bluuebunny/crossref_metadata_2025 huggingface dataset:
Establishing K-levels and prescribing transtibial prostheses using six-minute walk test and one-leg standing test on prosthesis: a retrospective audit
Authors: Majdič Neža , Vidmar Gaj , Burger Helena
Published: January 2020

Rehabilitation programs after amputation often include fitting a prosthesis, but prescriptions vary under similar circumstances. The US Medicare Functional Classification Level (K-level) is a scale for describing functional abilities of persons after lower-limb amputation (from 0 = no ability or potential to ambulate, to 4 = prosthetic demands of a child/active adult/athlete). Different outcome measures are used to assess K-level, including six-minute walk test (6MWT). We attempted to predict the assigned K-level of unilateral transtibial prosthesis users from their results of 6MWT and one-leg standing test on prosthesis (OLSTP). Outpatients who had been rehabilitated and fitted with transtibial prosthesis at the University Rehabilitation Institute in Ljubljana in 2014 were included in a retrospective audit. The data were analysed using receiver-operating-characteristics curves, linear discriminant analysis, classification trees and ordinal logistic regression. Among the 120 patients (aged 39–90, mean 67 years; 79% men), eight belonged to K1 level, 94 to K2, and 18 to K3 or K4; 61 could not stand on the prosthesis, eight stood on it for 1 s, and 51 stood on it for 2 s or more. With a simple classification rule based only on 6MWT (130 m threshold for K2/K3/K4 vs. K1, 340 m for K3/K4 vs. K1/K2), we observed sensitivity and specificity close to 90%. The more sophisticated statistical approaches yielded substantially similar and comparably accurate results. 6MWT and OLST could therefore be used as predictors for transtibial prosthesis prescription in clinical practice.
Embryonal Rhabdomyosarcoma of the Ovary and Fallopian Tube
Authors: McCluggage W. Glenn , Apellaniz-Ruiz Maria , Chong Anne-Laure , Hanley Krisztina Z. , Velázquez Vega Jose E. , McVeigh Terri P. , Foulkes William D.
Published: January 2020

DICER1 mutations (somatic or germline) are associated with a variety of uncommon neoplasms including cervical and genitourinary embryonal rhabdomyosarcoma (ERMS). We report a primary ovarian and 2 primary fallopian tube ERMS occurring in 60-, 13-, and 14-year-olds, respectively. The 3 neoplasms exhibited a similar morphologic appearance being polypoid and containing edematous hypocellular areas and hypercellular foci composed of small cells with scant cytoplasm exhibiting rhabdomyoblastic differentiation (desmin, myogenin, myoD1 positive). There was cellular cartilage in all cases and extensive foci of anaplasia, eosinophilic globules, and bone/osteoid in 1 case each. All 3 neoplasms exhibited DICER1 mutations; in 1 of the tubal cases, the patient had a germline mutation and in the other 2 cases, the DICER1 mutations were somatic. Accompanying DICER1 “second hits” were identified in all cases. In 2 of the neoplasms, SALL4-positive glandular structures were present which we speculate may represent an unusual primitive “metaplastic” phenomenon. Our study adds to the literature on ERMS at unusual sites associated with DICER1 mutations. ERMS arising at such sites, especially when they contain cartilage or bone/osteoid, are especially likely to be associated with DICER1 mutations. Pathologists should be aware of this as these may be the sentinel neoplasms in patients with DICER1 syndrome and confirming a germline mutation can facilitate the screening of the individual and affected family members for other neoplasms which occur in this syndrome.
Fungal infections of the skin and soft tissue
Authors: Gunaydin Sibel Dogan , Arikan-Akdagli Sevtap , Akova Murat
Published: January 2020

Purpose of review

This review aims to update on recent findings about epidemiology, risk factors and therapeutic options for fungi causing skin and soft tissue infections. The latest data on emerging antifungal resistance are also discussed.

Recent findings

In parallel with increased use of immunosuppression, the incidence of fungal infections is also on rise. This increase involves not only systemic infections but also infections with primary and secondary skin involvement. Antifungal resistance has become a major issue and covers several fungal pathogens including dermatophytes,Candidaspp. and,Aspergillus fumigatus. Multidisciplinary usage of newly targeted, immunomodulatory therapies may predispose patients to have fungal infections through mimicking an immunosuppressed status caused by genetic factors or the disease itself. Nonimmunosupressed patients, although less frequently than those with immunosuppression may also be vulnerable.

Physicians should be aware about skin and soft tissue findings related with systemic or locally occuring mycosis. Emerging antifungal resistance may hamper the success of the treatment. Antifungal susceptibility testing is advisable wherever available and particularly when a disseminated fungal infection is present.
Prolapse Recurrence After Sacrocolpopexy Mesh Removal: A Retrospective Cohort Study
Authors: Sassani Jessica C. , Ross James H. , Lopa Samia , Handzel Robert M. , Bradley Megan S. , Bonidie Michael
Published: January 2020

Objectives

There is limited literature regarding outcomes after sacrocolpopexy mesh removal. We sought to compare the proportion of prolapse recurrence in women after sacrocolpopexy mesh removal with women who underwent sacrocolpopexy without subsequent mesh removal. We hypothesize that more women will experience prolapse recurrence after mesh removal.

Methods

This is a retrospective cohort study of women who underwent sacrocolpopexy mesh removal between 2010 and 2019. These patients were time matched with women who had a sacrocolpopexy but did not undergo mesh removal. Prolapse recurrence was defined as the leading edge past the hymen or retreatment. Analysis was done using χ2, Wilcoxon rank-sum, or t test with a Cox proportional hazard model to assess the association between mesh removal and time to recurrence.

Results

We identified 26 mesh removals, which were matched with 78 patients without mesh removal. The most common indications for mesh removal were exposure (69.2%) and pain (57.7%). Women who underwent mesh removal were more likely to have Mersilene mesh (19.2% vs 1.3%, P = 0.006). Recurrence occurred in 46% of women who had mesh removal compared with 7.7% in those without (P < 0.001). When adjusted for age, parity, menopause, smoking, and diabetes status, those who had mesh removal had a 15 times higher hazard of prolapse recurrence (adjusted hazard ratio = 15.4, 95% confidence interval = 4.3–54.8, P = <.0001).

Conclusions

When compared with time-matched controls, women who underwent sacrocolpopexy mesh removal had a significantly higher proportion of prolapse recurrence. Prospective studies are needed to further explore the utility of concomitant prolapse repair at the time of mesh removal.
Surgeon-Team Separation in Robotic Theaters: A Qualitative Observational and Interview Study
Authors: El-Hamamsy Dina , Walton Thomas J. , Griffiths T.R. Leyshon , Anderson Elizabeth S. , Tincello Douglas G.
Published: January 2020

Background

The rapid uptake of robotic surgery has largely been driven by the improved technical aspects of minimally invasive surgery including improved ergonomics, wristed instruments, and 3-dimensional vision. However, little attention has been given to the effect of physical separation of the surgeon from the rest of the operating team.

Purpose

The aim of this study was to examine in depth how this separation affected team dynamics and staff emotions.

Methods

Robotic procedures were observed in 2 tertiary hospitals, and laparoscopic/open procedures were added for comparison; field notes were taken instantaneously. One-to-one interviews with theater team members were audio recorded and transcribed verbatim. Qualitative analysis was conducted via grounded theory approach using NVIVO11.

Results

Twenty-nine participants (26 interviewed) were recruited to the study (11 females) and 134 (109 robotic) hours of observation were completed across gynecology, urology, and colorectal surgery.

The following 3 main themes emerged with compounding factors identified: (a) communication challenge, (b) immersion versus distraction, and (c) emotional impact. Compounding factors included the following: individual and team experience, staffing levels, and the physical theater environment.

Conclusions

Our emergent theory is that “surgeon-team separation in robotic theaters poses communication challenges which impacts on situational awareness and staff emotions.” These can be ameliorated by staff training, increased experience, and team/procedure consistency.
Intrinsic excitation-inhibition imbalance affects medial prefrontal cortex differently in autistic men versus women
Authors: Trakoshis Stavros , Martínez-Cañada Pablo , Rocchi Federico , Canella Carola , You Wonsang , Chakrabarti Bhismadev , Ruigrok Amber N. V. , Bullmore Edward T. , Suckling John , Markicevic Marija , Zerbi Valerio ,   MRC AIMS Consortium, Baron-Cohen Simon , Gozzi Alessandro , Lai Meng-Chuan , Panzeri Stefano , Lombardo Michael V.
Published: January 2020

Excitation-inhibition (E:I) imbalance is theorized as an important pathophysiological mechanism in autism. Autism affects males more frequently than females and sex-related mechanisms (e.g., X-linked genes, androgen hormones) can influence E:I balance. This suggests that E:I imbalance may affect autism differently in males versus females. With a combination ofin-silicomodeling andin-vivochemogenetic manipulations in mice, we first show that a time-series metric estimated from fMRI BOLD signal, the Hurst exponent (H), can be an index for underlying change in the synaptic E:I ratio. In autism we find that H is reduced, indicating increased excitation, in the medial prefrontal cortex (MPFC) of autistic males but not females. Increasingly intact MPFC H is also associated with heightened ability to behaviorally camouflage social-communicative difficulties, but only in autistic females. This work suggests that H in BOLD can index synaptic E:I ratio and that E:I imbalance affects autistic males and females differently.
Biomolecular condensates undergo a generic shear-mediated liquid-to-solid transition
Authors: Shen Yi , Ruggeri Francesco Simone , Vigolo Daniele , Kamada Ayaka , Qamar Seema , Levin Aviad , Iserman Christiane , Alberti Simon , George-Hyslop Peter St , Knowles Tuomas P. J.
Published: January 2020

A wide range of systems containing proteins have been shown to undergo liquid-liquid phase separation (LLPS) forming membraneless compartments, such as processing bodies1, germ granules2, stress granules3and Cajal bodies4. The condensates resulting from this phase transition control essential cell functions, including mRNA regulation, cytoplasm structuring, cell signalling and embryogenesis1–4. RNA-binding Fused in Sarcoma (FUS) protein is one of the most studied systems in this context, due to its important role in neurodegenerative diseases5–7. It has recently been discovered that FUS condensates can undergo an irreversible phase transition which results in fibrous aggregate formation6. Gelation of protein condensates is generally associated with pathology. One case where liquid-to-solid transition (LST) of liquid-liquid phase separated proteins is functional, however, is that of silk spinning8,9, which is largely driven by shear, but it is not known what factors control the pathological gelation of functional condensates. Here we show that four proteins and one peptide system not related to silk, and with no function associated with fibre formation, have a strong propensity to undergo LST when exposed to even low levels of mechanical shear comparable to those found inside a living cell, once present in their liquid-liquid phase separated forms. Using microfluidics to control the application of mechanical shear, we generated fibres from single protein condensates and characterized their structures and material properties as a function of shear stress. Our results inform on the molecular grammar underlying protein LST and highlight generic backbone-backbone hydrogen bonding constraints as a determining factor in governing this transition. Taken together, these observations suggest that the shear plays an important role in the irreversible phase transition of liquid-liquid phase separated droplets, shed light on the role of physical factors in driving this transition in protein aggregation related diseases, and open a new route towards artificial shear responsive biomaterials.
Resting and functional pupil response metrics indicate features of reward sensitivity and Autism Spectrum Disorder in children
Authors: DiCriscio Antoinette Sabatino , Troiani Vanessa
Published: January 2020

Altered motivational drives and aberrant reward system function may contribute to the social impairments observed in autism spectrum disorders (ASD). Pupil metrics have been highlighted as peripheral indicators of autonomic arousal and reward system function, specifically noradrenergic and dopaminergic activity that influence motivational drive states. However, research on individual differences in the neurobiological correlates of reward responsivity and clinically relevant features associated with ASD is sparse. The goal of the current study was to examine the relationship between measures of sensitivity to punishment and reward, ASD features, and resting as well as functional pupil response metrics across a clinically heterogeneous pediatric sample. We assessed whether quantitative features of reward sensitivity are linearly related to core clinical features of ASD. Pupil metrics were measured using a passive eye tracking task. Scores on a parent-report measure of punishment and reward sensitivity were found to be positively correlated with ASD features. Given these relationships, we assessed whether pupil measurements could be used as a neurobiological correlate of reward sensitivity and predictor of clinically significant ASD traits. In a logistic regression model, we find that the amplitude of pupil dilation, along with sex and full-scale IQ, could be used to correctly classify 84.9% of participants as having an ASD diagnosis versus not having an ASD diagnosis. This research highlights individual differences of reward sensitivity that scale with ASD features. Furthermore, reported results emphasize that functional pupil response metrics and other objective patient-level variables can be used together as predictors of ASD diagnostic status.
Synaptic loss in primary tauopathies revealed by [11C]UCB-J positron emission tomography
Authors: Holland Negin , Jones P. Simon , Savulich George , Wiggins Julie K. , Hong Young T. , Fryer Tim D. , Manavaki Roido , Sephton Selena Milicevic , Boros Istvan , Malpetti Maura , Hezemans Frank H. , Aigbirhio Franklin I. , Coles Jonathan P. , O’Brien John , Rowe James B.
Published: January 2020

Background

Synaptic loss is a prominent and early feature of many neurodegenerative diseases.

Objectives

We tested the hypothesis that synaptic density is reduced in the primary tauopathies of progressive supranuclear palsy (PSP-Richardson’s syndrome) and amyloid-negative corticobasal syndrome (CBS).

Methods

Forty four participants (15 CBS, 14 PSP, and 15 age-/sex-/education-matched controls) underwent positron emission tomography (PET) with the radioligand [11C]UCB-J, which binds to synaptic vesicle glycoprotein 2A (SV2A), a marker of synaptic density; participants also had 3T magnetic resonance imaging and clinical and neuropsychological assessment.

Results

Nine CBS patients had negative amyloid biomarkers determined by [11C]PiB PET and hence were deemed likely to have corticobasal degeneration (CBD). Patients with PSP-Richardson’s syndrome and amyloid-negative CBS were impaired in executive, memory and visuospatial tasks. [11C]UCB-J binding was reduced across frontal, temporal, parietal, and occipital lobes, cingulate, hippocampus, insula, amygdala and subcortical structures in both PSP and CBD patients compared to controls (p<0.01), with median reductions up to 50%, consistent with post mortem data. Reductions of 20-30% were widespread even in the areas of the brain with minimal atrophy. There was a negative correlation between global [11C]UCB-J binding and the PSP and CBD rating scales (R= −0.61 p<0.002, R= −0.72 p<0.001, respectively) and a positive correlation with the revised Addenbrookes Cognitive Examination (R=0.52, p=0.01).

Conclusions

We confirm severe synaptic loss in PSP and CBD in proportion to disease severity, providing critical insight into the pathophysiology of primary degenerative tauopathies. [11C]UCB-J may facilitate treatment strategies for disease-modification, synaptic maintenance or restoration.
Streptococcus intermedius as a leading agent of brain abscess: retrospective analysis of a UK cohort
Authors: Darlow Christopher A , McGlashan Nicholas , Kerr Richard , Oakley Sarah , Pretorius Pieter , Jones Nicola , Matthews Philippa C
Published: January 2020

Background

Brain abscess is an uncommon condition, but carries high mortality. Current treatment guidelines are based on limited data. Surveillance of clinical, radiological and microbiology data is important to inform patient stratification, interventions, and antimicrobial stewardship.

Methods

We undertook a retrospective, observational study of patients with brain abscess, based on hospital coding, in a UK tertiary referral teaching hospital. We reviewed imaging data, laboratory microbiology, and antibiotic prescriptions.

Results

Over a 47 month period, we identified 47 adults with bacterial brain abscess (77% male, median age 47 years). Most of the abscesses were solitary frontal or parietal lesions. A microbiological diagnosis was secured in 39/47 (83%) of cases, among which the majority were of the Streptococcus milleri group (27/39; 69%), with a predominance of Streptococcus intermedius (19/27; 70%). Patients received a median of 6 weeks of intravenous antibiotics (most commonly ceftriaxone), followed by variable oral follow-on regimens. Ten patients (21%) died, up to 146 days after diagnosis. Mortality was significantly associated with increasing age, multiple abscesses, immunosuppression and the presence of an underlying cardiac anomaly.

Conclusion

Our data suggest that there has been a shift away from staphylococcal brain abscesses, towards S. intermedius as a dominant pathogen. In our setting, empiric current first line therapy with ceftriaxone remains appropriate on microbiological grounds and narrower spectrum therapy may sometimes be justified. Mortality of this condition remains high among patients with comorbidity. Prospective studies are required to inform optimum dose, route and duration of antimicrobial therapy.
Brain network dynamics fingerprints are resilient to data heterogeneity
Authors: Menara Tommaso , Lisi Giuseppe , Pasqualetti Fabio , Cortese Aurelio
Published: January 2020

Large multi-site neuroimaging datasets have significantly advanced our quest to understand brain-behaviour relationships and to develop biomarkers of psychiatric and neurodegenerative disorders. Yet, such data collections come at a cost, as the inevitable differences across samples may lead to biased or erroneous conclusions. Previous work has investigated this critical issue in resting-state functional magnetic resonance imaging (rs-fMRI) data in terms of effects on static measures, such as functional connectivity and brain parcellations. Here, we depart from prior approaches and utilize dynamical models to examine how diverse scanning factors in multi-site fMRI recordings affect our ability to infer the brain’s spatiotemporal wandering between large-scale networks of activity. Building upon this premise, we first confirm the emergence of robust subject-specific dynamical patterns of brain activity. Next, we exploit these individual fingerprints to show that scanning sessions belonging to different sites and days tend to induce high variability, while other factors, such as the scanner manufacturer or the number of coils, affect the same metrics to a lesser extent. These results concurrently indicate that we can recover the unique trajectories of brain activity changes in each individual, but also that our ability to infer such patterns is affected by how, where and when we try to do so.

Author summary

We investigate the important issue of data heterogeneity in large multi-site data collections of brain activity recordings. At a time in which appraising the source of variability in large datasets is gaining increasing attention, this study provides a novel point of view based on data-driven dynamical models. By employing subject-specific signatures of brain network dynamics, we find that certain scanning factors significantly affect the quality of resting-state fMRI data. More specifically, we first validate the existence of subject-specific brain dynamics fingerprints. As a proof of concept, we show that dynamical states can be estimated reliably, even across different datasets. Finally, we assess which scanning factors, and to what extent, influence the variability of such fingerprints.
Super-resolved live-cell imaging using Random Illumination Microscopy
Authors: Mangeat Thomas , Labouesse Simon , Allain Marc , Martin Emmanuel , Poincloux Renaud , Bouissou Anaïs , Cantaloube Sylvain , Courtaux Elise , Vega Elodie , Li Tong , Guénolé Aude , Rouvière Christian , Allard Sophie , Campo Nathalie , Suzanne Magali , Wang Xiaobo , Michaux Grégoire , Pinot Mathieu , Borgne Roland Le , Tournier Sylvie , Idier Jérôme , Sentenac Anne
Published: January 2020

Super-resolution fluorescence microscopy has been instrumental to progress in biology. Yet, the photo-induced toxicity, the loss of resolution into scattering samples or the complexity of the experimental setups curtail its general use for functional cell imaging. Here, we describe a new technology for tissue imaging reaching a 114nm/8Hz resolution at 30 µm depth. Random Illumination Microscopy (RIM) consists in shining the sample with uncontrolled speckles and extracting a high-fidelity super-resolved image from the variance of the data using a reconstruction scheme accounting for the spatial correlation of the illuminations. Super-resolution unaffected by optical aberrations, undetectable phototoxicity, fast image acquisition rate and ease of use, altogether, make RIM ideally suited for functional live cell imagingin situ. RIM ability to image molecular and cellular processes in three dimensions and at high resolution is demonstrated in a wide range of biological situations such as the motion of Myosin II minifilaments inDrosophila.
Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant
Authors: Chawla Harmeet Singh , Lee HueyTyng , Gabur Iulian , Tamilselvan-Nattar-Amutha Suriya , Obermeier Christian , Schiessl Sarah V. , Song Jia-Ming , Liu Kede , Guo Liang , Parkin Isobel A. P. , Snowdon Rod J.
Published: January 2020

Genome structural variation (SV) contributes strongly to trait variation in eukaryotic species and may have an even higher functional significance than single nucleotide polymorphism (SNP). In recent years there have been a number of studies associating large, chromosomal scale SV ranging from hundreds of kilobases all the way up to a few megabases to key agronomic traits in plant genomes. However, there have been little or no efforts towards cataloging small (30 to 10,000 bp) to mid-scale (10,000 bp to 30,000 bp) SV and their impact on evolution and adaptation related traits in plants. This might be attributed to complex and highly-duplicated nature of plant genomes, which makes them difficult to assess using high-throughput genome screening methods. Here we describe how long-read sequencing technologies can overcome this problem, revealing a surprisingly high level of widespread, small to mid-scale SV in a major allopolyploid crop species,Brassica napus. We found that up to 10% of all genes were affected by small to mid-scale SV events. Nearly half of these SV events ranged between 100 bp to 1000 bp, which makes them challenging to detect using short read Illumina sequencing. Examples demonstrating the contribution of such SV towards eco-geographical adaptation and disease resistance in oilseed rape suggest that revisiting complex plant genomes using medium-coverage, long-read sequencing might reveal unexpected levels of functional gene variation, with major implications for trait regulation and crop improvement.
PDZ and LIM domain protein 2 plays dual and context-dependent roles in breast cancer development
Authors: Maryas Josef , Pribyl Jan , Bouchalova Pavla , Skladal Petr , Bouchal Pavel
Published: January 2020

ABSTRACT

Background

PDZ and LIM domain protein 2 (PDLIM2) is a cytoskeletal and nuclear effector that regulates the activity of several transcription factors (e.g., NF-κB, STAT), and its deregulation has been associated with oncogenesis. Our recent study identified PDLIM2 as a protein associated with the lymph node metastasis of low grade luminal A breast cancer tissues. Here, we aim to understand this association at the molecular and cellular levels.

Methods

To investigate the link between PDLIM2 and epithelial-to-mesenchymal transition (EMT), stably transduced MCF7-PDLIM2 cells, and MCF7 or MCF10A cells with PDLIM2 protein levels modified using siRNA orPDLIM2gene carrying plasmid, were used. Additionally, MCF7 and MCF10A cells were exposed to hypoxic conditions and TGFβ1 treatment. EMT was monitored using immunoblotting of EMT markers and atomic force microscopy (AFM). The role of PDLIM2 in cell migration and/or invasion was investigated using Transwell assay and xCELLigence system.

Results

First, we observe a positive effect of PDLIM2 overexpression on EMT in MCF7 cells, a model of luminal A tumors, using EMT markers and AFM. On the other hand, PDLIM2 helps to maintain the epithelial phenotype in MCF10A cells, a model of normal breast epithelial cells. Second, we find that exposure of the MCF7 cells to hypoxic conditions increases levels of PDLIM2 and carbonic anhydrase-9 (CA-9), a marker of the response to hypoxia. However, none of these effects are observed in the MCF10A cells. Third, PDLIM2 overexpression promotes migration, invasion, and proliferation and decreases adhesion of the MCF7 cells, but an opposite effect is observed in the MCF10A cells.

Conclusions

Our data indicate that PDLIM2 plays a dual role: (i) as an EMT-supporting and hypoxia-responding oncoprotein in luminal breast cancer cells, and (ii) as an epithelial phenotype-maintaining tumor suppressor in normal epithelial breast cells.
Irrelevant Predictions: Distractor Rhythmicity Modulates Neural Encoding in Auditory Cortex
Authors: Makov Shiri , Zion-Golumbic Elana
Published: January 2020

Dynamic Attending Theory suggests that predicting the timing of upcoming sounds can assist in focusing attention towards them. However, whether similar predictive processes are also applied to background noises and assist in guiding attentionawayfrom potential distractors, remains an open question. Here we address this question by manipulating the temporal predictability of distractor sounds in a dichotic listening selective attention task. We tested the influence of distractors’ temporal predictability on performance and on the neural encoding of sounds, by comparing the effects of Rhythmic vs. Non-rhythmic distractors. Using Magnetoencephalography (MEG) we found that, indeed, the neural responses to both attended and distractor sounds were affected by distractors’ rhythmicity. Baseline activity preceding the onset of Rhythmic distractor sounds was enhanced relative to Non-rhythmic distractor sounds, and sensory response were suppressed. Moreover, when distractors were Rhythmic, responses to attended sounds were more strongly lateralized to the contra-lateral hemisphere. Behavioral performance also improved in the Rhythmic condition. These combined behavioral and neural results suggest that not only are temporal predictions formed for task-irrelevant sounds, but that these predictions bear functional significance for promoting selective attention and reducing distractibility.
Correlated motions of conserved polar motifs lay out a plausible mechanism of G protein-coupled receptor activation
Authors: Mitra Argha , Sarkar Arijit , Szabó Márton R. , Borics Attila
Published: January 2020

Recent advancements in the field of experimental structural biology have provided high-resolution structures of active and inactive state G protein-coupled receptors (GPCRs), a highly important pharmaceutical target family, but the process of transition between these states is poorly understood. According to the current theory, GPCRs exist in structurally distinct, dynamically interconverting functional states of which populations are shifted upon binding of ligands and intracellular signaling proteins. However, explanation of the activation mechanism on an entirely structural basis gets complicated when multiple activation pathways and active receptor states are considered. Our unbiased, atomistic molecular dynamics simulations of the mu-opioid receptor in a physiological environment revealed that external stimulus is propagated to the intracellular surface of the receptor through subtle, concerted movements of highly conserved polar amino acid side chains along the 7thtransmembrane helix. To amend the widely accepted theory we suggest that the initiation event of GPCR activation is the shift of macroscopic polarization between the ortho- and allosteric binding pockets and the intracellular G protein-binding interface.

Abstract Figure

Table of Contents Graphic
Simultaneous stimulation of RuBP regeneration and electron transport increases productivity and water use efficiency under field conditions
Authors: López-Calcagno Patricia E. , Brown Kenny L. , Simkin Andrew J. , Fisk Stuart J. , Lawson Tracy , Raines Christine A.
Published: January 2020

Previous studies have demonstrated that independent stimulation of either electron transport or RuBP regeneration can increase the rate of photosynthetic carbon assimilation and plant biomass. In this paper, we present evidence that a multi-gene approach to simultaneously manipulate these two processes provides a further stimulation of photosynthesis. We report on the introduction of the cyanobacterial bifunctional enzyme fructose-1,6-bisphosphatase/sedoheptulose-1,7-bisphosphatase or overexpression of the plant enzyme sedoheptulose-1,7-bisphosphatase, together with expression of the red algal protein cytochromec6, and show that a further increase in biomass accumulation under both glasshouse and field conditions can be achieved. Furthermore, we provide evidence that the simultaneous stimulation of electron transport and RuBP regeneration can lead to enhanced intrinsic water use efficiency under field conditions.

One sentence summary

Simultaneous stimulation of RuBP regeneration and electron transport results in improvements in biomass yield in glasshouse and field grown tobacco.
Dynamic Order in Allosteric Interactions
Authors: Türeli Sina , Haliloğlu Türkan
Published: January 2020

Allostery is an intrinsic dynamic phenomenon that underlies functional long-distance interactions in proteins, which we study here by stochastic calculus approach to elastic network models (ENMs). We show that once you drop the usually accepted high friction limit and include hydrodynamic interactions in ENMs, a simple measure that uses the pairwise difference in the time-delayed correlations of residue fluctuations provides insight about functional sites and their dynamical behaviour in allosteric communication. We present this with three exemplary cases Aspartate Carbamoyl transferase, Insulin Receptor and DNA-dependent Protein Kinase. We show that proteins possess characteristic pathways operating at different time-delay windows with slow to faster motions underlying the protein function. As these pathways help communication between key residues of functionality, they can also be used to identify their locations without any prior knowledge other than the protein crystal structure.
pH effect on strain-specific transcriptomes of the take-all fungus
Authors: Gazengel Kévin , Lebreton Lionel , Lapalu Nicolas , Amselem Joëlle , Guillerm-Erckelboudt Anne-Yvonne , Tagu Denis , Daval Stéphanie
Published: January 2020

The soilborne fungusGaeumannomyces graminisvar.tritici(Ggt) causes the take-all disease on wheat roots. Ambient pH has been shown to be critical in different steps ofGgtlife cycle such as survival in bulk soil, saprophytic growth, and pathogenicity on plants. There are however intra-specific variations and we previously found two types ofGgtstrains that grow preferentially either at acidic pH or at neutral/alkaline pH; gene expression involved in pH-signal transduction pathway and pathogenesis was differentially regulated in two strains representative of these types. To go deeper in the description of the genetic pathways and the understanding of this adaptative mechanism, transcriptome sequencing was achieved on two strains (PG6 and PG38) which displayed opposite growth profiles in two pH conditions (acidic and neutral). PG6, growing better at acidic pH, overexpressed in this condition genes related to energy production and protein deubiquitination. In contrast, PG38, which grew better at neutral pH, overexpressed in this condition genes involved in fatty acids metabolism. This strain also expressed stress resistance mechanisms at both pH, to assert a convenient growth under various ambient pH conditions. These differences in metabolic pathway expression between strains at different pH might buffer the effect of field or soil variation in wheat fields, and explain the success of the pathogen.
Water and phosphorus uptake by upland rice root systems unraveled under multiple scenarios: linking a 3D soil-root model and data
Authors: Mai Trung Hieu , Bauw Pieterjan De , Schnepf Andrea , Merckx Roel , Smolders Erik , Vanderborght Jan
Published: January 2020

Background and aims

Upland rice is often grown where water and phosphorus (P) are limited and these two factors interact on P bioavailability. To better understand this interaction, mechanistic models representing small-scale nutrient gradients and water dynamics in the rhizosphere of full-grown root systems are needed.

Methods

Rice was grown in large columns using a P-deficient soil at three different P supplies in the topsoil (deficient, suboptimal, non-limiting) in combination with two water regimes (field capacity versus drying periods). Root architectural parameters and P uptake were determined. Using a multiscale model of water and nutrient uptake, in-silico experiments were conducted by mimicking similar P and water treatments. First, 3D root systems were reconstructed by calibrating an architecure model with observed phenological root data, such as nodal root number, lateral types, interbranch distance, root diameters, and root biomass allocation along depth. Secondly, the multiscale model was informed with these 3D root architectures and the actual transpiration rates. Finally, water and P uptake were simulated.

Key results

The plant P uptake increased over threefold by increasing P and water supply, and drying periods reduced P uptake at high but not at low P supply. Root architecture was significantly affected by the treatments. Without calibration, simulation results adequately predicted P uptake, including the different effects of drying periods on P uptake at different P levels. However, P uptake was underestimated under P deficiency, a process likely related to an underestimated affinity of P uptake transporters in the roots. Both types of laterals (i.e. S- and L-type) are shown to be highly important for both water and P uptake, and the relative contribution of each type depend on both soil P availability and water dynamics. Key drivers in P uptake are growing root tips and the distribution of laterals.

Conclusions

This model-data integration demonstrates how multiple co-occurring single root phene responses to environmental stressors contribute to the development of a more efficient root system. Further model improvements such as the use of Michaelis constants from buffered systems and the inclusion of mycorrhizal infections and exudates are proposed.
Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near humanKRT8/18
Authors: Liu Huan , Duncan Kaylia , Helverson Annika , Kumari Priyanka , Mumm Camille , Xiao Yao , Carlson Jenna , Darbellay Fabrice , Visel Axel , Leslie Elizabeth , Breheny Patrick , Erives Albert , Cornell Robert A.
Published: January 2020

Genome wide association studies for non-syndromic orofacial cleft (OFC) have identified single nucleotide polymorphisms (SNPs) at loci where the presumed risk-relevant gene is expressed in oral periderm. The functional subsets of such SNPs are difficult to predict because the sequence underpinnings of periderm enhancers are unknown. We applied ATAC-seq to models of human palate periderm, including zebrafish periderm, mouse embryonic palate epithelia, and a human oral epithelium cell line, and to complementary mesenchymal cell types. We identified sets of enhancers specific to the epithelial cells and trained gapped-kmer support-vector-machine classifiers on these sets. We used the classifiers to predict the effect of 14 OFC-associated SNPs at 12q13 nearKRT18. All the classifiers picked the same SNP as having the strongest effect, but the significance was highest with the classifier trained on zebrafish periderm. Reporter and deletion analyses support this SNP as lying within a periderm enhancer regulatingKRT18/KRT8expression.
AERON: Transcript quantification and gene-fusion detection using long reads
Authors: Rautiainen Mikko , Durai Dilip A , Chen Ying , Xin Lixia , Low Hwee Meng , Göke Jonathan , Marschall Tobias , Schulz Marcel H.
Published: January 2020

Single-molecule sequencing technologies have the potential to improve measurement and analysis of long RNA molecules expressed in cells. However, analysis of error-prone long RNA reads is a current challenge. We present AERON for the estimation of transcript expression and prediction of gene-fusion events. AERON uses an efficient read-to-graph alignment algorithm to obtain accurate estimates for noisy reads. We demonstrate AERON to yield accurate expression estimates on simulated and real datasets. It is the first method to reliably call gene-fusion events from long RNA reads. Sequencing the K562 transcriptome, we used AERON and found known as well as novel gene-fusion events.
Environmental biases in the study of ecological networks at the planetary scale
Authors: Poisot Timothée , Bergeron Gabriel , Cazelles Kevin , Dallas Tad , Gravel Dominique , Macdonald Andrew , Mercier Benjamin , Violet Clément , Vissault Steve
Published: January 2020

Ecological networks are increasingly studied at large spatial scales, expanding their focus from a conceptual tool for community ecology into one that also adresses questions in biogeography and macroecology. This effort is supported by increased access to standardized information on ecological networks, in the form of openly accessible databases. Yet, there has been no systematic evaluation of the fitness for purpose of these data to explore synthesis questions at very large spatial scales. In particular, because the sampling of ecological networks is a difficult task, they are likely to not have a good representation of the diversity of Earth’s bioclimatic conditions, likely to be spatially aggregated, and therefore unlikely to achieve broad representativeness. In this paper, we analyze over 1300 ecological networks in the mangal.io database, and discuss their coverage of biomes, and the geographic areas in which there is a deficit of data on ecological networks. Taken together, our results suggest that while some information about the global structure of ecological networks is available, it remains fragmented over space, with further differences by types of eco-logical interactions. This causes great concerns both for our ability to transfer knowledge from one region to the next, but also to forecast the structural change in networks under climate change.
Antigenic variation by switching inter-chromosomal interactions with an RNA splicing locus in trypanosomes
Authors: Faria Joana , Luzak Vanessa , Müller Laura S.M. , Brink Benedikt G. , Hutchinson Sebastian , Glover Lucy , Horn David , Siegel T. Nicolai
Published: January 2020

Highly selective gene expression is a key requirement for antigenic variation in several pathogens, allowing evasion of host immune responses and maintenance of persistent infections. African trypanosomes, parasites that cause lethal diseases in humans and livestock, employ an antigenic variation mechanism that involves monogenic antigen expression from a pool of >2500 antigen coding genes. In other eukaryotes, the expression of individual genes can be enhanced by mechanisms involving the juxtaposition of otherwise distal chromosomal loci in the three-dimensional nuclear space. However, trypanosomes lack classical enhancer sequences or regulated transcription initiation and the monogenic expression mechanism has remained enigmatic. Here, we show that the single expressed antigen coding gene displays a specific inter-chromosomal interaction with a major mRNA splicing locus. Chromosome conformation capture (Hi-C), revealed a dynamic reconfiguration of this inter-chromosomal interaction upon activation of another antigen. Super-resolution microscopy showed the interaction to be heritable and splicing dependent. We find that the two genomic loci are connected by the antigen exclusion complex, whereby VEX1 associated with the splicing locus and VEX2 with the antigen coding locus. Following VEX2 depletion, loss of monogenic antigen expression was accompanied by increased interactions between previously silent antigen genes and the splicing locus. Our results reveal a novel mechanism to ensure monogenic expression, requiring the spatial integration of antigen transcription and mRNA splicing in a dedicated compartment. These findings suggest a new means of post-transcriptional gene regulation.
Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota
Authors: Shibata Takeo , Nakagawa Mayumi , Coleman Hannah N. , Owens Sarah M. , Greenfield William W. , Sasagawa Toshiyuki , Robeson Michael S.
Published: January 2020

Cervical microbiota (CM) are considered an important factor affecting the progression of cervical intraepithelial neoplasia (CIN) and are implicated in the persistence of human papillomavirus (HPV). Collection of liquid-based cytology (LBC) samples is routine for cervical cancer screening and HPV genotyping and can be used for long-term cytological biobanking. We sought to determine whether it is possible to access microbial DNA from LBC specimens, and compared the performance of four different extraction protocols: (ZymoBIOMICS DNA Miniprep Kit; QIAamp PowerFecal Pro DNA Kit; QIAamp DNA Mini Kit; and IndiSpin Pathogen Kit) and their ability to capture the diversity of CM from LBC specimens. LBC specimens from 20 patients (stored for 716 ± 105 days) with CIN values of 2 or 3 were each aliquoted for each of the four kits. Loss of microbial diversity due to long-term LBC storage could not be assessed due to lack of fresh LBC samples. Comparisons with other types of cervical sampling were not performed. We observed that all DNA extraction kits provided equivalent accessibility to the cervical microbial DNA within stored LBC samples. Approximately 80% microbial genera were shared among all DNA extraction protocols. Potential kit contaminants were observed as well. Variation between individuals was a significantly greater influence on the observed microbial composition than was the method of DNA extraction. We also observed that HPV16 was significantly associated with community types that were not dominated byLactobacillus iners.
Nelfinavir was predicted to be a potential inhibitor of 2019-nCov main protease by an integrative approach combining homology modelling, molecular docking and binding free energy calculation
Authors: Xu Zhijian , Peng Cheng , Shi Yulong , Zhu Zhengdan , Mu Kaijie , Wang Xiaoyu , Zhu Weiliang
Published: January 2020

2019-nCov has caused more than 80 deaths as of 27 January 2020 in China, and infection cases have been reported in more than 10 countries. However, there is no approved drug to treat the disease. 2019-nCov Mprois a potential drug target to combat the virus. We built homology models based on SARS Mprostructures, and docked 1903 small molecule drugs to the models. Based on the docking score and the 3D similarity of the binding mode to the known Mproligands, 4 drugs were selected for binding free energy calculations. Both MM/GBSA and SIE methods voted for nelfinavir, with the binding free energy of −24.69±0.52 kcal/mol and −9.42±0.04 kcal/mol, respectively. Therefore, we suggested that nelfinavir might be a potential inhibitor against 2019-nCov Mpro.
A paralog-specific role of the COPI pathway in the neuronal differentiation of murine pluripotent cells
Authors: Goyal Manu , Zhao Xiyan , Bozhinova Mariya , Andrade López Karla Lisette , de Heus Cecilia , Schulze-Dramac Sandra , Müller-McNicoll Michaela , Klumperman Judith , Béthune Julien
Published: January 2020

Coat protein complex I (COPI)-coated vesicles mediate membrane trafficking between Golgi cisternae as well as retrieval of proteins from the Golgi to the endoplasmic reticulum. There are several flavors of the COPI coat defined by paralogous subunits of the protein complex coatomer. However, whether paralogous COPI proteins have specific functions is currently unknown. Here we show that the paralogous coatomer subunits γ1-COP and γ2-COP are differentially expressed during the neuronal differentiation of mouse pluripotent cells. Moreover, through a combination of genome editing experiments, we demonstrate that whereas γ-COP paralogs are largely functionally redundant, γ1-COP specifically promotes neurite outgrowth. Our work stresses a role of the COPI pathway in neuronal polarization and provides evidence for distinct functions for coatomer paralogous subunits in this process.
Breaking down of healthcare system: Mathematical modelling for controlling the novel coronavirus (2019-nCoV) outbreak in Wuhan, China
Authors: Ming Wai-Kit , Huang Jian , Zhang Casper J. P.
Published: January 2020

Background

A novel coronavirus pneumonia initially identified in Wuhan, China and provisionally named 2019-nCoV has surged in the public. In anticipation of substantial burdens on healthcare system following this human-to-human spread, we aim to scrutinise the currently available information and evaluate the burden of healthcare systems during this outbreak in Wuhan.

Methods and Findings

We applied a modified SIR model to project the actual number of infected cases and the specific burdens on isolation wards and intensive care units (ICU), given the scenarios of different diagnosis rates as well as different public health intervention efficacy. Our estimates suggest, assuming 50% diagnosis rate if no public health interventions were implemented, that the actual number of infected cases could be much higher than the reported, with estimated 88,075 cases (as of 31stJanuary, 2020), and projected burdens on isolation wards and ICU would be 34,786 and 9,346 respectively The estimated burdens on healthcare system could be largely reduced if at least 70% efficacy of public health intervention is achieved.

Conclusion

The health system burdens arising from the actual number of cases infected by the novel coronavirus appear to be considerable if no effective public health interventions were implemented. This calls for continuation of implemented anti-transmission measures (e.g., closure of schools and facilities, suspension of public transport, lockdown of city) and further effective large-scale interventions spanning all subgroups of populations (e.g., universal facemask wear) aiming at obtaining overall efficacy with at least 70% to ensure the functioning of and to avoid the breakdown of health system.