bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-resolved metagenomics and detailed geochemical speciation analyses yield new insights into microbial mercury cycling in geothermal springs
Authors: Gionfriddo Caitlin M. , Stott Matthew B. , Power Jean F. , Ogorek Jacob M. , Krabbenhoft David P. , Wick Ryan , Holt Kathryn , Chen Lin-Xing , Thomas Brian C. , Banfield Jillian F. , Moreau John W.
Published: February 2020

Geothermal systems emit substantial amounts of aqueous, gaseous and methylated mercury, but little is known about microbial influences on mercury speciation. Here we report results from genome-resolved metagenomics and mercury speciation analysis of acid warm springs in the Ngawha Geothermal Field (<55 °C, pH < 4.5), Northland Region, Aotearoa (New Zealand). Our aim was to identify the microorganisms genetically equipped for mercury methylation, demethylation, or Hg(II) reduction to volatile Hg(0) in these springs. Dissolved total and methylated mercury concentrations in two adjacent springs with different mercury speciation ranked among the highest reported from natural sources (250–16000 ng L−1and 0.5–13.9 ng L−1, respectively). Total solid mercury concentrations in spring sediments ranged from 1273 to 7000 µg g−1. In the context of such ultra-high mercury levels, the geothermal microbiome was unexpectedly diverse, and dominated by acidophilic and mesophilic sulfur- and iron-cycling bacteria, mercury- and arsenic-resistant bacteria, and thermophilic and acidophilic archaea. Integrating microbiome structure and metagenomic potential with geochemical constraints, we constructed a conceptual model for biogeochemical mercury cycling in geothermal springs. The model includes abiotic and biotic controls on mercury speciation, and illustrates how geothermal mercury cycling may couple to microbial community dynamics and sulfur and iron biogeochemistry.

IMPORTANCE

Little is currently known about biogeochemical mercury cycling in geothermal systems. This manuscript presents an important new conceptual model, supported by genome-resolved metagenomic analysis and detailed geochemical measurements. This work provides a framework for studying natural geothermal mercury emissions globally. Specifically, our findings have implications for mercury speciation in wastewaters from geothermal power plants and the potential environmental impacts of microbially and abiotically formed mercury species, particularly where mobilized in spring waters that mix with surface- or ground-waters. Furthermore, in the context of thermophilic origins for microbial mercury volatilisation, this report yields new insights into how such processes may have evolved alongside microbial mercury methylation/demethylation, and the environmental constraints imposed by the geochemistry and mineralogy of geothermal systems.
Population movement, city closure and spatial transmission of the 2019-nCoV infection in China
Authors: Ai Siqi , Zhu Guanghu , Tian Fei , Li Huan , Gao Yuan , Wu Yinglin , Liu Qiyong , Lin Hualiang
Published: February 2020

The outbreak of pneumonia caused by a novel coronavirus (2019-nCoV) in Wuhan City of China obtained global concern, the population outflow from Wuhan has contributed to spatial expansion in other parts of China. We examined the effects of population outflow from Wuhan on the 2019-nCoV transmission in other provinces and cities of China, as well as the impacts of the city closure in Wuhan. We observed a significantly positive association between population movement and the number of cases. Further analysis revealed that if the city closure policy was implemented two days earlier, 1420 (95% CI: 1059, 1833) cases could be prevented, and if two days later, 1462 (95% CI: 1090, 1886) more cases would be possible. Our findings suggest that population movement might be one important trigger of the 2019-nCoV infection transmission in China, and the policy of city closure is effective to prevent the epidemic.
The impact of traffic isolation in Wuhan on the spread of 2019-nCov
Authors: Jin Gehui , Yu Jiayu , Han Liyuan , Duan Shiwei
Published: February 2020

The 2019-nCoV outbreak occurred near the Chinese Spring Festival transport period in Wuhan. As an important transportation center, the migration of Wuhan accelerated the spread of 2019-nCoV across mainland China. Based on the cumulative Baidu migration index (CBMI), we first analyzed the proportion of Wuhan’s migrant population to other cities. Our results confirm that there is a significant correlation between the export population of Wuhan and reported cases in various regions. We subsequently found that the mortality rate in Hubei Province was much higher than that in other regions of mainland China, while the investigation of potential cases in Wuhan was far behind other provinces in Mainland China, which indicates the effectiveness of early isolation.
Risk Assessment of Novel Coronavirus COVID-19 Outbreaks Outside China
Authors: Boldog Péter , Tekeli Tamás , Vizi Zsolt , Dénes Attila , Bartha Ferenc A. , Röst Gergely
Published: February 2020

We developed a computational tool to assess the risks of novel coronavirus outbreaks outside of China. We estimate the dependence of the risk of a major outbreak in a country from imported cases on key parameters such as: (i) the evolution of the cumulative number of cases in mainland China outside the closed areas; (ii) the connectivity of the destination country with China, including baseline travel frequencies, the effect of travel restrictions, and the efficacy of entry screening at destination; and (iii) the efficacy of control measures in the destination country (expressed by the local reproduction number Rloc). We found that in countries with low connectivity to China but with relatively high Rloc, the most beneficial control measure to reduce the risk of outbreaks is a further reduction in their importation number either by entry screening or travel restrictions. Countries with high connectivity but low Rloc benefit the most from policies that further reduce Rloc. Countries in the middle should consider a combination of such policies. Risk assessments were illustrated for selected groups of countries from America, Asia, and Europe. We investigated how their risks depend on those parameters, and how the risk is increasing in time as the number of cases in China is growing.
Dynamic Laser Speckle Imaging meets Machine Learning to enable Rapid Antibacterial Susceptibility Testing (DyRAST)
Authors: Zhou Keren , Zhou Chen , Sapre Anjali , Pavlock Jared Henry , Weaver Ashley , Muralidharan Ritvik , Noble Joshua , Kovac Jasna , Liu Zhiwen , Ebrahimi Aida
Published: February 2020

Rapid antibacterial susceptibility testing (RAST) methods which measure change of a bacterial phenotype in response to a given treatment are of significant importance in healthcare, as they can assist care-givers in timely administration of the right treatment. Various RAST techniques have been reported for tracking bacterial phenotypes, such as size, shape, motion, and metabolic activity. However, they still require bulky and expensive instruments (which hinders their application in resource-limited environments) and/or utilize labeling reagents (which can interfere with antibiotics and add to cost). Furthermore, the existing ultra-rapid methods do not address possible adaptation of gradual adaptation of bacteria to antibiotics, which can lead to false interpretation of resistance when using ultra-rapid methods. In this work, we present a RAST approach leveraging machine learning analysis of time-resolved dynamic laser speckle imaging (DLSI) results to accurately predict the minimum inhibitory concentration (MIC) of a model strain ofEscherichia coliin 60 minutes, compared to 6 hours using the currently FDA-approved phenotype-based RAST technique. To demonstrate the DLSI performance, we studied the effect of aβ-lactam ampicillin and an aminoglycoside gentamicin onEscherichia colistrain K-12. DLSI captures change of bacterial motion/division in response to treatment. The machine learning algorithm was trained and validated using the overnight results of gold standard, broth microdilution method. Empowered by machine learning, DyRAST can predict MIC with high accuracy comparable to gold standard methods through a voting strategy.
Association ofCDH11with ASD revealed by matched-gene co-expression analysis and mouse behavioral studies
Authors: Wu Nan , Wang Yue , Jia Jing-Yan , Pan Yi-Hsuan , Yuan Xiao-Bing
Published: February 2020

A large number of putative risk genes of autism spectrum disorder (ASD) have been reported. The functions of most of these susceptibility genes in developing brains remain unknown, and a causal relationship between their variations and autism traits has not been established. The aim of this study is to predict putative risk genes at the whole-genome level based on the analysis of gene co-expression with a group of high confidence ASD risk genes (hcASDs). Results showed that three gene features, including gene size, mRNA abundance, and guanine-cytosine content, affect genome-wide co-expression profiles of hcASDs. To circumvent the interference of these gene features on gene co-expression analysis (GCA), we developed a method to determine whether a gene is significantly co-expressed with hcASDs by statistically comparing the co-expression profile of this gene with hcASDs to that of this gene with permuted gene sets of feature-matched genes. This method is referred to as “matched-gene co-expression analysis” (MGCA). With MGCA, we demonstrated the convergence in developmental expression profiles of hcASDs and improved the efficacy of risk gene prediction. Results of analysis of two recently reported ASD candidate genes,CDH11andCDH9,suggested the involvement ofCDH11, but notCDH9, in ASD. Consistent with this prediction, behavioral studies showed thatCdh11-null mice, but notCdh9-null mice, have multiple autism-like behavioral alterations. This study highlighted the power of MGCA in revealing ASD-associated genes and the potential role of CDH11 in ASD.
Common variation at the LRRK2 locus is associated with survival in the primary tauopathy progressive supranuclear palsy
Authors: Jabbari Edwin , Tan Manuela M.X. , Reynolds Regina H. , Mok Kin Y. , Ferrari Raffaele , Murphy David P. , Valentino Rebecca R. , Ross Owen A. , Dickson Dennis W. , Al-Sarraj Safa , Gentleman Steve M. , Allinson Kieren S.J. , Jaunmuktane Zane , Holton Janice L. , Revesz Tamas , Warner Thomas T. , Lees Andrew J. , Cookson Mark R. , Gibbs J. Raphael , Ding Jinhui , Chia Ruth , Traynor Bryan J. , Scholz Sonja W. , Pantelyat Alexander , Viollet Coralie , Dalgard Clifton L. , Pletnikova Olga , Troncoso Juan C. , Boxer Adam L. , Respondek Gesine , Höglinger Günter U. , Burn David J. , Pavese Nicola , Gerhard Alexander , Kobylecki Christopher , Leigh P. Nigel , Church Alistair , Hu Michele T.M. , Rowe James B. , Ryten Mina , Hardy John , Shoai Maryam , Morris Huw R.
Published: February 2020

The genetic basis of variation in the rate of disease progression of primary tauopathies has not been determined. In two independent progressive supranuclear palsy cohorts, we show that common variation at theLRRK2locus determines survival from motor symptom onset to death, possibly through regulation of gene expression. This links together genetic risk in alpha-synuclein and tau disorders, and suggests that modulation of proteostasis and neuro-inflammation by LRRK2 inhibitors may have a therapeutic role across disorders.
eNOS-dependent S-nitrosylation of the NF-κB subunit p65 has neuroprotective effects
Authors: Caviedes Ariel , Maturana Barbara , Corvalán Katherina , Engler Alexander , Gordillo Felipe , Varas-Godoy Manuel , Smalla Karl-Heinz , Batiz Luis Federico , Lafourcade Carlos , Kaehne Thilo , Wyneken Ursula
Published: February 2020

Cell death by glutamate excitotoxicity, mediated by N-methyl-D-aspartate (NMDA) receptors, negatively impacts brain function, including but not limited to hippocampal neurons. The NF-κB transcription factor (composed mainly of p65/p50 subunits) contributes to neuronal death in excitotoxicity, while its inhibition should improve cell survival. Using the biotin switch method, subcellular fractionation, immunofluorescence and luciferase reporter assays, we found that NMDA stimulated NF-κB activity selectively in hippocampal neurons, while endothelial nitric oxide synthase (eNOS), an enzyme expressed in neurons, is involved in the S-nitrosylation of p65 and consequent NF-κB inhibition in cerebrocortical,i.e., resistant neurons. The S-nitro proteomes of cortical and hippocampal neurons revealed that different biological processes are regulated by S-nitrosylation in susceptible and resistant neurons, bringing to light that protein S-nitrosylation is a ubiquitous post-translational modification, able to influence a variety of biological processes including the homeostatic inhibition of the NF-κB transcriptional activity in cortical neurons exposed to NMDA receptor overstimulation.
Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation byE. coliRNA Polymerase: Upstream Wrapping and Downstream Bending Precede Clamp Opening and Insertion of the Downstream Duplex
Authors: Sreenivasan Raashi , Shkel Irina A. , Chhabra Munish , Drennan Amanda , Heitkamp Sara , Wang Hao-Che , Sridevi Malavika A. , Plaskon Dylan , McNerney Christina , Callies Katelyn , Cimperman Clare K. , Record M. Thomas
Published: February 2020

FRET (fluorescence energy transfer) between far-upstream (−100) and downstream (+14) cyanine dyes showed extensive bending/wrapping of λPRpromoter DNA onE. coliRNA polymerase (RNAP) in closed and open complexes (CC, OC). Here we determine the kinetics and mechanism of DNA bending/wrapping by FRET and of formation of RNAP contacts with −100 and +14 DNA by single-dye fluorescence enhancements (PIFE). FRET/PIFE kinetics exhibit two phases: rapidly-reversible steps forming a CC ensemble ({CC}c of four intermediates (initial (RPC), early (I1E), mid-(I1M), late (I1L)), followed by conversion of {CC} to OC via I1L. FRET and PIFE are first observed for I1E, not RPc. FRET/PIFE together reveal large-scale bending/wrapping of upstream and downstream DNA as RPCadvances to I1E, reducing −100/+14 distance to ∼75Å and making RNAP-DNA contacts at −100 and +14. We propose that far-upstream DNA wraps on the upper β’-clamp while downstream DNA contacts the top of the β-pincer in I1E. Converting I1Eto I1M(~1s time-scale)reducesFRET efficiency with little change in −100/+14PIFE, interpreted as clamp-opening that moves far-upstream DNA (on β’) away from downstream DNA (on β) to increase the −100/+14 distance by ~14Å. FRET increases greatly in converting I1Mto I1L, indicating bending of downstream duplex DNA into the clamp and clamp-closing to reduce the −100/+14 distance by ~21Å. In the subsequent rate-determining DNA-opening step, in which the clamp may also open, I1Lconverts to the initial unstable OC (I2). Implications for facilitation of CC-to-OC isomerization by upstream DNA and upstream-binding, DNA-bending transcription activators are discussed.

Abstract Figure
Periodicity Scoring of Time Series Encodes Dynamical Behavior of the Tumor Suppressor p53
Authors: Moosmüller Caroline , Tralie Christopher J. , Kooshkbaghi Mahdi , Belkhatir Zehor , Pouryahya Maryam , Reyes José , Deasy Joseph O. , Tannenbaum Allen R. , Kevrekidis Ioannis G.
Published: February 2020

In this paper, we analyze the dynamical behavior of the tumor suppressor protein p53, an essential player in the cellular stress response, which prevents a cell from dividing if severe DNA damage is present. When this response system is malfunctioning, e.g. due to mutations in p53, uncontrolled cell proliferation may lead to the development of cancer. Understanding the behavior of p53 is thus crucial to prevent its failing. It has been shown in various experiments that periodicity of the p53 signal is one of the main descriptors of its dynamics, and that its pulsing behavior (regular vs. spontaneous) indicates the level and type of cellular stress. In the present work, we introduce an algorithm to score the local periodicity of a given time series (such as the p53 signal), which we callDetrended Autocorrelation Periodicity Scoring(DAPS). It applies pitch detection (via autocorrelation) on sliding windows of the entire time series to describe the overall periodicity by a distribution of localized pitch scores. We apply DAPS to the p53 time series obtained from single cell experiments and establish a correlation between the periodicity scoring of a cell’s p53 signal and the number of cell division events. In particular, we show that high periodicity scoring of p53 is correlated to a low number of cell divisions and vice versa. We show similar results with a more computationally intensive state-of-the-art periodicity scoring algorithm based on topology known as Sw1PerS. This correlation has two major implications: It demonstrates that periodicity scoring of the p53 signal is a good descriptor for cellular stress, and it connects the high variability of p53 periodicity observed in cell populations to the variability in the number of cell division events.

AMS subject classification

92C42, 92C37, 62M10
Integrated profiling of single cell epigenomic and transcriptomic landscape of Parkinson’s disease mouse brain
Authors: Zhong Jixing , Tang Gen , Zhu Jiacheng , Qiu Xin , Wu Weiying , Li Ge , Lin Xiumei , Liang Langchao , Chai Chaochao , Zeng Yuying , Wang Feiyue , Luo Lihua , Li Jiankang , Chen Fang , Huang Zhen , Xu Xun , Tang Shengping , Zhu Shida , Chen Dongsheng
Published: February 2020

Parkinson’s disease (PD) is a neurodegenerative disease leading to the impairment of execution of movement. PD pathogenesis has been largely investigated, but either restricted in bulk level or at certain cell types, which failed to capture cellular heterogeneity and intrinsic interplays among distinct cell types. To overcome this, we applied single-nucleus RNA-seq and single cell ATAC-seq on cerebellum, midbrain and striatum of PD mouse and matched control. With 74,493 cells in total, we comprehensively depicted the dysfunctions under PD pathology covering proteostasis, neuroinflammation, calcium homeostasis and extracellular neurotransmitter homeostasis. Besides, by multi-omics approach, we identified putative biomarkers for early stage of PD, based on the relationships between transcriptomic and epigenetic profiles. We located certain cell types that primarily contribute to PD early pathology, narrowing the gap between genotypes and phenotypes. Taken together, our study provides a valuable resource to dissect the molecular mechanism of PD pathogenesis at single cell level, which could facilitate the development of novel methods regarding diagnosis, monitoring and practical therapies against PD at early stage.
Immunological role of primary cilia of dendritic cells in human skin disease
Authors: Toriyama Manami , Rizaldy Defri , Nakamura Motoki , Fujita Fumitaka , Okada Fumihiro , Morita Akimichi , Ishii Ken J.
Published: February 2020

Primary cilia are a unique organelle, known to provide a signaling hub for variety of cell activities. Their potential role(s) in human immune homeostasis and diseases, however, have yet to be explored. Here, we show that human dendritic cells (DCs) express primary cilia-like structure. The primary cilia growth during DC proliferation by GM-CSF was shut off by DC maturation agents, suggesting the role of primary cilia to transduce proliferation signaling. PDGFRα pathway, one of proliferation signal in primary cilia, promoted DC proliferation in a dependent manner of intra-flagellar transport system. In epidermis with atopic dermatitis patients, aberrant ciliated langerhans cells and keratinocytes with showing immature state were observed that may play a potential role in inflammation and skin barrier disorder.
A common problem in the purification of calicivirus raised by molecular sieving: balance between purification and loss of viral particles
Authors: Qu Zehui , Kang Hongtao , Cui Chenxi , Meng Kaiwen , Zhang Xinzheng , Qu Liandong , Meng Geng
Published: February 2020

Caliciviridae is a group of RNA viruses could lead to gastrointestinal disease in humans and acute oral or upper respiratory tract disease in felines, no efficient vaccine so far. The preparation of immunogen is a challenge to obtain a safe and efficient vaccine candidate. Molecular sieving, due to the advantage of simple and fast purifying, is considered as a very powerful tool in calicivirus purification; however, also introduce mechanical damage to the viron. In this study, we took Feline Calicivirus (FCV), a common natural pathogen in cats as well as a classic model for caliciviruses studies, as a research object. Here, with the help of the cryo-electron microscope (cryo-EM), we collected particle images in both conditions of with and without molecular sieving post-processing, the impact of molecular sieving on FCV particles was evaluated by building a flexibility evaluation system after 3D classification. The results indicated that the molecular sieving will impact the stability of P domains through increasing flexibility. In addition, we successfully built up a scoring system to describe this flexibility of FCV P-domains, which can be extended to assess the purification effect to the entire calicivirus.
Nanobody-directed targeting of optogenetic tools to study signaling in the primary cilium
Authors: Hansen Jan N. , Kaiser Fabian , Klausen Christina , Stüven Birthe , Chong Raymond , Bönigk Wolfgang , Mick David U. , Möglich Andreas , Jurisch-Yaksi Nathalie , Schmidt Florian I. , Wachten Dagmar
Published: February 2020

Compartmentalization of cellular signaling forms the molecular basis of cellular behavior. The primary cilium constitutes a subcellular compartment that orchestrates signal transduction independent from the cell body. Ciliary dysfunction causes severe diseases, termed ciliopathies. Analyzing ciliary signaling and function has been challenging due to the lack of tools to temporarily manipulate and analyze ciliary signaling. Here, we describe a nanobodybased targeting approach for optogenetic tools that is applicablein vitroandin vivoand allows to specifically analyze ciliary signaling and function. Thereby, we overcome the loss of protein function observed after direct fusion to a ciliary targeting sequence. We functionally localized modifiers of cAMP signaling, i.e. the photo-activated adenylate cyclase bPAC and the light-activated phosphodiesterase LAPD, as well as the cAMP biosensor mlCNBD-FRET to the cilium. Using this approach, we studied the contribution of spatial cAMP signaling in controlling cilia length. Combining optogenetics with nanobody-based targeting will pave the way to the molecular understanding of ciliary function in health and disease.
Sexually divergent effects of social dominance on chronic stress outcomes in mice
Authors: Karamihalev Stoyo , Brivio Elena , Flachskamm Cornelia , Stoffel Rainer , Schmidt Mathias V. , Chen Alon
Published: February 2020

Background

Sex and social context are two major factors in the development of depression and other stress-related disorders. However, few studies of the effects of stress on rodent behavior and physiology have investigated social context and fewer still have assessed the possibility of sex-specific effects of social context.

Methods

We assessed social dominance of group-living mice during several days of monitoring using a high-throughput automated behavioral tracking system. We then exposed groups from each sex to a three-week chronic mild stress (CMS) procedure, followed by a behavioral test battery. Finally, we used principle component analysis and post-hoc tests to explore the sources of variance in the behavioral outcome data.

Results

We found stable hierarchies in both sexes, however social dominance in males exhibited several additional associations with behaviors related to locomotion and exploration that were not seen in females. Crucially, pre-stress social dominance status was associated with opposing outcomes on multiple behavioral readouts between the two sexes following CMS. In particular, subordinate male mice and dominant female mice appeared more responsive to the environmental challenge, as observed in anxiety-like and locomotor behaviors.

Conclusions

This work demonstrates that sex differences interact with preexisting social dominance status to alter the effects of chronic stress. It highlights the importance of understanding the interplay between sex and social context and its contribution to individual differences in stress response.
Current achievements and future developments of a novel AI based visual monitoring of beehives in ecotoxicology and for the monitoring of landscape structures
Authors: Tausch Frederic , Schmidt Katharina , Diehl Matthias
Published: February 2020

Abstract in English

Honey bees are valuable bio-indicators. As such, they hold a vast potential to help shed light on the extent and interdependencies of factors influencing the decline in the number of insects. However, to date this potential has not yet been fully leveraged, as the production of reliable data requires large-scale study designs, which are very labour intensive and therefore costly.

A novel Artificial Intelligence (AI) based visual monitoring system could enable the partial automatization of data collection on activity, forager loss and impairment of the central nervous system. The possibility to extract features from image data could prospectively also allow an assessment of pollen intake and a differentiation of dead bees, drones and worker bees as well as other insects such as wasps or hornets.

The technology was validated in different studies with regards to its scalability and its ability to extract motion and feature related information.

The prospective possibilities were analyzed regarding their potential to enable advances both within ecotoxicological research and the monitoring of pollinator habitats.
The march of the Common Green Iguana (Iguana iguana): early establishment in Singapore and Thailand is facilitated by the pet trade and recreational parks
Authors: van den Burg Matthijs P. , Van Belleghem Steven M. , De Jesús Villanueva Christina N.
Published: February 2020

The popularity of the Common Green Iguana (Iguana iguana) as a pet has contributed to its global occurrence as an invasive alien species. Early detection and control of invasive alienI. iguanapopulations is necessary to prevent the need for large and financially demanding eradication actions. Here, we collated information from digital footage and interviews regarding sightings of free roamingI. iguanaspecimens in Singapore and Thailand, and present evidence of early-stage invasions and establishment. Using species distribution modeling, we find that large parts of Thailand and neighboring countries have suitable habitat, which could facilitate the expansion of these alien populations if left uncontrolled. Additionally, we report singularI. iguanasightings in Hong Kong and Peninsular Malaysia. We call for awareness of alienI. iguanain the Philippines due to the high number of pet iguanas and reported CITES importations as well as the availability of suitable habitat throughout the archipelago. Further, we identifyI. iguanapresence to be facilitated by the release of pet-traded specimens and uncontrolled exhibition practices in recreational parks. We provide recommendations for implementing monitoring and eradication efforts and strategy recommendations to halt future spread and release.
Radiation Induced Metabolic Alterations Associate with Tumor Aggressiveness and Poor Outcome in Glioblastoma
Authors: Gupta Kshama , Vuckovic Ivan , Zhang Song , Xiong Yuning , Carlson Brett L. , Jacobs Joshua , Olson Ian , Petterson Xuan-Mai , Macura Slobodan I. , Sarkaria Jann , Burns Terry C.
Published: February 2020

Glioblastoma (GBM) is uniformly fatal with a one year median survival rate, despite the best available treatment, including radiotherapy (RT). Impacts of prior RT on tumor recurrence are poorly understood but may increase tumor aggressiveness. Metabolic changes have been investigated in radiation-induced brain injury; however, the tumor-promoting effect following prior radiation is lacking. Since RT is vital to GBM management, we quantified the tumor-promoting effects of prior radiotherapy (RT) on patient-derived intracranial GBM xenografts and characterized the metabolic alterations associated with the protumorigenic microenvironment. Human xenografts (GBM143) were implanted into nude mice 24h following 20Gy cranial radiation vs. sham animals. Tumors in pre-radiated mice were more proliferative and more infiltrative, yielding faster mortality (p<0.0001). Histologic evaluation of tumor associated macrophage/microglia (TAMs) revealed cells with a more fully activated ameboid morphology in pre-radiated animals. Microdialyzates from the radiated brain at the margin of tumor infiltration contralateral to the site of implantation were analyzed by unsupervised liquid chromatography-mass spectrometry (LC-MS). In pre-radiated animals, metabolites known to be associated with tumor progression (like, modified nucleotides and polyols) were identified. Whole-tissue metabolomic analysis of the pre-radiated brain microenvironment for metabolic alterations in a separate cohort of nude mice using1H-NMR revealed significant decrease in levels of antioxidants (glutathione (GSH) and ascorbate (ASC)), NAD+, TCA intermediates, and increased ATP and GTP. Glutathione and ASC showed highest VIPpred (1.65) in OPLS-DA analysis. Involvement of ASC catabolism was further confirmed by GC-MS. To assess longevity of radiation effects, we compared survival with implantation occuring 2 months vs. 24h following radiation, finding worse survival in animals implanted at 2 months. These radiation-induced alterations are consistent with a chronic disease-like microenvironment characterized by reduced levels of antioxidants and NAD+, as well as elevated extracellular ATP and GTP serving as chemoattractants, promoting cell motility and vesicular secretion with decreased levels of GSH and ASC exacerbating oxidative stress. Taken together, these data suggest that IR induces tumor-permissive changes in the microenvironment with metabolomic alterations that may facilitate tumor aggressiveness with important implications for recurrent glioblastoma. Harnessing these metabolomic insights may provide opportunities to attenuate RT-associated aggressiveness of recurrent GBM.
Human Naïve Epiblast Cells Possess Unrestricted Lineage Potential
Authors: Guo Ge , Stirparo Giuliano Giuseppe , Strawbridge Stanley , Spindlow Daniel , Yang Jian , Clarke James , Dattani Anish , Yanagida Ayaka , Li Meng Amy , Myers Sam , Özel Buse Nurten , Nichols Jennifer , Smith Austin
Published: February 2020

Classical mouse embryology has established a paradigm of early development driven by sequential lineage bifurcations. Accordingly, mouse embryonic stem cells derived from early epiblast have lost the potency to produce extraembryonic trophectoderm. We show in contrast that human naïve epiblast cells readily make trophectoderm. Inhibition of ERK signalling, instrumental in naïve stem cell propagation, unexpectedly potentiates trophectoderm formation, an effect enhanced by Nodal inhibition. Transcriptome analyses authenticate conversion into trophectoderm with subsequent production of syncitiotrophoblast, cytotrophoblast and trophoblast stem cells. Genetic perturbations indicate that NANOG suppresses and TFAP2C enables trophectoderm induction. Consistent with post-implantation progression, trophectoderm potential is extinguished in conventional human pluripotent stem cells, which instead make amnion. Finally, human embryo epiblasts from late blastocysts efficiently generate trophectoderm and differentiated trophoblast. Thus, pluripotent cells in the human embryo retain extraembryonic lineage plasticity and regenerative potential until implantation. Harnessing this unanticipated regulative capacity may be beneficial for assisted reproduction technology.
Cell Atlas of Aqueous Humor Outflow Pathways in Eyes of Humans and Four Model Species Provides Insights into Glaucoma Pathogenesis
Authors: van Zyl Tavé , Yan Wenjun , McAdams Alexi , Peng Yi-Rong , Shekhar Karthik , Regev Aviv , Juric Dejan , Sanes Joshua R.
Published: February 2020

Increased intraocular pressure (IOP) represents a major risk factor for glaucoma, a prevalent eye disease characterized by death of retinal ganglion cells that carry information from the eye to the brain; lowering IOP is the only proven treatment strategy to delay disease progression. The main determinant of IOP is the equilibrium between production and drainage of aqueous humor, with compromised drainage generally viewed as the primary contributor to dangerous IOP elevations. Drainage occurs through two pathways in the anterior segment of the eye, called conventional and uveoscleral. To gain insights into the cell types that comprise these pathways, we used high-throughput single cell RNA sequencing (scRNA-seq). From ∼24,000 single cell transcriptomes, we identified 19 cell types with molecular markers for each and used histological methods to localize each type. We then performed similar analyses on four organisms used for experimental studies of IOP dynamics and glaucoma: cynomolgus macaque (Macaca fascicularis), rhesus macaque (Macaca mulatta), pig (Sus scrofa) and mouse (Mus musculus). Many human cell types had counterparts in these models, but differences in cell types and gene expression were evident. Finally, we identified the cell types that express genes implicated in glaucoma in all five species. Together, our results provide foundations for investigating the pathogenesis of glaucoma, and for using model systems to assess mechanisms and potential interventions.
SNF1-related protein kinase 2 directly regulate group C Raf-like protein kinases in abscisic acid signaling
Authors: Kamiyama Yoshiaki , Hirotani Misaki , Ishikawa Shinnosuke , Minegishi Fuko , Katagiri Sotaro , Takahashi Fuminori , Nomoto Mika , Ishikawa Kazuya , Kodama Yutaka , Tada Yasuomi , Takezawa Daisuke , Peck Scott C. , Shinozaki Kazuo , Umezawa Taishi
Published: February 2020

ABSTRUCT

A phytohormone abscisic acid (ABA) has a major role in abiotic stress responses in plants, and subclass III SNF1-related protein kinase 2 (SnRK2) mediates ABA signaling. In this study, we identified Raf36, a group C Raf-like protein kinase in Arabidopsis, as an interacting protein with SnRK2. A series of reverse genetic and biochemical analyses revealed that Raf36 negatively regulates ABA responses and is directly phosphorylated by SnRK2s. In addition, we found that Raf22, another C-type Raf-like kinase, functions partially redundantly with Raf36 to regulate ABA responses. Comparative phosphoproteomic analysis using Arabidopsis wild-type andraf22raf36-1plants identified proteins that are phosphorylated downstream of Raf36 and Raf22in planta. Together, these results reveal a novel subsection of ABA-responsive phosphosignaling pathways branching from SnRK2.
A designer FG-Nup that reconstitutes the selective transport barrier of the Nuclear Pore Complex
Authors: Fragasso Alessio , de Vries Hendrik W. , van der Sluis Eli O. , van der Giessen Erik , Onck Patrick R. , Dekker Cees
Published: February 2020

Nuclear Pore Complexes (NPCs) regulate bidirectional transport between the nucleus and the cytoplasm. Intrinsically disordered FG-Nups line the NPC lumen and form a selective barrier, where transport of most proteins is inhibited whereas specific transporter proteins freely pass. The mechanism underlying selective transport through the NPC is still debated. Here, we reconstitute the selective behaviour of the NPC bottom-up by introducing a rationally designed artificial FG-Nup that mimics natural Nups. Using QCM-D, we measure a strong affinity of the artificial FG-Nup brushes to the transport receptor Kap95, whereas no binding occurs to cytosolic proteins such as BSA. Solid-state nanopores with the artificial FG-Nups lining their inner walls support fast translocation of Kap95 while blocking BSA, thus demonstrating selectivity. Coarse-grained molecular dynamics simulations highlight the formation of a selective meshwork with densities comparable to native NPCs. Our findings show that simple design rules can recapitulate the selective behaviour of native FG-Nups and demonstrate that no specific spacer sequence nor a spatial segregation of different FG-motif types are needed to create functional NPCs.
Examination of the efficacy of small genetic panels in genomic conservation of companion animal populations
Authors: Sams Aaron J. , Ford Brett , Gardner Adam , Boyko Adam R.
Published: February 2020

In many ways dogs are an ideal model for the study of genetic erosion and population recovery, problems of major concern in the field of conservation genetics. Genetic diversity in many dog breeds has been declining systematically since the beginning of the 1800’s, when modern breeding practices came into fashion. As such, inbreeding in domestic dog breeds is substantial and widespread and has led to an increase in recessive deleterious mutations of high effect as well as general inbreeding depression. Pedigrees can in theory be used to guide breeding decisions, though are often incomplete and do not reflect the full history of inbreeding. Small microsatellite panels are also used in some cases to choose mating pairs to produce litters with low levels of inbreeding. However, the long-term impact of such practices have not been thoroughly evaluated. Here, we use forward simulation on a model of the dog genome to examine the impact of using limited markers panels to guide pairwise mating decisions on genome-wide population level genetic diversity. Our results suggest that in unsupervised mating schemes, where breeding decisions are made at the pairwise-rather than population-level, such panels can lead to accelerated loss of genetic diversity compared to random mating at regions of the genome unlinked to panel markers and demonstrate the importance of genome-wide genetic panels for managing and conserving genetic diversity in dogs and other companion animals.
BayeSuites: An open web framework for massive Bayesian networks focused on neuroscience
Authors: Michiels Mario , Larrañaga Pedro , Bielza Concha
Published: February 2020

BayeSuites is the first web framework for learning, visualizing, and interpreting Bayesian networks (BNs) that can scale to tens of thousands of nodes while providing fast and friendly user experience. All the necessary features that enable this are reviewed in this paper; these features include scalability, extensibility, interoperability, ease of use, and interpretability. Scalability is the key factor in learning and processing massive networks within reasonable time; for a maintainable software open to new functionalities, extensibility and interoperability are necessary. Ease of use and interpretability are fundamental aspects of model interpretation, fairly similar to the case of the recent explainable artificial intelligence trend. We present the capabilities of our proposed framework by highlighting a real example of a BN learned from genomic data obtained from Allen Institute for Brain Science. The extensibility properties of the software are also demonstrated with the help of our BN-based probabilistic clustering implementation, together with another genomic-data example.
Hnrnpul1 controls transcription, splicing, and modulates skeletal and limb development in vivo
Authors: Blackwell Danielle L , Fraser Sherri D , Caluseriu Oana , Vivori Claudia , Tyndall Amanda V , Lamont Ryan E , Parboosingh Jillian S , Innes A Micheil , Bernier François P , Childs Sarah J
Published: February 2020

Mutations in RNA binding proteins can lead to pleiotropic phenotypes including craniofacial, skeletal, limb and neurological symptoms. Heterogeneous Nuclear Ribonucleoproteins (hnRNPs) are involved in nucleic acid binding, transcription and splicing through direct binding to DNA and RNA, or through interaction with other proteins in the spliceosome. We show a developmental role for Hnrnpul1 in zebrafish, resulting in reduced craniofacial tendon length, severe adult-onset scoliosis and reduced fin size. We demonstrate a role of Hnrnpul1 in alternative splicing and transcriptional regulation using RNA sequencing. Given its cross-species conservation and role in splicing it would not be surprising if it had a role in human development but the developmental role of this gene in humans has not been explored. Whole exome sequencing detected a frameshift variant inHNRNPUL1in two siblings with congenital limb malformations which remain variants of unknown significance. Zebrafish Hnrnpul1 mutants suggest an important developmental role of hnRNPUL1 and provide motivation for exploring potential conservation of ancient regulatory circuits involving hnRNPUL1 in human development.
First study on age and growth of the deep-water Goblin Shark,Mitsukurina owstoni(Jordan, 1898)
Authors: Caltabellotta Fabio P. , Siders Zachary A. , Cailliet Gregor , Motta Fabio S. , Gadig Otto B. F.
Published: February 2020

Due to poorly mineralizing structures, ageing deep-water elasmobranchs requires nonconventional techniques. The aim of the present study was to develop a reliable ageing technique using the vertebral centrum to provide information about the age and growth parameters in the Goblin Shark,Mitsukurina owstoni(Jordan, 1898). One vertebral centrum from an individual measuring 315.2 cm in total length was analysed. A minimum age of 27 years was estimated. By incorporating priors based on the growth of deep-water sharks and an additional likelihood onL∞using data on large male Goblin Sharks, a Bayesian von Bertalanffy growth model was estimated with a maleL∞of 364 cm total length, weigh 215 kg atL∞, grow slowly with akequal to 0.049, mature at 16.5 years, and live up to 55 years. Our results are essential to provide useful life history information, with the aim of elucidating the cryptic ecology and biology of this deep-water shark.
Meiotic chromosome synapsis depends on multivalent SYCE1-SIX6OS1 interactions that are disrupted in cases of human infertility
Authors: Sánchez-Sáez Fernando , Gómez-H Laura , Dunne Orla M. , Gallego-Páramo Cristina , Felipe-Medina Natalia , Sánchez-Martín Manuel , Llano Elena , Pendas Alberto M. , Davies Owen R.
Published: February 2020

Meiotic reductional division is dependent on the synaptonemal complex (SC), a supramolecular protein assembly that mediates homologous chromosomes synapsis and promotes crossover formation. The mammalian SC is formed of eight structural components, including SYCE1, the only central element protein with known causative mutations in human infertility. We combine mouse genetics, cellular and biochemical studies to reveal that SYCE1 undergoes multivalent interactions with SC component SIX6OS1. The N-terminus of SIX6OS1 binds and disrupts SYCE1’s core dimeric structure to form a 1:1 complex, whilst their downstream sequences provide a distinct second interface. These interfaces are separately disrupted by SYCE1 mutations associated with non-obstructive azoospermia and premature ovarian failure, respectively. Mice harbouring SYCE1’s POF mutation and a targeted deletion within SIX6OS1’s N-terminus are infertile with failure of chromosome synapsis. We conclude that both SYCE1-SIX6OS1 binding interfaces are essential for SC assembly, thus explaining how SYCE1’s reported clinical mutations give rise to human infertility.
Neutrophils are required during immunization with the pneumococcal conjugate vaccine for protective antibody responses and host defense against infection
Authors: Tchalla Essi Y. I. , Wohlfert Elizabeth A. , Bou Ghanem Elsa N.
Published: February 2020

Neutrophils can shape adaptive immunity, however their role in vaccine-induced protection against infectionsin vivoremains unclear. Here, we tested their role in the clinically relevant polysaccharide conjugate vaccine againstStreptococcus pneumoniae(pneumococcus). We antibody depleted neutrophils during vaccination, allowed them to recover, and four weeks later challenged mice with pneumococci. We found that while isotype-treated vaccinated controls were protected against an otherwise lethal infection in naïve mice, full protection was lost upon neutrophil depletion. Compared to vaccinated controls, neutrophil-depleted mice had higher lung bacterial burdens, increased incidence of bacteremia and lower survival rates. Sera from neutrophil-depleted mice had less anti-pneumococcal IgG2c and IgG3, were less efficient at inducing opsonophagocytic killing of bacteria by neutrophilsin vitroand worse at protecting naïve mice against pneumococcal pneumonia. In summary, neutrophils are required during vaccination for optimal host protection, which has important implications for future vaccine design against pneumococci and other pathogens.
Stem Cell Transplantation Rescued A Primary Open-Angle Glaucoma Mouse Model
Authors: Xiong Siqi , Kumar Ajay , Tian Shenghe , Taher Eman E. , Yang Enzhi , Kinchington Paul R. , Xia Xiaobo , Du Yiqin
Published: February 2020

Glaucoma is a leading cause of irreversible blindness. In this study, we investigated if exogenous stem cells are able to rescue a glaucoma mouse model with transgenic myocilin Y437H mutation and explored the possible mechanisms. Human trabecular meshwork stem cells (TMSCs) were intracamerally transplanted which reduced mouse intraocular pressure, increased outflow facility, protected the retinal ganglion cells and preserved their function. TMSC transplantation also significantly increased the TM cellularity, promoted myocilin secretion from TM cells into the aqueous humor to reduce endoplasmic reticulum stress, repaired the TM tissue with extracellular matrix modulation and ultrastructural restoration. Co-culturing TMSCs with myocilin mutant TM cells in vitro promoted TMSCs differentiating into phagocytic functional TM cells. RNA sequencing revealed that TMSCs had upregulated genes related to TM regeneration and neuroprotection. Our results uncovered therapeutic potential of TMSCs for curing glaucoma and elucidated possible mechanisms by which TMSCs achieve the treatment effect.
The Hedgehog Co-Receptor BOC Differentially Regulates SHH Signaling During Craniofacial Development
Authors: Echevarría-Andino Martha L. , Allen Benjamin L.
Published: February 2020

The Hedgehog (HH) pathway controls multiple aspects of craniofacial development. HH ligands signal through the canonical receptor PTCH1, and three co-receptors– GAS1, CDON and BOC. Together, these co-receptors are required during embryogenesis to mediate proper HH signaling. Here we investigated the individual and combined contributions of GAS1, CDON and BOC to HH-dependent mammalian craniofacial development. Individual deletion of eitherGas1orCdonresults in variable holoprosencephaly phenotypes, characterized by the failure to divide and form the telencephalon and midfacial structures. In contrast, we find thatBocdeletion results in facial widening consistent with increased HH pathway activity. Additionally, the deletion ofBocin aGas1null background partially rescues the craniofacial defects observed inGas1single mutants; a phenotype that persists over developmental time. This contrasts with HH-dependent phenotypes in other tissues that significantly worsen following combined deletion ofGas1andBoc. Mechanistically, BOC selectively restricts neural crest-derived mesenchymal proliferation. Together, these data indicate that BOC acts as a multi-functional regulator of HH signaling during craniofacial development, alternately promoting or restraining HH pathway activity in a tissue-specific fashion.

Summary statement

Here we identify dual, tissue-specific roles for the Hedgehog co-receptor BOC in both the promotion and antagonism of Hedgehog signaling during craniofacial development.