bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of Partner-Related Social Harms on Women's Adherence to the Dapivirine Vaginal Ring During a Phase III Trial
Authors: Palanee-Phillips Thesla , Roberts Sarah T. , Reddy Krishnaveni , Govender Vaneshree , Naidoo Logashvari , Siva Samantha , Gafoor Zakir , Pather Arendevi , Matovu Flavia , Hlahla Kudzai , Makanani Bonus , Nair Gonasagrie , Schwartz Katie , Torjesen Kristine , Brown Elizabeth , Soto-Torres Lydia , Baeten Jared , Montgomery Elizabeth T. ,   on behalf of the MTN-020/ASPIRE Team
Published: September 2018

Background:

Long-acting female-initiated methods such as the dapivirine ring may give women greater agency in HIV-1 prevention. However, social harms, defined as nonmedical adverse consequences of study participation or dapivirine ring use, may reduce product adherence and consequently HIV-1 protection.

Methods:

We assessed whether experiencing social harms from male partners was associated with lower adherence to the dapivirine ring in the MTN-020/ASPIRE trial. Reports of social harms were solicited quarterly. Low adherence was defined by plasma dapivirine levels ≤95 pg/mL or residual dapivirine levels in returned rings >23.5 mg.

Results:

Among 2629 women enrolled in ASPIRE, 85 (3.2%) reported 87 social harms during a median follow-up of 1.6 years. Women were significantly more likely to have low adherence, measured by plasma dapivirine levels, at visits with a social harm in the past month than at visits where no social harm was reported (adjusted risk ratio 2.53, 95% confidence interval: 1.37 to 4.66, P = 0.003). There was no association for social harms reported ≥1 month prior, suggesting an acute, short-term effect. Women were significantly more likely to not return a ring at visits with a social harm reported (adjusted risk ratio 24.70, 95% confidence interval: 18.57 to 32.85, P < 0.001). In rings that were returned, social harms were not associated with residual dapivirine levels.

Conclusions:

Although social harms were uncommon (<5% of women with >1 year of use), participants reporting social harms by male partners had lower adherence to the dapivirine ring. Strategies to mitigate nonadherence to product use related to social harms should be evaluated in future studies of female-controlled HIV-1 prevention options.
Brief Report: PrEPTECH: A Telehealth-Based Initiation Program for HIV Pre-exposure Prophylaxis in Young Men of Color Who Have Sex With Men. A Pilot Study of Feasibility
Authors: Refugio Oliver N. , Kimble Mabel M. , Silva Cara L. , Lykens James E. , Bannister Christian , Klausner Jeffrey D.
Published: September 2018

Background:

In the United States, young men who have sex with men (YMSM) of color represent a high number of new HIV diagnoses annually. HIV pre-exposure prophylaxis (PrEP) is effective and acceptable to YMSM of color; yet, PrEP uptake is low in those communities because of barriers including stigma, cost, adherence concerns, and medical distrust. A telehealth-based approach to PrEP initiation may be a solution to those barriers. This pilot study investigates one such intervention called PrEPTECH.

Methods:

We enrolled 25 HIV-uninfected YMSM, aged 18–25 years, from the San Francisco Bay Area into a 180-day longitudinal study between November 2016 and May 2017. Participants received cost-free PrEP services through telehealth [eg, telemedicine visits, home delivery of Truvada, and sexually transmitted infection testing kits], except for 2 laboratory visits. Online survey assessments querying PrEPTECH features and experiences were administered to participants at 90 and 180 days.

Results:

Eighty-four percent of participants were YMSM of color. Among the 21 who completed the study, 11 of the 16 who wanted to continue PrEP were transitioned to sustainable PrEP providers. At least 75% felt that PrEPTECH was confidential, fast, convenient, and easy to use. Less than 15% personally experienced PrEP stigma during the study. The median time to PrEP initiation was 46 days. Sexually transmitted infection positivity was 20% and 19% at baseline and 90 days, respectively. No HIV infections were detected.

Conclusions:

Telehealth programs such as PrEPTECH increase PrEP access for YMSM of color by eliminating barriers inherent in traditional clinic-based models.
Where Have All the Patients Gone? Profile of US Adults Who Report Doctor-Diagnosed Arthritis But Are Not Being Treated
Authors: Theis Kristina A. , Brady Teresa J. , Sacks Jeffrey J.
Published: September 2018

Background

Patients only benefit from clinical management of arthritis if they are under the care of a physician or other health professional.

Objectives

We profiled adults who reported doctor-diagnosed arthritis who are not currently being treated for it to understand better who they are.

Methods

Individuals with no current treatment (NCT) were identified by “no” to “Are you currently being treated by a doctor or other health professional for arthritis or joint symptoms?” Demographics, current symptoms, physical functioning, arthritis limitations and interference in life activities, and level of agreement with treatment and attitude statements were assessed in this cross-sectional, descriptive study of noninstitutionalized US adults aged 45 years or older with self-reported, doctor-diagnosed arthritis (n = 1793).

Results

More than half of the study population, 52%, reported NCT (n = 920). Of those with NCT, 27% reported fair/poor health, 40% reported being limited by their arthritis, 51% had daily arthritis pain, 59% reported 2 or more symptomatic joints, and 19% reported the lowest third of physical functioning. Despite NCT, 83% with NCT agreed or strongly agreed with the importance of seeing a doctor for diagnosis and treatment.

Conclusions

Greater than half of those aged 45 years or older with arthritis were not currently being treated for it, substantial proportions of whom experienced severe symptoms and poor physical function and may benefit from clinical management and guidance, complemented by community-delivered public health interventions (self-management education, physical activity). Further research to understand the reasons for NCT may identify promising intervention points to address missed treatment opportunities and improve quality of life and functioning.
A Comparison of the Prevalence of Anxiety and Depression Between Uncomplicated and Complex IBD Patient Groups
Authors: Yongwen Ng Jeremy , Chauhan Usha , Armstrong David , Marshall John , Tse Frances , Moayyedi Paul , Reinisch Walter , Halder Smita
Published: September 2018

Our study aimed to assess the physical and mental health aspects and quality of life of patients with inflammatory bowel disease (IBD). We were interested in determining whether IBD patients with complex disease states had higher rates of anxiety and depression than those without complications. Complex and uncomplicated IBD patients were assessed using a demographic questionnaire, Short Form-12 (SF-12), and the Hospital Anxiety and Depression Scale (HADS). Complex IBD patients are defined as those specifically having active inflammation, nutritional, and/or surgical issues. All other IBD patients are defined as those with uncomplicated IBD. Analysis of SF-12 scores indicated that Physical Component Summary scores were below average in 71.9% and 56.0% of the complex and uncomplicated patients, respectively (p < .001), whereas Mental Component Summary scores were below average in 65.6% and 45.3% of the complex and uncomplicated patients, respectively (p < .001). HADS scores in the complex and uncomplicated IBD patients indicated that 29.2% and 18.5%, respectively, were anxiety cases (p < .1) and that 32.3% and 15.9%, respectively, were depression cases (p < .001). Efforts should be focused on the identification and management of anxiety and depression in complex IBD patients, as they may have higher likelihoods of anxiety and depression and lower quality of life.
PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level
Authors: Royer G. , Decousser J. W. , Branger C. , Dubois M. , Médigue C. , Denamur E. , Vallenet D.
Published: September 2018

Plasmid prediction may be of great interest when studying bacteria of medical importance such as Enterobacteriaceae as well as Staphylococcus aureus or Enterococcus. Indeed, many resistance and virulence genes are located on such replicons with major impact in terms of pathogenicity and spreading capacities. Beyond strain outbreak, plasmid outbreaks have been reported in particular for some extended-spectrum beta-lactamase- or carbapenemase-producing Enterobacteriaceae. Several tools are now available to explore the ‘plasmidome’ from whole-genome sequences with various approaches, but none of them are able to combine high sensitivity and specificity. With this in mind, we developed PlaScope, a targeted approach to recover plasmidic sequences in genome assemblies at the species or genus level. Based on Centrifuge, a metagenomic classifier, and a custom database containing complete sequences of chromosomes and plasmids from various curated databases, PlaScope classifies contigs from an assembly according to their predicted location. Compared to other plasmid classifiers, PlasFlow and cBar, it achieves better recall (0.87), specificity (0.99), precision (0.96) and accuracy (0.98) on a dataset of 70 genomes of Escherichia coli containing plasmids. In a second part, we identified 20 of the 21 chromosomal integrations of the extended-spectrum beta-lactamase coding gene in a clinical dataset of E. coli strains. In addition, we predicted virulence gene and operon locations in agreement with the literature. We also built a database for Klebsiella and correctly assigned the location for the majority of resistance genes from a collection of 12 Klebsiella pneumoniae strains. Similar approaches could also be developed for other well-characterized bacteria.
Oral Health-Related Quality of Life in Children and Adolescents with Osteogenesis Imperfecta: cross-sectional study
Authors: Najirad Mohammadamin , Ma Mang Shin , Rauch Frank , Sutton Vernon Reid , Lee Brendan , Retrouvey Jean-Marc ,   Members of the BBD, Esfandiari Shahrokh
Published: September 2018

Background

Osteogenesis imperfecta (OI) affects dental and craniofacial development and may therefore impair Oral Health-Related Quality of Life (OHRQoL). However, little is known about OHRQoL in children and adolescents with OI. The aim of this study was to explore the influence of OI severity on oral health-related quality of life in children and adolescents.

Methods

Children and adolescents aged 8-14 years were recruited in the context of a multicenter longitudinal study (Brittle Bone Disease Consortium) that enrolls individuals with OI in 10 centers across North America. OHRQoL was assessed using the Child Perceptions Questionnaire (CPQ) versions for 8 to 10-year-olds (CPQ8-10) and for 11 to 14-year-olds (CPQ11-14).

Results

A total of 138 children and adolescents (62% girls) diagnosed with OI types I, III, IV, V and VI (n=65, 30, 37, 4 and 2, respectively) participated in the study. CPQ8-10scores were similar between OI types in children aged 8 to 10 years. In the 11 to 14-year-old group, CPQ11-14-scores were significantly higher (i.e. worse) for OI types III (24.7 [SD 12.5]) and IV (23.1 [SD 14.8]) than for OI type I (16.5 [SD 12.8]) (P<0.05). The difference between OI types was due to the association between OI types and the functional limitations domain, as OI types III and IV were associated with significantly higher grade of functional limitations compared to OI type I.

Conclusion

The severity of OI impacts OHRQoL in adolescents aged 11 to 14 years, but not in children age 8 to 10 years.
Rifampicin and rifabutin resistance in 1000 Mycobacterium tuberculosis clinical isolates
Authors: Farhat Maha R , Sixsmith Jaimie , Calderon Roger , Hicks Nathan , Fortune Sarah , Murray Megan
Published: September 2018

Synopsis

Drug resistant tuberculosis (TB) remains a public health challenge with limited treatment options and high associated mortality. Rifamycins are among the most potent anti-TB drugs, and the loss of susceptibility to these agents, a hallmark of MDR TB, is considered a substantial therapeutic challenge. Rifamycins are known to target the RpoB subunit of RNA polymerase; however, our understanding of how rifamycin resistance is genetically encoded remains incomplete. Here we investigated rpoB genetic diversity and cross resistance between the two rifamycin drugs rifampicin (RIF) and rifabutin (RFB). We performed whole genome sequencing of 1005 MTB clinical isolates and measured minimum inhibitory concentration (MIC) to both agents on 7H10 agar using the indirect proportion method. Of the 1005 isolates, 767 were RIF resistant, and of these, 211 (27%) were sensitive to RFB at the critical concentration of 0.5ug/ml; 101/211 isolates had the rpoB mutation D435V (E.coli D516V). Isolates with discrepant resistance (RIF R and RFB S) 16.9 times more likely to harbor a D435V mutation as those resistant to both agents (OR 95% CI 10.5-27.9, P-value <10-40). To further understand this discrepancy, we generated both D435V and S450L (E.coli S531L) rpoB mutants in a laboratory strain and measured their antibiotic susceptibility using the alamar blue reduction assay. Compared with wildtype, D435V increased the 50% inhibitory concentration (IC50) to both RIF and RFB, however in both cases to a lesser degree than the S450L mutation. The observation that the rpoB D435V mutation produces an increase in the IC50 for both drugs contrasts with findings from previous smaller studies that suggested that isolates with D435V mutation remain RFB susceptible despite being RIF resistant. Our finding thus suggests that the recommended critical testing concentration for RFB should be revised.
Molecular changes during extended neoadjuvant letrozole treatment of breast cancer: distinguishing acquired resistance from dormant tumours
Authors: Selli Cigdem , Turnbull Arran K. , Pearce Dominic A. , Li Ang , Fernando Anu , Wills Jimi , Renshaw Lorna , Thomas Jeremy S. , Dixon J. Michael , Sims Andrew H.
Published: September 2018

Background

The risk of recurrence for endocrine-treated breast cancer patients persists for many years or even decades following surgery and apparently successful adjuvant therapy. This period of dormancy and acquired resistance is inherently difficult to investigate, previous efforts have been limited toin vitroorin vivoapproaches. In this study, sequential tumour samples from patients receiving extended neoadjuvant endocrine treatment were characterised as a novel clinical model.

Methods

Consecutive tumour samples from 62 patients undergoing extended (4-45 months) neoadjuvant aromatase inhibitor, letrozole, therapy were subjected to transcriptomic and proteomic analysis, representing before (≤0), early-on (13-120 days) and long-term (>120 days) neoadjuvant letrozole treatment. Patients with at least a 40% initial reduction in tumour size by 4 months of treatment were included. Of these, 42 patients with no subsequent progression were classified as “dormant”, and the remaining 20 patients as “acquired resistant”.

Results

Changes in gene expression in dormant tumours begin early and become more pronounced at later timepoints. Therapy-induced changes in resistant tumours were common features of treatment, rather than being specific to resistant phenotype. Comparative analysis of long-term treated dormant and resistant tumours highlighted changes in epigenetics pathways including DNA methylation and histone acetylation. DNA methylation marks 5-methylcytosine and 5-hydroxymethylcytosine were significantly reduced in resistant tumours compared to dormant tissues after extended letrozole treatment.

Conclusions

This is the first patient-matched gene expression study investigating long-term aromatase inhibitor-induced dormancy and acquired resistance in breast cancer. Dormant tumours continue to change during treatment whereas acquired resistant tumours more closely resemble their diagnostic samples. Global loss of DNA methylation was observed in resistant tumours under extended treatment. Epigenetic alterations may lead to escape from dormancy and drive acquired resistance in a subset of patients supporting a potential role for therapy targeted at these epigenetic alterations in the management of endocrine resistant breast cancer.
Cohort Profile: East London Genes & Health (ELGH), a community based population genomics and health study of British-Bangladeshi and British-Pakistani people
Authors: Finer Sarah , Martin Hilary C. , Khan Ahsan , Hunt Karen A , MacLaughlin Beverley , Ahmed Zaheer , Ashcroft Richard , Durham Ceri , MacArthur Daniel G , McCarthy Mark I , Robson John , Trivedi Bhavi , Griffiths Chris , Wright John , Trembath Richard C , van Heel David A
Published: September 2018

Cohort profile in a nutshell

East London Genes & Health (ELGH) is a large scale, community genomics and health study (to date >34,000 volunteers; target 100,000 volunteers).

ELGH was set up in 2015 to gain deeper understanding of health and disease, and underlying genetic influences, in British-Bangladeshi and British-Pakistani people living in east London.

ELGH prioritises studies in areas important to, and identified by, the community it represents. Current priorities include cardiometabolic diseases and mental illness, these being of notably high prevalence and severity. However studies in any scientific area are possible, subject to community advisory group and ethical approval.

ELGH combines health data science (using linked UK National Health Service (NHS) electronic health record data) with exome sequencing and SNP array genotyping to elucidate the genetic influence on health and disease, including the contribution from high rates of parental relatedness on rare genetic variation and homozygosity (autozygosity), in two understudied ethnic groups. Linkage to longitudinal health record data enables both retrospective and prospective analyses.

Through Stage 2 studies, ELGH offers researchers the opportunity to undertake recall-by-genotype and/or recall-by-phenotype studies on volunteers. Sub-cohort, trial-within-cohort, and other study designs are possible.

ELGH is a fully collaborative, open access resource, open to academic and life sciences industry scientific research partners.
The statistics of noisy growth with mechanical feedback in elastic tissues
Authors: Damavandi Ojan Khatib , Lubensky David K.
Published: September 2018

Tissue growth is a fundamental aspect of development and is intrinsically noisy. Stochasticity has important implications for morphogenesis, precise control of organ size, and regulation of tissue composition and heterogeneity. Yet, the basic statistical properties of growing tissues, particularly when growth induces mechanical stresses that can in turn affect growth rates, have received little attention. Here, we study the noisy growth of elastic sheets subject to mechanical feedback. Considering both isotropic and anisotropic growth, we find that the density-density correlation function shows power law scaling. We also consider the dynamics of marked, neutral clones of cells. We find that the areas (but not the shapes) of two clones are always statistically independent, even when they are adjacent. For anisotropic growth, we show that clone size variance scales like the average area squared and that the mode amplitudes characterizing clone shape show a slow 1/n decay, where n is the mode index. This is in stark contrast to the isotropic case, where relative variations in clone size and shape vanish at long times. The high variability in clone statistics observed in anisotropic growth is due to the presence of two soft modes—growth modes that generate no stress. Our results lay the groundwork for more in-depth explorations of the properties of noisy tissue growth in specific biological contexts.
The folded X-pattern is not necessarily a statistical signature of decision confidence
Authors: Rausch Manuel , Zehetleitner Michael
Published: September 2018

Recent studies have traced the neural correlates of confidence in perceptual choices using statistical signatures of confidence. The most widely used statistical signature is the folded X-pattern, which was derived from a standard model of confidence assuming an objective definition of confidence as the posterior probability of making the correct choice given the evidence. The folded X-pattern entails that confidence as the subjective probability of being correct equals the probability 0.75 if the stimulus in neutral about the choice options, increases with discriminability of the stimulus in correct trials, and decreases with discriminability in incorrect trials. Here, we show that the standard model of confidence is a special case in which there is no reliable trial-by-trial evidence about discriminability itself. According to a more general model, if there is enough evidence about discriminability, objective confidence is characterised by different pattern: For both correct and incorrect choices, confidence increases with discriminability. In addition, we demonstrate the consequence if discriminability is varied in discrete steps within the standard model: confidence in choices about neutral stimuli is no longer .75. Overall, identifying neural correlates of confidence by presupposing the folded X-pattern as a statistical signature of confidence is not legitimate.
RTHybrid: a standardized and open-source real-time software model library for experimental neuroscience
Authors: Amaducci Rodrigo , Reyes-Sanchez Manuel , Elices Irene , Rodriguez Francisco B. , Varona Pablo
Published: September 2018

Closed-loop technologies provide novel ways of online observation, control and bidirectional interaction with the nervous system, which help to study complex non-linear and partially observable neural dynamics. These protocols are often difficult to implement due to the temporal precision required when interacting with biological components, which in many cases can only be achieved using real-time technology. In this paper we introduce RTHybrid (www.github.com/GNB-UAM/RTHybrid), a free and open-source software that includes a neuron and synapse model library to build hybrid circuits with living neurons in a wide variety of experimental contexts. In an effort to encourage the standardization of real-time software technology in neuroscience research, we compared different open-source real-time operating system patches, RTAI, Xenomai 3 and Preempt-RT, according to their performance and usability. RTHybrid has been developed to run over Linux operating systems supporting both Xenomai 3 and Preempt-RT real-time patches, and thus allowing an easy implementation in any laboratory. We report a set of validation tests and latency benchmarks for the construction of hybrid circuits using this library. With this work we want to promote the dissemination of standardized, user-friendly and open-source software tools developed for open- and closed-loop experimental neuroscience.
The bacterial chromatin protein HupA can remodel DNA and associates with the nucleoid in Clostridium difficile
Authors: Oliveira Paiva Ana M. , Friggen Annemieke H. , Qin Liang , Douwes Roxanne , Dame Remus T. , Smits Wiep Klaas
Published: September 2018

The maintenance and organization of the chromosome plays an important role in the development and survival of bacteria. Bacterial chromatin proteins are architectural proteins that bind DNA, modulate its conformation and by doing so affect a variety of cellular processes. No bacterial chromatin proteins of C. difficile have been characterized to date.

Here, we investigate aspects of the C. difficile HupA protein, a homologue of the histone-like HU proteins of Escherichia coli. HupA is a 10 kDa protein that is present as a homodimer in vitro and self-interacts in vivo. HupA co-localizes with the nucleoid of C. difficile. It binds to the DNA without a preference for the DNA G+C content. Upon DNA binding, HupA induces a conformational change in the substrate DNA in vitro and leads to compaction of the chromosome in vivo.

The present study is the first to characterize a bacterial chromatin protein in C. difficile and opens the way to study the role of chromosomal organization in DNA metabolism and on other cellular processes in this organism.
Multicenter validation of a machine learning algorithm for 48 hour all-cause mortality prediction
Authors: Mohamadlou Hamid , Panchavati Saarang , Calvert Jacob , Lynn-Palevsky Anna , Barton Christopher , Fletcher Grant , Shieh Lisa , Stark Philip B , Chettipally Uli , Shimabukuro David , Feldman Mitchell , Das Ritankar
Published: September 2018

Purpose

This study evaluates a machine-learning-based mortality prediction tool.

Materials and Methods

We conducted a retrospective study with data drawn from three academic health centers. Inpatients of at least 18 years of age and with at least one observation of each vital sign were included. Predictions were made at 12, 24, and 48 hours before death. Models fit to training data from each institution were evaluated on hold-out test data from the same institution and data from the remaining institutions. Predictions were compared to those of qSOFA and MEWS using area under the receiver operating characteristic curve (AUROC).

Results

For training and testing on data from a single institution, machine learning predictions averaged AUROCs of 0.97, 0.96, and 0.95 across institutional test sets for 12-, 24-, and 48-hour predictions, respectively. When trained and tested on data from different hospitals, the algorithm achieved AUROC up to 0.95, 0.93, and 0.91, for 12-, 24-, and 48-hour predictions, respectively. MEWS and qSOFA had average 48-hour AUROCs of 0.86 and 0.82, respectively.

Conclusion

This algorithm may help identify patients in need of increased levels of clinical care.
Dual mechanism of TRKB activation by anandamide through CB1 and TRPV1 receptors
Authors: Craf Diniz , Biojone C , Joca SRL , Rantamäki T , Castrén E , Guimarães FS , Casarotto PC
Published: September 2018

Background

administration of anandamide (AEA) or 2-arachidonoylglycerol (2AG) induces CB1 coupling and activation of TRKB receptors, regulating the neuronal migration and maturation in the developing cortex. However, at higher concentrations AEA also engages vanilloid receptor - TRPV1, usually with opposed consequences on behavior.

Methods and Results

Using primary cell cultures from the cortex of rat embryos (E18) we determined the effects of AEA on phosphorylated TRKB (pTRK). We observed that AEA (at 100 and 200nM) induced a significant increase in pTRK levels. Such effect of AEA at 100nM was blocked by pretreatment with the CB1 antagonist AM251 (200nM) and, at the higher concentration of 200nM by the TRPV1 antagonist capsazepine (200nM), but mildly attenuated by AM251. Interestingly, the effect of AEA or capsaicin (a TRPV1 agonist, also at 200nM) on pTRK was blocked by TRKB.Fc (a soluble form of TRKB able to bind BDNF) or capsazepine, suggesting a mechanism dependent on BDNF release. Using the marble-burying test (MBT) in mice, we observed that the local administration of ACEA (a CB1 agonist) into the prelimbic region of prefrontal cortex (PL-PFC) was sufficient to reduce the burying behavior, while capsaicin or BDNF exerted the opposite effect, increasing the number of buried marbles. In addition, both ACEA and capsaicin effects were blocked by previous administration of k252a (an antagonist of TRK receptors) into PL-PFC. The effect of systemically injected CB1 agonist WIN55,212-2 was blocked by previous administration of k252a. We also observed a partial colocalization of CB1 /TRPV1 /TRKB in the PL-PFC, and the localization of TRPV1 in CaMK2+ cells.

Conclusion

taken together, our data indicate that anandamide engages a coordinated activation of TRKB, via CB1 and TRPV1. Thus, acting upon CB1 and TRPV1, AEA could regulate the TRKB-dependent plasticity in both pre- and postsynaptic compartments.
A well-controlled BioID design for endogenous bait proteins
Authors: Vandemoortele Giel , De Sutter Delphine , Moliere Aline , Pauwels Jarne , Gevaert Kris , Eyckerman Sven
Published: September 2018

The CRISPR/Cas9 revolution is profoundly changing the way life sciences technologies are used. Many assays now rely on engineered clonal cell lines to eliminate overexpression of bait proteins. Control cell lines are typically non-engineered cells or engineered clones implying a considerable risk for artefacts because of clonal variation. Genome engineering can also transform BioID, a proximity labelling method that relies on fusing a bait protein to a promiscuous biotin ligase, BirA*, resulting in the tagging of vicinal proteins. We here propose an innovative design to enable BioID for endogenous proteins wherein we introduce a T2A-BirA* module at the C-terminus of endogenous p53 by genome engineering, leading to bi-cistronic expression of both p53 and BirA* under control of the endogenous promoter. By targeting a Cas9-cytidine deaminase base editor to the T2A auto-cleavage site, we can efficiently derive an isogenic population expressing a functional p53-BirA* fusion protein. Using quantitative proteomics we show significant benefits over classical ectopic expression of p53-BirA*, and we provide a first well-controlled view on the proximal proteins of endogenous p53 in colon carcinoma cells. This novel application for base editors expands the CRISPR/Cas9 toolbox and can be a valuable addition for synthetic biology.
Adaptive genomic variation associated with environmental gradients along a latitudinal cline inRana temporaria
Authors: van Rensburg Alexandra Jansen , Cortazar-Chinarro Maria , Laurila Annsi , Van Buskirk Josh
Published: September 2018

Rana temporariaoccur across a large geographic and environmental gradient in Scandinavia. Several studies involving common garden experiments have established adaptive divergence across the gradient. The main objective of this study was to determine the extent of neutral and adaptive genetic divergence across the latitudinal gradient. Here we sequence genome-wide markers for 15 populations from six regions sampled from southern Sweden to Finland. Using a multivariate approach we find that 68% of the genomic variation is associated with climate or geographically structured climate. Using outlier scans and environmental association analyses we identify a set of potentially adaptive loci and examine their change in allele frequency associated with different climatic variables. Using a gradient forest analysis we identify points along three of the climate variables where allele frequencies change more rapidly than expected if it were a linear association. We identify a large threshold effect associated with BIO5 (mean temperature during the warmest month) which is seen as a rapid change in southern Sweden. By comparing the change in neutral and adaptive allele frequencies across the whole gradient, we identify southern Sweden as a region with the largest divergence between the datasets. This suggests small changes in the climate may result in a mismatch between the adaptive genotypes and the environment in these populations. Overall this study shows that genomic analyses can provide a powerful complement to common garden experiments to improve our understanding of adaptive divergence across heterogeneous landscapes.
Macrophages protect against loss of adipose tissue during cancer cachexia
Authors: Erdem Merve , Möckel Diana , Jumpertz Sandra , John Cathleen , Fragoulis Athanassios , Rudolph Ines , Wulfmeier Johanna , Springer Jochen , Horn Henrike , Koch Marco , Lurje Georg , Lammers Twan , der Kroft Gregory van , Gremse Felix , Cramer Thorsten
Published: September 2018

Cancer cachexia represents a central obstacle in medical oncology as it is associated with poor therapy response and reduced overall survival. Systemic inflammation is considered to be a key driver of cancer cachexia, however, clinical studies with anti-inflammatory drugs failed to show a robust cachexia-inhibiting effect. To address this contradiction, we investigated the functional importance of innate immune cells for hepatocellular carcinoma (HCC)-associated cachexia. To this end, we used a transgenic HCC mouse model intercrossed with mice harboring a defect in myeloid cell-mediated inflammation. We identified robust cachexia in the HCC mouse model as evidenced by a marked loss of visceral fat and lean mass. Computed tomography-based analyses demonstrated that a subgroup of human HCC patients displays reduced visceral fat mass, complementing the murine data. While the myeloid cell-mediated inflammation defect resulted in reduced expression of pro-inflammatory cytokines in the serum of HCC-bearing mice, this unexpectedly did not translate into diminished, but rather enhanced cachexia-associated fat loss. Defective myeloid cell-mediated inflammation was associated with decreased macrophage abundance in visceral adipose tissue, suggesting a role for local macrophages in the regulation of cancer-induced fat loss. Taken together, myeloid cell-mediated inflammation displays a rather unexpected beneficial function in a murine HCC model. These results demonstrate that immune cells are capable of protecting the host against cancer-induced tissue wasting, adding a further layer of complexity to the pathogenesis of cachexia and providing a potential explanation for the contradictory results of clinical studies with anti-inflammatory drugs.
The nuclear RNAi factor, NRDE2, prevents the accumulation of DNA damage during mitosis in stressful growth conditions
Authors: Asundi Aarati , Venkataramanan Srivats , Cuellar Gina Caldas , Suzuki Atsushi , Floor Stephen N. , Goga Andrei , L’Etoile Noelle
Published: September 2018

Organisms have evolved multiple mechanisms to prevent and repair DNA damage to protect the integrity of the genome, particularly under stressful conditions. Unrepaired DNA damage leads to genomic instability, aneuploidy, and an increased risk for cancer. Before the cell can divide, it must repair damaged DNA and it is thought that this process requires global silencing of most transcription. In C. elegans, NRDE-2, in complex with other nuclear factors and guided by small RNA, directs heterochromatin formation and transcriptional silencing of targeted genes. Additionally, when C. elegans are cultivated at high temperatures, NRDE-2 is required to maintain germ line immortality. However, the role of NRDE-2 in maintaining the physical integrity of the genome is not understood. We show here that loss of NRDE2 in either nematode or human cells induces the accumulation of DNA damage specifically under conditions of stress, such as cultivation at a high temperature in C. elegans or Aurora B Kinase oncogenic overexpression in the MCF10A epithelial breast cell line. In addition, we found that NRDE2 interacts with β-actin in unstressed mammalian cells. This interaction is dramatically reduced upon DNA damage. Monomeric nuclear actin binds to heterochromatin remodeling factors and transcriptional activators while filamentous actin has been implicated in DNA repair processes. Thus, NRDE2 may dissociate from actin when it becomes filamentous as a result of DNA damage. In this way, heterochromatin factors may associate with the actin dependent DNA repair process to allow appropriate mitotic progression and maintain genomic integrity.
Biomarker de-Mendelization: principles, potentials and limitations of a strategy to improve biomarker prediction by reducing the component of variance explained by genotype
Authors: Kjaergaard Alisa D , Bojesen Stig E , Nordestgaard Børge G , Johansen Julia S , Smith George Davey
Published: September 2018

In observational studies, the Mendelian randomization approach can be used to circumvent confounding, bias and reverse causation, and to assess a potential causal association between a biomarker and risk of disease. If, on the other hand, a substantial component of variance of a non-causal biomarker is explained by genotype, then genotype could potentially attenuate the observational association and the strength of the prediction. In order to reduce the component of variance explained by genotype, an approach that can be seen as the inverse of Mendelian randomization - biomarker de-Mendelization - appears plausible.Plasma YKL-40 is a good candidate for demonstrating principles of biomarker de-Mendelization because it is a non-causal biomarker with a substantial component of variance explained by genotype. This approach is an attempt to improve the observational association and the strength of a predictive biomarker; it is explicitly not aimed at detection of causal effects.

We studied 21 161 individuals form the Danish general population with measurements of YKL-40 concentration and rs4950928 genotype. Four different methods for biomarker de-Mendelization are explored for alcoholic liver cirrhosis and lung cancer.

De-Mendelization methods only improved predictive ability slighly. We observed an interaction between genotype and markers of developing disease with respect to YKL-40 concentration.

Even when genotype explains 14% of the variance in a non-causal biomarker, we found no useful empirical improvement in risk prediction by biomarker de-Mendelization. This could reflect the predictive interaction between genotype and disease development being removed which counterbalanced any beneficial properties of the method in this situation.
Whole genome bisulfite sequencing of Down syndrome brain reveals regional DNA hypermethylation and novel disorder insights
Authors: Laufer Benjamin I. , Hwang Hyeyeon , Vogel Ciernia Annie , Mordaunt Charles E. , LaSalle Janine M.
Published: September 2018

Down Syndrome (DS) is the most common genetic cause of intellectual disability, in which an extra copy of human chromosome 21 (HSA21) affects regional DNA methylation profiles across the genome. Although DNA methylation has been previously examined at select regulatory regions across the genome in a variety of DS tissues and cells, differentially methylated regions (DMRs) have yet to be examined in an unbiased sequencing-based approach. Here, we present the first analysis of DMRs from whole genome bisulfite sequencing (WGBS) data of human DS and matched control brain, specifically frontal cortex. While no global differences in DNA methylation were observed, we identified 3,152 DS-DMRs across the entire genome, the majority of which were hypermethylated in DS. DS-DMRs were significantly enriched at CpG islands and de-enriched at specific gene body and regulatory regions. Functionally, the hypermethylated DS-DMRs were enriched for one-carbon metabolism, membrane transport, and glutamatergic synaptic signaling, while the hypomethylated DMRs were enriched for proline isomerization, glial immune response, and apoptosis. Furthermore, in a cross-tissue comparison to previous studies of DNA methylation from diverse DS tissues and reference epigenomes, hypermethylated DS-DMRs showed a strong cross-tissue concordance, while a more tissue-specific pattern was observed for the hypomethylated DS-DMRs. Overall, this approach highlights that low-coverage WGBS of clinical samples can identify epigenetic alterations to known biological pathways, which are potentially relevant to therapeutic treatments and include metabolic pathways. These results also provide new insights into the genome-wide effects of genetic alterations on DNA methylation profiles indicative of altered neurodevelopment and brain function.
Imaging of red-shifted photons from bioluminescent tumours using fluorescence by unbound excitation from luminescence
Authors: Sônego Fabiane , Bouccara Sophie , Pons Thomas , Lequeux Nicolas , Danckaert Anne , Tinevez Jean-Yves , Alam Israt S. , Shorte Spencer L. , Tournebize Régis
Published: September 2018

Early detection of tumours is today a major challenge and requires sensitive imaging methodologies coupled with new efficient probes. Bioluminescence imaging has been widely used in the field of oncology and several cancer cell lines have been genetically modified to provide bioluminescence signals. However, photons that are emitted by the majority of commonly used luciferases are usually in the blue part of the visible spectrum, where tissue absorption is still very high, making deep tissue imaging non-optimal and calling for optimised optical imaging methodologies. We have previously shown that red-shifting of bioluminescence signal by Fluorescence Unbound Excitation from Luminescence (FUEL) is a mean to increase bioluminescence signal sensitivity detection in vivo. Here, we applied FUEL to tumour detection in two different subcutaneous tumour models: the auto-luminescent human embryonic kidney (HEK293) cell line and the murine B16-F10 melanoma cell line previously transfected with the plasmid Luc2. Tumour size and bioluminescence were measured over time and tumour vascularization characterized. We then locally injected near infrared emitting Quantum Dots (NIR QDs)in the tumour site and observed a red-shifting of bioluminescence signal by (FUEL) indicating that FUEL could be used to allow deeper tumour detection.
CrRLK1L receptor-like kinases HERCULES RECEPTOR KINASE 1 and ANJEA are female determinants of pollen tube reception
Authors: Galindo-Trigo Sergio , Blanco-Touriñán Noel , DeFalco Thomas A. , Wells Eloise S. , Gray Julie E , Zipfel Cyril , Smith Lisa M
Published: September 2018

Communication between the gametophytes is vital for angiosperm fertilisation. Multiple CrRLK1L-type receptor kinases prevent premature pollen tube burst, while another CrRLK1L protein, FERONIA (FER), is required for pollen tube burst in the female gametophyte. We report here the identification of two additional CrRLK1L homologues, HERCULES RECEPTOR KINASE 1 (HERK1) and ANJEA (ANJ), which act redundantly to promote pollen tube burst at the synergid cells. HERK1 and ANJ localise to the filiform apparatus of the synergid cells in unfertilised ovules, and in herk1 anj mutants a majority of ovules remain unfertilised due to pollen tube overgrowth, together indicating that HERK1 and ANJ act as female determinants for fertilisation. As in fer mutants, the synergid cell-specific, endomembrane protein NORTIA (NTA) is not relocalised after pollen tube reception; however, unlike fer mutants, reactive oxygen species levels are unaffected in herk1 anj double mutants. Both ANJ and HERK1 associate with FER and its proposed co-receptor LORELEI (LRE) in planta. Together, our data indicate that HERK1 and ANJ act with FER to mediate female-male gametophyte interactions during plant fertilisation.
MiR-146a-dependent regulation of CD24/AKT/β-catenin axis drives cancer stem cell phenotype in oral squamous cell carcinoma
Authors: Ghuwalewala Sangeeta , Ghatak Dishari , Das Sumit , Das Pijush , Butti Ramesh , Gorain Mahadeo , Kundu Gopal C , Roychoudhury Susanta
Published: September 2018

Cancer stem cells (CSCs) are known to potentiate tumor initiation and maintenance in Oral Squamous Cell Carcinoma (OSCC). Increasing evidences suggest that CD44highCD24low population in OSCC are potential CSCs. MicroRNAs (miRNAs) have emerged as crucial players in tumor development. However, their role in maintenance of OSCC stem cells remains unclear. Here we report that CD44highCD24low population within OSCC cells and primary HNSCC tumors have an elevated expression of miR-146a. Moreover, over-expression of miR-146a results in enhanced stemness phenotype by augmenting CD44highCD24low population. We demonstrate that miR-146a induces stemness by stabilizing β-catenin with concomitant loss of E-cadherin and CD24. Interestingly, CD24 is identified as a novel functional target of miR-146a and ectopic expression of CD24 abrogates miR-146a driven potential CSC phenotype. Mechanistic analysis reveals that higher CD24 levels inhibit AKT phosphorylation leading to β-catenin degradation. Using stably expressing miR-146a/CD24 OSCC cell lines, we also validate that the miR-146a/ CD24/AKT loop significantly alters tumorigenic ability in vivo. Furthermore, we confirmed that β-catenin trans-activates miR-146a, thereby forming a positive feedback loop contributing to stem cell maintenance. Collectively, our study demonstrates that miR-146a regulate CSCs in OSCC through CD24-AKT-β-catenin axis.

Highlights

MiR-146a induces cancer stem cell characteristics in OSCC by targeting CD24

CD24 abrogates miR-146a mediated stemness via β-catenin degradation in non-CSCs

Akt/Wnt pathway is critical for sustenance of miR-146a driven potential CSCs

The miR-146a/CD24/AKT loop significantly alters tumorigenic ability in vivo
Movement Dynamics of Divisome and Penicillin-Binding Proteins (PBPs) in Cells of Streptococcus pneumoniae
Authors: Perez Amilcar J. , Cesbron Yann , Shaw Sidney L. , Villicana Jesus Bazan , Tsui Ho-Ching T. , Boersma Michael J , Ye Ziyun A. , Tovpeko Yanina , Dekker Cees , Holden Seamus , Winkler Malcolm E.
Published: September 2018

Bacterial cell division and peptidoglycan (PG) synthesis are orchestrated by the coordinated dynamic movement of essential protein complexes. Recent studies show that bidirectional treadmilling of FtsZ filaments/bundles is tightly coupled to and limiting for both septal PG synthesis and septum closure in some bacteria, but not in others. Here we report the dynamics of FtsZ movement leading to septal and equatorial ring formation in the ovoid-shaped pathogen, Streptococcus pneumoniae (Spn). Conventional and single-molecule total internal reflection fluorescence microscopy (TIRFm) showed that nascent rings of FtsZ and its anchoring and stabilizing proteins FtsA and EzrA move out from mature septal rings coincident with MapZ rings early in cell division. This mode of continuous nascent ring movement contrasts with a failsafe streaming mechanism of FtsZ/FtsA/EzrA observed in a ΔmapZ mutant and another Streptococcus species. This analysis also provides several parameters of FtsZ treadmilling in nascent and mature rings, including treadmilling velocity in wild-type cells and ftsZ(GTPase) mutants, lifetimes of FtsZ subunits in filaments and of entire FtsZ filaments/bundles, and the processivity length of treadmilling of FtsZ filament/bundles. In addition, we delineated the motion of the septal PBP2x transpeptidase and its FtsW glycosyl transferase binding partner relative to FtsZ treadmilling in Spn cells. Five lines of evidence support the conclusion that movement of the bPBP2x:FtsW complex in septa depends on PG synthesis and not on FtsZ treadmilling. Together, these results support a model in which FtsZ dynamics and associations organize and distribute septal PG synthesis, but do not control its rate in Spn.

Significance

This study answers two long-standing questions about FtsZ dynamics and its relationship to septal PG synthesis in Spn for the first time. In previous models, FtsZ concertedly moves from midcell septa to MapZ rings that have reached the equators of daughter cells. Instead, the results presented here show that FtsZ, FtsA, and EzrA filaments/bundles move continuously out from early septa as part of MapZ rings. In addition, this study establishes that the movement of bPBP2x:FtsW complexes in septal PG synthesis depends on and likely mirrors new PG synthesis and is not correlated with the treadmilling of FtsZ filaments/bundles. These findings are consistent with a mechanism where septal FtsZ rings organize directional movement of bPBP2x:FtsW complexes dependent on PG substrate availability.