our clustering approach adapts a “coreset” approach for data reduction and uses efficient inference methods in a Dirichlet process mixture model framework to dramatically improve the scalability and reliability of the entire pipeline. The “triaged” waveforms are then finally recovered with matching-pursuit deconvolution techniques. The proposed methods improve on the state-of-the-art in terms of accuracy and stability on both real and biophysically-realistic simulated MEA data. Furthermore, the proposed pipeline is efficient, learning templates and clustering much faster than real-time for a ≃ 500-electrode dataset, using primarily a single CPU core.
Reflected Stochastic Differential Equation Models for Constrained Animal Movement
Authors: Hanks Ephraim M. , Johnson Devin S. , Hooten Mevin B.
Published: June 2017

Movement for many animal species is constrained in space by barriers such as rivers, shore-lines, or impassable cliffs. We develop an approach for modeling animal movement constrained in space by considering a class of constrained stochastic processes, reflected stochastic differential equations. Our approach generalizes existing methods for modeling unconstrained animal movement. We present methods for simulation and inference based on augmenting the constrained movement path with a latent unconstrained path and illustrate this augmentation with a simulation example and an analysis of telemetry data from a Steller sea lion(Eumatopias jubatus)in southeast Alaska.
Feedback inhibition of Ras activity coordinates cell fusion with cell-cell contact
Authors: Merlini Laura , Khalili Bita , Dudin Omaya , Michon Laetitia , Vincenzetti Vincent , G Martin Sophie
Published: June 2017

In fission yeastSchizosaccharomyces pombe, pheromone signalling engages a GPCR-Ras-MAPK cascade to trigger sexual differentiation leading to gamete fusion. Cell-cell fusion necessitates local cell wall digestion, the location of which relies on an initially dynamic actin fusion focus that becomes stabilized upon local enrichment of the signalling cascade. We constructed a live-reporter of active Ras1 (Ras1-GTP), also functional inS. cerevisiae, which revealed Ras activity at polarity sites peaking on the fusion structure before fusion. Remarkably, constitutive Ras1 activation promoted fusion focus stabilization and fusion attempts irrespective of cell-cell pairing, leading to cell lysis. Ras1 activity is restricted by the GTPase activating protein (GAP) Gap1, itself recruited to sites of Ras1-GTP. While the GAP domain on its own does not suffice for this localization, its recruitment to Ras1-GTP sites is essential to block untimely fusion attempts. We conclude that negative feedback control of Ras activity restrains the MAPK signal and couples fusion with cell-cell engagement.
Inter-organ regulation ofDrosophilaintestinal stem cell proliferation by a hybrid organ boundary zone
Authors: Sawyer Jessica K. , Cohen Erez , Fox Donald T.
Published: June 2017

SUMMARY STATEMENT

Gene expression at theDrosophilamidgut-hindgut boundary is a hybrid of both organs. Hybrid cells repress stem cell division, but boundary injury activates stem cell division through inter-organ JAK-STAT signaling.

The molecular identities and regulation of cells at inter-organ boundaries are often unclear, despite the increasingly appreciated role of organ boundaries in disease. UsingDrosophilaas a model, here we show that a specific population of adult midgut organ boundary intestinal stem cells (OB-ISCs) is regulated by the neighboring hindgut, a developmentally distinct organ. This distinct OB-ISCs control is due to proximity to a specialized transition zone between the endodermal midgut and ectodermal hindgut that shares molecular signatures of both organs, which we term the hybrid zone (HZ). During homeostasis, proximity to the HZ restrains OB-ISC proliferation. However, injury to the adult HZ/hindgut drives up-regulation ofupaired-3cytokine and OB-ISC hyperplasia. If HZ disruption is severe, hyperplastic OB-ISCs expand across the inter-organ boundary. Our data suggest that inter-organ signaling plays an important role in controlling OB-ISCs in homeostasis and injury repair, which is likely critical in prevention of disease.
Silver microwires from treating tooth decay with silver diamine fluoride
Authors: Seto Jong , Horst Jeremy A. , Parkinson Dilworth Y. , Frachella John C. , DeRisi Joseph L.
Published: June 2017

Silver diamine fluoride (SDF) is a brush-on treatment for tooth decay that stops 81% of cavitated caries lesions (dental cavities). Before this innovation, caries was treatable only with operative approaches (dental fillings). SDF-treated lesions harden and become resistant to further decay. We hypothesized that the hardening is due to reaction with silver, rather than classic fluoride-mediated remineralization, because infected dentin is not amenable to remineralization. Using synchrotron microCT with 1.3 μm resolution, we observe filamentous densities up to 500 μm in length and 0.25-7.0 μm in diameter, formedin situby applying SDF to caries lesions. We show that these “microwires” fill voids in the lesion caused by disease, and permeate through surrounding dentinal tubules. Using spectroscopy, we confirm that the chemical composition of the observed microwires is predominantly silver. To our knowledge, this represents the first structural microscale observations resulting from clinical SDF treatment. These novel observations hint at mechanistic explanations for the first clinical method to harden carious dentin besides remineralization. We hypothesize that SDF may not only achieve its antimicrobial functions by biochemical interactions, but also through its inherent ability to integrate into dentin.
t-Darpp is an elongated monomer that binds to calcium and is phosphorylated by cyclin-dependent kinases 1 and 5
Authors: Momand Jamil , Magdziarz Patrycja , Feng You , Jiang Dianlu , Parga Elizabeth , Celis Arianna , Denny Erin , Wang Xiaoying , Phillips Martin L. , Monterroso Estuardo , Kane Susan E. , Zhou Feimeng
Published: June 2017

t-Darpp is a protein encoded by the PPP1R1B gene and is expressed in breast, colon, esophageal, gastric, and prostate cancers, as well as in normal adult brain striatal cells. Overexpression of t-Darpp in cultured cells leads to increased protein kinase A activity and increased phosphorylation of AKT (protein kinase B). In HER2+ breast cancer cells t-Darpp confers resistance to the chemotherapeutic agent trastuzumab. To shed light on t-Darpp function, we studied its secondary structure, oligomerization status, metal-binding properties, and phosphorylation by cyclin dependent kinases 1 and 5. t-Darpp exhibits 12% alpha helix, 29% beta strand, 24% beta turn and 35% random coil structures. t-Darpp binds to calcium, but not to other metals commonly found in biological systems. The T39 site, critical for t-Darpp activation of the AKT signaling pathway, is a substrate for phosphorylation by cyclin-dependent kinase 1 (CDK1) and cyclin-dependent kinase 5 (CDK5). Gel filtration chromatography, sedimentation equilibrium analysis, blue native gel electrophoresis, and glutaraldehyde-mediated crosslinking experiments demonstrate that the majority of t-Darpp exists as a monomer, but forms low levels (< 3%) of hetero-oligomers with its longer isoform Darpp-32. t-Darpp has a large Stokes radius of 4.4 nm relative to its mass of 19 kDa, indicating that it has an elongated structure.
TheDrosophilaFormin Fhod Nucleates Actin Filaments
Authors: Patel Aanand A. , Oztug Durer Zeynep A. , van Loon Aaron P. , Quinlan Margot E.
Published: June 2017

Formins are a conserved group of proteins that nucleate and processively elongate actin filaments. Among them, the formin homology domain-containing protein (FHOD) family of formins contributes to contractility of striated muscle and cell motility in several contexts. However, the mechanisms by which they carry out these functions remain poorly understood. Unlike other formins, mammalian FHOD1 and FHOD3 do not accelerate actin assemblyin vitro, and have instead been suggested to act as barbed end cappers or bundlers. Here, we show that purifiedDrosophilaFhod, in contrast with the mammalian homologues, potently accelerates actin assembly by nucleation. We found that Fhod binds tightly to barbed ends, where it slows elongation in the absence of profilin and allows elongation in the presence of profilin. Fhod protects barbed ends from capping protein, but dissociates from barbed ends relatively quickly. Finally, we used cosedimentation assays to determine that Fhod binds the sides of actin filaments and bundles filaments. This work establishes that Fhod shares the capacity of other formins to nucleate and bundle actin filaments, but is notably less effective at processively elongating barbed ends.
Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome
Authors: Evrony Gilad D. , Cordero Dwight R. , Shen Jun , Partlow Jennifer N. , Yu Timothy W. , Rodin Rachel E. , Hill R. Sean , Coulter Michael E. , Lam Anh-Thu N. , Jayaraman Divya , Gerrelli Dianne , Diaz Diana G. , Santos Chloe , Morrison Victoria , Galli Antonella , Tschulena Ulrich , Wiemann Stefan , Martel M. Jocelyne , Spooner Betty , Ryu Steven C. , Elhosary Princess C. , Richardson Jillian M. , Tierney Danielle , Robinson Christopher A. , Chibbar Rajni , Diudea Dana , Folkerth Rebecca , Wiebe Sheldon , Barkovich A. James , Mochida Ganeshwaran H. , Irvine James , Lemire Edmond G. , Blakley Patricia , Walsh Christopher A.
Published: June 2017

While next-generation sequencing has accelerated the discovery of human disease genes, progress has been largely limited to the “low hanging fruit” of mutations with obvious exonic coding or canonical splice site impact. In contrast, the lack of high-throughput, unbiased approaches for functional assessment of most noncoding variants has bottlenecked gene discovery. We report the integration of transcriptome sequencing (RNA-seq), which surveys all mRNAs to reveal functional impacts of variants at the transcription level, into the gene discovery framework for a unique human disease, microcephaly-micromelia syndrome (MMS). MMS is an autosomal recessive condition described thus far in only a single First Nations population and causes intrauterine growth restriction, severe microcephaly, craniofacial anomalies, skeletal dysplasia, and neonatal lethality. Linkage analysis of affected families, including a very large pedigree, identified a single locus on Chromosome 21 linked to the disease (LOD > 9). Comprehensive genome sequencing did not reveal any pathogenic coding or canonical splicing mutations within the linkage region but identified several nonconserved noncoding variants. RNA-seq analysis detected aberrant splicing in DONSON due to one of these noncoding variants, showing a causative role for DONSON disruption in MMS. We show that DONSON is expressed in progenitor cells of embryonic human brain and other proliferating tissues, is co-expressed with components of the DNA replication machinery, and that Donson is essential for early embryonic development in mice as well, suggesting an essential conserved role for DONSON in the cell cycle. Our results demonstrate the utility of integrating transcriptomics into the study of human genetic disease when DNA sequencing alone is not sufficient to reveal the underlying pathogenic mutation.
Accuracy of stress measurement by Laue microdiffraction (Laue-DIC method): the influence of image noise, calibration errors and spot number
Authors: Zhang F. G. , Bornert M. , Petit J. , Castelnau O.
Published: June 2017

Laue microdiffraction, available at several synchrotron radiation facilities, is well suited for measuring the intragranular stress field in deformed materials thanks to the achievable submicrometer beam size. The traditional method for extracting elastic strain (and hence stress) and lattice orientation from a microdiffraction image relies on fitting each Laue spot with an analytical function to estimate the peak position on the detector screen. The method is thus limited to spots exhibiting ellipsoidal shapes, thereby impeding the study of specimens plastically deformed. To overcome this difficulty, the so-called Laue-DIC method introduces digital image correlation (DIC) for the evaluation of the relative positions of spots, which can thus be of any shape. This paper is dedicated to evaluating the accuracy of this Laue-DIC method. First, a simple image noise model is established and verified on the data acquired at beamline BM32 of the European Synchrotron Radiation Facility. Then, the effect of image noise on errors on spot displacement measured by DIC is evaluated by Monte Carlo simulation. Finally, the combined effect of the image noise, calibration errors and the number of Laue spots used for data treatment is investigated. Results in terms of the uncertainty of stress measurement are provided, and various error regimes are identified.