bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct medical costs of hospitalized patients with idiopathic pulmonary fibrosis in China
Authors: Zheng Xiaofen , Xie Bingbing , Liu Yan , Zhu Ming , Zhang Shu , Ban Chengjun , Geng Jing , Jiang Dingyuan , Ren Yanhong , Dai Huaping , Wang Chen
Published: October 2019

Background

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive fibrosing interstitial pneumonia of unknown cause. The incidence of IPF is increasing year by year, as well as the mortality rates, which is really a burden both for the family and the society. However few data concerning the economic burden of the patients with IPF is available, especially in China.

Objective

This study aimed to examine the direct medical costs of hospitalized patients with IPF and to determine the contributing factors.

Methods

This retrospective analysis used the cost-of-illness framework in order to analyze the direct medical costs of patients with IPF. The study used data from the pneumology department of Beijing Chao-Yang Hospital affiliated to Capital Medical University from year 2012 to 2015. The direct medical costs included drug fee, auxiliary examination fee, treatment fee and other fee. Patients’ characteristics, medical treatment, and the direct medical costs were analyzed by descriptive statistics and multivariable regression.

Results

There were 219 hospitalized patients meeting the diagnosis of IPF, 91% male. The mean age was 65 years old. For the direct medical costs of hospitalized patients with IPF, the mean(SD) of the total costs per IPF patient per admission was 14882.3 (30975.8)CNY. The largest parts were the examination fee of 6034.5 (15651.2)CNY and the drug fee of 5048.9 (3855.1)CNY. By regression analysis we found that length of stay, emergency treatment, ventilator use and being a Beijing native were significantly (P<0.05) associated with total hospitalization costs, and the length of stay had the biggest impact. Complications or comorbidities contributated to the direct medical costs as follows: respiratory failure with 30898.3CNY (P=0.004), pulmonary arterial hypertension(PAH) with 26898.2CNY (P=0.098), emphysema with 25368.3CNY (P=0.033), and high blood pressure with 24659.4CNY (P=0.026). Using DLCO or DLCO% pred to reflect the severity of IPF, there was no significant correlation between DLCO or DLCO% pred and patients’ direct medical costs. While, the worse the diffusion function, the higher the drug fee.

Conclusion

This study showed that IPF has a major impact on the direct medical costs. Thus, appropriate long-term interventions are recommended to lower the economic burden of IPF.

Strengths and limitations of this study

It was the first time in China to discuss the economic burden of diseases and its influencing factors in patients with IPF.

The results of this study might be of reference for the establishment of IPF disease-related medical policies in future.

The retrospective cross-sectional design does not allow for establishing any causal relationships.

It was a a single-center study, resulting a slightly smaller sample size. A large sample of multicenter studies is needed to confirm this.
Increased ultra-rare variant load in an isolated Scottish population impacts exonic and regulatory regions
Authors: Halachev Mihail , Meynert Alison , Taylor Martin S , Vitart Veronique , Kerr Shona M , Klaric Lucija ,   SGP Consortium, Aitman Timothy J , Haley Chris S , Prendergast James G , Pugh Carys , Hume David A , Harris Sarah E , Liewald David C , Deary Ian J , Semple Colin A , Wilson James F
Published: October 2019

Human population isolates provide a snapshot of the impact of historical demographic processes on population genetics. Such data facilitate studies of the functional impact of rare sequence variants on biomedical phenotypes, as strong genetic drift can result in higher frequencies of variants that are otherwise rare. We present the first whole genome sequencing (WGS) study of the VIKING cohort, a representative collection of samples from the isolated Shetland population in northern Scotland, and explore how its genetic characteristics compare to a mainland Scottish population. Our analyses reveal the strong contributions played by the founder effect and genetic drift in shaping genomic variation in the VIKING cohort. About one tenth of all high-quality variants discovered are unique to the VIKING cohort or are seen at frequencies at least ten fold higher than in more cosmopolitan control populations. Multiple lines of evidence also suggest relaxation of purifying selection during the evolutionary history of the Shetland isolate. We demonstrate enrichment of ultra-rare VIKING variants in exonic regions and for the first time we also show that ultra-rare variants are enriched within regulatory regions, particularly promoters, suggesting that gene expression patterns may diverge relatively rapidly in human isolates.

Author Summary

Population isolates provide a valuable window on the roles of rare genetic variation in human phenotypes, as a result of their unusual evolutionary histories, that often lead to relatively high frequencies of variants that are exceptionally rare elsewhere. Such populations show increased levels of background relatedness among individuals and are often subject to stronger genetic drift, leading to a higher frequency of deleterious variants. Here, for the first time, we present whole genome sequencing data from the Shetland population in Northern Scotland, encompassing 500 individuals, and compare these genomes to the mainland Scottish population. As expected we find the imprint of Shetland population history in the Shetland genome, with strong evidence for founder effects and genetic drift, but we also discover a relaxation of selective constraint across the genome. These influences have combined to endow the Shetland genome with thousands of ultra-rare genetic variants, not observed previously in other populations. Surprisingly these variants are significantly enriched in functional regions including protein coding regions of genes and regulatory elements. Among regulatory regions, promoters are particularly enriched for ultra-rare variants, suggesting the potential for rapid divergence of gene expression in isolates.
CPlantBox, a whole plant modelling framework for the simulation of water and carbon related processes
Authors: Zhou Xiao-Ran , Schnepf Andrea , Vanderborght Jan , Leitner Daniel , Lacointe André , Vereecken Harry , Lobet Guillaume
Published: October 2019

The interaction between carbon and flows within the plant is at the center of most growth and developmental processes. Understanding how these fluxes influence each other, and how they respond to heterogeneous environmental conditions, is important to answer diverse questions in forest, agriculture and environmental sciences. However, due to the high complexity of the plant-environment system, specific tools are needed to perform such quantitative analyses.

Here we present CPlantBox, full plant modelling framework based on the root system model CRootBox. CPlantbox is capable of simulating the growth and development of a variety of plant architectures (root and shoot). In addition, the flexibility of CPlantBox enables its coupling with external modeling tools. Here, we connected it to an existing mechanistic model of water and carbon flows in the plant, PiafMunch.

The usefulness of the CPlantBox modelling framework is exemplified in four case studies. Firstly, we illustrate the range of plant structures that can be simulated using CPlantBox. In the second example, we simulated diurnal carbon and water flows, which corroborates published experimental data. In the third case study, we simulated impacts of heterogeneous environment on carbon and water flows. Finally, we showed that our modelling framework can be used to fit phloem pressure and flow speed to (published) experimental data.

The CPlantBox modelling framework is open-source, highly accessible and flexible. Its aim is to provide a quantitative framework for the understanding of plant-environment interaction.
An integrated platform to systematically identify causal variants and genes for polygenic human traits
Authors: Downes Damien J. , Schwessinger Ron , Hill Stephanie J. , Nussbaum Lea , Scott Caroline , Gosden Matthew E. , Hirschfeld Priscila P. , Telenius Jelena M. , Eijsbouts Chris Q. , McGowan Simon J. , Cutler Antony J. , Kerry Jon , Davies Jessica L. , Dendrou Calliope A. , Inshaw Jamie R.J. , Larke Martin S.C. , Marieke Oudelaar A. , Bozhilov Yavor , King Andrew J. , Brown Richard C. , Suciu Maria C. , Davies James O.J. , Hublitz Philip , Fisher Chris , Kurita Ryo , Nakamura Yukio , Lunter Gerton , Taylor Stephen , Buckle Veronica J. , Todd John A. , Higgs Douglas R. , Hughes Jim R.
Published: October 2019

Genome-wide association studies (GWAS) have identified over 150,000 links between common genetic variants and human traits or complex diseases. Over 80% of these associations map to polymorphisms in non-coding DNA. Therefore, the challenge is to identify disease-causing variants, the genes they affect, and the cells in which these effects occur. We have developed a platform using ATAC-seq, DNaseI footprints, NG Capture-C and machine learning to address this challenge. Applying this approach to red blood cell traits identifies a significant proportion of known causative variants and their effector genes, which we show can be validated by direct in vivo modelling.
On the relation of phase separation and Hi-C maps to epigenetics
Authors: Singh Prim B. , Newman Andrew G.
Published: October 2019

The relationship between compartmentalisation of the genome and epigenetics is long and hoary. In 1928 Heitz defined heterochromatin as the largest differentiated chromatin compartment in eukaryotic nuclei. Müller’s (1930) discovery of position-effect variegation (PEV) went on to show that heterochromatin is a cytologically-visible state of heritable (epigenetic) gene repression. Current insights into compartmentalisation have come from a high-throughput top-down approach where contact frequency (Hi-C) maps revealed the presence of compartmental domains that segregate the genome into heterochromatin and euchromatin. It has been argued that the compartmentalisation seen in Hi-C maps is due to the physiochemical process of phase separation. Oddly, the insights provided by these experimental and conceptual advances have remained largely silent on how Hi-C maps and phase separation relate to epigenetics. Addressing this issue directly in mammals, we have made use of a bottom-up approach starting with the hallmarks of constitutive heterochromatin, heterochromatin protein 1 (HP1) and its binding partner the H3K9me2/3 determinant of the histone code. They are key epigenetic regulators in eukaryotes. Both hallmarks are also found outside mammalian constitutive heterochromatin as constituents of larger (0.1-5Mb) heterochromatin-likedomains and smaller (less than 100Kb) complexes. The well-documented ability of HP1 proteins to function as bridges between H3K9me2/3-marked nucleosomes enables cross-linking within and between chromatin fibres that contributes to polymer-polymer phase separation (PPPS) that packages epigenetically-heritable chromatin states during interphase. Contacts mediated by HP1 “bridging” are likely to have been detected in Hi-C maps, as evidenced by the B4 heterochromatic sub-compartment that emerges from contacts between large KRAB-ZNF heterochromatin-likedomains. Further, mutational analyses have revealed a finer, innate, compartmentalisation in Hi-C experiments that likely reflect contacts involving smaller domains/complexes. Proteins that bridge (modified) DNA and histones in nucleosomal fibres – where the HP1-H3K9me2/3 interaction represents the most evolutionarily-conserved paradigm – could drive and generate the fundamental compartmentalisation of the interphase nucleus. This has implications for the mechanism(s) that maintains cellular identity, be it a terminally-differentiated fibroblast or a pluripotent embryonic stem cell.
A sparse observation model to quantify species interactions in time and space
Authors: Ait Kaci Azzou Sadoune , Singer Liam , Aebischer Thierry , Caduff Madleina , Wolf Beat , Wegmann Daniel
Published: October 2019

Camera traps and acoustic recording devices are essential tools to quantify the distribution, abundance and behavior of mobile species. Varying detection probabilities among device locations must be accounted for when analyzing such data, which is generally done using occupancy models. We introduce a Bayesian Time-dependent Observation Model for Camera Trap data (Tomcat), suited to estimate relative event densities in space and time.Tomcatallows to learn about the environmental requirements and daily activity patterns of species while accounting for imperfect detection. It further implements a sparse model that deals well will a large number of potentially highly correlated environmental variables. By integrating both spatial and temporal information, we extend the notation of overlap coefficient between species to time and space to study niche partitioning. We illustrate the power ofTomcatthrough an application to camera trap data of eight sympatrically occurring duikerCephalophinaespecies in the savanna - rainforest ecotone in the Central African Republic and show that most species pairs show little overlap. Exceptions are those for which one species is very rare, likely as a result of direct competition.
Transduction of mechanical cellular oscillation by the plasma-membrane mechanosensitive channel MSL10
Authors: Tran Daniel , Girault Tiffanie , Guichard Marjorie , Thomine Sébastien , Leblanc-Fournier Nathalie , Moulia Bruno , de Langre Emmanuel , Allain Jean-Marc , Frachisse Jean-Marie
Published: October 2019

Throughout their life, plants are submitted to recurrent cyclic mechanical loading due to wind. The resulting passive oscillation movements of stem and foliage is an important phenomenon for biological and ecological issues such as photosynthesis optimization 1–3 and thermal exchange 4. The induced motions at plant scale are well described and analyzed, with oscillations at typically 1 to 3 Hz in trees 5–10. However, the cellular perception and transduction of such recurring mechanical signals remains an open question. Multimeric protein complexes forming mechanosensitive (MS) channels embedded in the membrane provide an efficient system to rapidly convert mechanical tension into electrical signal 11. Here we show that the plasma membrane mechanosensitive channel MscS-LIKE 10 (MSL10) from the model plant Arabidopsis thaliana responds to pulsed membrane stretching with rapid activation and relaxation kinetics in the range of one second. Under sinusoidal membrane stretching MSL10 presents a greater activity than under static stimulation and behaves as a large bandpass oscillation “follower” without filtering the signal in the range of 0.3 to 3 Hz. With a localization in aerial organs naturally submitted to oscillations, our results suggest that the mechanosensitive channel MSL10 represents a molecular component of a universal system of oscillatory perception in plants.
The BIR2/BIR3-interacting Phospholipase D gamma 1 negatively regulates immunity in Arabidopsis
Authors: Schlöffel Maria A. , Salzer Andrea , Wan Wei-Lin , van Wijk Ringo , Šemanjski Maja , Symeonidi Efthymia , Slaby Peter , Kilian Joachim , Maček Boris , Munnik Teun , Gust Andrea A.
Published: October 2019

Plants have evolved effective strategies to defend themselves against pathogen invasion. Starting from the plasma membrane with the recognition of microbe-associated molecular patterns (MAMPs) via pattern recognition receptors, internal cellular signaling pathways are induced to ultimately fend off the attack. Phospholipase D (PLD) hydrolyzes membrane phospholipids to produce phosphatidic acid (PA), which has been proposed to play a second messenger role in immunity. The Arabidopsis PLD family consists of 12 members and for some a specific function in resistance towards a subset of pathogens has been shown. We demonstrate here that Arabidopsis PLDγ1, but not its close homologs PLDγ2 and PLDγ3, is specifically involved in plant immunity. Genetic inactivation of PLDγ1 resulted in increased resistance towards the virulent bacterium Pseudomonas syringae pv. tomato DC3000 and the necrotrophic fungus Botrytis cinerea. As pldγ1 mutant plants responded with elevated levels of reactive oxygen species to MAMP-treatment, a negative regulatory function for this PLD isoform is proposed. Importantly, PA levels in pldγ1 mutants were not affected compared to stressed wild-type plants, suggesting that alterations in PA levels are unlikely the cause for the enhanced immunity in the pldγ1 line. Instead, the plasma-membrane-attached PLDγ1 protein colocalized and associated with the receptor-like kinases BIR2 and BIR3, which are known negative regulators of pattern-triggered immunity. Moreover, complex formation of PLDγ1 and BIR2 was further promoted upon MAMP-treatment. Hence, we propose that PLDγ1 acts as a negative regulator of plant immune responses in complex with immunity-related proteins BIR2 and BIR3.

One-sentence summary

A phospholipase D is a novel negative regulator of plant immunity and forms complexes with regulatory receptor-like kinases.
The Brassica napus Wall-Associated Kinase-Like (WAKL) gene Rlm9 provides race-specific blackleg resistance
Authors: Larkan Nicholas J. , Ma Lisong , Haddadi Parham , Buchwaldt Miles , Parkin Isobel A. P. , Djavaheri Mohammad , Borhan M. Hossein
Published: October 2019

In plants, race-specific defense against microbial pathogens is facilitated by resistance (R) genes which correspond to specific pathogen avirulence (Avr) genes. This study reports the cloning of a blackleg R gene from Brassica napus (canola); Rlm9, which encodes a wall-associated kinase-like (WAKL) protein, a newly-discovered class of race-specific plant RLK resistance genes. Rlm9 provides race-specific resistance against isolates of Leptosphaeria maculans carrying the corresponding avirulence gene AvrLm5-9, representing only the second WAKL-type R gene described to date. The Rlm9 protein is predicted to be cell membrane-bound yet appears to have no direct interaction with AvrLm5-9. Rlm9 forms part of a distinct evolutionary family of RLK proteins in B. napus, and while little is yet known about WAKL function, the Brassica-Leptosphaeria pathosystem may prove to be a model system by which the mechanism of fungal avirulence protein recognition by WAKL-type R genes can be determined.
Host relatedness and landscape connectivity shape pathogen spread in a large secretive carnivore
Authors: Fountain-Jones Nicholas M. , Kraberger Simona , Gagne Roderick , Trumbo Daryl R. , Salerno Patricia , Funk W. Chris , Crooks Kevin , Biek Roman , Alldredge Mathew , Logan Ken , Baele Guy , Dellicour Simon , Ernest Holly B , VandeWoude Sue , Carver Scott , Craft Meggan E.
Published: October 2019

Urban expansion can fundamentally alter wildlife movement and gene flow, but how urbanization alterspathogenspread is poorly understood. Here we combine high resolution host and viral genomic data with landscape variables to examine the context of viral spread in puma from two contrasting regions: one bounded by the wildland urban interface (WUI) and one unbounded with minimal anthropogenic development. We found landscape variables and host gene flow explained significant amounts of variation of feline immunodeficiency virus (FIV) spread in the WUI, but not in the unbounded region. The most important predictors of viral spread also differed; host spatial proximity, host relatedness, and mountain ranges played a role in FIV spread in the WUI, whereas unpaved roads were more important in the unbounded region. Our research demonstrates how anthropogenic landscapes can alter pathogen spread, providing a more nuanced understanding of host-pathogen relationships to inform disease ecology in free-ranging species.
Broad-Spectrum Antifungal Activities and Mechanism of Drimane Sesquiterpenoids
Authors: Edouarzin Edruce , Horn Connor , Paduyal Anuja , Zhang Cunli , Lu Jianyu , Tong Zongbo , Giaever Guri , Nislow Corey , Veerapandian Raja , Hua Duy H. , Vediyappan Govindsamy
Published: October 2019

Eight drimane sesquiterpenoids including (-)-drimenol and (+)-albicanol were synthesized from (+)-sclareolide and evaluated for their antifungal activities. Three compounds, (-)-drimenol, (+)-albicanol, and (1R,2R,4aS,8aS)-2-hydroxy-2,5,5,8a-tetramethyl-decahydronaphthalene-1-carbaldehyde (4) showed strong activity against C. albicans. (-)-Drimenol, the strongest inhibitor of the three, (at concentrations of 8 – 64 μg/ml, causing 100% death of fungi), acts not only against C. albicans as a fungicidal manner, but also inhibits other fungi such as Aspergillus, Cryptococcus, Pneumocystis, Blastomyces, Fusarium, Rhizopus, Saksenaea and FLU resistant strains of C. albicans, C. glabrata, C. krusei, C. parapsilosis and C. auris. These observations suggest drimenol is a broad-spectrum antifungal agent. At high concentration (100 μg/ml), drimenol caused a rupture of the fungal cell wall/membrane. In a nematode model of C. albicans infection, drimenol rescued the worms from C. albicans-mediated death, indicating drimenol is tolerable and bioactive in a metazoan. Genome-wide fitness profiling assays of both S. cerevisiae (nonessential homozygous and essential heterozygous) and C. albicans (Tn-insertion mutants) collections revealed putative genes and pathways affected by drimenol. Using a C. albicans mutants spot assay, the Crk1 kinase associated gene products, Ret2, Cdc37, and novel putative targets orf19.759, orf19.1672, and orf19.4382 were revealed to be the potential targets of drimenol. Further, computational modeling results suggest possible modification of the structure of drimenol including the A ring for improving antifungal activity.
A framework for effective application of machine learning to microbiome-based classification problems
Authors: Topçuoğlu Begüm D. , Lesniak Nicholas A. , Ruffin Mack , Wiens Jenna , Schloss Patrick D.
Published: October 2019

Machine learning (ML) modeling of the human microbiome has the potential to identify microbial biomarkers and aid in the diagnosis of many diseases such as inflammatory bowel disease, diabetes, and colorectal cancer. Progress has been made towards developing ML models that predict health outcomes using bacterial abundances, but inconsistent adoption of training and evaluation methods call the validity of these models into question. Furthermore, there appears to be a preference by many researchers to favor increased model complexity over interpretability. To overcome these challenges, we trained seven models that used fecal 16S rRNA sequence data to predict the presence of colonic screen relevant neoplasias (SRNs; n=490 patients, 261 controls and 229 cases). We developed a reusable open-source pipeline to train, validate, and interpret ML models. To show the effect of model selection, we assessed the predictive performance, interpretability, and training time of L2-regularized logistic regression, L1 and L2-regularized support vector machines (SVM) with linear and radial basis function kernels, decision trees, random forest, and gradient boosted trees (XGBoost). The random forest model performed best at detecting SRNs with an AUROC of 0.695 [IQR 0.651-0.739] but was slow to train (83.2 h) and not inherently interpretable. Despite its simplicity, L2-regularized logistic regression followed random forest in predictive performance with an AUROC of 0.680 [IQR 0.625-0.735], trained faster (12 min), and was inherently interpretable. Our analysis highlights the importance of choosing an ML approach based on the goal of the study, as the choice will inform expectations of performance and interpretability.

Importance

Diagnosing diseases using machine learning (ML) is rapidly being adopted in microbiome studies. However, the estimated performance associated with these models is likely over-optimistic. Moreover, there is a trend towards using black box models without a discussion of the difficulty of interpreting such models when trying to identify microbial biomarkers of disease. This work represents a step towards developing more reproducible ML practices in applying ML to microbiome research. We implement a rigorous pipeline and emphasize the importance of selecting ML models that reflect the goal of the study. These concepts are not particular to the study of human health but can also be applied to environmental microbiology studies.
Syncytins enable novel possibilities to transduce human or mouse primary B cells and to achieve well-toleratedin vivogene transfer
Authors: Coquin Y. , Ferrand M. , Seye A. , Menu L. , Galy A.
Published: October 2019

Syncytins are cellular transmembrane glycoproteins with fusogenic and immunosuppressive properties that are encoded by endogenous retroviral envelope sequences in mammalian genomes. Based on their properties, syncytins may be useful to pseudotype lentiviral gene transfer vectors (LV) and to obtain well-toleratedin vivogene delivery but their cellular targets are unknown in this context. We pseudotyped LV with human or murine syncytins. Such LV-Syn particles were infectiousin vitrobut required a transduction additive, as do other retroviral envelope LV pseudotypes. In these conditions, LV-Syn remarkably transduced quiescent human or murine primary B cells at high levelin vitroincluding naïve blood B cells or B cell precursors from murine bone marrow. Transduced human B cells could be expanded in culture and were functional. Human or murine T cells were transduced less efficiently than B cells, in agreement with lower levels of syncytin receptors on T cells compared to B cells. Well-toleratedin vivogene transfer was possible without additive, as demonstrated with murine syncytin A-mediated gene delivery in C57BL/6 mice. A single intravenous injection of LV-SynA vector to mice led to stable gene transfer into spleen germinal center B cells. LV-SynA were also intrinsically less immunogenic than LV-VSVG, leading to low antibody responses against the vector capsid. This is the first evidence of interactions between syncytins and B cells, providing novel opportunities for B cell genetic engineering and for well-tolerated gene transferin vivo. The findings also suggest that some immunosuppressive properties of syncytins could be mediated by B cells.

One Sentence Summary

Syncytins are fusogenic cellular proteins that can pseudotype lentiviral gene transfer vector particles, achieving efficient gene transfer into primary quiescent B cells and reducing thein vivoimmunogenicity of the particles following systemic administration.
MNase profiling of promoter chromatin inS. typhimurium-stimulated GM12878 cells reveals dynamic and response-specific nucleosome architecture
Authors: Cole Lauren , Dennis Jonathan
Published: October 2019

The nucleosome is the primary unit of chromatin structure and commonly imputed as a regulator of nuclear events, although the exact mechanisms remain unclear. Recent studies have shown that certain nucleosomes can have different sensitivities to micrococcal nuclease (MNase) digestion, resulting in the release of populations of nucleosomes dependent on the concentration of MNase. Mapping MNase sensitivity of nucleosomes at transcription start sites genome-wide reveals an important functional nucleosome organization that correlates with gene expression levels and transcription factor binding. In order to understand nucleosome distribution and sensitivity dynamics during a robust genome response, we mapped nucleosome position and sensitivity using multiple concentrations of MNase. We use the innate immune response as a model system to understand chromatin-mediated regulation. Herein we demonstrate that stimulation of a human lymphoblastoid cell line (GM12878) with heat-killedSalmonella typhimurium(HKST) results in widespread nucleosome remodeling of response-specific loci. We further show that the response alters the sensitivity of promoter nucleosomes. Finally, we correlate the increased sensitivity with response-specific transcription factor binding. These results indicate that nucleosome distribution and sensitivity dynamics are integral to appropriate cellular response and pave the way for further studies that will deepen our understanding of the specificity of genome response.
Characterization of splice isoform switching during human kidney development
Authors: Wineberg Yishay , Kanter Itamar , Ben-Haim Nissim , Pode-Shakked Naomi , Bucris Efrat , Bar-Lev Tali Hana , Oriel Sarit , Yehuda Yishai , Gershon Rotem , Shukrun Rachel , Bar-Lev Dekel Dov , Urbach Achia , Dekel Benjamin , Kalisky Tomer
Published: October 2019

Nephrons are the functional units of the kidney. During kidney development, cells from the cap mesenchyme – a transient kidney-specific progenitor state – undergo a mesenchymal to epithelial transition (MET) and subsequently differentiate into the various epithelial cell types that create the tubular structures of the nephron. Faults in this transition can lead to a pediatric malignancy of the kidney called Wilms’ tumor that mimics normal kidney development. While kidney development has been characterized at the gene expression level, a comprehensive characterization of alternative splicing is lacking. We therefore performed RNA sequencing on cell populations representing early, intermediate, and late developmental stages of the human fetal kidney, as well as three blastemal-predominant Wilms’ tumor patient-derived xenografts. We identified a set of transcripts that are alternatively spliced between the different developmental stages. Moreover, we found that cells from the earliest developmental stage have a mesenchymal splice-isoform profile that is similar to that of blastemal-predominant Wilms’ tumors. RNA binding motif enrichment analysis suggests that the mRNA binding proteins ESRP1, ESRP2, RBFOX2, and QKI regulate mRNA splice isoform switching during human kidney development. These findings illuminate new molecular mechanisms involved in kidney development and pediatric kidney tumors.

HIGHLIGHTS

During fetal kidney development, kidney progenitor cells undergo a mesenchymal to epithelial transition (MET) and subsequently differentiate into the various epithelial cell types that create the tubular structures of the nephron.

RNA sequencing identifies a set of transcripts that undergo splice isoform switching during the mesenchymal to epithelial transition (MET) that occurs in the course of human fetal kidney development.

Cells in the early stages of kidney development have a mesenchymal splice-isoform profile that is similar to that observed in blastemal-predominant Wilms’ tumor patient-derived xenografts (WT-PDX) that represent an aggressive subtype of Wilms’ tumors.

RNA binding motif enrichment analysis indicates that the mRNA binding proteins ESRP1, ESRP2, RBFOX2, and QKI regulate splice isoform switching during human kidney development.
Temporal models using environmental variables to predict Aedes aegypti oviposition activity in a temperate region of Argentina
Authors: Benitez Elisabet M. , Estallo Elizabet L. , Grech Marta , Frías-Céspedes Maria , Almirón Walter R. , Ludueña-Almeida Francisco F.
Published: October 2019

Environmental variables are some of the factors that more impact on Aedes aegypti, vector of Dengue, Chikungunya and Zika viruses. In this study, the Ae. aegypti oviposition activity was related to satellite and meteorological variables, in Córdoba City (Argentina). Eggs were collected using ovitraps placed throughout the city from 2009 to 2012, replaced them weekly. Generalized Linear Mixed Models were developed with negative binomial distributions of errors, modeling average number of eggs collected weekly as a function of satellite and meteorological variables with time lags. The best model included a vegetation index, vapor pressure of water, precipitation and photoperiod, lagged between 3 and 4 weeks. By each increment unit in vegetation index, vapor pressure (hPa) and light hour, the average number of eggs increases by 72%, 20% and 29%, respectively, in the following 3 or 4 weeks. In addition, the average number of eggs decreases a 50% in the following month by each millimeter of rain. The results evince the relevant importance of the vegetation, maybe due to the shade that provide to the containers as breeding habitat of this species and the shelter for adults. On the other hand, the negative effect of precipitation could be a consequence of abundant rainfalls that fulfill containers avoiding females to lay eggs in there. Although no significant effect of the photoperiod on the vector abundance has been detected in the north of the country, in Córdoba City an important effect is observed when it is presented together with other variables, producing different effects of these variables in different regions. Lastly, it is necessary to emphasize the importance of the minimum temperature in temperate zones, since it would be a limiting factor that prevents the Ae. aegypti oviposition activity.
Radiographic and clinical risk factors of total knee arthroplasty in asymptomatic knees; a 15-year follow-up study
Authors: Nielsen Flemming Kromann , Jurik Anne Grethe , Jørgensen Anette , Egund Niels
Published: October 2019

Background

Radiographic signs of osteoarthritis (OA) are frequent in knees without symptoms. The long-term impact of these findings is not completely elucidated. We wanted to evaluate whether radiographic or clinical baseline findings are associated with the risk of total knee arthroplasty (TKA) in knees without symptomatic OA but with clinical OA of the other knee during a mean follow-up period of 15 years.

Methods

A follow-up analysis was performed in 100 persons with unilateral, clinical knee OA according to the ACR (American College of Rheumatology) criteria, who participated in a clinical trial between 2000 and 2002. Baseline radiographs of the contralateral, non-symptomatic knee were available in 88 participants at follow-up. Data on TKA procedures were extracted from the Danish National Patient Register at follow-up. Radiographic and clinical findings were analyzed for associations with subsequent TKA.

Results

At follow-up, 40% had received a TKA in their non-symptomatic knee. The risk of TKA was significantly associated with baseline joint space narrowing (risk ratio (RR) 1.6 (95% confidence interval (95% CI) 1.4 to 1.9)), osteophytes (RR 1.5 (95% CI 1.3 to 1.8)) and subchondral sclerosis (RR 2.4 (95% CI 1.6 to 3.7)). Among the clinical findings, only baseline body mass index (BMI) was significantly associated with the risk of TKA (RR 1.4 (95& CI 1.1 to 1.8)).

Conclusions

Radiographic OA changes and BMI at baseline were significantly associated with the long-term risk of TKA in persons without symptomatic knee OA but with symptomatic OA in the contralateral knee, implying that radiographic OA findings are important prognostic factors regardless of symptoms.
An integrated platform for genome engineering and gene expression perturbation in Plasmodium falciparum
Authors: Nasamu Armiyaw S. , Falla Alejandra , Pasaje Charisse Flerida A. , Wall Bridget A. , Wagner Jeffrey C. , Ganesan Suresh M. , Goldfless Stephen J. , Niles Jacquin C.
Published: October 2019

Establishing robust genome engineering methods in the malarial parasite, Plasmodium falciparum, has the potential to substantially improve the efficiency with which we gain understanding of this pathogen’s biology to propel treatment and elimination efforts. Methods for manipulating gene expression and engineering the P. falciparum genome have been validated. However, a significant barrier to fully leveraging these advances is the difficulty associated with assembling the extremely high AT content DNA constructs required for modifying the P. falciparum genome. These are frequently unstable in commonly-used circular plasmids. We address this bottleneck by devising a DNA assembly framework leveraging the improved reliability with which large AT-rich regions can be efficiently manipulated in linear plasmids. This framework integrates several key functional genetics outcomes via CRISPR/Cas9 and other methods from a common, validated framework. Overall, this molecular toolkit enables P. falciparum genetics broadly and facilitates deeper interrogation of parasite genes involved in diverse biological processes.
Cohesin depleted cells rebuild functional nuclear compartments after endomitosis
Authors: Cremer Marion , Brandstetter Katharina , Maiser Andreas , Rao Suhas S P , Schmid Volker , Guirao-Ortiz Miguel , Mitra Namita , Mamberti Stefania , Klein Kyle N , Gilbert David M , Leonhardt Heinrich , Cardoso Maria Cristina , Aiden Erez Lieberman , Harz Hartmann , Cremer Thomas
Published: October 2019

Cohesin plays an essential role in chromatin loop extrusion, but its impact on a compartmentalized nuclear architecture, linked to nuclear functions, is debatable. Using live-cell and super-resolved 3D microscopy, we demonstrate that cohesin depleted cells pass through an endomitosis and rebuild a single multilobulated nucleus (MLN) with chromosome territories (CTs) pervaded by interchromatin channels. CTs contain chromatin domain clusters with a zonal organization of repressed chromatin domains in the interior and transcriptionally competent domains located at the periphery. Splicing speckles are located nearby within the lining channel system. These clusters form microscopically defined, active and inactive compartments, which correspond to A/B compartments, detected with ensemble Hi-C. Functionality of MLN despite continuous absence of cohesin was demonstrated by their ability to pass through S-phase with typical spatio-temporal patterns of replication domains. Evidence for structural changes of these domains compared to controls suggests that cohesin is required for their full integrity.
Genetic control of the human brain proteome
Authors: Robins Chloe , Wingo Aliza P. , Fan Wen , Duong Duc M. , Meigs Jacob , Gerasimov Ekaterina S. , Dammer Eric B. , Cutler David J. , Jager Philip L. De , Bennett David A. , Lah James J. , Levey Allan I. , Seyfried Nicholas T. , Wingo Thomas S.
Published: October 2019

Alteration of protein abundance and conformation are widely believed to be the hallmark of neurodegenerative diseases. Yet relatively little is known about the genetic variation that controls protein abundance in the healthy human brain. The genetic control of protein abundance is generally thought to parallel that of RNA expression, but there is little direct evidence to support this view. Here, we performed a large-scale protein quantitative trait locus (pQTL) analysis using single nucleotide variants (SNVs) from whole-genome sequencing and tandem mass spectrometry-based proteomic quantification of 12,691 unique proteins (7,901 after quality control) from the dorsolateral prefrontal cortex (dPFC) in 144 cognitively normal individuals. We identified 28,211 pQTLs that were significantly associated with the abundance of 864 proteins. These pQTLs were compared to dPFC expression quantitative trait loci (eQTL) in cognitive normal individuals (n=169; 81 had protein data) and a meta-analysis of dPFC eQTLs (n=1,433). We found that strong pQTLs are generally only weak eQTLs, and that the majority of strong eQTLs are not detectable pQTLs. These results suggest that the genetic control of mRNA and protein abundance may be substantially distinct and suggests inference concerning protein abundance made from mRNA in human brain should be treated with caution.
Persistent chromatin states, pervasive transcription, and sharedcis-regulatory sequences have shaped theC. elegansgenome
Authors: Bellush James M. , Whitehouse Iestyn
Published: October 2019

Despite highly conserved chromatin states andcis-regulatory elements, studies of metazoan genomes reveal that gene organization and the strategies to control mRNA expression can vary widely among animal species.C. elegansgene regulation is often assumed to be similar to that of other model organisms, yet evidence suggests the existence of distinct molecular mechanisms to pattern the developmental transcriptome, including extensive post-transcriptional RNA control pathways, widespread splice leader (SL) trans-splicing of pre-mRNAs, and the organization of genes into operons. Here, we performed ChIP-seq for histone modifications in highly synchronized embryos cohorts representing three major developmental stages, with the goal of better characterizing whether the dynamic changes in embryonic mRNA expression are accompanied by changes to the chromatin state. We were surprised to find that thousands of promoters are persistently marked by active histone modifications, despite a fundamental restructuring of the transcriptome. We employed global run-on sequencing using a long-read nanopore format to map nascent RNA transcription across embryogenesis, finding that the invariant open chromatin regions are persistently transcribed by Pol II at all stages of embryo development, even though the mature mRNA is not produced. By annotating our nascent RNA sequencing reads into directional transcription units, we find extensive evidence of polycistronic RNA transcription genome-wide, suggesting that nearby genes inC. elegansare linked by shared transcriptional regulatory mechanisms. We present data indicating that the sharing of cis-regulatory sequences has constrainedC. elegansgene positioning and likely explains the remarkable retention of syntenic gene pairs over long evolutionary timescales.
Step-wise Hydration of Magnesium by Four Water Molecules Precedes Phosphate Release in a Myosin Motor
Authors: Mugnai M.L. , Thirumalai D.
Published: October 2019

Molecular motors, such as myosin, kinesin, and dynein, convert the energy released by the hydrolysis of ATP into mechanical work, which allows them to undergo directional motion on cytoskeletal tracks. This process is achieved through synchronization between the catalytic activity of the motor and the associated changes in its conformation. A pivotal step in the chemomechanical transduction in myosin motors occurs after they bind to the actin filament, which triggers the release of phosphate (Pi, product of ATP hydrolysis) and the rotation of the lever arm. Here, we investigate the mechanism of phosphate release in myosin VI, which has been debated for over two decades, using extensive molecular dynamics simulations involving multiple trajectories each severalμslong. Because the escape of phosphate is expected to occur on time-scales on the order of milliseconds in myosin VI, we observed Pirelease only if the trajectories were initiated with a rotated phosphate inside the nucleotide binding pocket. The rotation provided the needed perturbation that enabled successful expulsions of Piin several trajectories. Analyses of these trajectories lead to a robust mechanism of Pirelease in the class of motors belonging to the myosin super family. We discovered that although Pipopulates the traditional “back door” route, phosphate exits through various other gateways, thus establishing the heterogeneity in the escape routes. Remarkably, we observe that the release of phosphate is preceded by a step-wise hydration of the ADP-bound magnesium ion. In particular, the release of the anion occurredonly after four water moleculeshydrate the cation (Mg2+). By performing comparative structural analyses, we suggest that the hydration of magnesium is the key step in the phosphate release in a number of ATPases and GTPases that share a similar structure in the nucleotide binding pocket. Thus, nature may have evolved hydration of Mg2+by discrete water molecules as a general molecular switch for Pirelease, which is a universal step in the catalytic cycle of many machines which share little sequence or structural similarity.
Image-based Cell Phenotyping Using Deep Learning
Authors: Berryman Samuel , Matthews Kerryn , Lee Jeong Hyun , Duffy Simon P. , Ma Hongshen
Published: October 2019

The ability to phenotype cells is fundamentally important in biological research and medicine. Current methods rely primarily on fluorescence labeling of specific markers. However, there are many situations where this approach is unavailable or undesirable. Machine learning has been used for image cytometry but has been limited by cell agglomeration and it is unclear if this approach can reliably phenotype cells indistinguishable to the human eye. Here, we show disaggregated single cells can be phenotyped with a high degree of accuracy using low-resolution bright-field and non-specific fluorescence images of the nucleus, cytoplasm, and cytoskeleton. Specifically, we trained a convolutional neural network using automatically segmented images of cells from eight standard cancer cell-lines. These cells could be identified with an average classification accuracy of 94.6%, tested using separately acquired images. Our results demonstrate the potential to develop an “electronic eye” to phenotype cells directly from microscopy images indistinguishable to the human eye.
Identification and dynamic quantification of regulatory elements using total RNA
Authors: Duttke Sascha H. , Chang Max W. , Heinz Sven , Benner Christopher
Published: October 2019

The spatial and temporal regulation of transcription initiation is pivotal for controlling gene expression. Here, we introduce capped-small RNA-seq (csRNA-seq), which uses total RNA as starting material to detect transcription start sites (TSSs) of both stable and unstable RNAs at single-nucleotide resolution. csRNA-seq is highly sensitive to acute changes in transcription and identifies an order of magnitude more regulated transcripts than does RNA-seq. Interrogating tissues from species across the eukaryotic kingdoms identified unstable transcripts resembling enhancer RNAs, pri-miRNAs, antisense transcripts, and promoter upstream transcripts in multicellular animals, plants, and fungi spanning 1.6 billion years of evolution. Integration of epigenomic data from these organisms revealed that histone H3 trimethylation (H3K4me3) was largely confined to TSSs of stable transcripts, whereas H3K27ac marked nucleosomes downstream from all active TSSs, suggesting an ancient role for posttranslational histone modifications in transcription. Our findings show that total RNA is sufficient to identify transcribed regulatory elements and capture the dynamics of initiated stable and unstable transcripts at single-nucleotide resolution in eukaryotes.
Synthesis and structural characterization of the type-I clathrates K8AlxSn46–xand Rb8AlxSn46–x(x≃ 6.4–9.7)
Authors: Baranets Sviatoslav , Schäfer Marion , Bobev Svilen
Published: October 2019

Exploratory studies in the systemsA–Al–Sn (A= K and Rb) yielded the clathrates K8AlxSn46–x(potassium aluminium stannide) and Rb8AlxSn46–x(rubidium aluminium stannide), both with the cubic type-I structure (space groupPm\overline{3}n, No. 223;a≃ 12.0 Å). The Al:Sn ratio is close to the idealizedA8Al8Sn38composition and it is shown that it can be varied slightly, in the range ofca±1.5, depending on the experimental conditions. Both the (Sn,Al)20and the (Sn,Al)24cages in the structure are fully occupied by the guest alkali metal atoms,i.e.K or Rb. TheA8Al8Sn38formula has a valence electron count that obeys the valence rules and represents an intrinsic semiconductor, while the experimentally determined compositionsA8Al8±xSn38∓xsuggest the synthesized materials to be nearly charge-balanced Zintl phases,i.e.they are likely to behave as heavily dopedp- orn-type semiconductors.