bluuebunny/crossref_metadata_2025 huggingface dataset:
Plasmin improves oedematous blood-gas barrier by cleaving epithelial sodium channels
Authors: Zhao Runzhen , Ali Gibran , Nie Hong-Guang , Chang Yongchang , Bhattarai Deepa , Su Xuefeng , Zhao Xiaoli , Matthay Michael A. , Ji Hong-Long
Published: February 2020

Background and Purpose

Lung oedema in association with suppressed fibrinolysis is a hallmark of lung injury. We aimed to test whether plasmin cleaves epithelial sodium channels (ENaC) to resolve lung oedema fluid.

Experimental Approaches

Human lungs and airway acid-instilled mice were used for analysing fluid resolution.In silicoprediction, mutagenesis,Xenopusoocytes, immunoblotting, voltage clamp, mass spectrometry, protein docking, and alveolar fluid clearance were combined for identifying plasmin specific cleavage sites and benefits.

Key Results

Plasmin led to a marked increment in lung fluid resolution in both human lungs ex vivo and injured mice. Plasmin specifically activated αβγENaC channels in oocytes in a time-dependent manner. Deletion of four consensus proteolysis tracts (αΔ432-444, γΔ131-138, γΔ178-193, and γΔ410-422) eliminated plasmin-induced activation significantly. Further, immunoblotting assays identified 7 cleavage sites (K126, R135, K136, R153, K168, R178, K179) for plasmin to trim both furin-cleaved C-terminal fragments and full-length human γENaC proteins. In addition to confirming the 7 cleavage sites, 9 new sites (R122, R137, R138, K150, K170, R172, R180, K181, K189) in synthesized peptides were found to be cleaved by plasmin with mass spectrometry. These cleavage sites were located in the finger and the thumb, particularly the GRIP domain of human ENaC 3D model composed of two proteolytic centres for plasmin. Novel uncleaved sites beyond the GRIP domain in both α and γ subunits were identified to interrupt the plasmin cleavage-induced conformational change in ENaC channel complexes. Additionally, plasmin could regulate ENaC activity via the G protein signal.

Conclusion and Implications

We demonstrate that plasmin could cleave ENaC to benefit the blood-gas exchange by resolving oedema fluid as a potent fibrinolytic therapy for oedematous pulmonary diseases.

Bullet point summary

What is already know

Serine proteases proteolytically cleave epithelial sodium channels, including plasmin and uPA acutely.

Activity of epithelial sodium channels is increased post proteolysis.

What this study adds

Plasmin cleaves up to 16 sites composed of two proteolytic centres in both full-length and furin-cleaved human γ subunit of epithelial sodium channels in hours.

Non-proteolytic sites in both α and γ subunits interrupt the plasmin cleavage-induced channel gating.

Intratracheally instilled plasmin facilitates alveolar fluid clearance in normal human and injured mouse lungs.

Clinical significance

Activation of human lung epithelial sodium channels by plasmin may benefit lung oedema resolution as a novel therapy for ARDS.
Bursty Expression Enhances Reliability of Messaging in Gene Networks
Authors: Gama Leonardo R. , Giovanini Guilherme , Balázsi Gábor , Ramos Alexandre F.
Published: February 2020

The promoter state of a gene and its expression levels are modulated by the amounts of transcription factors interacting with its regulatory regions. Hence, one may interpret a gene network as a communicating system in which the state of the promoter of a gene (thesource) is communicated by the amounts of transcription factors that it expresses (themessage) to modulate the state of the promoter and expression levels of another gene (thereceptor). The reliability of the gene network dynamics can be quantified by the Shannon’s entropy of the message and the mutual information between the message and the promoter state. Here we consider a stochastic model for a binary gene and use its exact steady state solutions to calculate the entropy and mutual information. We show that a slow switching promoter having long and equally standing ON and OFF states maximizes the mutual information and reduces entropy. That is a bursty regime generating a high variance message governed by a bimodal probability distribution with peaks of the same height. Our results indicate that Shannon’s theory can be a powerful framework for understanding how bursty gene expression conciliates with the striking spatio-temporal precision exhibited in pattern formation of developing organisms.
BET Bromodomain Proteins Regulate Transcriptional Reprogramming in Genetic Dilated Cardiomyopathy
Authors: Antolic Andrew , Wakimoto Hiroko , Jiao Zhe , Gorham Joshua M. , DePalma Steven R. , Conner David A. , Lee Da Young , Qi Jun , Seidman Jonathan G. , Bradner James E. , Brown Jonathan D. , Haldar Saptarsi M. , Seidman Christine E. , Burke Michael A.
Published: February 2020

The bromodomain and extraterminal (BET) family of epigenetic reader proteins are key regulators of pathologic gene expression in the heart. Using mice carrying a human mutation in phospholamban (PLNR9C) that develop progressive dilated cardiomyopathy (DCM), we previously identified the activation of inflammatory gene networks as a key early driver of DCM. We reasoned that BETs control this inflammatory process, representing a key node in the progression of genetic DCM. Using a chemical genetic strategy, PLNR9Cor age-matched wild type mice were treated longitudinally with the BET inhibitor JQ1 or vehicle. JQ1 abrogated DCM, reduced cardiac fibrosis, and prolonged survival in PLNR9Cmice by inhibiting inflammatory gene network expression at all disease stages. Cardiac fibroblast proliferation was also substantially reduced by JQ1. Interestingly, JQ1 had profound effects on pathologic gene network expression in cardiac fibroblasts, while having little effect on transcription in cardiomyocytes. Using co-immunoprecipitation, we identified BRD4 as a direct and essential regulator of NFκB-mediated inflammatory gene transcription in cardiac fibroblasts. In this this model of chronic, heritable DCM, BETs activate inflammatory gene networks in cardiac fibroblasts via an NFκB-dependent mechanism, marking them as critical effectors of pathologic gene expression.
ScaleQC: A Scalable Lossy to Lossless Solution for NGS Sequencing Data Compression
Authors: Yu Rogshan , Yang Wenxian
Published: February 2020

Motivation

Per-base quality values in NGS sequencing data take a significant portion of storage even after compression. Lossy compression technologies could further reduce the space used by quality values. However, in many applications lossless compression is still desired. Hence, sequencing data in multiple file formats have to be prepared for different applications.

Results

We developed a scalable lossy to lossless compression solution for quality values named ScaleQC. ScaleQC is able to provide bit-stream level scalability. More specifically, the losslessly compressed bit-stream by ScaleQC can be further truncated to lower data rates without re-encoding. Despite its scalability, ScaleQC still achieves same or better compression performance at both lossless and lossy data rates compared to the state-of-the-art lossless or lossy compressors.

Availability

ScaleQC has been integrated with SAMtools as a special quality value encoding mode for CRAM. Its source codes can be obtained from our integrated SAMtools (https://github.com/xmuyulab/samtools) with dependency on integrated HTSlib (https://github.com/xmuyulab/htslib).
Genome-wide molecular effects of the neuropsychiatric 16p11 CNVs in an iPSC-to-iN neuronal model
Authors: Ward Thomas R. , Zhang Xianglong , Leung Louis C. , Zhou Bo , Muench Kristin , Roth Julien G. , Khechaduri Arineh , Plastini Melanie J. , Charlton Carol , Pattni Reenal , Ho Steve , Ho Marcus , Huang Yiling , Hallmayer Joachim F. , Mourrain Phillippe , Palmer Theo D. , Urban Alexander E.
Published: February 2020

Copy number variants (CNVs), either deletions or duplications, at the 16p11.2 locus in the human genome are known to increase the risk for autism spectrum disorders (ASD), schizophrenia, and for several other developmental conditions. Here, we investigate the global effects on gene expression and DNA methylation using a 16p11.2 CNV patient-derived induced pluripotent stem cell (iPSC) to induced neuron (iN) cell model system. This approach revealed genome-wide and cell-type specific alterations to both gene expression and DNA methylation patterns and also yielded specific leads on genes potentially contributing to some of the known 16p11.2 patient phenotypes. PCSK9 is identified as a possible contributing factor to the symptoms seen in carriers of the 16p11.2 CNVs. The protocadherin (PCDH) gene family is found to have altered DNA methylation patterns in the CNV patient samples. The iPSC lines used for this study are available through a repository as a resource for research into the molecular etiology of the clinical phenotypes of 16p11.2 CNVs and into that of neuropsychiatric and neurodevelopmental disorders in general.
Gut microbiome modulates behaviour and life history in two wild rodents
Authors: Jameson Joël W. , Réale Denis , Kembel Steven W.
Published: February 2020

Laboratory studies demonstrate that the gut microbiome can regulate host anxiety and exploratory behaviour. While this has implications for human health, it could have ecological and evolutionary implications for wild populations, a hitherto untested hypothesis. We tested whether the microbiome can directly modulate host behaviour and thereby affect life history in wild mice (Peromyscus maniculatus) and voles (Myodes gapperi). We compared the microbiome composition, exploration and anxiety behaviours, and home range of mice and voles before and after chronic antibiotic treatment and measured survival during treatment. Treated animals had lower diversity and relative abundance of most bacterial phyla save for Proteobacteria which increased in relative abundance. In mice, antibiotic treatment increased exploration and decreased home range without impacting survival. In voles, it lowered survival such that we could not test its effect on behaviour. Therefore, the microbiome can directly impact behaviour and host life history in the wild.
Continuous Aerosol Medication Therapy in an in vitro High-Flow System Using Wire Mesh Technology
Authors: Cappiello Jhaymie , Bremenour Carla , Boyle Jason , Lumbard Jessica , Ghadimi Kamrouz
Published: February 2020

BACKGROUND

Jet nebulizers are commonly used to provide continuous aerosolized medication therapy (CAMT). We observed the function of our CAMT system that utilizes the Aeroneb Solo nebulizer system (Aerogen Ltd, Galway, Ireland). METHODS: An observational study was performed on 2 CAMT systems with 15 Aeroneb nebulizers for each system. CAMT was simulated for 1, 2 and 3 hours. Continuous nebulization was monitored and residual volumes were recorded at the end of each simulation. Our primary endpoint was established as intermittent nebulization observed by nebulizer filling of > 1 ml during CAMT simulation. Secondary endpoint was a residual volume of < 0.1 ml.

RESULTS

Out of 30 simulations in two arms, a fluid level was observed to accumulate intermittently in three nebulizers with a residual volume of 0.7 mls in one of these three. This produced a total success rate of 90%, Arm-A 80%, Arm B-100%, for our primary endpoint. Our secondary endpoint was achieved in 29 of the 30 nebulizers for an overall 97% success rate, Arm A-93%, Arm B-100%. CONCLUSION: Our Aerogen Solo CAMT system successfully emitted the set dose with 90% accuracy.
Predicting and elucidating the etiology of fatty liver disease using a machine learning-based approach: an IMI DIRECT study
Authors: Atabaki-Pasdar Naeimeh , Ohlsson Mattias , Viñuela Ana , Frau Francesca , Pomares-Millan Hugo , Haid Mark , Jones Angus G , Thomas E Louise , Koivula Robert W , Kurbasic Azra , Mutie Pascal M , Fitipaldi Hugo , Fernandez Juan , Dawed Adem Y , Giordano Giuseppe N , Forgie Ian M , McDonald Timothy J , Rutters Femke , Cederberg Henna , Chabanova Elizaveta , Dale Matilda , De Masi Federico , Thomas Cecilia Engel , Allin Kristine H , Hansen Tue H , Heggie Alison , Hong Mun-Gwan , Elders Petra JM , Kennedy Gwen , Kokkola Tarja , Pedersen Helle Krogh , Mahajan Anubha , McEvoy Donna , Pattou Francois , Raverdy Violeta , Häussler Ragna S , Sharma Sapna , Thomsen Henrik S , Vangipurapu Jagadish , Vestergaard Henrik , ‘t Hart Leen M , Adamski Jerzy , Musholt Petra B , Brage Soren , Brunak Søren , Dermitzakis Emmanouil , Frost Gary , Hansen Torben , Laakso Markku , Pedersen Oluf , Ridderstråle Martin , Ruetten Hartmut , Hattersley Andrew T , Walker Mark , Beulens Joline WJ , Mari Andrea , Schwenk Jochen M , Gupta Ramneek , McCarthy Mark I , Pearson Ewan R , Bell Jimmy D , Pavo Imre , Franks Paul W
Published: February 2020

Background

Non-alcoholic fatty liver disease (NAFLD) is highly prevalent and causes serious health complications in type 2 diabetes (T2D) and beyond. Early diagnosis of NAFLD is important, as this can help prevent irreversible damage to the liver and ultimately hepatocellular carcinomas.

Methods and Findings

Utilizing the baseline data from the IMI DIRECT participants (n=1514) we sought to expand etiological understanding and develop a diagnostic tool for NAFLD using machine learning. Multi-omic (genetic, transcriptomic, proteomic, and metabolomic) and clinical (liver enzymes and other serological biomarkers, anthropometry, and measures of beta-cell function, insulin sensitivity, and lifestyle) data comprised the key input variables. The models were trained on MRI image-derived liver fat content (<5% or ≥5%). We applied LASSO (least absolute shrinkage and selection operator) to select features from the different layers of omics data and Random Forest analysis to develop the models. The prediction models included clinical and omics variables separately or in combination. A model including all omics and clinical variables yielded a cross-validated receiver operator characteristic area under the curve (ROCAUC) of 0.84 (95% confidence interval (CI)=0.82, 0.86), which compared with a ROCAUC of 0.82 (95% CI=0.81, 0.83) for a model including nine clinically-accessible variables. The IMI DIRECT prediction models out-performed existing non-invasive NAFLD prediction tools.

Conclusions

We have developed clinically useful liver fat prediction models (see:www.predictliverfat.org) and identified biological features that appear to affect liver fat accumulation.
A non-APOE Polygenic score for Alzheimer’s disease and APOE-ε4 have independent associations with dementia in the Health and Retirement Study
Authors: Bakulski Kelly M. , Vadari Harita S. , Faul Jessica D. , Heeringa Steven G. , Kardia Sharon LR , Langa Kenneth M , Smith Jennifer A. , Manly Jennifer J. , Mitchell Colter M. , Benke Kelly S. , Ware Erin B.
Published: February 2020

INTRODUCTION

Alzheimer’s disease (AD) is a common and costly neurodegenerative disorder. A large proportion of risk is heritable and many genetic risk factors for AD have been identified. The cumulative genetic risk of known markers has not been benchmarked for dementia in a population-based sample.

METHODS

In the United States population-based Health and Retirement Study (HRS) (waves 1995-2014), we evaluated the role of cumulative genetic risk for AD, with and without the APOE-ε4 alleles, on dementia status (dementia, cognitive impairment without dementia, borderline cognitive impairment without dementia, cognitively normal). We used logistic regression, accounting for demographic covariates and genetic principal components, and analyses were stratified by European and African genetic ancestry.

RESULTS

In the European ancestry sample (n=8399), both AD polygenic score excluding the APOE genetic region (odds ratio (OR)=1.10; 95% confidence interval (CI): 1.00, 1.20) and the presence of any APOE-ε4 alleles (OR=2.42; 95% CI: 1.99, 2.95) were associated with the odds of dementia relative to normal cognition in a mutually-adjusted model. In the African ancestry sample (n=1605), the presence of any APOE-ε4 alleles was associated with 1.77 (95% CI: 1.20, 2.61) times higher odds of dementia, while the AD polygenic score excluding the APOE genetic region was not significantly associated with the odds of dementia relative to normal cognition 1.06 (95% CI: 0.97, 1.30).

DISCUSSION

Cumulative genetic risk for AD and APOE-ε4 are both independent predictors of dementia. This study provides important insight into the polygenic nature of dementia and demonstrates the utility of polygenic scores in dementia research.
Epidemiological and clinical features of the 2019 novel coronavirus outbreak in China
Authors: Yang Yang , Lu Qing-Bin , Liu Ming-Jin , Wang Yi-Xing , Zhang An-Ran , Jalali Neda , Dean Natalie E. , Longini Ira , Halloran M. Elizabeth , Xu Bo , Zhang Xiao-Ai , Wang Li-Ping , Liu Wei , Fang Li-Qun
Published: February 2020

Our manuscript was based on surveillance cases of COVID-19 identified before January 26, 2020. As of February 20, 2020, the total number of confirmed cases in mainland China has reached 18 times of the number in our manuscript. While the methods and the main conclusions in our original analyses remain solid, we decided to withdraw this preprint for the time being, and will replace it with a more up-to-date version shortly. Should you have any comments or suggestions, please feel free to contact the corresponding author.
Normative modelling using deep autoencoders: a multi-cohort study on mild cognitive impairment and Alzheimer’s disease
Authors: Pinaya Walter H. L. , Scarpazza Cristina , Garcia-Dias Rafael , Vieira Sandra , Baecker Lea , da Costa Pedro F. , Redolfi Alberto , Frisoni Giovanni B. , Pievani Michela , Calhoun Vince D. , Sato João R. , Mechelli Andrea ,   the Alzheimer’s Disease Neuroimaging Initiative,   the Australian Imaging Biomarkers and Lifestyle flagship study of ageing
Published: February 2020

Normative modelling is an emerging method for quantifying how individuals deviate from the healthy populational pattern. Several machine learning models have been implemented to develop normative models to investigate brain disorders, including regression, support vector machines and Gaussian process models. With the advance of deep learning technology, the use of deep neural networks has also been proposed. In this study, we assessed normative models based on deep autoencoders using structural neuroimaging data from patients with Alzheimer’s disease (n=206) and mild cognitive impairment (n=354). We first trained the autoencoder on an independent dataset (UK Biobank dataset) with 11,034 healthy controls. Then, we estimated how each patient deviated from this norm and established which brain regions were associated to this deviation. Finally, we compared the performance of our normative model against traditional classifiers. As expected, we found that patients exhibited deviations according to the severity of their clinical condition. The model identified medial temporal regions, including the hippocampus, and the ventricular system as critical regions for the calculation of the deviation score. Overall, the normative model had comparable cross-cohort generalizability to traditional classifiers. In order to promote open science, we are making all scripts and the trained models available to the wider research community.
Plasticity in gene expression facilitates invasion of the desert environment in house mice
Authors: Bittner Noëlle K. J. , Mack Katya L. , Nachman Michael W.
Published: February 2020

Understanding how organisms adapt to new environments is a key problem in evolution, yet it remains unclear whether phenotypic plasticity generally facilitates or hinders this process. Here we studied the evolved and plastic responses to water stress in lab-born descendants of wild house mice (Mus musculus domesticus) collected from desert and non-desert environments. Using a full sib design, we measured organismal phenotypes and gene expression under normal (hydrated) and water stressed (dehydrated) conditions. After many generations in the lab, mice from the desert consumed significantly less water than mice from other localities, indicating that this difference has a genetic basis. Under water stress, desert mice lost less weight than non-desert mice, and desert mice exhibited differences in blood chemistry related to osmoregulatory function. Gene expression in the kidney revealed evolved differences between mice from different environments as well as plastic responses between hydrated and dehydrated mice. Desert mice showed reduced gene expression plasticity under water stress compared to non-desert mice. Importantly, the non-desert mice generally showed shifts towards desert-like expression under water stress, consistent with adaptive plasticity. Finally, patterns of gene expression identified several candidate genes for adaptation to the desert, includingAqp1andApoe. These findings provide evidence for local adaptation in a recently introduced species and suggest that adaptive plasticity may have facilitated the colonization of the desert environment.
Protein allocation and enzymatic constraints explainEscherichia coliwildtype and mutant phenotypes
Authors: Alter Tobias B. , Blank Lars M. , Ebert Birgitta E.
Published: February 2020

Proteins have generally been recognized to constitute the key cellular component in shaping microbial phenotypes. Due to limited cellular resources and space, optimal allocation of proteins is crucial for microbes to facilitate maximum proliferation rates while allowing a flexible response to environmental changes. Regulatory patterns of protein allocation were utilized to account for the condition-dependent proteome in a genome-scale metabolic reconstruction ofEscherichia coliby linearly linking mass concentrations of protein sectors and single metabolic enzymes to flux variables. The resulting protein allocation model (PAM) correctly approximates wildtype phenotypes and flux distributions for various substrates, even under data scarcity. Moreover, we showed the ability of the PAM to predict metabolic responses of single gene deletion mutants by additionally assuming growth-limiting, transcriptional restrictions. Thus, we promote the integration of protein allocation constraints into classical constraint-based models to foster their predictive capabilities and application for strain analysis and metabolic engineering purposes.
Insulin-Like Growth Factor I Modulates Vulnerability to Stress Through Orexin Neurons
Authors: Fernandez de Sevilla ME , Pignatelli J , Mendez P. , Zegarra-Valdivia J , Torres Alemán I
Published: February 2020

Knowledge of mechanisms involved in vulnerability/resilience to stress disorders is crucial for prevention and treatment schemes. We previously documented that insulin-like growth factor I (IGF-I) is associated to vulnerability to stress both in mice and humans. Since hypothalamic orexin neurons express IGF-I receptors and are involved in responses to stress, we analyzed their role in the modulatory actions of IGF-I on stress. Anxiolytic actions of IGF-I after exposure to a predator were absent in mice lacking IGF-I receptors in orexin neurons (Firoc mice). Based on these observations we speculated that Firoc mice may be prone to develop fear-related disturbances, including post-traumatic stress disorder (PTSD)-like symptoms when confronted to fear learning, a process that is postulated to be altered in PTSD. Firoc mice submitted to fear conditioning showed increased freezing responses, suggesting aberrant fear learning. Exaggerated freezing was accompanied by increased levels of orexin, together with enhanced c-fos staining of these neurons –an indicator of increased cell activity, and of noradrenergic neurons of the locus coeruleus nucleus, a region downstream of orexinergic activation. After fear conditioning, Firoc mice developed PTSD-like behavioral traits such as prolonged context-dependent fear and post-stress anhedonia. Since abnormal fear learning was ameliorated by chemogenetic (DREADD) inhibition of orexin neurons, reduced IGF-I input to orexin neurons in Firoc mice seems to enhance their excitability to fear-related inputs. Collectively, these results suggest that IGF-I input to orexin neurons is an important determinant of vulnerability to stress disorders, which provides additional targets for therapy of these high social impact conditions.
A genome-wide screen in mice to identify cell-extrinsic regulators of pulmonary metastatic colonisation
Authors: van der Weyden Louise , Swiatkowska Agnieszka , Iyer Vivek , Speak Anneliese O. , Adams David J.
Published: February 2020

Metastatic colonisation, whereby a disseminated tumour cell is able to survive and proliferate at a secondary site, involves both tumour cell-intrinsic and -extrinsic factors. To identify tumour cell-extrinsic (microenvironmental) factors that regulate the ability of metastatic tumour cells to effectively colonise a tissue, we performed a genome-wide screen utilising the experimental metastasis assay on mutant mice. Mutant and wildtype (control) mice were tail vein-dosed with murine metastatic melanoma B16-F10 cells and 10 days later the number of pulmonary metastatic colonies were counted. Of the 1,300 genes/genetic locations (1,344 alleles) assessed in the screen 34 genes were determined to significantly regulate pulmonary metastatic colonisation (15 increased and 19 decreased;P<0.005 and genotype effect <-60 or >+60). Whilst several of these genes have known roles in immune system regulation (Bach2, Cyba, Cybb, Cybc1, Id2, Igh-6, Irf1, Irf7, Ncf1, Ncf2, Ncf4andPik3cg) most are involved in a disparate range of biological processes, ranging from ubiquitination (Herc1) to diphthamide synthesis (Dph6) to Rho GTPase-activation (Arhgap30andFgd4), with no previous reports of a role in the regulation of metastasis. Thus, we have identified numerous novel regulators of pulmonary metastatic colonisation, which may represent potential therapeutic targets.
Temperature, but not excess of glycogen, regulate post-mortem AMPK activity in muscle of steer carcasses.
Authors: Strobel Pablo , Galaz A , Villaroel-Espíndola Franz , Apaoblaza Ariel , Slebe Juan Carlos , Jerez-Timaure Nancy , Gallo Carmen , Ramírez-Reveco Alfredo
Published: February 2020

Post-mortem muscle temperature affects the rate of decline in pH in a linear manner from 37.5 °C down near 0 °C, and this pH decline is correlated with the enzymatic degradation of glycogen to lactate. This transformation occurs in an anaerobic context that includes the metabolic splice between glycogenolysis and glycolysis; and both processes are strongly upregulated by AMPK enzyme. In this study we reported changes (0.5 h and 24 h post-mortem) in muscle glycogen concentration, lactate and AMPK activity from 12 samples of Longissimus dorsi from 38 steers that produced high pH (>5.9) and normal pH (<5.8) carcasses at 24 h post-mortem. Moreover, we evaluated changes in AMPK activity in samples from both categories incubated at 37, 25, 17 and 5 °C and supplemented with exogenous glycogen. Finally, we analysed if there were structural differences between polymers from both categories. Our analyses show that enzymatic AMPK activity was significantly higher at 17 °C than at 37 °C or 25 °C (p<0.0001 and p<0.05 in samples from normal and high pH categories, respectively), and was near zero at 5 °C. On the other hand, AMPK activity did not change in relation with excess glycogen and we did not detect structural differences in the polymers present in samples from both categories. We concluded that post-mortem AMPK activity level is highly sensitive to temperature and not at in vitro changes in glycogen concentration. Their results suggest that that normal levels of pre-mortem muscle glycogen and an adequate cooling managing of carcasses are relevant to let an efficient glycogenolytic/glycolytic flow required for lactate accumulation and pH decline, trough of post-mortem AMPK signalling pathway.
Automated flight interception traps for interval sampling of insects
Authors: Bolliger Janine , Collet Marco , Hohl Michael , Wermelinger Beat , Obrist Martin K.
Published: February 2020

Recent debates on insect decline require sound assessments on the relative drivers that may negatively impact insect populations. Often, baseline data rely on insect monitorings that integrates catches over long time periods. If, however, effects of time-critical environmental factors (e.g., light pollution) are of interest, higher temporal resolution of insect observations during specific time intervals are required (e.g., between dusk and dawn). Conventional time-critical insect trapping is labour-intensive (manual activation/deactivation) and temporally inaccurate as not all traps can be serviced synchronically at different sites. Also, temporal shifts of environmental conditions (e.g., sunset/sunrise) are not accounted for. We provide a battery-driven automated insect flight-interception trap which samples insects during seven user-defined time intervals. A commercially available flight-interception trap is fitted to a rotating platform containing seven flasks and a passage hole. The passage hole avoids unwanted sampling during time-intervals not of interest. Comparisons between two manual and two automated traps during 71 nights in 2018 showed no difference in caught insects. An experiment using 20 automated traps during 104 nights in 2019 proved that the automated flight interception traps is reliable. The automated trap opens new research possibilities as any insect-sampling interval can be defined. It is efficient and saves manpower and associated costs as activation/deactivation is required only every seven sampling intervals. Also, the traps are accurate because all traps sample exactly the same intervals. The trap is low maintenance and robust due to straightforward technical design. It can be controlled manually or via Bluetooth and smartphone.
Cysteamine-bicalutamide combination treatment restores alpha-ketoglutarate and corrects proximal tubule phenotype in cystinosis
Authors: Jamalpoor Amer , van Gelder Charlotte AGH , Yousef Yengej Fjodor A , Zaal Esther A , Berlingerio Sante Princiero , Veys Koenraad R , Casellas Carla Pou , Voskuil Koen , Essa Khaled , Ammerlaan Carola ME , Rega Laura Rita , van der Welle Reini , Lilien Marc R , Rookmaaker Maarten B , Clevers Hans , Klumperman Judith , Levtchenko Elena , Berkers Celia R , Verhaar Marianne C , Altelaar Maarten , Masereeuw Rosalinde , Janssen Manoe J
Published: February 2020

Nephropathic cystinosis is a severe monogenetic kidney disorder caused by mutations inCTNS, encoding the lysosomal transporter cystinosin, resulting in lysosomal cystine accumulation. The sole treatment, cysteamine, slows down the disease progression, but does not correct the established proximal tubulopathy. Here, we developed a new therapeutic strategy by applying an omics-based strategy to expand our knowledge on the complexity of the disease and prioritize drug targets in cystinosis. We identified alpha-ketoglutarate as a key metabolite linking cystinosin loss, lysosomal autophagy defect and proximal tubular impairment in cystinosis. This insight offered a bicalutamide-cysteamine combination treatment as a novel dual target pharmacological approach for the phenotypical correction of cystinotic proximal tubule cells, patient-derived kidney tubuloids and cystinotic zebrafish.
Activation of Rab11a and endocytosis by Phosphatidylinositol 4-kinase III beta promotes oncogenic signaling in breast cancer
Authors: MacDonald Spencer A , Harding Katherine , Bilodeau Patricia , de Souza Christiano T , Campa Carlo Cosimo , Hirsch Emilio , Auer Rebecca C , Lee Jonathan M
Published: February 2020

Endosomes are now recognized as important sites for regulating signal transduction. Here we show that the lipid kinase phosphatidylinositol 4-kinase III beta (PI4KIIIβ) regulates both endocytic kinetics and receptor signaling in breast cancer cells. PI4KIIIβ generates phosphatidylinositol 4-phosphate from phosphatidylinositol and is highly expressed in a subset of breast cancers. However, the molecular mechanism by which PI4KIIIβ promotes breast cancer is unclear. We demonstrate that ectopic PI4KIIIβ expression increases the rates of both endocytic internalization and recycling. PI4KIIIβ deletion reduces endocytic kinetics accompanied by a concomitant decrease in activity of the Rab11a GTPase, a protein required for endocytic function. Finally, we find that PI4KIIIβ activates IGF-IRβ signaling dependent on endosome function. Regulation of endocytic function by PI4KIIIβ is independent of its kinase activity but requires interaction with the Rab11a. This suggests that PI4KIIIβ controls endosomal kinetics and signaling by directly modulating Rab11a function. Our work suggests a novel regulatory role for PI4KIIIβ in endosome function and plasma membrane receptor signaling.
Importin-9 regulates chromosome segregation and packaging inDrosophilagerm cells
Authors: Palacios Victor , Kimble Garrett C , Tootle Tina L. , Buszczak Michael
Published: February 2020

Germ cells undergo distinct nuclear processes as they differentiate into gametes. While these events must be coordinated to ensure proper maturation, the stage-specific transport of proteins in and out of germ cell nuclei remains incompletely understood.

Our efforts to genetically characterizeDrosophilagenes that exhibit enriched expression in germ cells led to the finding that loss of the highly-conserved Importin β/karyopherin family member Importin-9 (Ipo9) results in female and male sterility.

Immunofluorescence and fluorescent in situ hybridization (FISH) revealed thatIpo9KOmutants display chromosome condensation and segregation defects during meiosis. In addition,Ipo9KOmutant males form abnormally structured sperm and fail to properly exchange histones for protamines. Ipo9 physically interacts with proteasome proteins andIpo9mutant males exhibit loss of nuclear ubiquitination and disruption of the nuclear localization of several proteasome components. Thus, Ipo9 coordinates the nuclear import of functionally related factors necessary for the completion of gametogenesis.

Highlights

DrosophilaImportin-9 functions in female and male meiosis

Loss of Importin-9 disrupts the histone to protamine transition during spermiogenesis Importin-9 physically interacts with components of the proteasome

Importin-9 is required for the efficient nuclear transport of proteasome proteins during spermiogenesis
A pedigree-based prediction model identifies carriers of deleteriousde novomutations in families with Li-Fraumeni syndrome
Authors: Gao Fan , Pan Xuedong , Dodd-Eaton Elissa B. , Recio Carlos Vera , Montierth Matthew D. , Bojadzieva Jasmina , Mai Phuong L. , Zelley Kristin , Johnson Valen E. , Braun Danielle , Nichols Kim E. , Garber Judy E. , Savage Sharon A. , Strong Louise C. , Wang Wenyi
Published: February 2020

De novomutations (DNMs) are increasingly recognized as rare disease causal factors. Identifying DNM carriers will allow researchers to study the likely distinct molecular mechanisms of DNMs. We developed Famdenovo to predict DNM status (DNM or familial mutation (FM)) of deleterious autosomal dominant germline mutations for any syndrome. We introduce Famdenovo.TP53 for Li-Fraumeni syndrome (LFS) and analyze 324 LFS family pedigrees from four US cohorts: a validation set of 186 pedigrees and a discovery set of 138 pedigrees. The concordance index for Famdenovo.TP53 prediction was 0.95 (95% CI: [0.92, 0.98]). Forty individuals (95% CI: [30, 50]) were predicted as DNM carriers, increasing the total number from 42 to 82. We compared clinical and biological features of FM versus DNM carriers: 1) cancer and mutation spectra along with parental ages were similarly distributed; 2) ascertainment criteria like early-onset breast cancer (age 20 to 35 years) provides a condition for an unbiased estimate of the DNM rate: 48% (23 DNMs versus 25 FMs); 3) hotspot mutation R248W was not observed in DNMs, although it was as prevalent as hotspot mutation R248Q in FMs. Furthermore, we introduce Famdenovo.BRCA for hereditary breast and ovarian cancer syndrome, and apply it to a small set of family data from the Cancer Genetics Network. In summary, we introduce a novel statistical approach to systematically evaluate deleterious DNMs in inherited cancer syndromes. Our approach may serve as a foundation for future studies evaluating how new deleterious mutations can be established in the germline, such as those inTP53.
Imaging and tracking mRNA in live mammalian cells via fluorogenic photoaffinity labeling
Authors: Ayele Tewoderos M. , Loya Travis , Valdez-Sinon Arielle N. , Bassell Gary J. , Heemstra Jennifer M.
Published: February 2020

Cellular RNA labeling using light-up aptamers that bind to and activate fluorogenic molecules has gained interest in recent years as an alternative to protein-based RNA labeling approaches. Aptamer-based systems are genetically encodable and cover the entire visible spectrum. However, the relatively weak nature of the non-covalent aptamer-fluorogen interaction limits the utility of these systems in that multiple copies of the aptamer are often required, and in most cases the aptamer must be expressed on a second scaffold such as a transfer RNA. We propose that these limitations can be averted through covalent RNA labeling, and here we describe a photoaffinity approach in which the aptamer ligand is functionalized with a photoactivatable reactive group such that irradiation with UV light results in covalent attachment to the RNA of interest. In addition to the robustness of the covalent linkage, this approach benefits from the ability to temporally control RNA labeling. To demonstrate this method, we incorporated a photoaffinity linker onto malachite green and fused the malachite green aptamer to a specific mRNA reporter of interest. We observed markedly improved sensitivity for fixed cell imaging of mRNA using this approach compared toin situhybridization. Additionally, we demonstrate visualization of RNA dynamics in live cells using an mRNA having only a single copy of the aptamer, minimizing perturbation of the structure and localization. Our initial biological application utilizes the photoaffinity labeling approach to monitor RNA stress granule dynamics and we envision future application of this method for a wide range of investigations into the cellular localization, dynamics, and protein binding properties of cellular RNAs.
Mobile Element Insertions and Associated Structural Variants in Longitudinal Breast Cancer Samples
Authors: Steely Cody J. , Russell Kristi L. , Feusier Julie E. , Qiao Yi , Tavtigian Sean V. , Marth Gabor , Jorde Lynn B.
Published: February 2020

While mobile elements are largely inactive in healthy somatic tissues, increased activity has been found in cancer tissues, with significant variation among different cancer types. In addition to insertion events, mobile elements have also been found to mediate many structural variation events in the genome. Here, to better understand the timing and impact of mobile element insertions and structural variants involving existing mobile elements in cancer, we examined their activity in longitudinal samples of four metastatic breast cancer patients. With whole-genome sequencing data from multiple timepoints through tumor progression, we used mobile element detection software followed by visual confirmation of the insertions. We identified 11 mobile element insertions or structural variants involving existing elements and found that the majority of these occurred early in tumor progression. Two of the identified insertions were SVA elements, which have rarely been found in previous cancer studies. Most of the variants appear to impact intergenic regions; however, we identified a translocation interruptingMAP2K4involvingAluelements and a deletion inYTHDF2involving mobile elements that likely inactivate reported tumor suppressor genes. The high variant allele fraction of theMAP2K4translocation, the loss of the other copy ofMAP2K4, the recurrent loss-of-function mutations found in this gene in other human cancers, and the important function ofMAP2K4indicate that this translocation is potentially a driver mutation. Overall, using a unique longitudinal dataset, we find that most variants are likely passenger mutations in the four patients we examined, but some variants impact tumor progression.
Seed-skewness algorithm for X-ray diffraction signal detection in time-resolved synchrotron Laue photocrystallography
Authors: Szarejko Dariusz , Kamiński Radosław , Łaski Piotr , Jarzembska Katarzyna N.
Published: February 2020

A one-dimensional seed-skewness algorithm adapted for X-ray diffraction signal detection is presented and discussed. The method, primarily designed for photocrystallographic time-resolved Laue data processing, was shown to work well for the type of data collected at the Advanced Photon Source and European Synchrotron Radiation Facility. Nevertheless, it is also applicable in the case of standard single-crystal X-ray diffraction data. The reported algorithm enables reasonable separation of signal from the background in single one-dimensional data vectors as well as the capability to determine small changes of reflection shapes and intensities resulting from exposure of the sample to laser light. Otherwise, the procedure is objective, and relies only on skewness computation and its subsequent minimization. The new algorithm was proved to yield comparable results to the Kruskal–Wallis test method [Kalinowski, J. A. et al. (2012). J. Synchrotron Rad.
19, 637], while the processing takes a similar amount of time. Importantly, in contrast to the Kruskal–Wallis test, the reported seed-skewness approach does not need redundant input data, which allows for faster data collections and wider applications. Furthermore, as far as the structure refinement is concerned, the reported algorithm leads to the excited-state geometry closest to the one modelled using the quantum-mechanics/molecular-mechanics approach reported previously [Jarzembska, K. N. et al. (2014). Inorg. Chem.
53, 10594], when the t and s algorithm parameters are set to the recommended values of 0.2 and 3.0, respectively.
Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1
Authors: Zivanov Jasenko , Nakane Takanori , Scheres Sjors H. W.
Published: February 2020

Methods are presented that detect three types of aberrations in single-particle cryo-EM data sets: symmetrical and antisymmetrical optical aberrations and magnification anisotropy. Because these methods only depend on the availability of a preliminary 3D reconstruction from the data, they can be used to correct for these aberrations for any given cryo-EM data set, a posteriori. Using five publicly available data sets, it is shown that considering these aberrations improves the resolution of the 3D reconstruction when these effects are present. The methods are implemented in version 3.1 of the open-source software package RELION.
The atomic structure of the Bergman-type icosahedral quasicrystal based on the Ammann–Kramer–Neri tiling
Authors: Buganski Ireneusz , Wolny Janusz , Takakura Hiroyuki
Published: February 2020

In this study, the atomic structure of the ternary icosahedral ZnMgTm quasicrystal (QC) is investigated by means of single-crystal X-ray diffraction. The structure is found to be a member of the Bergman QC family, frequently found in Zn–Mg–rare-earth systems. Theab initiostructure solution was obtained by the use of theSuperflipsoftware. The infinite structure model was founded on the atomic decoration of two golden rhombohedra, with an edge length of 21.7 Å, constituting the Ammann–Kramer–Neri tiling. The refined structure converged well with the experimental diffraction diagram, with the crystallographicRfactor equal to 9.8%. The Bergman clusters were found to be bonded by four possible linkages. Only two linkages,bandc, are detected in approximant crystals and are employed to model the icosahedral QCs in the cluster approach known for the CdYb Tsai-type QC. Additional shortbandalinkages are found in this study. Short interatomic distances are not generated by those linkages due to the systematic absence of atoms and the formation of split atomic positions. The presence of four linkages allows the structure to be pictured as a complete covering by rhombic triacontahedral clusters and consequently there is no need to define the interstitial part of the structure (i.e.that outside the cluster). The 6D embedding of the solved structure is discussed for the final verification of the model.
5-Methyl-4-(5-methyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)-2-phenyl-1H-pyrazol-3(2H)-one
Authors: Powell Gregory L. , Rix Brad A.
Published: February 2020

The title compound, C20H18N4O2, known as bispyrazolone, was crystallized from dimethyl sulfoxide. The structure has orthorhombic (Pbca) symmetry at 150 K, and displays both intra- and intermolecular hydrogen bonding through C—H...O and N—H...O contacts, respectively. None of the phenyl and pyrazolone rings in the molecule are coplanar. The dihedral angle between the pyrazolone rings is 66.18 (5)°.
Music subculture as a source of conspicuous consumption practices: a qualitative content analysis of “altered movement” songs and music videos
Authors: Castillo-Villar Fernando Rey , Cavazos-Arroyo Judith , Kervyn Nicolas
Published: February 2020

Purpose

The purpose of this study is to focus on analyzing the role of music subcultures in the communication and promotion of conspicuous consumption practices. The object of study is the “altered movement” as the music style of the drug subculture in Mexico.

Design/methodology/approach

A qualitative content analysis of 78 lyrics and music videos of “altered movement” was carried out between August and December 2018.

Findings

The analysis of lyrics and music videos leads to the identification of four narratives (from poor to rich, power through violence, lavish lifestyle and power over women) and diverse symbolic markers (luxury brands mainly) that together, display messages aimed at promoting conspicuous consumption practices.

Originality/value

The current research expands the body of literature of music subcultures in the consumer research area by contesting the common conception of this phenomenon as a healthy source of self-identity formation and deepening into its role as a source of conspicuous consumption practices.
MCMC and GLMs for estimating regression parameters
Authors: ELsayed Mahmoud , Soliman Amr
Published: February 2020

Purpose

The purpose of this study is to estimate the linear regression parameters using two alternative techniques. First technique is to apply the generalized linear model (GLM) and the second technique is the Markov Chain Monte Carlo (MCMC) method.

Design/methodology/approach

In this paper, the authors adopted the incurred claims of Egyptian non-life insurance market as a dependent variable during a 10-year period. MCMC uses Gibbs sampling to generate a sample from a posterior distribution of a linear regression to estimate the parameters of interest. However, the authors used the R package to estimate the parameters of the linear regression using the above techniques.

Findings

These procedures will guide the decision-maker for estimating the reserve and set proper investment strategy.

Originality/value

In this paper, the authors will estimate the parameters of a linear regression model using MCMC method via R package. Furthermore, MCMC uses Gibbs sampling to generate a sample from a posterior distribution of a linear regression to estimate parameters to predict future claims. In the same line, these procedures will guide the decision-maker for estimating the reserve and set proper investment strategy.