bluuebunny/crossref_metadata_2025 huggingface dataset:
Incidence of Laryngotracheal Stenosis after Thermal Inhalation Airway Injury
Authors: Lowery Anne Sun , Dion Greg , Thompson Callie , Weavind Liza , Shinn Justin , McGrane Stuart , Summitt Blair , Gelbard Alexander
Published: July 2019

Inhalation injury is independently associated with burn mortality, yet little information is available on the incidence, risk factors, or functional outcomes of thermal injury to the airway. In patients with thermal inhalation injury, we sought to define the incidence of laryngotracheal stenosis (LTS), delineate risk factors associated with LTS development, and assess long-term tracheostomy dependence as a proxy for laryngeal function. Retrospective cohort study of adult patients treated for thermal inhalation injury at a single institution burn critical care unit from 2012 to 2017. Eligible patients’ records were assessed for LTS (laryngeal, subglottic, or tracheal stenosis). Patient characteristics, burn injury characteristics, and treatment-specific covariates were assessed. Descriptive statistics, Mann–Whitney U-tests, odds ratio, and chi-square tests compared LTS versus non-LTS groups. Of 129 patients with thermal inhalation injury during the study period, 8 (6.2%) developed LTS. When compared with the non-LTS group, patients with LTS had greater mean TBSA (mean 30.3, Interquartile Range 7–57.5 vs 10.5, Interquartile Range 0–15.12, P = .01), higher grade of inhalation injury (mean 2.63 vs 1.80, P = .05), longer duration of intubation (12.63 vs 5.44; P < .001), and greater inflammatory response (mean white blood cell count on presentation 25.8 vs 14.9, P = .02, mean hyperglycemia on presentation 176.4 vs 136.9, P = .01). LTS patients had a significantly higher rate of tracheostomy dependence at last follow-up (50 vs 1.7%, P < .001). Six percent of patients with thermal inhalation injury develop LTS. LTS was associated with more severe thermal airway injury, longer duration of intubation, and more severe initial host inflammation. Patients with inhalation injury and LTS are at high risk for tracheostomy dependence. In burn patients with thermal inhalation injury, laryngeal evaluation and directed therapy should be incorporated early into multispecialty pathways of care.
Challenges and perspectives for structural biology of lncRNAs—the example of the Xist lncRNA A-repeats
Authors: Jones Alisha N , Sattler Michael
Published: July 2019

Following the discovery of numerous long non-coding RNA (lncRNA) transcripts in the human genome, their important roles in biology and human disease are emerging. Recent progress in experimental methods has enabled the identification of structural features of lncRNAs. However, determining high-resolution structures is challenging as lncRNAs are expected to be dynamic and adopt multiple conformations, which may be modulated by interaction with protein binding partners. The X-inactive specific transcript (Xist) is necessary for X inactivation during dosage compensation in female placental mammals and one of the best-studied lncRNAs. Recent progress has provided new insights into the domain organization, molecular features, and RNA binding proteins that interact with distinct regions of Xist. The A-repeats located at the 5′ end of the transcript are of particular interest as they are essential for mediating silencing of the inactive X chromosome. Here, we discuss recent progress with elucidating structural features of the Xist lncRNA, focusing on the A-repeats. We discuss the experimental and computational approaches employed that have led to distinct structural models, likely reflecting the intrinsic dynamics of this RNA. The presence of multiple dynamic conformations may also play an important role in the formation of the associated RNPs, thus influencing the molecular mechanism underlying the biological function of the Xist A-repeats. We propose that integrative approaches that combine biochemical experiments and high-resolution structural biology in vitro with chemical probing and functional studies in vivo are required to unravel the molecular mechanisms of lncRNAs.
High Resiliency Linked to Short-Term Patient Reported Outcomes and Return to Duty Following Arthroscopic Knee Surgery
Authors: Drayer Nicholas J , Wallace Christopher S , Yu Henry H , Mansfield Taylor D , Cummings Danielle L , Hood Debra K , Arrington Edward D , Kang Daniel G
Published: July 2019

Introduction

Resilience is a psychometric construct of a patient’s ability to recover from adversity and has been used to predict outcomes but its use in orthopedics has been limited. The purpose of this study was to examine the association between resilience and outcomes.

Materials and Methods

We performed a retrospective analysis of prospectively collected data of patient who underwent sports knee surgery at a single institution performed by 6 orthopedic surgeons from January 2017 to December 2017. We included active-duty patients with complete preoperative outcomes and a minimum of 6 month follow-up. All patients completed the Brief Resilience Scale (BRS), Veteran’s Rand-12 (VR-12), Patient-Reported Outcomes Measurement Information System 43 (PROMIS-43), International Knee Documentation Committee function score (IKDC), and Knee Injury and Osteoarthritis Outcome Score (KOOS). Patients were divided into low resilience (LR) and high resilience (HR) groups based on a score of less than 24 for low and greater than or equal to 24 according to BRS. Outcomes were then compared.

Results

We identified 50 active-duty patients who had complete preoperative and postoperative outcomes at a minimum of 6 months. Mean preoperative and postoperative BRS were significantly different (25.8 HR v 18.6 LR, p < 0.001). We found a difference in postop KOOS in pain, sports, and short form (pain 70.9 HR v 55.7 LR, p = 0.03; sports 50.3 HR v 32.2 LR, p = 0.03; short form (72.1 HR v 62.5 LR, p = 0.04). Similarly, there was a significant difference in postoperative IKDC score (58.0 HR v 44.0 LR, p = 0.03). Similarly we found significant differences in postoperative PROMIS-43 (anxiety 44.4 HR v 60.3 LR, p = 0.004; depression 41.6 HR v 58.1 LR, p = 0.004; fatigue 45.1 HR v 58.6 LR, p = 0.001; sleep 52.6 HR v 62.5 LR, p = 0.02; social participation 36.2 HR v 47.6 LR, p < 0.001). Postoperative VR-12 mental was also statistically different between the two groups (53.5 HR v 41.6 LR; p = 0.01). In addition, 2.3% of the HR group changed MOS as a result of their sports knee surgery compared to 22.2% of the LR group.

Conclusions

Active-military patients with high preoperative resilience appear to have significantly better early postoperative outcomes following sports knee surgery in terms of PROMIS-43, KOOS, and IKDC. There was also a lower rate of changing MOS secondary to sports knee surgery in patients with high resilience.
Complementary roles of Pif1 helicase and single stranded DNA binding proteins in stimulating DNA replication through G-quadruplexes
Authors: Sparks Melanie A , Singh Saurabh P , Burgers Peter M , Galletto Roberto
Published: July 2019

G-quadruplexes (G4s) are stable secondary structures that can lead to the stalling of replication forks and cause genomic instability. Pif1 is a 5′ to 3′ helicase, localized to both the mitochondria and nucleus that can unwind G4s in vitro and prevent fork stalling at G4 forming sequences in vivo. Using in vitro primer extension assays, we show that both G4s and stable hairpins form barriers to nuclear and mitochondrial DNA polymerases δ and γ, respectively. However, while single-stranded DNA binding proteins (SSBs) readily promote replication through hairpins, SSBs are only effective in promoting replication through weak G4s. Using a series of G4s with increasing stabilities, we reveal a threshold above which G4 through-replication is inhibited even with SSBs present, and Pif1 helicase is required. Because Pif1 moves along the template strand with a 5′-3′-directionality, head-on collisions between Pif1 and polymerase δ or γ result in the stimulation of their 3′-exonuclease activity. Both nuclear RPA and mitochondrial SSB play a protective role during DNA replication by preventing excessive DNA degradation caused by the helicase-polymerase conflict.
Delayed occupational asthma from epoxy exposure
Authors: Brock Jacobsen I , Baelum J , Carstensen O , Skadhauge L R , Feary J , Cullinan P , Sherson D L
Published: July 2019

Background

A delayed asthma reaction occurring several hours after exposure is difficult to diagnose.

Aims

To confirm a delayed asthma reaction in five workers following epoxy exposure.

Case report

Working conditions with exposure to epoxy encountered at the workplace were reproduced in a challenge chamber. Specific inhalation challenge (SIC) with epoxy was compared to a control challenge. All five cases had delayed a asthma response 6–15 h after epoxy exposure.

Conclusions

Our study confirms that SIC is a useful tool in diagnosing delayed asthma response.
The Benefits of Limited Orbitotomy on the Supraorbital Approach: An Anatomic and Morphometric Study in Virtual Reality
Authors: Tai Alexander X , Sack Kenneth D , Herur-Raman Aalap , Jean Walter C
Published: July 2019

BACKGROUND

Cadaveric studies on surgical anatomy and approaches are hampered by the limited number of specimens. Virtual reality (VR) technology can overcome this limitation, allowing for more in-depth statistical analysis of the data.

OBJECTIVE

To determine the benefit of a supraorbital ridge osteotomy in a supraorbital craniotomy targeting (1) the anterior communicating artery complex (ACOM), and (2) a lesion 25 mm above tuberculum sellae, using a large dataset generated by VR.

METHODS

Computed tomography scans of 30 subjects without cranial osseous pathology were identified for use with VR technology. After correlating VR and DICOM datasets, supraorbital craniotomies were simulated without and with removal of supraorbital ridge, bilaterally (n = 60). Area of freedom (AOF) from the outer table to the targets and the vertical center angle (VCA) to targets were calculated, before and after the orbitotomy.

RESULTS

For the ACOM, AOF averaged 496 mm2 (range: 322-805) and increased 8.9% to an average of 547 mm2 with the removal of the supraorbital ridge (P < .001). VCA increased from 18.5 to 20.3 degrees. For the suprasellar target, AOF averaged 507 mm2 (range 324-772) and increased 42.5% to 722 mm2 after orbitotomy (P < .001). VCA increased from 22.1 to 30.8 degrees.

CONCLUSION

VR technology is an emerging tool to study neurosurgical approaches. Here, we demonstrate with VR that the removal of the supraorbital ridge in a supraorbital craniotomy affords greater access to superiorly located lesions of the anterior fossa floor; however, deeper and lower lesions require a more aggressive orbital roof osteotomy to widen the exposure.
Aging Back Clinics—a Geriatric Syndrome Approach to Treating Chronic Low Back Pain in Older Adults: Results of a Preliminary Randomized Controlled Trial
Authors: Weiner Debra K , Gentili Angela , Rossi Michelle , Coffey-Vega Katherine , Rodriguez Keri L , Hruska Kristina L , Hausmann Leslie , Perera Subashan
Published: July 2019

Objective

Treating chronic low back pain (CLBP) with spine-focused interventions is common, potentially dangerous, and often ineffective. This preliminary trial tests the feasibility and efficacy of caring for CLBP in older adults as a geriatric syndrome in Aging Back Clinics (ABC).

Design

Randomized controlled trial.

Setting

Outpatient clinics of two VA Medical Centers.

Subjects

Fifty-five English-speaking veterans aged 60–89 with CLBP and no red flags for serious underlying illness, prior back surgery, dementia, impaired communication, or uncontrolled psychiatric illness.

Methods

Participants were randomized to ABC care or usual care (UC) and followed for six months. ABC care included 1) a structured history and physical examination to identify pain contributors, 2) structured participant education, 3) collaborative decision-making, and 4) care guided by condition-specific algorithms. Primary outcomes were low back pain severity (0–10 current and seven-day average/worst pain) and pain-related disability (Roland Morris). Secondary outcomes included the SF-12 and health care utilization.

Results

ABC participants experienced significantly greater reduction in seven-day average (–1.22 points, P = 0.023) and worst pain (–1.70 points, P = 0.003) and SF-12 interference with social activities (50.0 vs 11.5%, P = 0.0030) at six months. ABC participants were less likely to take muscle relaxants (16.7 vs 42.3%, P = 0.0481). Descriptively, UC participants were more likely to experience pain-related emergency room visits (45.8% vs 30.8%) and to be exposed to non-COX2 nonsteroidal anti-inflammatory drugs (73.1% vs 54.2%).

Conclusions

These preliminary data suggest that ABC care for older veterans with CLBP is feasible and may reduce pain and exposure to other potential morbidity.
Quantitative Immunology for Physicists
Authors: Altan-Bonnet Grégoire , Mora Thierry , Walczak Aleksandra M.
Published: July 2019

The adaptive immune system is a dynamical, self-organized multiscale system that protects vertebrates from both pathogens and internal irregularities, such as tumours. For these reason it fascinates physicists, yet the multitude of different cells, molecules and sub-systems is often also petrifying. Despite this complexity, as experiments on different scales of the adaptive immune system become more quantitative, many physicists have made both theoretical and experimental contributions that help predict the behaviour of ensembles of cells and molecules that participate in an immune response. Here we review some recent contributions with an emphasis on quantitative questions and methodologies. We also provide a more general methods section that presents some of the wide array of theoretical tools used in the field.
The histone chaperone FACT induces Cas9 multi-turnover behavior and modifies genome manipulation in human cells
Authors: Wang Alan S. , Chen Leo , Wu R. Alex , Richardson Christopher D. , Gowen Benjamin G. , Kazane Katelynn R. , Vu Jonathan T. , Wyman Stacia K. , Shin Jiyung , Walter Johannes C. , Corn Jacob E.
Published: July 2019

Cas9 is a prokaryotic RNA-guided DNA endonuclease that binds substrates tightly in vitro but turns over rapidly when used to manipulate genomes in eukaryotic cells. Little is known about the factors responsible for dislodging Cas9 or how they influence genome engineering. Using a proximity labeling system for unbiased detection of transient protein interactions in cell-free Xenopus laevis egg extract, we identified the dimeric histone chaperone FACT as an interactor of substrate-bound Cas9. Immunodepletion of FACT subunits from extract potently inhibits Cas9 unloading and converts Cas9’s activity from multi-turnover to single-turnover. In human cells, depletion of FACT delays genome editing and alters the balance between indel formation and homology directed repair. Depletion of FACT also increases epigenetic marking by dCas9-based transcriptional effectors with concomitant enhancement of transcriptional modulation. FACT thus shapes the intrinsic cellular response to Cas9-based genome manipulation most likely by determining Cas9 residence times.
MUC5AC drives COPD exacerbation severity through amplification of virus-induced airway inflammation
Authors: Singanayagam Aran , Footitt Joseph , Kasdorf Benjamin T , Marczynski Matthias , Cross Michael T , Finney Lydia J , Trujillo Torralbo Maria-Belen , Calderazzo Maria , Zhu Jie , Aniscenko Julia , Clarke Thomas B , Molyneaux Philip L , Bartlett Nathan W , Moffatt Miriam F , Cookson William O , Wedzicha Jadwiga , Evans Christopher M , Lieleg Oliver , Mallia Patrick , Johnston Sebastian L
Published: July 2019

The respiratory tract surface is protected from inhaled pathogens by a secreted layer of mucus that is rich in mucin glycoproteins. Disrupted mucus production is a cardinal feature of chronic respiratory diseases but how this alteration affect interactions between mucins and pathogens is complex and poorly understood. Here, we identify a central and unexpected role for the major airway mucin MUC5AC in pathogenesis of virus-induced exacerbations of chronic obstructive pulmonary disease (COPD). Virus induction of MUC5AC is augmented in COPD compared to healthy subjects, is enhanced in frequent exacerbators and correlates with inflammation, symptom severity and secondary bacterial infection during exacerbation. MUC5AC is functionally related to inflammation as MUC5AC-deficient (Muc5ac-/-) mice had attenuated rhinovirus-induced airway inflammation whilst exogenous MUC5AC glycoprotein administration augmented virus-induced inflammatory responses and bacterial load. Mechanistically, MUC5AC-augmentation of rhinovirus-induced inflammation occurred through release of extracellular adenosine triphosphate (ATP). Therapeutic suppression of virus-induced MUC5AC release using an epidermal growth factor receptor (EGFR) inhibitor ameliorated exaggerated pro-inflammatory responses in a mouse COPD exacerbation model. Collectively, these studies demonstrate previously unrecognised pro-inflammatory effects of MUC5AC during infection and thus highlight a key unforeseen role in driving COPD exacerbation severity.
TWO-SIGMA: a novel TWO-component SInGle cell Model-based Association method for single-cell RNA-seq data
Authors: Van Buren Eric , Hu Ming , Weng Chen , Jin Fulai , Li Yan , Wu Di , Li Yun
Published: July 2019

In this paper, we develop TWO-SIGMA, a TWO-component SInGle cell Model-based Association method for differential expression (DE) analyses in single-cell RNA-seq (scRNA-seq) data. The first component models the probability of “drop-out” with a mixed-effects logistic regression model and the second component models the (conditional) mean expression with a mixed-effects negative binomial regression model. TWO-SIGMA is extremely flexible in that it: (i) does not require a log-transformation of the outcome, (ii) allows for overdispersed and zero-inflated counts, (iii) accommodates a correlation structure between cells from the same biological sample via random effect terms, (iv) can analyze unbalanced designs (in which the number of cells does not need to be identical for all samples), (v) can control for additional sample-level and cell-level covariates including batch effects, (vi) provides interpretable effect size estimates, and (vii) enables general tests of DE beyond two-group comparisons. To our knowledge, TWO-SIGMA is the only method for analyzing scRNA-seq data that can simultaneously accomplish each of these features. Simulations studies show that TWO-SIGMA outperforms alternative regression-based approaches in both type-I error control and power enhancement when the data contains even moderate within-sample correlation. A real data analysis using pancreas islet single-cells exhibits the flexibility of TWO-SIGMA and demonstrates that incorrectly failing to include random effect terms can have dramatic impacts on scientific conclusions. TWO-SIGMA is implemented in the R package twosigma available at https://github.com/edvanburen/twosigma.
Notes on the endemic cloud forest plants of the Cameroon Highlands and the new, Endangered,Tricalysia elmar(Coffeeae-Rubiaceae)
Authors: Cheek Martin , Causon Isla , Tchiengue Barthelemy , House Eden
Published: July 2019

Background and aims

This paper reports a further discovery in the context of a long-term botanical survey in the Cross River-Sanaga interval of west-central Africa, focussing on species discovery and conservation.

Methods

Normal practices of herbarium taxonomy have been applied to study the material collected. The relevant collections are stored in the Herbarium of the Royal Botanic Gardens, Kew, London and at the Institute of Research in Agronomic Development – National Herbarium of Cameroon.

Key results

New species to science continue to be discovered from the cloud (submontane) forests of the Cameroon Highlands in Cameroon. Most of these species are rare, highly localised, and threatened by habitat destruction. These discoveries increase the justification for improved conservation management of surviving habitat.Tricalysia elmarCheek (Coffeeae-Rubiaceae) is described as an additional species new to science and is compared with similar species of the genus. Restricted so far to four locations, Mt Kupe, Bali Ngemba, Lebialem and Nta Ali, its conservation status is assessed as Endangered (EN B1+2ab(iii)) according to the 2012 criteria of IUCN.
Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales
Authors: Holt Kathryn E. , Lassalle Florent , Wyres Kelly L. , Wick Ryan , Mostowy Rafal J.
Published: July 2019

Bacterial capsules and lipopolysaccharides are diverse surface polysaccharides (SPs) that serve as the frontline for interactions with the outside world. While SPs can evolve rapidly, their diversity and evolutionary dynamics across different taxonomic scales has not been investigated in detail. Here, we focused on the bacterial order Enterobacteriales (including the medically-relevant Enterobacteriaceae), to carry out comparative genomics of two SP locus synthesis regions,cpsandkps, using 27,334 genomes from 45 genera. We identified high-qualitycpsloci in 22 genera andkpsin 11 genera, around 4% of which were detected in multiple species. We found SP loci to be highly dynamic genetic entities: their evolution was driven by high rates of horizontal gene transfer (HGT), both of whole loci and component genes, and relaxed purifying selection, yielding large repertoires of SP diversity. In spite of that, we found the presence of (near-)identical locus structures in distant taxonomic backgrounds that could not be explained by recent exchange, pointing to long-term selective preservation of locus structures in some populations. Our results reveal differences in evolutionary dynamics driving SP diversity within different bacterial species, with lineages ofEscherichia coli,Enterobacter hormacheiandKlebsiella aerogenesmost likely to share SP loci via recent exchange; and lineages ofSalmonella enterica,Citrobacter sakazakiiandSerratia marcescensmost likely to share SP loci via other mechanisms such as long-term preservation. Overall, the evolution of SP loci in Enterobacteriales is driven by a range of evolutionary forces and their dynamics and relative importance varies between different species.
NASQAR: A web-based platform for high-throughput sequencing data analysis and visualization
Authors: Yousif Ayman , Drou Nizar , Rowe Jillian , Khalfan Mohammed , Gunsalus Kristin C
Published: July 2019

Background

As high-throughput sequencing applications continue to evolve, the rapid growth in quantity and variety of sequence-based data calls for the development of new software libraries and tools for data analysis and visualization. Often, effective use of these tools requires computational skills beyond those of many researchers. To ease this computational barrier, we have created a dynamic web-based platform, NASQAR (Nucleic Acid SeQuence Analysis Resource).

Results

NASQAR offers a collection of custom and publicly available open-source web applications that make extensive use of a variety of R packages to provide interactive data analysis and visualization. The platform is publicly accessible at http://nasqar.abudhabi.nyu.edu/. Open-source code is on GitHub at https://github.com/nasqar/NASQAR, and the system is also available as a Docker image at https://hub.docker.com/r/aymanm/nasqarall. NASQAR is a collaboration between the core bioinformatics teams of the NYU Abu Dhabi and NYU New York Centers for Genomics and Systems Biology.

Conclusions

NASQAR empowers non-programming experts with a versatile and intuitive toolbox to easily and efficiently explore, analyze, and visualize their Transcriptomics data interactively. Popular tools for a variety of applications are currently available, including Transcriptome Data Preprocessing, RNA-seq Analysis (including Single-cell RNA-seq), Metagenomics, and Gene Enrichment.
Spatial patterns emerging from a stochastic process near criticality
Authors: Peruzzo Fabio , Mobilia Mauro , Azaele Sandro
Published: July 2019

There is mounting empirical evidence that many communities of living organisms display key features which closely resemble those of physical systems at criticality. We here introduce a minimal model framework for the dynamics of a community of individuals which undergoes local birth-death, immigration and local jumps on a regular lattice. We study its properties when the system is close to its critical point. Even if this model violates detailed balance, within a physically relevant regime dominated by fluctuations, it is possible to calculate analytically the probability density function of the number of individuals living in a given volume, which captures the close-to-critical behavior of the community across spatial scales. We find that the resulting distribution satisfies an equation where spatial effects are encoded in appropriate functions of space, which we calculate explicitly. The validity of the analytical formulæ is confirmed by simulations in the expected regimes. We finally discuss how this model in the critical-like regime is in agreement with several biodiversity patterns observed in tropical rain forests.
Centrioles control the capacity, but not the specificity, of cytotoxic T cell killing
Authors: Tamzalit Fella , Tran Diana , Jin Weiyang , Boyko Vitaly , Bazzi Hisham , Kepecs Ariella , Kam Lance C. , Anderson Kathryn V. , Huse Morgan
Published: July 2019

Immunological synapse formation between cytotoxic T lymphocytes (CTLs) and the target cells they aim to destroy is accompanied by reorientation of the CTL centrosome to a position beneath the synaptic membrane. Centrosome polarization is thought to enhance the potency and specificity of killing by driving lytic granule fusion at the synapse and thereby the release of perforin and granzymes toward the target cell. To test this model, we employed a genetic strategy to delete centrioles, the core structural components of the centrosome. Centriole deletion altered microtubule architecture, as expected, but surprisingly had no effect on lytic granule polarization and directional secretion. Nevertheless, CTLs lacking centrioles did display substantially reduced killing potential, which was associated with defects in both lytic granule biogenesis and synaptic actin remodeling. These results reveal an unexpected role for the intact centrosome in controlling the capacity, but not the specificity, of cytotoxic killing.
PIN FORMED 2 facilitates the transport of Arsenite inArabidopsis thaliana
Authors: Ashraf Mohammad Arif , Umetsu Kana , Ponomarenko Olena , Saito Michiko , Aslam Mohammad , Antipova Olga , Dolgova Natalia , Kiani Cheyenne D. , Nezhati Susan , Tanoi Keitaro , Minegishi Katsuyuki , Nagatsu Kotaro , Kamiya Takehiro , Fujiwara Toru , Luschnig Christian , Tanino Karen , Pickering Ingrid , George Graham N. , Rahman Abidur
Published: July 2019

Arsenic contamination is a major environmental issue as it may lead to serious health hazard. Reduced trivalent form of inorganic arsenic, arsenite, is in general more toxic to plants compared with the fully oxidized pentavalent arsenate. The uptake of arsenite in plants has been shown to be mediated through a large subfamily of plant aquaglyceroporins, nodulin 26-like intrinsic proteins (NIPs). However, the efflux mechanisms, as well as the mechanism of arsenite-induced root growth inhibition, remain poorly understood. Using molecular physiology, synchrotron imaging, and root transport assay approaches, we show that the cellular transport of trivalent arsenicals inArabidopsis thalianais strongly modulated by PIN FORMED 2 (PIN2) auxin efflux transporter. Direct transport assay using radioactive arsenite, X-ray fluorescence imaging (XFI) coupled with X-ray absorption spectroscopy (XAS), and ICP-MS analysis revealed thatpin2plants accumulate higher concentrations of arsenite in root compared to wild-type. At the cellular level, arsenite specifically targets intracellular cycling of PIN2 and thereby alters the cellular auxin homeostasis. Consistently, loss of PIN2 results in aresenite hypersensitivity in root. XFI coupled with XAS further revealed that loss of PIN2 results in specific accumulation of arsenical species, but not the other metals like iron, zinc or calcium in the root tip. Collectively, these results demonstrate that PIN2 serves as a putative transporter of arsenical speciesin planta.
Systematic variation in marine dissolved organic matter stoichiometry and remineralization ratios as a function of lability
Authors: Zakem Emily J. , Levine Naomi M.
Published: July 2019

Remineralization of organic matter by heterotrophic organisms regulates the biological sequestration of carbon, thereby mediating atmospheric CO2. While surface nutrient supply impacts the elemental ratios of primary production, stoichiometric control by remineralization remains unclear. Here we develop a mechanistic description of remineralization and its stoichiometry in a marine microbial ecosystem model. The model simulates the observed elemental plasticity of phytoplankton and the relatively constant, lower C:N of heterotrophic biomass. In addition, the model captures the observed decreases in DOC:DON and the C:N remineralization ratio with depth for more labile substrates, which are driven by a switch in the dominant source of labile DOM from phytoplankton to heterotrophic biomass. Only a model version with targeted remineralization of N-rich components is able to simulate the observed profiles of preferential remineralization of DON relative to DOC and the elevated C:N of bulk DOM. The model suggests that more labile substrates are associated with C-limited heterotrophic growth and not with preferential remineralization, while more recalcitrant substrates are associated with growth limited by processing rates and with preferential remineralization. The resulting patterns of variable remineralization stoichiometry mediate the extent to which a proportional increase in carbon production resulting from changes in phytoplankton stoichiometry can increase the efficiency of the biological pump. Results emphasize the importance of understanding the physiology of both phytoplankton and heterotrophs for anticipating changes in biologically driven ocean carbon storage.
A direct role for SNX9 in the biogenesis of filopodia
Authors: Jarsch IK , Gadsby JR , Nuccitelli A , Mason J , Shimo H , Pilloux L , Marzook B , Mulvey CM , Dobramysl U , Lilley KS , Hayward RD , Vaughan TJ , Dobson CL , Gallop JL
Published: July 2019

Filopodia are finger-like actin-rich protrusions that extend from the cell surface and are important for cell-cell communication and pathogen internalization. The small size and transient nature of filopodia combined with shared usage of actin regulators within cells confounds attempts to identify filopodial proteins. Here, we used phage display phenotypic screening to isolate antibodies that alter the actin morphology of filopodia-like structuresin vitro. We found that all of the antibodies that cause shorter FLS interact with SNX9, an actin regulator that binds phosphoinositides during endocytosis and in invadopodia. In cells, we discover SNX9 at specialised filopodia inXenopusdevelopment and that SNX9 is an endogenous component of filopodia that are hijacked byChlamydiaentry. We show the use of antibody technology to identify proteins used in filopodia-like structures, and a role for SNX9 in filopodia.
Analysis of stochastic timing of intracellular events with gene switching
Authors: Ghusinga Khem Raj , Singh Abhyudai
Published: July 2019

An important step in execution of several cellular processes is accumulation of a regulatory protein up to a specific threshold level. Since production of a protein is inherently stochastic, the time at which its level crosses a threshold exhibits cell-to-cell variation. A problem of interest is to characterize how the statistics of event timing is affected by various steps of protein expression. Our previous work studied this problem by considering a gene expression model where gene was always active. Here we extend our analysis to a scenario where gene stochastically switches between active and inactive states. We formulate event timing as the first-passage time for a protein’s level to cross a threshold and investigate how the rates of gene activation/inactivation affect the distribution and moments of the first-passage time. Our results show that both the time-scale of gene switching with respect to the protein degradation rate as well as the ratio of the gene inactivation to gene activation rates are important parameters in shaping the event-timing distribution.
Quantification ofnosZgenes and transcripts in activated sludge microbiomes with novel group-specific qPCR methods validated with metagenomic analyses
Authors: Kim DaeHyun D. , Park Doyoung , Yoon Hyun , Yun Taeho , Song Min Joon , Yoon Sukhwan
Published: July 2019

Substantial N2O emission results from activated sludge nitrogen removal processes. The importance of N2O-reducers possessing NosZ-type N2O reductases have been recognized as the only N2O sinkin situkey to determination of the net N2O emissions; however, reliable quantification methods fornosZgenes and transcripts have yet to be developed. Here,nosZgenes and transcripts in activated sludge tank microbiomes were analyzed with the group-specific qPCR assays designedde novocombining culture-based and computational approach. A sewage sample was enriched in a batch reactor fed continuous stream of N2containing 20-10,000 ppmv N2O, where 14 genera of potential N2O-reducers were identified. All available amino acid sequences of NosZ affiliated to these taxa were grouped into five subgroups (two clade I and three clade II groups), and primer/probe sets exclusively and comprehensively targeting the subgroups were designed and validated within silicoPCR. Four distinct activated sludge samples from three different wastewater treatment plants in Korea were analyzed with the qPCR assays and the results were validated by comparison with the shotgun metagenome analysis results. With the validated qPCR assays, thenosZgenes and transcripts of six additional activated sludge samples were analyzed and the results of the analyses clearly indicated the dominance of two clade IInosZsubgroups (Flavobacterium-like andDechloromonas-like) among bothnosZgene and transcript pools.
Composition and Diversity of CRISPR-Cas13a systems in the genus Leptotrichia
Authors: Watanabe Shinya , Cui Bintao , Kiga Kotaro , Aiba Yoshifumi , Tan Xin-Ee , Sato’o Yusuke , Kawauchi Moriyuki , Boonsiri Tanit , Thitiananpakorn Kanate , Taki Yusuke , Li Fen-Yu , Azam Aa Haeruman , Nakada Yumi , Sasahara Teppei , Cui Longzhu
Published: July 2019

Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas13a, previously known as CRISPR-C2c2, is the most recently identified RNA-guided RNA-targeting CRISPR-Cas system and has the unique characteristics of both targeted and collateral single-stranded RNA (ssRNA) cleavage activities, which was first identified in Leptotrichia shahii CRISPR-Cas13a. Here, the complete whole genome sequences of 11 Leptotrichia strains were determined and compared with 18 publicly available Leptotrichia genomes in regard to the composition, occurrence and diversity of the CRISPR-Cas13a and other CRISPR-Cas systems. Various types of CRISPR-Cas systems, I-B, II-C, III-A, III-D, III-like and VI-A, were unevenly distributed among the Leptotrichia genomes, accounting for 10 (34.4%), 1 (2.6%), 6 (15.4%), 6 (15.4%), 3 (7.7%) and 11 (37.9%) of the 29 strains, respectively, while 8 (20.5%) strains had no CRISPR-Cas system. The Cas13a effectors were highly divergent with amino acid sequence similarities ranging from 61% to 90% to that of L. shahii and their collateral ssRNA cleavage activities, resulting in cytotoxicity to host cell, were found to be maintained. CRISPR-Cas spacers represent a sequential achievement of former intruder encounters, and the retained spacers reflect the evolutionary phylogeny or relatedness of strains. Analysis of spacer contents and numbers among Leptotrichia species showed considerable diversity with only 2 (0.5%) of 400 spacers through CRIPSR-Cas I-VI were shared by two strains. The organisation and distribution of CRISPR-Cas systems (type I-VI) encoded by all registered Leptotrichia species revealed that effector or spacer sequences of the CRISPR-Cas systems were very divergent, and the prevalence of types I, III and VI was almost equal. There was only one strain carrying type II, while none carried type IV or V. These results provide new insights into the characteristics and divergences of CRISPR-Cas systems among Leptotrichia species.
MGSE regulates crosstalk from the mucin pathway to the TFE3 pathway of the Golgi stress response
Authors: Jamaludin Mohamad Ikhwan , Wakabayashi Sadao , Sasaki Kanae , Komori Ryota , Kawamura Hirotada , Takase Hayataka , Sakamoto Miyu , Yoshida Hiderou
Published: July 2019

The Golgi apparatus is an organelle where membrane or secretory proteins receive post-translational modifications such as glycosylation and sulfation, after which the proteins are selectively transported to their final destinations through vesicular transport. When the synthesis of secretory or membrane proteins is increased and overwhelms the capacity of the Golgi (Golgi stress), eukaryotic cells activate a homeostatic mechanism called the Golgi stress response to augment the capacity of the Golgi. Four response pathways of the Golgi stress response have been identified, namely the TFE3, CREB3, HSP47, and proteoglycan pathways, which regulate the general function of the Golgi, apoptosis, cell survival, and proteoglycan glycosylation, respectively. Here, we identified a novel response pathway that augments the expression of glycosylation enzymes for mucins in response to insufficiency in mucin-type glycosylation in the Golgi (mucin-type Golgi stress), and we found that expression of glycosylation enzymes for mucins such as GALNT5, GALNT8, and GALNT18 was increased upon mucin-type-Golgi stress. We named this pathway the mucin pathway. Unexpectedly, mucin-type Golgi stress induced the expression and activation of TFE3, a key transcription factor regulating the TFE3 pathway, suggesting that the activated mucin pathway sends a crosstalk signal to the TFE3 pathway. We identified an enhancer element regulating transcriptional induction of TFE3 upon mucin-type Golgi stress, and named it the mucin-type Golgi stress response element, of which consensus was ACTTCC(N9)TCCCCA. These results suggested that crosstalk from the mucin pathway to the TFE3 pathway has an important role in the regulation of the mammalian Golgi stress response.
Diversity, dynamics and effects of LTR retrotransposons in the model grassBrachypodium distachyon
Authors: Stritt C , Wyler M , Gimmi EL , Pippel M , Roulin AC
Published: July 2019

Transposable elements (TEs) are the main reason for the high plasticity of plant genomes, where they occur as communities of diverse evolutionary lineages. Because research has typically focused on single abundant families or summarized TEs at a coarse taxonomic level, our knowledge about how these lineages differ in their effects on genome evolution is still rudimentary.

Here we investigate the community composition and dynamics of 32 long terminal repeat retrotransposon (LTR-RT) families in the 272 Mb genome of the Mediterranean grassBrachypodium distachyon.

We find that much of the recent transpositional activity in theB. distachyongenome is due to centromericGypsyfamilies andCopiaelements belonging to the Angela lineage. With a half-life as low as 66 ky, the latter are the most dynamic part of the genome and an important source of within-species polymorphisms. Second, GC-richGypsyelements of the Retand lineage are the most abundant TEs in the genome. Their presence explains more than 20 percent of the genome-wide variation in GC content and is associated to higher methylation levels.

Our study shows how individual TE lineages change the genetic and epigenetic constitution of the host beyond simple changes in genome size.
Parallel ecological and evolutionary responses to selection in a natural bacterial community
Authors: Hesse Elze , Luján Adela M. , O’Brien Siobhan , Newbury Arthur , McAvoy Terence , Pascual Jesica Soria , Bayer Florian , Hodgson Dave J. , Buckling Angus
Published: July 2019

Evolution can occur over ecological timescales, suggesting a potentially important role for rapid evolution in shaping community trait distributions. However, evidence of concordant eco-evolutionary dynamics often comes fromin vitrostudies of highly simplified communities, and measures of ecological and evolutionary dynamics are rarely directly comparable. Here, we quantified how ecological species sorting and rapid evolution simultaneously shape community trait distributions by tracking within and between-species changes in a key trait in a complex bacterial community. We focused on the production of siderophores; bacteria use these costly secreted metabolites to scavenge poorly soluble iron and to detoxify environments polluted with toxic non-ferrous metals. We found that responses to copper-imposed selection within and between species were ultimately the same – intermediate siderophore levels were favored – and occurred over similar timescales. Despite being a social trait, this level of siderophore production was selected regardless of whether species evolved in isolation or in a community context. Our study suggests that evolutionary selection can play a pivotal role in shaping community trait distributions within natural, highly complex, bacterial communities. Furthermore, trait evolution may not always be qualitatively affected by interactions with other community members.

Significance

Bacterial communities possess remarkable taxonomic and metabolic diversity and play a key role in nearly every biogeochemical process on Earth. Rapid evolution (occurring over ecological time scales) can in principle shape these processes, yet we have little understanding of its importance in natural communities. Here, we quantified how the production of metal-detoxifying siderophores is driven by species compositional changes and evolution in a compost community in response to copper stress. We found that siderophore production converged at intermediate levels, with evolutionary and ecological changes occurring at similar rates. Understanding how ecological and evolutionary processes contribute to shaping trait distributions will improve our ability to predict ecosystem responses to global change, and aid in the engineering of microbial consortia.
Stable Biomarker Identification For Predicting Schizophrenia in the Human Connectome
Authors: Gutiérrez-Gómez Leonardo , Vohryzek Jakub , Chiêm Benjamin , Baumann Philipp S. , Conus Philippe , Do Cuenod Kim , Hagmann Patric , Delvenne Jean-Charles
Published: July 2019

Schizophrenia, as a psychiatric disorder, has recognized brain alterations both at the structural and at the functional magnetic resonance imaging level. The developing field of connec-tomics has attracted much attention as it allows researchers to take advantage of powerful tools of network analysis in order to study structural and functional connectivity abnormalities in schizophrenia. Many methods have been proposed to identify biomarkers in schizophrenia, focusing mainly on improving the classification performance or performing statistical comparisons between groups. However, the stability of biomarkers selection has been for long overlooked in the connectomics field. In this study, we follow a machine learning approach where the identification of biomarkers is addressed as a feature selection problem for a classification task. We perform a recursive feature elimination and support vector machines (RFE-SVM) approach to identify the most meaningful biomarkers from the structural, functional, and multi-modal connectomes of healthy controls and patients. Furthermore, the stability of the retrieved biomarkers is assessed across different subsamplings of the dataset, allowing us to identify the affected core of the pathology. Considering our technique altogether, it demonstrates a principled way to achieve both accurate and stable biomarkers while highlighting the importance of multi-modal approaches to brain pathology as they tend to reveal complementary information.
Addressing lipid structural diversity in signalling: Photochemical probes for live-cell lipid biochemistry
Authors: Schuhmacher Milena , Grasskamp Andreas T. , Wagner Nicolai , Lombardot Benoit , Schuhmacher Jan S. , Sala Pia , Lohmann Annett , Henry Ian , Shevchenko Andrej , Coskun Ünal , Walter Alexander M. , Nadler André
Published: July 2019

Every cell produces thousands of distinct lipid species, but methodology for studying the biological roles of individual lipids is insufficient. Using the example of diacylglycerols, prominent second messengers, we here investigate whether lipid chemical diversity can provide a basis for cellular signal specification. We developed novel photo-caged lipid probes, which allow acute manipulation of distinct diacylglycerol species in the plasma membrane. Combining uncaging experiments with mathematical modelling enabled the determination of binding constants for diacylglycerol-protein interactions and kinetic parameters for diacylglycerol transbilayer movement and turnover in quantitative live-cell experiments. Strikingly, we find that affinities and kinetics vary by orders of magnitude due to diacylglycerol structural diversity. These differences are sufficient to explain differential recruitment of diacylglycerol binding proteins and thus differing downstream phosphorylation patterns. Our approach represents a generally applicable method for elucidating the biological function of single lipid species on subcellular scales.
Heat dissipation capacity influences reproductive performance in an aerial insectivore
Authors: Tapper Simon , Nocera Joseph J. , Burness Gary
Published: July 2019

Climatic warming will likely increase the frequency of extreme weather events, which may reduce an individual’s capacity for sustained activity due to thermal limits. We tested whether the risk of overheating may limit parental provisioning of an aerial insectivorous bird in population decline. For many seasonally breeding birds, parents are thought to operate close to an energetic ceiling during the 2-3 week chick-rearing period. The factors determining the ceiling remain unknown, although it may be set by an individual’s capacity to dissipate body heat (the heat dissipation limitation hypothesis). To test this hypothesis, over two breeding seasons we experimentally trimmed the ventral feathers of female tree swallows (Tachycineta bicolor) to provide a thermal window. We then monitored maternal provisioning rates, nestling growth rates, and fledging success. We found the effect of our experimental treatment was context-dependent and varied with environmental conditions. Females with trimmed plumage fed their nestlings at higher rates than controls when conditions were hot and non-windy, but the reverse was true under cool and windy conditions. On average, nestlings of trimmed females were heavier than controls, and had a higher probability of fledging. We suggest that removal of a thermal constraint allowed females to increase provisioning rates, but additionally provided nestlings with a thermal advantage via increased heat transfer during maternal brooding. Our data provide partial support for the heat dissipation limitation hypothesis, and suggest that depending on weather patterns, heat dissipation capacity can influence reproductive success in aerial insectivores.