bluuebunny/crossref_metadata_2025 huggingface dataset:
Factor Structure, Reliability and Validity of the Institutional Culture Assessment Scale (ICAS)
Authors: Monteiro Gabriela Massaro Carneiro , Moser Carolina Meira , de Oliveira Luciana Terra , Gabbard Glen Owens , Laskoski Pricilla Braga , Hauck Simone
Published: September 2020

Introduction

Work environment can affect the employees, fostering well-being versus emotional burden. The aim of this study was to develop the Institutional Culture Assessment Scale (ICAS), and evaluate its Factor Structure, Reliability and Validity in a Brazilian sample of medical students and physicians in different settings and phases of the medical career.

Method

2,537 individuals were evaluated by an online questionnaire. The sample was split in half for independent testing of Exploratory Factor Analysis and Confirmatory Factor Analysis. We then used Confirmatory Factor Analysis (CFA) to test the best solutions in the second half of the sample. Then, considering a unidimensional model solution, an item response theory (IRT) analysis was conducted. Simple linear regression analysis was performed to investigate associations between ICAS factor scores and internal validators (burnout scores), using again the second half of the sample.

Result

Parallel analysis revealed two factors. The first factor encompassed items involving the institution and supervisors. The second factor encompassed items involving peers. We decided to performed the next analysis with a unidimensional construct based solely on institution/supervisor items. A unidimensional model including the remaining seven items from the ICAS instrument revealed an excellent fit with the data. All items loaded significantly on the unidimensional latent trait with factor loadings ranging from 0.583 to 0.869. McDonald’s Omega was 0.89, showing a high internal consistency.

Conclusion

This study presents a valid and reliable scale to assess aspects of institutional culture connected to the relationships with superiors/supervisors and to the relation to the institutions themselves.
Stage-differentiated modelling of methylation patterns uncovers salient biomarkers and prognostic signatures in colorectal cancer progression
Authors: Raghavendran Abirami , Muthamilselvan Sangeetha , Palaniappan Ashok
Published: September 2020

Background

Aberrant methylation of DNA acts epigenetically to skew the gene transcription rate up or down. In this study, we have developed a comprehensive computational framework for the stage-specific analysis of methylation patterns in colorectal cancer.

Methods

Combining public-domain methylation and clinical data from TCGA, the methylation β - matrix was converted into M-value matrix, annotated with sample stages and analysed for stage-specific genes using multiple approaches involving stage-differentiated linear modelling of methylation patterns or their correlation with the phenotype and expression patterns. Differentially methylated genes (DMGs) were identified using a contrast against control samples (adjusted p-value <0.001 and |log fold-change of M-value| >2). These results were further filtered using a series of all possible pairwise stage contrasts (p-value <0.05) to obtain stage-specific DMGs. These were then subjected to a consensus analysis, followed by Kaplan–Meier survival analysis to explore the relationship between methylation and prognosis for the consensus stage-salient biomarkers.

Results

We found significant genome-wide changes in methylation patterns in cancer samples relative to controls agnostic of stage. Our stage-differentiated analysis yielded the following stage-salient genes: one stage-I gene (“FBN1”), one stage II specific gene (“FOXG1”), one stage III specific gene (“HCN1”) and four stage IV specific genes (“NELL1”, “ZNF135”, “FAM123A”, “LAMA1”), which could be used for stage-specific diagnosis. All the biomarkers were hypermethylated, indicating down-regulation and signifying a CpG island Methylator Phenotype (CIMP) manifestation. A prognostic signature consisting of FBN1 and FOXG1was significantly associated with patient survival (p-value < 0.01) and could be used as a biomarker panel for early-stage CRC prognosis.

Conclusion

Our workflow for stage-differentiated consensus analysis has yielded stage-salient diagnostic biomarkers as well as an early-stage prognostic biomarker panel. In addition, our studies have affirmed a novel CIMP-like signature in colorectal cancer, urging clinical validation.

Supplementary Information

Supplementary information could be found at https://doi.org/10.6084/m9.figshare.13013852
A Data-Driven Evaluation Approach for Assessing Student Nurse Training Effectiveness in Clinical Practice Using A Fuzzy Mathematics Model
Authors: Liu Yanmei , Chen Yuwen
Published: September 2020

The overall performance of student nurses during training and subsequent medical treatment practice has a direct effect on the quality of healthcare they provide in hospitals. The evaluation of student nurses’ overall performance is usually not straightforward, as the evaluation criteria includes many aspects and it’s difficult to develop a generic metric. Fuzzy mathematics provides a mathematical tool for processing data with fuzziness. Using fuzzy mathematics theory enables data-driven evaluation of the overall performance of student nurses after their training program.
Light-induced modulation of DNA recognition by the Rad4/XPC damage sensor protein
Authors: Tavakoli Amirrasoul , Paul Debamita , Mu Hong , Kuchlyan Jagannath , Baral Saroj , Ansari Anjum , Broyde Suse , Min Jung-Hyun
Published: September 2020

Biomolecular structural changes upon binding/unbinding are key to their functions. However, characterization of such dynamical processes with high spatial and temporal resolutions is difficult as it requires ways to rapidly trigger the assembly/disassembly as well as ways to monitor the structural changes over time. Recently, various chemical strategies have been developed to use light to trigger changes in oligonucleotide structures, thereby their activities. Here we report that photoswitchable DNA can be used to modulate the DNA binding of the Rad4/XPC DNA repair complex using light. Rad4/XPC specifically binds to diverse helix-destabilizing/distorting lesions including bulky organic adducts and functions as a key initiator for the eukaryotic nucleotide excision repair (NER) pathway. We show that the 6-nitropiperonyloxymethyl (NPOM)-modified DNA is recognized by the Rad4 protein as a specific substrate and that the specific binding can be abolished by light-induced cleavage of the NPOM group from DNA in a dose-dependent manner. Fluorescence lifetime-based analyses of the DNA conformations suggest that free NPOM-DNA retains B-DNA-like conformations despite its bulky NPOM adduct, but Rad4-binding renders it to be heterogeneously distorted. Subsequent extensive conformational searches and molecular dynamics simulations demonstrate that NPOM in DNA can be housed in the major groove of the DNA, with stacking interactions among the nucleotide pairs remaining largely unperturbed and thus retaining overall B-DNA conformation. Our work suggests that photoactivable DNA can be used as a DNA lesion surrogate to study DNA repair mechanisms such as nucleotide excision repair.

Abstract Figure

Graphical Summary

This work shows that a photolabile 6-nitropiperonyloxymethyl (NPOM)-modified DNA is specifically recognized by the Rad4/XPC damage sensor protein complex that initiates the nucleotide excision repair pathway; light-induced cleavage of NPOM abolishes the specific binding to Rad4/XPC.
Genomic prediction of arsenic tolerance and grain yield in rice. Contribution of trait-specific markers and multi environment models
Authors: Ahmadi Nourollah , Cao Tuong-Vi , Frouin Julien , Norton Gareth J. , Price Adam H.
Published: September 2020

Many rice-growing areas are affected by high concentrations of arsenic (As). Rice varieties that preventAsuptake and/or accumulation can mitigateAsthreats to human health. Genomic selection is known to facilitate rapid selection of superior genotypes for complex traits. We explored the predictive ability (PA) of genomic prediction with single-environment models, accounting or not for trait-specific markers, multi-environment models, and multi-trait and multi-environment models, using the genotypic (1600 K SNP) and phenotypic (grain arsenic content, grain yield and days to flowering, observed under two irrigation systems over two years) data of the Bengal and AssamAusPanel (BAAP). Under the base-line single environment model, PA of up to 0.707 and 0.654 was obtained for grain yield and grainAsrespectively, the three prediction methods (BL, GBLUP and RKHS) considered performed similarly, and marker selection based on linkage disequilibrium allowed to reduce the number of SNP to 17 K, without negative effect on PA of genomic predictions. Single environment models giving distinct weight to trait-specific markers in the genomic relationship matrix outperformed the base-line models up to 32%. Multi-environment models, accounting for G × E interactions, and multi-trait and multi-environment models outperformed the base-line models by up to 47% and 61%, respectively. Among the multi-trait and multi-environment models, the Bayesian multi-output regressor stacking function obtained the highest PA (0.831 for grainAs) with much higher efficiency for computing time. These findings pave the way for breeding forAs-tolerance in the progenies of biparental crosses involving members of the BAAP. It also applies to breeding for other complex traits evaluated under multiple environments.
Smart bionic graspers: background study and design process
Authors: Li Xinrui , Chizari Mahmoud
Published: September 2020

This paper has focused on reviewing passive bionic grasper and designing a virtual prototype using a computer modelling technique. The main aim of this study is to review existing research and compare their functionalities. This has been followed by introducing a concept design with suitable components. To start the project, generating a clear overview form the most updated and relative knowledge and information on existing designs was the intention of the study. The concept design part of this study uses an iterative process (similar to the Double Diamond Model introduced by Frances et al (2019)) including Discover, Define, Develop and Deliver to complete the design components. Following the concept design process, the detailed theoretical considerations and the features of components selection were then defined. In Develop Phase, the goal was to decide the final design and generate the computer model using SolidWorks. The fourth phase of process was Delivery leading the design evaluation and validation of the generated model or virtual prototype. By completing the process, it is possible to determine the feasibility of the design and the need for improvement. In final stage of the design, a finite element approach using SolidWorks Simulation was performed on the concept. Final design was decided after comparing the concepts in terms of several considerations. A series of simulations were performed on the design to evaluate the durability of the design and extend its functionality. The results showed that the supporting pad was robust enough when dropped down from 1.5 meters height, while the hinge which connecting the finger straps would need further improvement to avoid failure during its practical loading.
Simulation of bacterial populations with SLiM
Authors: Cury Jean , Haller Benjamin C. , Achaz Guillaume , Jay Flora
Published: September 2020

Simulation of genomic data is a key tool in population genetics, yet, to date, there is no forward-in-time simulator of bacterial populations that is both computationally efficient and adaptable to a wide range of scenarios. Here we demonstrate how to simulate bacterial populations with SLiM, a forward-in-time simulator built for eukaryotes. SLiM has gained many users in recent years, due to its speed and power, and has extensive documentation showcasing various scenarios that it can simulate. This paper focuses on a simple demographic scenario, to explore unique aspects of modeling bacteria in SLiM’s scripting language. In addition, we illustrate the flexibility of SLiM by simulating the growth of bacteria on a Petri dish with antibiotic. To foster the development of bacterial simulations based upon this recipe, we explain the inner workings of its code. We also validate the simulator, by extensively testing the results of simulations against existing simulators, and against theoretical expectations for some summary statistics. This protocol, with the flexibility and power of SLiM, will enable the community to simulate bacterial populations efficiently under a wide range of evolutionary scenarios.
Amyloid beta acts synergistically as a pro-inflammatory cytokine
Authors: LaRocca Thomas J. , Cavalier Alyssa N. , Roberts Christine M. , Lemieux Maddie R. , Link Christopher D.
Published: September 2020

The amyloid beta (Aβ) peptide is believed to play a central role in Alzheimer’s disease (AD), the most common age-related neurodegenerative disorder. However, the natural, evolutionarily-selected functions of Aβ are incompletely understood. Here, we report that nanomolar concentrations of Aβ act synergistically with known cytokines to promote pro-inflammatory activation in primary human astrocytes (a cell type increasingly implicated in brain aging and AD). Using transcriptomics (RNA-seq), we show that Aβ can directly substitute for the complement component C1q in a cytokine cocktail previously shown to induce astrocyte immune activation. Furthermore, we show that astrocytes synergistically activated by Aβ have a transcriptional signature similar to neurotoxic “A1” astrocytes known to accumulate with age and in AD. Interestingly, we find that this biological action of Aβ at low concentrations is distinct from the transcriptome changes induced by the high/supraphysiological doses of Aβ often used inin vitrostudies. Collectively, our results suggest an important, cytokine-like function for Aβ and a novel mechanism by which it may directly contribute to the neuroinflammation associated with brain aging and AD.
Effect of Cellular and ECM Aging on Human iPSC-derived Cardiomyocyte Performance, Maturity and Senescence
Authors: Ozcebe S. Gulberk , Bahcecioglu Gokhan , Yue Xiaoshan S. , Zorlutuna Pinar
Published: September 2020

Cardiovascular diseases are the leading cause of death worldwide and their occurrence is highly associated with age. However, lack of knowledge in cardiac tissue aging is a major roadblock in devising novel therapies. Here, we studied the effects of cell and cardiac extracellular matrix (ECM) aging on the induced pluripotent stem cell (iPSC)-derived cardiomyocyte cell state, function, as well as response to myocardial infarction (MI)-mimicking stress conditionsin vitro. Within 3-weeks, young ECM promoted proliferation and drug responsiveness in young cells, and induced cell cycle re-entry, and protection against stress in the aged cells. Adult ECM improved cardiac function, while aged ECM accelerated the aging phenotype, and impaired cardiac function and stress defense machinery of the cells. In summary, we have gained a comprehensive understanding of cardiac aging and highlighted the importance of cell-ECM interactions. This study is the first to investigate the individual effects of cellular and environmental aging and identify the biochemical changes that occur upon cardiac aging.
Epigenomic features related to microglia are associated with attenuated effect of APOE ε4 on alzheimer’s disease risk in humans
Authors: Ma Yiyi , Yu Lei , Olah Marta , Smith Rebecca , Oatman Stephanie R. , Allen Mariet , Pishva Ehsan , Zhang Bin , Menon Vilas , Ertekin-Taner Nilüfer , Lunnon Katie , Bennett David A. , Klein Hans-Ulrich , De Jager Philip L.
Published: September 2020

INTRODUCTION

Not allAPOEε4 carriers who survive to advanced age develop Alzheimer’s disease (AD); factors attenuating the risk of ε4 on AD may exist.

METHODS

Guided by the top ε4-attenuating signals from methylome-wide association analyses (N=572, ε4+ and ε4-) of neurofibrillary tangles and neuritic plaques, we conducted a meta-analysis for pathological AD within the ε4+ subgroups (N=235) across four independent collections of brains. Cortical RNA-seq and microglial morphology measurements were used in functional analyses.

RESULTS

Three out of the four significant CpG dinucleotides were captured by one principle component (PC1), which interacts with ε4 on AD, and is associated with expression of innate immune genes and activated microglia. In ε4 carriers, reduction in each unit of PC1 attenuated the odds of AD by 58% (OR=2.39, 95%CI=[1.64,3.46],P=7.08×10−6).

DISCUSSION

An epigenomic factor associated with a reduced proportion of activated microglia appears to attenuate the risk of ε4 on AD.
Sonographic Analysis of Abscess Maturation in a Porcine Model
Authors: Leotta Daniel F. , Bruce Matthew , Wang Yak-Nam , Kucewicz John , Khokhlova Tatiana , Chan Keith , Monsky Wayne , Matula Thomas J.
Published: September 2020

Abscesses are walled-off collections of infected fluids that often develop as complications in the setting of surgery and trauma. Abscess care depends on size, location, composition and complexity, among other patient factors. The goal of this work is to describe, using the latest ultrasound imaging technologies, the progression of abscess development in a porcine animal model. Intramuscular or subcutaneous injections of bacteria plus dextran particles as an irritant led to identifiable abscesses over a 2- to 3-week period. The abscesses were imaged at least weekly with B-mode, 3D B-mode, shear-wave elastography (SWE) and color flow imaging. Mature abscesses were characterized by a well-defined core of varying echogenicity surrounded by a hypoechoic capsule that was highly vascularized on Doppler imaging. Size and shape changes during development were quantified with 3D imaging. With SWE, the lesion stiffness varied interiorly and generally decreased over time. These ultrasound features potentially provide biomarkers to facilitate improved selection of treatment strategies for abscesses.
The novel anti-CRISPR AcrIIA22 relieves DNA torsion in target plasmids and impairs SpyCas9 activity
Authors: Forsberg Kevin J. , Schmidtke Danica T. , Werther Rachel , Uribe Ruben V. , Hausman Deanna , Sommer Morten O.A. , Stoddard Barry L. , Kaiser Brett K. , Malik Harmit S.
Published: September 2020

To overcome CRISPR-Cas defense systems, many phages and mobile genetic elements encode CRISPR-Cas inhibitors called anti-CRISPRs (Acrs). Nearly all characterized Acrs directly bind Cas proteins to inactivate CRISPR immunity. Here, using functional metagenomic selection, we describe AcrIIA22, an unconventional Acr found in hypervariable genomic regions of clostridial bacteria and their prophages from human gut microbiomes. AcrIIA22 does not bind strongly to SpyCas9 but nonetheless potently inhibits its activity against plasmids. To gain insight into its mechanism, we obtained an X-ray crystal structure of AcrIIA22, which revealed homology to PC4-like nucleic-acid binding proteins. Based on mutational analyses and functional assays, we deduced thatacrIIA22encodes a DNA nickase that relieves torsional stress in supercoiled plasmids. This may render them less susceptible to SpyCas9, which uses free energy from negative supercoils to form stable R-loops. Modifying DNA topology may provide an additional route to CRISPR-Cas resistance in phages and mobile genetic elements.
Genome-wide analysis of experimentally evolvedCandida aurisreveals multiple novel mechanisms of multidrug-resistance
Authors: Carolus Hans , Pierson Siebe , Muñoz José F. , Subotić Ana , Cruz Rita B. , Cuomo Christina A. , Van Dijck Patrick
Published: September 2020

Candida aurisis globally recognized as an opportunistic fungal pathogen of high concern, due to its extensive multidrug-resistance (MDR). Still, molecular mechanisms of MDR are largely unexplored. This is the first account of genome wide evolution of MDR inC. aurisobtained through serialin vitroexposure to azoles, polyenes and echinocandins. We show the stepwise accumulation of multiple novel mutations in genes known and unknown in antifungal drug resistance, albeit almost all new forC. auris. Echinocandin resistance evolved through a codon deletion inFKS1accompanied by a substitution inFKS1hot spot 3. Mutations inERG3andCIS2further increased the echinocandin MIC. Decreased azole susceptibility was acquired through a gain of function mutation in transcription factorTAC1byielding overexpression of the drug efflux pump Cdr1; a segmental duplication of chromosome 1 containingERG11; and a whole chromosome 5 duplication, which containsTAC1b. The latter was associated with increased expression ofERG11, TAC1bandCDR2, but notCDR1. The simultaneous emergence of nonsense mutations inERG3andERG11, presumably leading to the abrogation of ergosterol synthesis, was shown to decrease amphotericin B susceptibility, accompanied with fluconazole cross resistance. A mutation inMEC3, a gene mainly known for its role in DNA damage homeostasis, further increased the polyene MIC. Overall, this study shows the alarming potential and diversity for MDR development inC. auris, even in a clade until now not associated with MDR (clade II), hereby stressing its clinical importance and the urge for future research.

Importance

C. aurisis a recently discovered human fungal pathogens and has shown an alarming potential for multi- and pan-resistance towards all classes of antifungals most commonly used in the clinic. Currently,C. aurishas been globally recognized as a nosocomial pathogen of high concern due to this evolutionary potential. So far, this is the first study in which the stepwise progression of MDR inC. aurisis monitoredin vitro. Multiple novel mutations in known ‘resistance genes’ and genes previously not or vaguely associated with drug resistance reveal rapid MDR evolution in aC. aurisclade II isolate. Additionally, this study shows thatin vitroexperimental evolution can be a powerful tool to discover new drug resistance mechanisms, although it has its limitations.
Coding Complete Genome Sequences of Twenty-three SARS-CoV-2 Strains Isolated in the Philippines
Authors: Velasco John Mark , Chinnawirotpisan Piyawan , Joonlasak Khajohn , Manasatienkij Wudtichai , Huang Angkana , Valderama Ma.. Theresa , Diones Paula Corazon , Leonardia Susie , Timbol Ma.Leanor , Navarro Fatima Claire , Villa Vicente , Tabinas Henry , Chua Domingo , Fernandez Stefan , Jones Anthony , Klungthong Chonticha
Published: September 2020

Here, we report the coding complete genome sequences of 23 severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) strains from the Philippines. Sequences were obtained from nasopharyngeal and oropharyngeal swabs from COVID-19 positive patients. Mutation analysis showed the presence of the D614G mutation in the spike protein in 22 of 23 genomes.
Healthcare use and cost trajectories during the last year of life: A national population administrative secondary care data linkage study
Authors: Diernberger Katharina , Luta Xhyljeta , Bowden Joanna , Fallon Marie , Droney Joanne , Lemmon Elizabeth , Gray Ewan , Marti Joachim , Hall Peter S
Published: September 2020

Background

People who are nearing the end of life are high users of healthcare. The cost to providers is high and the value of care is uncertain.

Objectives

To describe the pattern, trajectory and drivers of secondary care use and cost by people in Scotland in their last year of life.

Methods

Retrospective whole-population secondary care administrative data linkage study of Scottish decedents of 60 years and over between 2012 and 2017 (N=274,048).

Results

Secondary care use was high in the last year of life with a sharp rise in inpatient admissions in the last three months. The mean cost was £10,000. Cause of death was associated with differing patterns of healthcare use: dying of cancer was preceded by the greatest number of hospital admissions and dementia the least. Greater age was associated with lower admission rates and cost. There was higher resource use in the urban areas. No difference was observed by deprivation.

Conclusions

Hospitalisation near the end of life was least frequent for older people and those living rurally, although length of stay for both groups, when they were admitted, was longer. Research is required to understand if variation in hospitalisation is due to variation in the quantity or quality of end of life care available, varying community support, patient preferences or an inevitable consequence of disease-specific needs.
A common model for the breathlessness experience
Authors: Finnegan Sarah L. , Pattinson Kyle T.S. , Sundh Josefin , Sköld Magnus , Janson Christer , Blomberg Anders , Sandberg Jacob , Ekström Magnus
Published: September 2020

Introduction

Chronic breathlessness occurs across many different diseases, independently of severity. Yet, despite being strongly linked to adverse outcomes, chronic breathlessness is generally not considered a stand-alone treatment target. Here we move focus from identifying the “best” measurement tool and use data-driven techniques to identify and confirm the stability of underlying features (factors) driving breathlessness across different cardiorespiratory diseases. Such frameworks could provide an opportunity to address the underlying mechanisms of breathlessness and over-come issues with co-morbidities, particularly when medical therapies have been optimised.

Methods

Longitudinal study of questionnaire data on 182 participants with main diagnoses of asthma (21.4%), COPD (24.7%), heart failure (19.2%), idiopathic pulmonary fibrosis (18.7%), other interstitial lung disease (5.5%), and “other diagnoses” (8.8%) were entered into an exploratory factor analysis (EFA). Participants were stratified based on their EFA factor scores, allowing us to examine whether the breathlessness experience differed across disease diagnosis. We then examined model stability after six months and established through an iterative process the most compact, and therefore least burdensome assessment tool.

Results

From the 25 input measures, 16 measures were retained for model validation. The resulting model contained four factors to which we assigned the following descriptive labels: body burden, 2) affect/mood, 3) breathing burden and 4) anger/frustration. Stratifying patients by their scores across the four factors revealed two groups corresponding to high and low burden. These were not found to be predictive of primary disease diagnosis and did remain stable after six months.

Conclusions

We have identified four stable and disease-independent factors that seem to underlie the experience of breathlessness. We suggest that interventions may target factors within this framework to answer the question of whether they are also driving the experience itself.
Population structure, biogeography and transmissibility ofMycobacterium tuberculosis
Authors: Freschi Luca , Vargas Roger , Hussain Ashek , Kamal S M Mostofa , Skrahina Alena , Tahseen Sabira , Ismail Nazir , Barbova Anna , Niemann Stefan , Cirillo Daniela Maria , Dean Anna S , Zignol Matteo , Farhat Maha Reda
Published: September 2020

Mycobacterium tuberculosisis a clonal pathogen proposed to have co-evolved with its human host for millennia, yet our understanding of its genomic diversity and biogeography remains incomplete. Here we use a combination of phylogenetics and dimensionality reduction to reevaluate the population structure ofM. tuberculosis, providing the first in-depth analysis of the ancient East African Indian Lineage 1 and the modern Central Asian Lineage 3 and expanding our understanding of Lineages 2 and 4. We assess sub-lineages using genomic sequences from 4,939 pan-susceptible strains and find 30 new genetically distinct clades that we validate in a dataset of 4,645 independent isolates. We characterize sub-lineage geographic distributions and demonstrate a consistent geographically restricted and unrestricted pattern for 20 groups, including three groups of Lineage 1. We assess the transmissibility of the four major lineages by examining the distribution of terminal branch lengths across theM. tuberculosisphylogeny and identify evidence supporting higher transmissibility in Lineages 2 and 4 than 3 and 1 on a global scale. We define a robust expanded barcode of 95 single nucleotide substitutions (SNS) that allows for the rapid identification of 69Mtbsub-lineages and 26 additional internal groups. Our results paint a higher resolution picture of theMtbphylogeny and biogeography.
The Abl-interactor Abi suppresses the function of the BRAG2 GEF family member Schizo
Authors: Lübke Stefanie , Braukmann Carina , Rexer Karl-Heinz , Cigoja Lubjinka , Önel Susanne F.
Published: September 2020

Guanine nucleotide exchange factors (GEF) of the BRAG subfamily activate small Arf GTPases, which are pivotal regulators of intracellular membrane traffic and actin dynamics. Here, we demonstrate a novel interaction between the Abl-interactor (Abi) and the BRAG family member Schizo. We mapped the SH3 domain of Abi to interact with the N-terminal region of Schizo. This region is additionally involved in the binding of the cytodomain of the cell adhesion molecule N-cadherin. Inschizoloss of function mutants, we detected increased amounts of N-cadherin. In contrast, the expression of the GEF (Sec7) and the membrane-binding (pleckstrin homology) domains decreased amounts of N-cadherin, indicating a crucial role of the Sec7-PH module in regulating N-cadherin levels. Unlike other Sec7 GEFs, where the catalytic Sec7 domain is autoinhibited, the Sec7 and PH domain of BRAG2 are constitutively accessible, raising the question how GEF activity is controlled in a spatial and temporal manner. Our genetic analyzes demonstrate that the nature of the Abi Schizo interaction is to antagonize Schizo function and to restore wild-type amounts of N-cadherin.
CDK-Mediated Phosphorylation of FANCD2 Promotes Mitotic Fidelity
Authors: Cantres-Velez Juan A. , Blaize Justin L. , Vierra David A. , Boisvert Rebecca A. , Garzon Jada M. , Piraino Benjamin , Tan Winnie , Deans Andrew J. , Howlett Niall G.
Published: September 2020

Fanconi anemia (FA) is a rare genetic disease characterized by increased risk for bone marrow failure and cancer. The FA proteins function together to repair damaged DNA. A central step in the activation of the FA pathway is the monoubiquitination of the FANCD2 and FANCI proteins under conditions of cellular stress and during S-phase of the cell cycle. The regulatory mechanisms governing S-phase monoubiquitination, in particular, are poorly understood. In this study, we have identified a CDK regulatory phospho-site (S592) proximal to the site of FANCD2 monoubiquitination. FANCD2 S592 phosphorylation was detected by LC-MS/MS and by immunoblotting with a S592 phospho-specific antibody. Mutation of S592 leads to abrogated monoubiquitination of FANCD2 during S-phase. Furthermore, FA-D2 (FANCD2-/-) patient cells expressing S592 mutants display reduced proliferation under conditions of replication stress and increased mitotic aberrations, including micronuclei and multinucleated cells. Our findings describe a novel cell cycle-specific regulatory mechanism for the FANCD2 protein that promotes mitotic fidelity.

Author Summary

Fanconi anemia (FA) is a rare genetic disease characterized by high risk for bone marrow failure and cancer. FA has strong genetic and biochemical links to hereditary breast and ovarian cancer. The FA proteins function to repair DNA damage and to maintain genome stability. The FANCD2 protein functions at a critical stage of the FA pathway and its posttranslational modification is defective in >90% of FA patients. However, the function, and regulation of FANCD2, particularly under unperturbed cellular conditions, remains remarkably poorly characterized. In this study, we describe a novel mechanism of regulation of the FANCD2 protein during S-phase of the cell cycle. CDK-mediated phosphorylation of FANCD2 on S592 promotes the ubiquitination of FANCD2 during S-phase. Disruption of this phospho-regulatory mechanism results in compromised mitotic fidelity and an increase in mitotic chromosome instability.
Sniffing the Human Body-Volatile Hexadecanal Blocks Aggression in Men but Triggers Aggression in Women
Authors: Mishor Eva , Amir Daniel , Weiss Tali , Honigstein Danielle , Weissbrod Aharon , Livne Ethan , Gorodisky Lior , Karagach Shiri , Ravia Aharon , Snitz Kobi , Karawani Diyala , Zirler Rotem , Weissgross Reut , Soroka Timna , Endevelt-Shapira Yaara , Agron Shani , Rozenkrantz Liron , Reshef Netta , Furman-Haran Edna , Breer Heinz , Strotmann Joerg , Sobel Noam
Published: September 2020

Body-volatiles can effectively trigger or block conspecific aggression in terrestrial mammals. Here we tested whether hexadecanal (HEX), a human body-volatile implicated as a mammalian-wide social cue, impacts human aggression. Using validated behavioural paradigms, we observed a remarkable dissociation: sniffing HEX blocked aggression in men, but triggered aggression in women. Next, using functional brain imaging, we uncovered a pattern of brain activity mirroring behaviour: In both men and women, HEX increased activity in the left angular gyrus, an area implicated in perception of social cues. Hex then modulated functional connectivity between the angular gyrus and a brain network implicated in social appraisal (temporal pole) and aggressive execution (amygdala and orbitofrontal cortex) in a sex-dependent manner consistent with behaviour: increasing connectivity in men, but decreasing connectivity in women. These findings implicate sex-specific social chemosignaling at the mechanistic heart of human aggressive behaviour.
Impaired p53-mediated DNA damage response contributes to microcephaly in Nijmegen Breakage Syndrome patient-derived cerebral organoids
Authors: Martins Soraia , Erichsen Lars , Datsi Angeliki , Wruck Wasco , Goering Wolfgang , Chrzanowska Krystyna , Adjaye James
Published: September 2020

Nijmegen Breakage Syndrome (NBS) is a rare autosomal recessive genetic disorder caused by mutations withinNBN, a DNA-damage repair protein. Hallmarks of NBS include several clinical manifestations such growth retardation, chromosomal instability, immunodeficiency and progressive microcephaly. However, the etiology of microcephaly in NBS patients remains elusive. Here, we employed induced pluripotent stem cell-derived brain organoids from two NBS patients to analyze the underlying mechanisms of microcephaly. We show that NBS-organoids carrying the homozygous 647del5NBNmutation are significantly smaller in size with disrupted cyto-architecture Patient-derived organoids exhibit premature differentiation together with neuronatin (NNAT) overexpression and key pathways related to DNA damage response and cell cycle are differentially regulated compared to controls. Moreover, we show that after exposure to bleomycin, NBS organoids undergo a delayed p53-mediated DNA damage response and aberrant trans-synaptic signalling, which ultimately leads to neuronal apoptosis. Our data provide insights into how mutations withinNBNalters neurogenesis in NBS patients, thus providing a proof of concept that cerebral organoids are a valuable tool for studying DNA damage-related disorders.
The Positive Switching RSFP Padron2 Enables Live-Cell RESOLFT Nanoscopy Without Sequential Irradiation Steps
Authors: Konen Timo , Grotjohann Tim , Jansen Isabelle , Jensen Nickels , Hell Stefan W. , Jakobs Stefan
Published: September 2020

Reversibly switchable fluorescent proteins (RSFPs) can be repeatedly transferred between a fluorescent on- and a non-fluorescent off-state in response to irradiation with light of different wavelengths. Negative switching RSFPs are switched from the on- to the off-state with the same wavelength which also excites fluorescence. Positive switching RSFPs have a reversed light response where the fluorescence excitation wavelength induces the transition from the off- to the on-state. Reversible saturable optical linear (fluorescence) transitions (RESOLFT) nanoscopy utilizes these switching states to achieve diffraction-unlimited resolution, but so far has primarily relied on negative switching RSFPs by using time sequential switching schemes.

Based on the green fluorescent RSFP Padron, we engineered the positive switching RSFP Padron2. Compared to its predecessor, it can undergo 50-fold more switching cycles while displaying a contrast ratio between the on- and the off-state of more than 100:1. Because of its robust switching behavior, Padron2 supports a RESOLFT imaging scheme that entirely refrains from sequential switching as it only requires beam scanning of two spatially overlaid light distributions. Using Padron2, we demonstrate live-cell RESOLFT nanoscopy without sequential irradiation steps.
Studies on CRMP2 SUMOylation-deficient transgenic mice reveal novel insights into the trafficking of NaV1.7 channels
Authors: Gomez Kimberly , Ran Dongzhi , Madura Cynthia L. , Moutal Aubin , Khanna Rajesh
Published: September 2020

Voltage-gated sodium channels are key players in neuronal excitability and pain signaling. Functional expression of the voltage-gated sodium channel NaV1.7 is under the control of SUMOylated collapsin response mediator protein 2 (CRMP2). If not SUMOylated, CRMP2 forms a complex with the endocytic proteins Numb, the epidermal growth factor receptor pathway substrate 15 (Eps15), and the E3 ubiquitin ligase Nedd4-2 to promote clathrin-mediated endocytosis of NaV1.7. We recently reported that CRMP2 SUMO-null knock-in (CRMP2K374A/K374A) female mice have reduced NaV1.7 membrane localization and currents in their sensory neurons. Preventing CRMP2 SUMOylation was sufficient to reverse mechanical allodynia in CRMP2K374A/K374Afemale mice with neuropathic pain. Here we report that inhibiting clathrin assembly in nerve-injured male and female CRMP2K374A/K374Amice, increased pain sensitivity in allodynia-resistant animals. Furthermore, Numb, Nedd4-2 and Eps15 expression was not modified in basal conditions in the dorsal root ganglia (DRG) of male and female CRMP2K374A/K374Amice. Finally, silencing these proteins in DRG neurons from female CRMP2K374A/K374Amice, restored the loss of sodium currents. Our study shows that the endocytic complex composed of Numb, Nedd4-2 and Eps15, is necessary for non SUMOylated CRMP2-mediated internalization of sodium channelsin vivo.
APEX-based proximity labeling inPlasmodiumidentifies a membrane protein with dual functions during mosquito infection
Authors: Kehrer Jessica , Ricken Dominik , Strauss Leanne , Pietsch Emma , Heinze Julia M. , Frischknecht Friedrich
Published: September 2020

Transmission of the malaria parasitePlasmodiumto mosquitoes necessitates gamete egress from red blood cells to allow zygote formation and ookinete motility to enable penetration of the midgut epithelium. Both processes are dependent on the secretion of proteins from distinct sets of specialized vesicles. Inhibiting some of these proteins has shown potential for blocking parasite transmission to the mosquito. To identify new transmission blocking vaccine candidates, we defined the microneme content from ookinetes of the rodent model organismPlasmodium bergheiusing APEX2-mediated rapid proximity-dependent biotinylation. Besides known proteins of ookinete micronemes, this identified over 50 novel candidates and sharpened the list of a previous survey based on subcellular fractionation. Functional analysis of a first candidate uncovered a dual role for this membrane protein in male gametogenesis and ookinete midgut traversal. Mutation of a putative trafficking motif in the C-terminus led to its mis-localization in ookinetes and affected ookinete to oocyst transition but not gamete formation. This suggests the existence of distinct functional and transport requirements for Plasmodium proteins in different parasite stages.

Significance

The genome of the malaria parasitePlasmodiumcontains over 5500 genes, of which over 30% have no assigned function. Transmission ofPlasmodium spp. to the mosquito contains several essential steps that can be inhibited by antibodies or chemical compounds. Yet few proteins involved in these processes are characterized, thus limiting our capacity to generate transmission interfering tools. Here, we establish a method to rapidly identify proteins in a specific compartment within the parasite that is essential for establishment of an infection within the mosquito, and identify over 50 novel candidate proteins. Functional analysis of the top candidate identifies a protein with two independent essential functions in subsequent steps along thePlasmodiumlife cycle within the mosquito.

Highlights

first use of APEX based proximity ligation in Apicomplexa

identification of >50 putative ookinete surface proteins

novel membrane protein essential for microgamete egress and ookinete migration

putative trafficking motif essential in ookinetes but not gametes
An adipocyte-specific lncRAP2 – Igf2bp2 complex enhances adipogenesis and energy expenditure by stabilizing target mRNAs
Authors: Alvarez-Dominguez Juan R. , Winther Sally , Hansen Jacob B. , Lodish Harvey F. , Knoll Marko
Published: September 2020

lncRAP2 is a conserved cytoplasmic adipocyte-specific lncRNA required for adipogenesis. Using hybridization-based purification combined within vivointeractome analyses, we show that lncRAP2 forms ribonucleoprotein complexes with several mRNA stability and translation modulators, among them Igf2bp2. Transcriptome-wide identification of Igf2bp2 client mRNAs in white adipocytes reveals selective binding to mRNAs encoding adipogenic effectors and regulators. Depleting either lncRAP2 or Igf2bp coordinately downregulates these same target proteins. Ribosome profiling and quantitative proteomics show that this occurs predominantly at the level of mRNA, as binding of the lncRAP2-Igf2bp complex does not affect mRNA translation. Suppressing lncRAP2 or Igf2bp2 selectively destabilizes many mRNAs encoding proteins essential for energy expenditure, including Adiponectin, reducing adipocyte lipolytic capacity. Genome-wide association studies reveal specific association of genetic variants within both lncRAP2 and Igf2bp2 with body mass and type 2 diabetes, and we find that adipose lncRAP2 and Igf2bp2 are suppressed during obesity and diabetes progression. Thus, the lncRAP2-Igf2bp complex potentiates adipose development and energy expenditure and is associated with susceptibility to obesity-linked diabetes.
Generated randomly and selected functionally? The nature of enterovirus recombination
Authors: Alnaji Fadi G. , Bentley Kirsten , Pearson Ashley , Woodman Andrew , Moore Jonathan , Fox Helen , MacAdam Andrew , Evans David J.
Published: September 2020

Genetic recombination in RNA viruses is an important evolutionary mechanism. It contributes to population diversity, host/tissue adaptation and compromises vaccine efficacy. Both the molecular mechanism and initial products of recombination are relatively poorly understood. We used an established poliovirus-basedin vitrorecombination assay to investigate the roles of sequence identity and RNA structure, both implicated or inferred from analysis of circulating recombinant viruses, in the process. In addition, we used next generation sequencing to investigate the early products of recombination after cellular co-infection with different poliovirus serotypes. In independent studies we find no evidence for a role for RNA identity or structure in determining recombination junctions location. Instead, genome function and fitness are of greater importance in determining the identity of recombinant progeny. These studies provide further insights into this important evolutionary mechanism and emphasise the critical nature of the selection process on a mixed virus population.
Effects of petrophysical parameters on attenuation and dispersion of seismic waves in the simplified poroelastic theory: Comparison between the Biot's theory and viscosity‐extended theory
Authors: Zhao Haixia , Wu Bangyu , Gao Jinghuai
Published: September 2020

The simplified macro‐equations of porous elastic media are presented based on Hickey's theory upon ignoring effects of thermomechanical coupling and fluctuations of porosity and density induced by passing waves. The macro‐equations with definite physical parameters predict two types of compressional waves (P wave) and two types of shear waves (S wave). The first types of P and S waves, similar to the fast P wave and S wave in Biot's theory, propagate with fast velocity and have relatively weak dispersion and attenuation, while the second types of waves behave as diffusive modes due to their distinct dispersion and strong attenuation. The second S wave resulting from the bulk and shear viscous loss within pore fluid is slower than the second P wave but with strong attenuation at lower frequencies. Based on the simplified porous elastic equations, the effects of petrophysical parameters (permeability, porosity, coupling density and fluid viscosity) on the velocity dispersion and attenuation of P and S waves are studied in brine‐saturated sandstone compared with the results of Biot's theory. The results show that the dispersion and attenuation of P waves in simplified theory are stronger than those of Biot's theory and appear at slightly lower frequencies because of the existence of bulk and shear viscous loss within pore fluid. The properties of the first S wave are almost consistent with the S wave in Biot's theory, while the second S wave not included in Biot's theory even dies off around its source due to its extremely strong attenuation. The permeability and porosity have an obvious impact on the velocity dispersion and attenuation of both P and S waves. Higher permeabilities make the peaks of attenuation shift towards lower frequencies. Higher porosities correspond to higher dispersion and attenuation. Moreover, the inertial coupling between fluid and solid induces weak velocity dispersion and attenuation of both P and S waves at higher frequencies, whereas the fluid viscosity dominates the dispersion and attenuation in a macroscopic porous medium. Besides, the heavy oil sand is used to investigate the influence of high viscous fluid on the dispersion and attenuation of both P and S waves. The dispersion and attenuation in heavy oil sand are stronger than those in brine‐saturated sandstone due to the considerable shear viscosity of heavy oil. Seismic properties are strongly influenced by the fluid viscosity; thus, viscosity should be included in fluid properties to explain solid–fluid combination behaviour properly.