bluuebunny/crossref_metadata_2025 huggingface dataset:
Nicotine dependence among adolescents in the European Union: How many and who are affected?
Authors: Coban F R , Kunst A E , Van Stralen M M , Richter M , Rathmann K , Perelman J , Alves J , Federico B , Rimpelä A , Lorant V , Kuipers M A G
Published: August 2018

Background

Nicotine dependence during adolescence increases the risk of continuing smoking into adulthood. The magnitude of nicotine dependence among adolescents in the European Union (EU) has not been established. We aimed to estimate the number of nicotine dependent 15-year-old adolescents in the EU, and identify high-risk groups.

Methods

The number of nicotine dependent 15-year-olds in the EU was derived combining: (i) total number of 15-year-olds in the EU (2013 Eurostat), (ii) smoking prevalence among 15-year-olds (2013/2014 HBSC survey) and (iii) proportion of nicotine dependent 15-year-olds in six EU countries (2013 SILNE survey). Logistic regression analyses identified high-risk groups in the SILNE dataset.

Results

We estimated 172 636 15-year-olds were moderately to highly nicotine dependent (3.2% of all 15 years old; 35.3% of daily smokers). In the total population, risk of nicotine dependence was higher in males, adolescents with poor academic achievement, and those with smoking parents or friends. Among daily smokers, only lower academic achievement and younger age of smoking onset were associated with nicotine dependence.

Conclusion

According to our conservative estimates, more than 172 000 15-year-old EU adolescents were nicotine dependent in 2013. Prevention of smoking initiation, especially among adolescents with poor academic performance, is necessary to prevent a similar number of adolescents getting addicted to nicotine each consecutive year.
Clinician knowledge, attitudes, and barriers to management of vulvovaginal atrophy: variations in primary care and gynecology
Authors: Vesco Kimberly K. , Beadle Kate , Stoneburner Ashley , Bulkley Joanna , Leo Michael C. , Clark Amanda L.
Published: August 2018

Objective:

Vulvovaginal atrophy is a common, but under-recognized condition affecting postmenopausal women. To guide development of an intervention to boost its detection and treatment, we surveyed primary care and gynecology clinicians practicing in an integrated healthcare system.

Methods:

We constructed a three-part survey that contained (1) eight multiple-choice knowledge questions; (2) three Likert-scale questions regarding clinicians’ likelihood of assessing for vulvovaginal atrophy symptoms at a routine (well) visit, confidence in advising patients about symptoms and counseling about therapy; and (3) a 12-item check list of potential barriers to diagnosis and treatment. Analyses were performed using multiple regression.

Results:

Of the 360 clinicians who were sent an e-mail request, 119 (90 primary care, 29 gynecology) completed the survey (33%). Responders and nonresponders did not differ by age, specialty, or clinician type. The proportion with correct responses to knowledge questions differed between primary care (63%) and gynecology (77%) (adjusted mean difference [AMD] =16, 95% CI [10-22]). Primary care clinicians were less likely than gynecology clinicians to assess for symptoms (AMD = 1.04, 95% CI [0.55-1.52]), and were less confident about their ability to advise on symptoms (AMD = 0.66, 95% CI [0.33-0.99]) and to counsel patients about treatment (AMD = 0.76, 95% CI [0.42-1.10]). Lack of time (71%) and educational materials (44%) were the most common barriers to diagnosis and treatment.

Conclusions:

Primary care and gynecology clinicians differ in their knowledge and confidence in managing vulvovaginal atrophy but report similar practice barriers. Addressing identified knowledge deficits and practice barriers may lead to improved management of vulvovaginal atrophy.
Amenorrhea after lung cancer treatment
Authors: Cathcart-Rake Elizabeth J. , Ruddy Kathryn J. , Gupta Ruchi , Kremers Walter , Gast Kelly , Su H. Irene , Partridge Ann H. , Stewart Elizabeth A. , Liu Han , He Yanqi , Yang Ping
Published: August 2018

Objective:

More than 5,000 premenopausal women are diagnosed with lung cancer annually in the United States. Limited data exist regarding the risk of treatment-related amenorrhea, a surrogate for infertility and early menopause, after systemic therapies for lung cancer.

Methods:

Premenopausal women diagnosed with lung cancer under age 50 were surveyed at diagnosis and annually thereafter about their menstrual status as a part of the Mayo Clinic Epidemiology and Genetics of Lung Cancer Research Program. Types of lung cancer-directed treatments were recorded, and frequencies of self-reported menopause at each survey were calculated.

Results:

A cohort of 182 premenopausal women were included in this study, with average age at lung cancer diagnosis 43 years (SD 6). Among the 85 patients who received chemotherapy, 64% self-reported that they had become menopausal within a year of diagnosis. Platinum salts were universally included in these chemotherapy regimens, and the majority of these women also received taxanes within 1 year of diagnosis. Only 15% of the 94 patients who did not receive systemic therapy within 1 year of diagnosis experienced self-reported menopause. Three patients received targeted therapy alone, two of whom remained premenopausal at the final qualifying survey, completed a median of 3 years after diagnosis.

Conclusions:

Chemotherapy for lung cancer patients appears to increase risk of early loss of menses in survivors.
Improving Outcomes in Oncological Colorectal Surgery by Prehabilitation
Authors: Bruns Emma R.J. , van Rooijen Stefanus J. , Argillander Tanja E. , van der Zaag Edwin S. , van Grevenstein Wilhelmina M.U. , van Duijvendijk Peter , Buskens Christianne J. , Bemelman Willem A. , van Munster Barbara C. , Slooter Gerrit D. , van den Heuvel Baukje
Published: August 2018

Introduction

The cornerstone in the treatment of colorectal cancer is surgery. A surgical event poses a significant risk of decreased functional decline and impaired health-related quality of life. Prehabilitation is defined as the multimodal preoperative enhancement of a patient's condition. It may serve as a strategy to improve postoperative outcomes. Prehabilitation requires a multidisciplinary effort of medical health care professionals and a behavioral change of the patient.

Methods

The goal of prehabilitation is threefold: (1) to reduce postoperative complications, (2) to enhance and accelerate the recovery of the patient, and (3) to improve overall quality of life. In this article, we introduce the FIT model illustrating a possible framework toward the implementation of both evidence-based and tailor-made prehabilitation for patients undergoing surgery for colorectal cancer.

Results

The model is composed of three pillars: “facts” (how to screen patients and evidence on what content to prescribe), “integration” (data of own questionnaires assessing motivation of patients and specialists), and finally “tools” (which outcome measurements to use).

Discussion

Developing implementable methods and defining standardized outcome instruments will help establish a solid base for patient-centered prehabilitation programs. Any party introducing prehabilitation requiring multidisciplinary teamwork and behavioral change can potentially use this framework.
Patient Self-Reported Adherence to Ritonavir-Boosted Darunavir Combined With Either Raltegravir or Tenofovir Disoproxil Fumarate/Emtricitabine in the NEAT001/ANRS143 Trial
Authors: Ammassari Adriana , Stöhr Wolfgang , Antinori Andrea , Molina Jean-Michel , Schwimmer Christine , Domingo Pere , Thalme Anders , Di Pietro Massimo , Wallet Cedrick , Pozniak Anton , Richert Laura , Raffi François ,   the NEAT001/ANRS143 Trial Study Group
Published: August 2018

Background:

The NEAT001/ANRS143 trial demonstrated noninferiority of ritonavir-boosted darunavir combined with either raltegravir (RAL + DRV/r) or tenofovir disoproxil fumarate/emtricitabine (TDF/FTC + DRV/r) in HIV-positive, antiretroviral-naive adults. In post hoc analyses, however, RAL + DRV/r showed inferiority in patients with baseline CD4+ <200/mm3 and HIV-1 RNA ≥100,000 copies per milliliter. This preplanned ancillary study was conducted to assess whether differences in adherence might explain efficacy results.

Setting:

Phase III, open-label, randomized, multicenter study in 15 European countries (ClinicalTrials.gov, NCT01066962).

Methods:

Seven hundred seventy-four participants self-reported adherence (modified AIDS Clinical Trials Group questionnaire) over 96 weeks [383 RAL + DRV/r (twice daily; 5 pills/day), 391 TDF/FTC + DRV/r (once daily; 4 pills/day)]. Primary endpoint was ≥95% versus <95% adherence to prescribed doses recorded (1) over the last 4 days or (2) on the visual analogue scale over the last 30 days.

Results:

Characteristics, except age, were similar between arms; 9% had CD4+ <200 cells/mm3 and HIV-1 RNA ≥100,000 copies per milliliter. Adherence ≥95% in the last 4 days (P = 0.029) or at the visual analogue scale (P = 0.0072) was higher with TDF/FTC + DRV/r than with RAL + DRV/r. Adherence ≥95% over the last 4 days was associated with lower probability of virological failure (P = 0.015). Adherence in patients with baseline CD4+ <200 cells/mm3 and HIV-1 RNA ≥100,000 copies per milliliter was similar to the rest of the population, and not significantly associated with efficacy measures, with no significant differences between arms.

Conclusion:

Adherence was high and slightly better in the TDF/FTC + DRV/r than in the RAL + DRV/r arm. No convincing evidence was found that higher failure rate in the RAL + DRV/r arm in the subgroup with worse baseline viroimmunological status is caused by adherence differences.
Isolated Fourth Nerve Palsy in Nontraumatic Tentorial Hemorrhage
Authors: Walter Eyal , Trobe Jonathan D.
Published: August 2018

A 46-year-old woman being treated with warfarin for antiphospholipid antibody syndrome experienced a rise in international normalized ratio (INR) to 5.4 and developed sudden headache and diplopia. Neuro-ophthalmologic examination disclosed a right fourth nerve palsy. Noncontrast computed tomography revealed a subdural hematoma layered along the right tentorium cerebelli, directly in the path of the nerve. With normalization of the INR, the palsy markedly improved over subsequent weeks. This is a unique case of a nontraumatic subdural hematoma causing a fourth nerve palsy.
Visual Field Mean Deviation at Diagnosis of Idiopathic Intracranial Hypertension Predicts Visual Outcome
Authors: Mikkilineni Shravani , Trobe Jonathan D. , Cornblath Wayne T. , De Lott Lindsey
Published: August 2018

Background:

A robust predictor of visual outcome in idiopathic intracranial hypertension (IIH) would be useful in management, but there is limited information on this point. The purpose of this study was to ascertain whether visual field mean deviation on standard static perimetry performed at diagnosis in a large patient cohort is a reliable predictor of visual outcome.

Methods:

We retrospectively reviewed the automated visual field mean deviations at diagnosis and at final encounter in 79 patients with IIH examined in the neuro-ophthalmology clinics at a single academic medical center from 1999 to 2015.

Results:

Of the 79 study patients, 66 (84%) entered with visual field mean deviations of −7 dB or better. Of those 66 patients, 59 (89%) had final mean deviations of −4 dB or better and 33 (56%) had final mean deviations of −2 dB or better. The single patient who had an initial mean deviation of −7 dB or better and a poor final mean deviation (−32 dB) was nonadherent to prescribed medication. Of the 13 (21%) patients who entered with mean deviations worse than −7 dB, 11 (85%) ended up with poor visual outcomes, their final mean deviations ranging from −5 dB to −32 dB. Over half of those 13 patients had required surgery for IIH, often within 3 weeks of diagnosis, owing to severe papilledema and visual dysfunction at the time of diagnosis.

Conclusions:

Based on this retrospective study, patients with IIH who have relatively mild visual dysfunction at diagnosis are likely to have a favorable visual outcome, provided they are adherent to recommended treatment. Many of those with poor visual function at diagnosis will have unfavorable visual outcomes despite aggressive treatment.
A probable genetic origin for pit defects on the molars of Paranthropus robustus
Authors: Towle Ian , Irish Joel D.
Published: August 2018

We report the frequencies of linear enamel hypoplasia (LEH) and, specifically, pitting enamel hypoplasia (PEH) defects in the teeth of Paranthropus robustus, for comparison with four other South African hominin species and three extant nonhuman primate species. Unlike LEH, the lesser known PEH is characterized by multiple circular depression defects across a tooth crown and is often difficult to interpret in terms of developmental timing and etiology. Teeth in all samples were examined macroscopically with type, position and number of defects recorded. Frequencies of teeth with LEH vary among hominin species, but the differences in PEH are considerable. That is, P. robustus has much higher rates of pitting defects, with 47% of deciduous teeth and 14% of permanent teeth affected, relative to 6.7% and 4.3%, respectively, for all other hominin teeth combined; none of the extant primate samples evidence comparable rates. The defects on P. robustus molars are unlike those in other species, with entire crowns often covered in small circular depressions. The PEH is most consistent with modern human examples of amelogenesis imperfecta. Additionally, the defects are: 1) not found on anterior teeth, 2) uniform in shape and size, and 3) similar in appearance/severity on all molars. A possible reason for this form of PEH is as a side effect of selection on another phenotype that shares the same coding gene(s), i.e., a genetic origin. Recent research on the ENAM gene provides one such possibility. Paranthropus likely underwent rapid evolution in the ENAM loci, with changes in this gene contributing to larger posterior teeth and thicker enamel. This same gene is associated with amelogenesis imperfecta; therefore, pleiotropy effects, relating to high selection on this gene during Paranthropus evolution, could have yielded this unique condition.
UNCROSS2: identification of cross-talk in 16S rRNA OTU tables
Authors: Edgar Robert C.
Published: August 2018

Next-generation amplicon sequencing is widely used for surveying biological diversity in applications such as microbial metagenomics, immune system repertoire analysis and targeted tumor sequencing of cancer-associated genes. In such studies, assignment of reads to incorrect samples (cross-talk) is a well-documented problem that is rarely considered in practice. Here, I describe UNCROSS2, an algorithm designed to detect and filter cross-talk in OTU tables generated by next-generation sequencing of the 16S ribosomal RNA gene. On eight published datasets, cross-talk rates are estimated to range from 0.4% to 1.5% mis-assigned reads. On a mock community test, UNCROSS2 identifies spurious counts due to cross-talk with sensitivity ∼80% to 90% and error rate from ∼1% to ∼20%, but it is not clear whether the accuracy of the algorithm is sufficient to decisively improve diversity rates in practice.
Real-time non-invasive intracranial state estimation using unscented Kalman filter
Authors: Park Chanki , Ryu Seungjun , Jung Bonghyun , Lee Sangpyong , Hong Changkie , Kim Yongbae , Lee Boreom
Published: August 2018

Intracranial pressure (ICP) monitoring is desirable as a first-line measure to assist decision-making in cases of increased ICP. Clinically, non-invasive ICP monitoring is also required to avoid infection and hemorrhage in patients. The relationships among the arterial blood pressure (Pa), ICP, cerebral blood flow, and its velocity (QCBFv) measured by transcranial Doppler ultrasound measurement have been reported. However, real-time non-invasive ICP estimation using these modalities is less well documented. Here, we present a novel algorithm for real-time and non-invasive ICP monitoring with QCBFv and Pa, called direct-current (DC)-ICP. This technique is compared with invasive ICP for 11 traumatic-brain-injury patients admitted to Cheju Halla Hospital and Gangnam Severance Hospital from July 2017 to June 2018. The inter-subject correlation coefficient between true and estimate was 0.70. The AUCs of the ROCs for prediction of increased ICP for the DC-ICP methods are 0.816. Thus, QCBFv monitoring can facilitate reliable real-time ICP tracking with our novel DC-ICP algorithm, which can provide valuable information under clinical conditions.
e-workflow for recording of glycomic mass spectrometric data in compliance with reporting guidelines
Authors: Rojas-Macias Miguel A. , Mariethoz Julien , Andersson Peter , Jin Chunsheng , Venkatakrishnan Vignesh , Aoki Nobuyuki P. , Shinmachi Daisuke , Ashwood Christopher , Madunic Katarina , Zhang Tao , Miller Rebecca L. , Horlacher Oliver , Struwe Weston B. , Levander Fredrik , Kolarich Daniel , Rudd Pauline M. , Wuhrer Manfred , Kettner Carsten , Packer Nicolle H. , Aoki-Kinoshita Kiyoko F. , Lisacek Frédérique , Karlsson Niclas G.
Published: August 2018

Glycomics targets released glycans from proteins, lipids and proteoglycans. High throughput glycomics is based on mass spectrometry (MS) that increasingly depends on exchange of data with databases and the use of software. This requires an agreed format for accurately recording of experiments, developing consistent storage modules and granting public access to glycomic MS data. The introduction of the MIRAGE (Mimimum Requirement for A Glycomics Experiment) reporting standards for glycomics was the first step towards automating glycomic data recording. This report describes a glycomic e-infrastructure utilizing a well established glycomics recording format (GlycoWorkbench), and a dedicated web tool for submitting MIRAGE-compatible MS information into a public experimental repository, UniCarb-DR. The submission of data to UniCarb-DR should be a part of the submission process for publications with glycomics MSn that conform to the MIRAGE guidelines. The structure of this pipeline allows submission of most MS workflows used in glycomics.
The influence of X chromosome variants on trait neuroticism
Authors: Luciano Michelle , Davies Gail , Summers Kim M , Hill W David , Hayward Caroline , Liewald David C , Porteous David J , Gale Catharine R. , McIntosh Andrew M , Deary Ian J
Published: August 2018

Autosomal variants have successfully been associated with trait neuroticism in genome-wide analysis of adequately-powered samples. But such studies have so far excluded the X chromosome from analysis. Here, we report genetic association analyses of X chromosome and XY pseudoautosomal single nucleotide polymorphisms (SNPs) and trait neuroticism using UK Biobank samples (N = 405,274). Significant association was found with neuroticism on the X chromosome for 204 markers found within three independent loci (a further 783 were suggestive). Most of these significant neuroticism-related X chromosome variants were located in intergenic regions (n = 713). Involvement of HS6ST2, which has been previously associated with sociability behaviour in the dog, was supported by single SNP and gene-based tests. We found that the amino acid and nucleotide sequences are highly conserved between dogs and humans. From the suggestive X chromosome variants, there were 19 nearby genes which could be linked to gene ontology information. Molecular function was primarily related to binding and catalytic activity; notable biological processes were cellular and metabolic, and nucleic acid binding and transcription factor protein classes were most commonly involved. X-variant heritability of neuroticism was estimated at 0.34% (SE = 0.07). A polygenic X-variant score created in an independent sample (maximum N ≈ 7300) did not predict significant variance in neuroticism, psychological distress, or depressive disorder. We conclude that the X chromosome harbours significant variants influencing neuroticism, and might prove important for other quantitative traits and complex disorders.
Where did you come from, where did you go: Refining Metagenomic Analysis Tools for HGT characterisation
Authors: Seiler Enrico , Trappe Kathrin , Renard Bernhard Y.
Published: August 2018

Horizontal gene transfer (HGT) has changed the way we regard evolution. Instead of waiting for the next generation to establish new traits, especially bacteria are able to take a shortcut via HGT that enables them to pass on genes from one individual to another, even across species boundaries. Existing HGT detection approaches usually first identify genes of foreign nature, e.g., using composition-based methods, and then exploit phylogenetic discrepancies of the corresponding gene tree compared to a species tree. These approaches depend on fully sequenced HGT organisms and computable phylogenetic species trees. The tool Daisy offers a different approach based on read mapping that provides complementary evidence compared to existing methods at the cost of relying on the acceptor and donor references of the HGT organism being known. Acceptor and donor identification is akin to species identification in metagenomic samples based on sequencing reads, a problem addressed by metagenomic profiling tools. However, acceptor and donor references have certain properties such that these methods can not be directly applied. We propose DaisyGPS, a mapping-based pipeline that is able to identify acceptor and donor candidates of an HGT organism based on sequencing reads. To do that, DaisyGPS leverages metagenomic profiling strategies and refines them for HGT candidate identification. These candidates can then be further evaluated by tools like Daisy to establish HGT regions. We successfully validated our approach on both simulated and real data, and show its benefits in an investigation of MRSA outbreak data. DaisyGPS is freely available from https://gitlab.com/rki_bioinformatics/.
Reconstructing meaning from bits of information
Authors: Kivisaari Sasa L. , Vliet Marijn van , Hultén Annika , Lindh-Knuutila Tiina , Faisal Ali , Salmelin Riitta
Published: August 2018

We can easily identify a dog merely by the sound of barking or an orange by its citrus scent. In this work, we study the neural underpinnings of how the brain combines bits of information into meaningful object representations. Modern theories of semantics posit that the meaning of words can be decomposed into a unique combination of individual semantic features (e.g., “barks”, “has citrus scent”). Here, participants received clues of individual objects in form of three isolated semantic features, given as verbal descriptions. We used machine-learning-based neural decoding to learn a mapping between individual semantic features and BOLD activation patterns. We discovered that the recorded brain patterns were best decoded using a combination of not only the three semantic features that were presented as clues, but a far richer set of semantic features typically linked to the target object. We conclude that our experimental protocol allowed us to observe how fragmented information is combined into a complete semantic representation of an object and suggest neuroanatomical underpinnings for this process.
Enemy release mitigates inbreeding depression in native and invasive Silene latifolia populations: experimental insight into the role of inbreeding × environment interactions in invasion success
Authors: Schrieber Karin , Wolf Sabrina , Wypior Catherina , Höhlig Diana , Keller Stephen R. , Hensen Isabell , Lachmuth Susanne
Published: August 2018

Inbreeding and enemy infestation are common in plants and can synergistically reduce their performance. This inbreeding × environment (I×E) interaction may be of particular importance for the success of plant invasions if introduced populations experience a release from attack by natural enemies relative to their native conspecifics. Using native and invasive plant populations, we investigate whether inbreeding affects infestation damage, whether inbreeding depression in performance is mitigated by enemy release and whether genetic differentiation among native and invasive plants modifies these I×E interactions. We used the plant invader Silene latifolia and its natural enemies as a study system. We performed two generations of experimental out- and inbreeding within eight native (European) and eight invasive (North American) S. latifolia populations under controlled conditions using field-collected seeds. Subsequently, we exposed the offspring to an enemy exclusion and inclusion treatment in a common garden in the species’ native range to assess the interactive effects of population origin (range), breeding treatment and enemy treatment on infestation damage as well as plant performance. Inbreeding increased flower and leaf infestation damage in plants from both ranges, but had opposing effects on fruit damage in native versus invasive plants. Both inbreeding and enemy infestation had negative effects on plant performance, whereby inbreeding depression in fruit number was higher in enemy inclusions than exclusions in plants from both ranges. Moreover, the magnitude of inbreeding depression in fruit number was lower in invasive than native populations. Our results support that inbreeding increases enemy susceptibility of S. latifolia, which magnifies inbreeding depression in the presence of enemies. Enemy release in the invaded habitat may thus increase the persistence of inbred founder populations and thereby contribute to successful invasion. Moreover, our findings emphasize that genetic differentiation among native and invasive plants can shape the magnitude and even the direction of inbreeding effects.
The Desmosome is a Mesoscale Lipid Raft-Like Membrane Domain
Authors: Lewis Joshua D , Caldara Amber L , Zimmer Stephanie E , Seybold Anna , Strong Nicole L , Stahley Sara N , Frangakis Achilleas S , Levental Ilya , Wahl James K , Mattheyses Alexa L , Sasaki Takashi , Nakabayashi Kazuhiko , Hata Kenichiro , Matsubara Yoichi , Ishida-Yamamoto Akemi , Amagai Masayuki , Kubo Akiharu , Kowalczyk Andrew P
Published: August 2018

Desmogleins are cadherin family adhesion molecules essential for epidermal integrity. Previous studies have shown that desmogleins associate with lipid rafts, but the significance of this association was not clear. Here, we report that the desmoglein transmembrane domain (TMD) is the primary determinant of raft association. Further, we identify a novel mutation in the DSG1 TMD (G562R) that causes severe dermatitis, multiple allergies, and metabolic wasting (SAM) syndrome. Molecular modeling predicts that this G to R mutation shortens the DSG1 TMD, and experiments directly demonstrate that this mutation compromises both lipid raft association and desmosome incorporation. Finally, cryo-electron tomography (cryo-ET) indicates that the lipid bilayer within the desmosome is ~10% thicker than adjacent regions of the plasma membrane. These findings suggest that differences in bilayer thickness influence the organization of adhesion molecules within the epithelial plasma membrane, with cadherin TMDs recruited to the desmosome via establishment of a specialized mesoscale lipid raft-like membrane domain.
Depletion of microbiome-derived molecules in the host using Clostridium genetics
Authors: Guo Chun-Jun , Allen Breanna M. , Hiam Kamir J. , Dodd Dylan , van Treuren Will , Higginbottom Steven , Fischer Curt R. , Sonnenburg Justin L. , Spitzer Matthew H. , Fischbach Michael A.
Published: August 2018

The gut microbiota produce hundreds of molecules that are present at high concentrations in circulation and whose levels vary widely among humans. In most cases, molecule production has not been linked to specific bacterial strains or metabolic pathways, and unraveling the contribution of each molecule to host biology remains difficult. A general system to ‘toggle’ molecules in this pool on/off in the host would enable interrogation of the mechanisms by which they modulate host biology and disease processes. Such a system has been elusive due to limitations in the genetic manipulability of Clostridium and its relatives, the source of many molecules in this pool. Here, we describe a method for reliably constructing clean deletions in a model commensal Clostridium, C. sporogenes (Cs), including multiply mutated strains. We demonstrate the utility of this method by using it to ‘toggle’ off the production of ten Cs-derived molecules that accumulate in host tissues. By comparing mice colonized by wild-type Cs versus a mutant deficient in the production of branched short-chain fatty acids, we discover a previously unknown IgA-modulatory activity of these abundant microbiome-derived molecules. Our method opens the door to interrogating and sculpting a highly concentrated pool of chemicals from the microbiome.
Zinc Boosts EGCG’s hIAPP Amyloid Inhibition Both in Solution and Membrane
Authors: Lee Young-Ho , Lin Yuxi , Cox Sarah J. , Kinoshita Misaki , Sahoo Bikash R. , Ivanova Magdalena , Ramamoorthy Ayyalusamy
Published: August 2018

Amyloid aggregation of human islet amyloid polypeptide (hIAPP) is linked to insulin-producing islet cell death in type II diabetes. Previous studies have shown the amyloid inhibiting effects of zinc (Zn) and insulin that are co-present with hIAPP in islet cells, and the lipid membrane has been shown to significantly influence the aggregation kinetics. Increasing number of studies report the importance of developing small molecule inhibitors to suppress the hIAPP’s toxicity. Particularly, the ability of epigallocatechin-gallate (EGCG) to inhibit amyloid aggregation of a variety of amyloid peptide/proteins including hIAPP initiated numerous studies including the development of compounds to potentially treat amyloid diseases. In this study, by using a combination of thioflavin-T fluorescence and transmission electron microscopy experiments, we demonstrate a significant enhancement in EGCG’s efficiency, when mixed with Zn, to significantly suppress hIAPP amyloid aggregation both in presence and absence of lipid membrane. Circular dichroism experiments indicate the formation and stabilization of a helical structure of hIAPP in presence of EGCG:Zn complex. Our results also reveal the ability of EGCG or EGCG:Zn to suppress hIAPP’s cellular toxicity and that the ability of EGCG to chelate with Zn suppresses zinc’s cellular toxicity. We suggest that the reported results would be useful to develop strategies to trap hIAPP intermediates for further biophysical and structural studies, and also to devise approaches to abolish amyloid aggregation and cellular toxicity.
Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains
Authors: Jurisic Anamarija , Robin Chloe , Tarlykov Pavel , Siggens Lee , Schoell Brigitte , Jauch Anna , Ekwal Karl , Sørensen Claus Storgaard , Lipinski Marc , Shoaib Muhammad , Ogryzko Vasily
Published: August 2018

Analysis of large-scale interphase genome positioning with reference to a nuclear landmark has recently been studied using sequencing-based single cell approaches. However, these approaches are dependent upon technically challenging, time consuming and costly high throughput sequencing technologies, requiring specialized bioinformatics tools and expertise. Here, we propose a novel, affordable and robust microscopy-based single cell approach, termed Topokaryotyping, to analyze and reconstruct the interphase positioning of genomic loci relative to a given nuclear landmark, detectable as banding pattern on mitotic chromosomes. This is accomplished by proximity-dependent histone labeling, where biotin ligase BirA fused to nuclear envelope marker Emerin was coexpressed together with Biotin Acceptor Peptide (BAP)-histone fusion followed by (i) biotin labeling, (ii) generation of mitotic spreads, (iii) detection of the biotin label on mitotic chromosomes and (iv) their identification by karyotyping. Using Topokaryotyping, we identified both cooperativity and stochasticity in the positioning of emerin-associated chromatin domains in individual cells. Furthermore, the chromosome-banding pattern showed dynamic changes in emerin-associated domains upon physical and radiological stress. In summary, Topokaryotyping is a sensitive and reliable technique to quantitatively analyze spatial positioning of genomic regions interacting with a given nuclear landmark at the single cell level in various experimental conditions.
Activation of innate immune responses by a CpG oligonucleotide sequence composed entirely of threose nucleic acid
Authors: Lange Margaret J. , Burke Donald H. , Chaput John C.
Published: August 2018

Recent advances in synthetic biology have led to the development of nucleic acid polymers with backbone structures distinct from those found in nature, termed xeno-nucleic acids (XNAs). Several unique properties of XNAs make them attractive as nucleic acid therapeutics, most notably their high resistance to serum nucleases and ability to form Watson-Crick base-pairing with DNA and RNA. The ability of XNAs to induce immune responses has not been investigated. Threose nucleic acid (TNA), a type of XNA, is recalcitrant to nuclease digestion and capable of undergoing Darwinian evolution to produce high affinity aptamers; thus, TNA is an attractive candidate for diverse applications, including nucleic acid therapeutics. Here, we evaluated a TNA oligonucleotide derived from a CpG oligonucleotide sequence known to activate TLR9-dependent immune signaling in B cell lines. We observed a slight induction of relevant mRNA signals, robust B cell line activation, and negligible effects on cellular proliferation.
Whole genome sequencing for drug resistance profile prediction inMycobacterium tuberculosis
Authors: Gygli Sebastian M. , Keller Peter M. , Ballif Marie , Blöchliger Nicolas , Hömke Rico , Reinhard Miriam , Loiseau Chloé , Ritter Claudia , Sander Peter , Borrell Sonia , Loo Jimena Collantes , Avihingsanon Anchalee , Gnokoro Joachim , Yotebieng Marcel , Egger Matthias , Gagneux Sebastien , Böttger Erik C.
Published: August 2018

Whole genome sequencing allows rapid detection of drug-resistantM. tuberculosisisolates. However, high-quality data linking quantitative phenotypic drug susceptibility testing (DST) and genomic data have thus far been lacking.

We determined drug resistance profiles of 176 genetically diverse clinicalM. tuberculosisisolates from Democratic Republic of the Congo, Ivory Coast, Peru, Thailand and Switzerland by quantitative phenotypic DST for 11 antituberculous drugs using the BD BACTEC MGIT 960 system and 7H10 agar dilution to generate a cross-validated phenotypic DST readout. We compared phenotypic drug susceptibility results with predicted drug resistance profiles inferred by whole genome sequencing.

Both phenotypic DST methods identically classified the strains into resistant/susceptible in 73-99% of the cases, depending on the drug. Changes in minimal inhibitory concentrations were readily explained by mutations identified by whole genome sequencing. Using the whole genome sequences we were able to predict quantitative drug resistance levels where wild type and mutant MIC distributions did not overlap. The utility of genome sequences to predict quantitative levels of drug resistance was partially limited due to incompletely understood mechanisms influencing the expression of phenotypic drug resistance. The overall sensitivity and specificity of whole genome-based DST were 86.8% and 94.5%, respectively.

Despite some limitations, whole genome sequencing has high predictive power to infer resistance profiles without the need for time-consuming phenotypic methods.

One sentence summary

Whole genome sequencing of clinicalM. tuberculosisisolates accurately predicts drug resistance profiles and may replace culture-based drug susceptibility testing in the future.
The RNA-Binding Protein DND1Acts Sequentially as a Negative Regulator of Pluripotency and a Positive Regulator of Epigenetic Modifiers Required for Germ Cell Reprogramming
Authors: Ruthig Victor A. , Friedersdorf Matthew B. , Garness Jason A. , Munger Steve C. , Bunce Corey , Keene Jack D. , Capel Blanche
Published: August 2018

The adult spermatogonial stem cell population arises from pluripotent primordial germ cells (PGCs) that enter the fetal testis around embryonic day 10.5 (E10.5). These cells undergo rapid mitotic proliferation, then enter a prolonged period of cell cycle arrest (G1/G0) during which they transition to pro-spermatogonia. In mice homozygous for theTermutation in the RNA-binding proteinDND1(DND1Ter/Ter), many germ cells fail to enter G1/G0, and give rise to teratomas, tumors in which many embryonic cell types are represented. To investigate the origin of these tumors, we sequenced the transcriptome of male germ cells inDND1Ter/Termutants at E12.5, E13.5, and E14.5, just prior to the formation of teratomas, and correlated this information with direct targets of DND1identified by DO-RIP-Seq. Consistent with previous results, we found that DND1controls the down regulation of many genes associated with pluripotency and active cell cycle, including elements of the mTor, Hippo and Bmp/Nodal signaling pathways. However, DND1targets also include genes associated with male differentiation including a large group of chromatin regulators activated in wild type but not mutant germ cells during the transition between E13.5and E14.5. These results suggest multiple functions of DND1, and link DND1to the initiation of epigenetic modifications in male germ cells.
Description of novel marine bioflocculant-producing bacteria isolated from biofloc of Pacific whiteleg shrimp,Litopenaeus vannameiculture ponds
Authors: Che Hashim Nurul Fakriah , Ghazali Nurarina Ayuni , Amin Nakisah Mat , Ismail Noraznawati , Kasan Nor Azman
Published: August 2018

Description of marine bioflocculant-producing bacteria isolated from biofloc of Pacific whiteleg shrimp,Litopenaeus vannameiculture ponds was prompted to explore the bacteria that enhanced bioflocculation process in aquaculture wastewater treatment. Certain marine bacteria were potentially secreted extracellular polymeric substances (EPS) which response to the physiological stress encountered in the natural environment that can act as bioflocculants. This study aimed to identify marine bioflocculant-producing bacteria isolated from biofloc; to evaluate their flocculating activities; and to characterize their protein in EPS. Phenotypic and genotypic identification of the bacteria including morphological and molecular approaches were employed, while their flocculating activities were examined via Kaolin clay suspension method and statistically analyzed. The EPS that acted as bioflocculants were extracted using cold ethanol precipitation method. Protein concentration was determined by Bradford assay and protein profiling was finally completed with Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE) method. Six species of marine bacteria known asHalomonas venusta, Bacillus cereus, Bacillus subtilis, Bacillus pumilus, Nitratireductor aquimarinusandPseudoalteromonassp. were successfully identified as bioflocculant-producing bacteria. The highest flocculating activity was exhibited byBacillus cereusat 93%, whileHalomonas venustashowed the lowest record at 59%. All bioflocculant-producing bacteria species showed different protein concentration that ranged between 1.377 μg/mL to 1.455 μg/mL. Several protein bands with different molecular weight that ranged between 16 kDa to 100 kDa were observed. This study revealed that all the identified bacteria species have high potential characteristics to initiate aquaculture wastewater treatment and may play important roles in bioflocculation process.

Importance

Six species of marine bacteria isolated from biofloc of Pacific whiteleg shrimp,Litopenaeus vannameiculture ponds were identified as bioflocculant-producing bacteria. Among those six species,Bacillus cereus,Bacillus pumilus,Nitratireductor aquimarinusandPseudoalteromonassp. were highly potential to be used as booster for rapid formation of biofloc due to their high flocculating activities. Protein content in EPS of novel marine biofocculant-producing bacteria has beneficial consequences on degradation process of organic substances, denitrification of wastes and ions elimination from aquaculture wastes.
Screening Mycobacterium tuberculosis secreted proteins identifies Mpt64 as eukaryotic membrane-binding virulence factor
Authors: Stamm Chelsea E. , Pasko Breanna L. , Chaisavaneeyakorn Sujittra , Franco Luis H. , Nair Vidhya R. , Weigele Bethany A. , Alto Neal M. , Shiloh Michael U.
Published: August 2018

Mycobacterium tuberculosis(Mtb), the causative agent of tuberculosis, is one of the most successful human pathogens. One reason for its success is that Mtb can reside within host macrophages, a cell type that normally functions to phagocytose and destroy infectious bacteria. However, Mtb is able to evade macrophage defenses in order to survive for prolonged periods of time. Many intracellular pathogens secret virulence factors targeting host membranes and organelles to remodel their intracellular environmental niche. We hypothesized that Mtb exported proteins that target host membranes are vital for Mtb to adapt to and manipulate the host environment for survival. Thus, we characterized 200 exported proteins from Mtb for their ability to associate with eukaryotic membranes using a unique temperature sensitive yeast screen and to manipulate host trafficking pathways using a modified inducible secretion screen. We identified five Mtb exported proteins that both associated with eukaryotic membranes and altered the host secretory pathway. One of these secreted proteins, Mpt64, localized to the endoplasmic reticulum during Mtb infection of murine and human macrophages and was necessary for Mtb survival in primary human macrophages. These data highlight the importance of exported proteins in Mtb pathogenesis and provide a basis for further investigation into their molecular mechanisms.

Importance

Advances have been made to identify exported proteins ofMycobacterium tuberculosisduring animal infections. These data, combined with transposon screens identifying genes important forM. tuberculosisvirulence, have generated a vast resource of potentialM. tuberculosisvirulence proteins. However, the function of many of these proteins inM. tuberculosispathogenesis remains elusive. We have integrated three cell biological screens to characterize nearly 200M. tuberculosisexported proteins for eukaryotic membrane binding, host subcellular localization and interactions with host vesicular trafficking. In addition, we observed the localization of one exported protein, Mpt64, duringM. tuberculosisinfection of macrophages. Interestingly, although Mpt64 is exported by the Sec pathway, its delivery into host cells was dependent upon the action of the Type VII Secretion System. Finally, we observed that Mpt64 contributes to the virulence ofM. tuberculosisduring infection of primary human macrophages.
Epigenetic signatures of starting and stopping smoking
Authors: McCartney Daniel L , Stevenson Anna J , Hillary Robert F , Walker Rosie M , Bermingham Mairead L , Morris Stewart W , Clarke Toni-Kim , Campbell Archie , Murray Alison D , Whalley Heather C , Porteous David J , Visscher Peter M , McIntosh Andrew M , Evans Kathryn L , Deary Ian J , Marioni Riccardo E
Published: August 2018

Background

Multiple studies have made robust associations between differential DNA methylation and exposure to cigarette smoke. But whether a DNA methylation phenotype is established immediately upon exposure, or only after prolonged exposure is less well-established. Here, we assess DNA methylation patterns in current smokers in response to dose and duration of exposure, along with the effects of smoking cessation on DNA methylation in former smokers.

Methods

Dimensionality reduction was applied to DNA methylation data at 90 previously identified smoking-associated CpG sites for over 4,900 individuals in the Generation Scotland cohort. K-means clustering was performed to identify clusters associated with current and never smoker status based on these methylation patterns. Cluster assignments were assessed with respect to duration of exposure in current smokers (years as a smoker), time since smoking cessation in former smokers (years), and dose (cigarettes per day).

Results

Two clusters were specified, corresponding to never smokers (97.5% of whom were assigned to Cluster 1) and current smokers (81.1% of whom were assigned to Cluster 2). The exposure time point from which >50% of current smokers were assigned to thesmoker-enrichedcluster varied between 5-9 years in heavier smokers and between 15-19 years in lighter smokers. Low-dose former smokers were more likely to be assigned to thenever smoker-enrichedcluster from the first year following cessation. In contrast, a period of at least two years was required before the majority of former high-dose smokers were assigned to the never smoker-enriched cluster.

Conclusions

Our findings suggest that smoking-associated DNA methylation changes are a result of prolonged exposure to cigarette smoke, and can be reversed following cessation. The length of time in which these signatures are established and recovered is dose dependent. Should DNA methylation-based signatures of smoking status be predictive of smoking-related health outcomes, our findings may provide an additional criterion on which to stratify risk.