bluuebunny/crossref_metadata_2025 huggingface dataset:
Inhibiting DDX3X triggers tumor-intrinsic type I interferon response and enhances anti-tumor immunity
Authors: Choi Hyeongjwa , Kwon Juntae , Sun Jiafang , Cho Min Soon , Sun Yifan , Casey John L , Toretsky Jeffrey , Han Cecil
Published: September 2020

Accumulating evidence has shown that cellular double-stranded RNAs (dsRNAs) induce antiviral innate immune responses in human normal and malignant cancer cells. However, it is not fully understood how endogenous ‘self’ dsRNA homeostasis is regulated in the cell. Here, we show that an RNA-binding protein, DEAD-box RNA helicase 3X (DDX3X), prevents the aberrant accumulation of cellular dsRNAs. Loss of DDX3X induces dsRNA sensor-mediated type I interferon signaling and innate immune response in breast cancer cells due to abnormal cytoplasmic accumulation of dsRNAs. Dual depletion of DDX3X and a dsRNA-editing protein, ADAR1 synergistically activates the cytosolic dsRNA pathway in breast cancer cell. Moreover, inhibiting DDX3X enhances the antitumor activity by increasing tumor intrinsic-type I interferon response, antigen presentation, and tumor-infiltration of cytotoxic T cells as well as dendritic cells in breast tumors, which may lead to the development of breast cancer therapy by targeting DDX3X in combination with immune checkpoint blockade.
Transcriptional reprogramming during effector/flg22-triggered immune is independent of defense phytohormone signaling networks
Authors: Zhang Nailou , Fan Zhijin
Published: September 2020

Plants rely on the innate immune system to sense and respond to a wide range of lifestyle pathogens and to facilitate their survival in natural ecosystems. Pathogen-associated molecular patterns (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI) are designated as a two-branched system of innate immunity. Although PTI/ETI share a series of downstream molecular events, systematic analysis of convergent and divergent signaling in PTI/ETI is currently lacking. The phytohormones salicylic acid (SA) and jasmonic acid (JA) are considered to constitute the hormonal backbone of plant immunity, are functionally antagonistic, and play essential roles in defending against biotrophic and necrotrophic pathogens, respectively. However, the distinct performance of two phytohormones in PTI/ETI remains unclear. Here, we systemically investigate and validate the reprogramming of molecular networks during PTI and ETI. Using publicly availableArabidopsisRNA sequence data from 560 samples, we construct a co-expression network under Mock conditions and then explore the differential expression/co-expression changes during PTI, ETI, andPtoDC3000 infection. During PTI and ETI, one-third of genes in theArabidopsisgenome exhibit the same directional differential expression in a manner independent of JA/ethylene/PAD4/SA signaling but show differential co-expression patterns. However, the defense phytohormone network is required for defense againstPtoDC3000 infection. We also exhibit the use of this network in prioritizing genes that functioned closely with the proteins directly targeted by elicitors. Overall, this study will deepen our understanding of plant transcriptome in plant immunity and provide new insights into the mode of action of elicitors.
LIQA: Long-read Isoform Quantification and Analysis
Authors: Hu Yu , Fang Li , Chen Xuelian , Zhong Jiang F. , Li Mingyao , Wang Kai
Published: September 2020

Long-read RNA sequencing (RNA-seq) technologies have made it possible to sequence full-length transcripts, facilitating the exploration of isoform-specific gene expression (isoform relative abundance and isoform-level TPM) over conventional short-read RNA-seq. However, long-read RNA-seq suffers from high per-base error rate, presence of chimeric reads or alternative alignments, and other biases, which require different analysis methods than short-read RNA-seq. Here we present LIQA (Long-read IsoformQuantification andAnalysis), an Expectation-Maximization based statistical method to quantify isoform expression and detect differential alternative splicing (DAS) events using long-read RNA-seq data. Rather than summarizing isoform-specific read counts directly as done in short-read methods, LIQA incorporates base-pair quality score and isoform-specific read length information to assign different weights across reads, which reflects alignment confidence. Moreover, LIQA can detect DAS events between conditions using isoform usage estimates. We evaluated LIQA’s performance on simulated data and demonstrated that it outperforms other approaches in characterizing isoforms with low read coverage and in detecting DAS events between two groups. We also generated one direct mRNA sequencing dataset and one cDNA sequencing dataset using the Oxford Nanopore long-read platform, both with paired short-read RNA-seq data and qPCR data on selected genes, and we demonstrated that LIQA performs well in isoform discovery and quantification. Finally, we evaluated LIQA on a PacBio dataset on esophageal squamous epithelial cells, and demonstrated that LIQA recovered DAS events that failed to be detected in short-read data. In summary, LIQA leverages the power of long-read RNA-seq and achieves higher accuracy in estimating isoform abundance than existing approaches, especially for isoforms with low coverage and biased read distribution. LIQA is freely available athttps://github.com/WGLab/LIQA.
Epigenetic clock and methylation studies in vervet monkeys
Authors: Jasinska Anna J. , Haghani Amin , Zoller Joseph A. , Li Caesar Z. , Arneson Adriana , Ernst Jason , Kavanagh Kylie , Jorgensen Matthew J , Mattison Julie A. , Wojta Kevin , Choi Oi-Wa , DeYoung Joseph , Li Xinmin , Rao Andrew W. , Coppola Giovanni , Freimer Nelson B. , Woods Roger P. , Horvath Steve
Published: September 2020

DNA methylation-based biomarkers of aging have been developed for many mammals but not yet for the vervet monkey (Chlorocebus sabaeus), which is a valuable non-human primate model for biomedical studies. We generated novel DNA methylation data from vervet cerebral cortex, blood, and liver using highly conserved mammalian CpGs represented on a custom array (HorvathMammalMethylChip40). We present six DNA methylation-based estimators of age: vervet multi-tissue epigenetic clock and tissue-specific clocks for brain cortex, blood, and liver. In addition, two dual species clocks (human-vervet clocks) for measuring chronological age and relative age, respectively. Relative age was defined as ratio of chronological age to maximum lifespan to address the species differences in maximum lifespan. The high accuracy of the human-vervet clocks demonstrates that epigenetic aging processes are evolutionary conserved in primates. When applying these vervet clocks to tissue samples from another primate species, rhesus macaque, we observed high age correlations but strong offsets. We characterized CpGs that correlate significantly with age in the vervet. CpG probes hypermethylated with age across tissues were located near the targets of Polycomb proteins SUZ12 and EED, and genes possessing the trimethylated H3K27 mark in their promoters.

The epigenetic clocks are expected to be useful for age estimation of wild-born animals and anti-aging studies in vervets.
Novel regulatory and transcriptional networks associated with resistance to platinum-based chemotherapy in ovarian cancer
Authors: Topouza Danai G. , Choi Jihoon , Nesdoly Sean , Tarnouskaya Anastasiya , Nicol Christopher J.B. , Duan Qing Ling
Published: September 2020

Background

High-grade serous ovarian cancer (HGSOC) is a highly lethal gynecologic cancer, in part due to resistance to platinum-based chemotherapy reported among 20% of patients. This study aims to elucidate the biological mechanisms underlying chemotherapy resistance, which remain poorly understood.

Methods

Sequencing data (mRNA and microRNA) from HGSOC patients were analyzed to identify differentially expressed genes and co-expressed transcript networks associated with chemotherapy response. Initial analyses used datasets from The Cancer Genome Atlas and then replicated in two independent cancer cohorts. Moreover, transcript expression datasets and genomics data (i.e. single nucleotide polymorphisms) were integrated to determine potential regulation of the associated mRNA networks by microRNAs and expression quantitative trait loci (eQTLs).

Results

In total, 196 differentially expressed mRNAs were enriched for adaptive immunity and translation, and 21 differentially expressed microRNAs were associated with angiogenesis. Moreover, co-expression network analysis identified two mRNA networks associated with chemotherapy response, which were enriched for ubiquitination and lipid metabolism, as well as three associated microRNA networks enriched for lipoprotein transport and oncogenic pathways. In addition, integrative analyses revealed potential regulation of the mRNA networks by the associated microRNAs and eQTLs.

Conclusion

We report novel transcriptional networks and pathways associated with resistance to platinum-based chemotherapy among HGSOC patients. These results aid our understanding of the effector networks and regulators of chemotherapy response, which will improve drug efficacy and identify novel therapeutic targets for ovarian cancer.
Modulating the activities of chloroplasts and mitochondria promotes ATP production and plant growth
Authors: Voon Chia Pao , Law Yee-Song , Guan Xiaoqian , Lim Shey-Li , Xu Zhou , Chu Wing-Tung , Zhang Renshan , Sun Feng , Labs Mathias , Leister Dario , Pribil Mathias , Hronková Marie , Kubásek Jiří , Cui Yong , Jiang Liwen , Tsuyama Michito , Gardeström Per , Tikkanen Mikko , Lim Boon Leong
Published: September 2020

Efficient photosynthesis requires a balance of ATP and NADPH production/consumption in chloroplasts and the exportation of reducing equivalents from chloroplasts is important for balancing stromal ATP/NADPH ratio. Here we showed that the overexpression of purple acid phosphatase 2 on the outer membranes of chloroplasts and mitochondria can streamline the production and consumption of reducing equivalents in these two organelles, respectively. A higher capacity of consumption of reducing equivalents in mitochondria can indirectly help chloroplasts to balance the ATP/NADPH ratio in stroma and recycle NADP+, the electron acceptors of the linear electron flow. A higher rate of ATP and NADPH production from the linear electron flow, a higher capacity of carbon fixation by the Calvin-Benson-Bassham cycle and a greater consumption of NADH in mitochondria, enhance photosynthesis in the chloroplasts, ATP production in the mitochondria, sucrose synthesis in the cytosol, and eventually boosting plant growth and seed yields in the overexpression lines.
Epigenomic patterns reflect irrigation and grafting in the grapevine clone ‘Chambourcin’
Authors: Williams Brigette R. , Edwards Christine E. , Kwasniewski Misha T. , Miller Allison J.
Published: September 2020

Although DNA methylation has largely been shown to be stable in plants, mounting evidence indicates methylation patterns may reflect environmental sensitivity. Perennial plants experience seasonal and inter-annual environmental variation, and clonal replicates of some long-lived plants, including many perennial crops, survive in a broad range of environments. This makes perennial crops a compelling study system to investigate links between the plant epigenome and environmental variation. In this study, we used whole genome bisulfite sequencing and small RNA sequencing to characterize the epigenome in 12 clonal replicates of the winegrape cultivar ‘Chambourcin.’ We asked whether DNA methylation varied in response to a full factorial combination of irrigation and grafting treatments. We found signatures of both irrigation and grafting in the ‘Chambourcin’ epigenome, as well as compelling evidence for a unique interaction effect whereby grafting appeared to override or mitigate epigenomic changes associated with irrigation in ungrafted vines. These findings indicate that the epigenome responds to environmental and agronomic manipulations, suggesting the epigenome might be a mechanism underlying how long-lived, clonal plants respond at the molecular level to their environment. Further research is needed to assess the potential relevance of variation in DNA methylation to plant form and function, and to address the implications of environmentally-inducible patterns of DNA methylation on the adaptive capacity of long-lived woody perennials in nature and under cultivation.
Major oscillations in spontaneous home-cage activity with an infraradian periodicity in C57Bl/6 mice housed under constant conditions
Authors: Pernold K. , Rullman E. , Ulfhake B.
Published: September 2020

Using 14-20 months of cumulative 24/7 home-cage activity recorded with a non-intrusive technique and a data driven analytical approach, we here provide evidence for the existence of a circannual oscillation (1-2 SD of the mean, on average 65% higher during peak of highs than lows; P=7E-50) in spontaneous activity of male and female C57BL/6 mice held under constant barrier conditions (dark-light cycle 12/12 h (DL), temperature 21±1°C, humidity 40-60%). The periodicity of the season-like oscillation is in the range of 2-4 months (on average 97 days across cohorts of cages) and off-sets also responses to environmental stimuli but does not significantly alter the preference for activity during the dark hours of this nocturnal mouse strain (P=0.11 difference between highs and lows).

The significance of this hitherto not recognized slow rhythmic alteration in spontaneous activity is further substantiated by its co-variation with the feeding behaviour of the mice. The absence of coordination within and between cohorts of cages or synchronization to the seasons of the year, suggests that the oscillation of in-cage activity and behavioural responses is generated by a free-running intrinsic oscillator devoid of synchronization with an out-of-cage environmental time-keeper. Since the variation over time has such a magnitude and correlate with the feeding behaviour it is likely that it will impact a range of long term experiments conducted on laboratory mice if left unrecognized.
Topological Assembly of a Deployable Hoberman Flight Ring from DNA
Authors: Li Ruixin , Chen Haorong , Choi Jong Hyun
Published: September 2020

Deployable geometries are finite auxetic structures that preserve their overall shapes during expansion and contraction. The topological behaviors emerge from intricately arranged elements and their connections. Despite considerable utility of such configurations in nature and in engineering, deployable nanostructures have never been demonstrated. Here we show a deployable flight ring, a simplified planar structure of Hoberman sphere, using DNA origami. The DNA flight ring consists of topologically assembled six triangles in two layers that can slide against each other, thereby switching between two distinct (open and closed) states. The origami topology is a trefoil knot, and its auxetic reconfiguration results in negative Poisson’s ratios. This work shows the feasibility of deployable nanoarchitectures, providing a versatile platform for topological studies and opening new opportunities for bioengineering.
Glioblastoma Cell Migration is Directed by Electrical Signals
Authors: Clancy Hannah , Pruski Michal , Lang Bing , Ching Jared , McCaig Colin D.
Published: September 2020

Background:

Electric field (EF) directed cell migration (electrotaxis) is known to occur in glioblastoma multiforme (GBM) and neural stem cells, with key signaling pathways frequently dysregulated in GBM. One such pathway is EGFR/PI3K/Akt, which is down-regulated by peroxisome proliferator activated receptor gamma (PPARγ) agonists. We investigated the effect of electric fields on GBM differentiated and stem cell migration and whether this was affected by treatment with the PPARγ agonist pioglitazone.

Methods

Primary GBM cell lines were cultured as differentiated and glioma stem cells (GSCs) and then exposed to EFs using electrotaxis chambers and imaged with time lapse microscopy. Cells were then treated with varying concentrations of pioglitazone and/or its inhibitor GW9662 and their responses to EFs examined.

Results

We demonstrated that GBM differentiated and GSCs have opposing preferences for anodal and cathodal migration, respectively. Pioglitazone treatment resulted in significantly decreased directed cell migration in both cell types. Western blot analysis did not demonstrate any change in PPARγ expression with and without exposure to EF.

Conclusions

Opposing EF responses in primary GBM differentiated cells and GSCs can be inhibited chemically by pioglitazone, implicating GBM EF modulation as a potential target in preventing tumour recurrence.
Modeling the hemodynamic response function using simultaneous EEG-fMRI data and convolutional sparse coding analysis with rank-1 constraints
Authors: Prokopiou Prokopis C. , Kassinopoulos Michalis , Xifra-Porxas Alba , Boudrias Marie-Hélène , Mitsis Georgios D.
Published: September 2020

Over the last few years, an increasing body of evidence points to the hemodynamic response function as an important confound of resting-state functional connectivity. Several studies in the literature proposed using blind deconvolution of resting-state fMRI data to retrieve the HRF, which can be subsequently used for hemodynamic deblurring. A basic hypothesis in these studies is that relevant information of the resting-state brain dynamics is condensed in discrete events resulting in large amplitude peaks in the BOLD signal. In this work, we showed that important information of resting-state activity, in addition to the larger amplitude peaks, is also concentrated in lower amplitude peaks. Moreover, due to the strong effect of physiological noise and head motion on the BOLD signal, which in many cases may not be completely removed after preprocessing, the neurophysiological origin of the large amplitude BOLD signal peaks is questionable. Hence, focusing on the large amplitude BOLD signal peaks may yield biased HRF estimates. To define discrete events of neuronal origins, we proposed using simultaneous EEG-fMRI along with convolutional sparse coding analysis. Our results suggested that events detected in the EEG are able to describe the slow oscillations of the BOLD signal and to obtain consistent HRF shapes across subjects under both task-based and resting-state conditions.
Long time-scale study of von Willebrand factor multimers in extensional flow
Authors: Kania S. , Oztekin A. , Cheng X. , Zhang X. F. , Webb E. B.
Published: September 2020

Extensional flow-induced transitions from a compact to an unfolded conformation are explored for the human glycoprotein von Willebrand factor (vWF). Multimer unfolding is a crucial step in the process of blood clotting and protein size maintenance. Previous studies have shown that flow-induced conformational transitions are initiated by a thermally nucleated polymeric protrusion. Below a certain strain rate, such a transition is a rare event that cannot be studied using standard stochastic dynamic simulation. In the present study, we have employed Weighted Ensemble Brownian dynamic (WEBD) simulations to study rare events of conformation transition in extensional flow. Results are presented for the transition rate of VWF multimer unfolding, with concomitant analysis of the likelihood of pathological unfolding as a function of strain rate. Relative to the typical half-life of vWF proteins in the human body, results here indicate that pathological unfolding would not manifest for strain rate less than 2000 s−1.

Statement of Significance

vWF multimers, as they transit through the circulation, are exposed to extensional flow multiple times, and the total exposure time to such intermittent extensional flow can be on the order of minutes to an hour. However, due to the time-scale limitation of Brownian dynamics simulation, all the present studies of vWF multimers are limited to a few seconds in total duration. Here, we have applied an enhanced sampling technique, i.e., Weighted Ensemble, in combination with Brownian dynamics to analyze the behavior of multimers in extensional flow at physiologically relevant time-scales of hours and longer. The findings presented here provide new physical insights into vWF behavior, including how it relates to hematological pathology, while also illustrating the time-scale bridging capability of the WEBD method.
Polee: RNA-Seq analysis using approximate likelihood
Authors: Jones Daniel C. , Ruzzo Walter L.
Published: September 2020

The analysis of mRNA transcript abundance with RNA-Seq is a central tool in molecular biology research, but often analyses fail to account for the uncertainty in these estimates, which can be significant, especially when trying to disentangle isoforms or duplicated genes. Preserving un-certainty necessitates a full probabilistic model of the all the sequencing reads, which quickly becomes intractable, as experiments can consist of billions of reads. To overcome these limitations, we propose a new method of approximating the likelihood function of a sparse mixture model, using a technique we call the Pólya tree transformation. We demonstrate that substituting this approximation for the real thing achieves most of the benefits with a fraction of the computational costs, leading to more accurate detection of differential transcript expression.

Availability

The method is implemented in a Julia package available fromhttps://github.com/dcjones/polee

Contact

dcjones@cs.washington.edu
Interactions between specific breeding system and ploidy play a critical role in increasing niche adaptability in a global food crop
Authors: Fumia Nathan , Rubinoff Daniel , Zenil-Ferguson Rosana , Khoury Colin K. , Pironon Samuel , Gore Michael A. , Kantar Michael B.
Published: September 2020

Understanding the factors driving ecological and evolutionary interactions of economically important plant species is important for sustainability. Niches of crop wild relatives, including wild potatoes (SolanumsectionPetota), have received attention, however, such information has not been analyzed in combination with phylogenetic histories, genomic composition and reproductive systems. We used a combination of ordinary least-squares (OLS) and phylogenetic generalized least-squares (PGLM) analyses to identify the discrete climate classes that wild potato species inhabit in the context of breeding system and ploidy. Self-incompatible diploid or self-compatible polyploid species significantly increase the number of discrete climate niches inhabited. This result was sustained when correcting for phylogenetic non-independence in the linear model. Our results support the idea that specific breeding system and ploidy combinations increase niche divergence through the decoupling of geographical range and niche diversity, and therefore, these species may be of particular interest for crop adaptation to a changing climate.
Integration of constraint-based modelling with faecal metabolomics reveals large deleterious effects ofFusobacteriaspecies on community butyrate production
Authors: Hertel Johannes , Heinken Almut , Martinelli Filippo , Thiele Ines
Published: September 2020

Integrating constraint-based community modelling with population statistics, we introduce new theoretical concepts for interrogating the metabolic functions of the microbiome, applying them to a public metagenomic dataset consisting of 365 colorectal cancer cases (CRC) and 251 healthy controls. We found that 1) glutarate production capability was significantly enriched in CRC microbiomes and mechanistically linked to lysine fermentation inFusobacteriaspecies, 2) acetate and butyrate production potentials were lowered in CRC, 3) Fusobacteria presence had large negative ecological effects on community butyrate production in CRC and healthy controls. Validating the model predictions against faecal metabolomics, ourin silicoframeworks correctly predictedin vivospecies metabolite correlations with high accuracy. In conclusion, highlighting the value of combining statistical association studies within silicomodelling, this study delivers insights on the metabolic role ofFusobacteriain the gut, while providing a proof of concept for the validity of constraint-based community modelling.
Investigating the role of root exudates in recruitingStreptomycesbacteria to theArabidopsis thalianaroot microbiome
Authors: Worsley Sarah F. , Macey Michael , Prudence Sam , Wilkinson Barrie , Murrell J. Colin , Hutchings Matthew I.
Published: September 2020

Streptomycesspecies are saprophytic soil bacteria that produce a diverse array of specialised metabolites, including half of all known antibiotics. They are also rhizobacteria and plant endophytes that can promote plant growth and protect against disease. Several studies have shown that streptomycetes are enriched in the rhizosphere and endosphere of the model plantArabidopsis thaliana. Here, we set out to test the hypothesis that they are attracted to plant roots by root exudates, and specifically by the plant phytohormone salicylate, which they might use as a nutrient source. We confirmed a previously published report that salicylate over-producingcpr5plants are colonised more readily by streptomycetes but found that salicylate-deficientsid2-2andpad4plants had the same levels of root colonisation byStreptomycesbacteria as the wild-type plants. We then tested eight genome sequencedStreptomycesendophyte strainsin vitroand found that none were attracted to or could grow on salicylate as a sole carbon source. We next used13CO2DNA stable isotope probing to test whetherStreptomycesspecies can feed off a wider range of plant metabolites but found thatStreptomycesbacteria were outcompeted by faster growing proteobacteria and did not incorporate photosynthetically fixed carbon into their DNA. We conclude that, given their saprotrophic nature and under conditions of high competition, streptomycetes most likely feed on more complex organic material shed by growing plant roots. Understanding the factors that impact the competitiveness of strains in the plant root microbiome could have consequences for the effective application of biocontrol strains.

Importance

Streptomycesbacteria are ubiquitous in soil but their role as rhizobacteria is less well studied. Our recent work demonstrated that streptomycetes isolated fromA. thalianaroots can promote growth and protect against disease across plant species and that plant growth hormones can modulate the production of bioactive specialised metabolites by these strains. Here we used13CO2DNA stable isotope probing to identify which bacteria feed on plant metabolites in theA. thalianarhizosphere and, for the first time, in the endosphere. We found thatStreptomycesspecies are outcompeted for these metabolites by faster growing proteobacteria and instead likely subsist on more complex organic material such as cellulose derived from plant cell material that is shed from the roots. This work thus reveals the “winners and losers” in the battle between soil bacteria for plant metabolites and could inform the development of methods to apply streptomycetes as plant growth-promoting agents.
A simple permutation-based test of intermodal correspondence
Authors: Weinstein Sarah M. , Vandekar Simon N. , Adebimpe Azeez , Tapera Tinashe M. , Robert-Fitzgerald Timothy , Gur Ruben C. , Gur Raquel E. , Raznahan Armin , Satterthwaite Theodore D. , Alexander-Bloch Aaron F. , Shinohara Russell T.
Published: September 2020

Many key findings in neuroimaging studies involve similarities between brain maps, but statistical methods used to measure these findings have varied. Current state-of-the-art methods involve comparing observed group-level brain maps (after averaging intensities at each image location across multiple subjects) against spatial null models of these group-level maps. However, these methods typically make strong and potentially unrealistic statistical assumptions, such as covariance stationarity. To address these issues, in this paper we propose using subject-level data and a classical permutation testing framework to test and assess similarities between brain maps. Our method is comparable to traditional permutation tests in that it involves randomly permuting subjects to generate a null distribution of intermodal correspondence statistics, which we compare to an observed statistic to estimate ap-value. We apply and compare our method in simulated and real neuroimaging data from the Philadelphia Neurodevelopmental Cohort. We show that our method performs well for detecting relationships between modalities known to be strongly related (cortical thickness and sulcal depth), and it is conservative when an association would not be expected (cortical thickness and activation on then-back working memory task). Notably, our method is the most flexible and reliable for localizing intermodal relationships within subregions of the brain and allows for generalizable statistical inference.
The phosphatase inhibitor LB-100 acts synergistically with the NPR2 agonist BMN-111 to improve bone growth
Authors: Shuhaibar Leia C. , Kaci Nabil , Egbert Jeremy R. , Loisay Léa , Vigone Giulia , Uliasz Tracy F. , Dambroise Emilie , Swingle Mark R. , Honkanen Richard E. , Jaffe Laurinda A. , Legeai-Mallet Laurence
Published: September 2020

Activating mutations in fibroblast growth factor receptor 3 (FGFR3) and inactivating mutations in the natriuretic peptide receptor 2 (NPR2) guanylyl cyclase both result in decreased production of cyclic GMP (cGMP) in chondrocytes and severe short stature, causing achondroplasia (ACH) and acrosomelic dysplasia type Maroteaux, respectively. Previously we showed that an NPR2 agonist BMN-111 (vosoritide) increases bone growth in mice mimicking ACH (Fgfr3Y367C/+), and that in control growth plate chondrocytes, FGFR3 signaling decreases NPR2 activity by dephosphorylating the NPR2 protein. Here we tested whether a phosphatase inhibitor (LB-100) could enhance bone growth in ACH. Inex vivoimaging experiments using a FRET sensor to measure cGMP production in chondrocytes of living tibias from newborn mice, LB-100 counteracts the FGF-induced dephosphorylation and inactivation of NPR2. Inex vivoexperiments withFgfr3Y367C/+mice, LB-100 in combination with BMN-111 increases the rate of femur growth by ∼25% vs BMN-111 alone, restores chondrocyte terminal differentiation, increases the proliferative growth plate area of the femur, and reduces the activity of the MAP kinase pathway. Our results provide a proof of concept that a phosphatase inhibitor could be used together with an NPR2 agonist to enhance cGMP production as a therapy for ACH.

GRAPHICAL ABSTRACT
Coordination of two enhancers drives expression of olfactory trace amine-associated receptors
Authors: Fei Aimei , Wu Wanqing , Tan Longzhi , Tang Cheng , Xu Zhengrong , Huo Xiaona , Bao Hongqiang , Johnson Mark , Hartmann Griffin , Talay Mustafa , Yang Cheng , Riegler Clemens , Joseph Kristian , Engert Florian , Xie X. Sunney , Barnea Gilad , Liberles Stephen D. , Yang Hui , Li Qian
Published: September 2020

Olfactory sensory neurons (OSNs) are functionally defined by their expression of a unique odorant receptor (OR). Mechanisms underlying singular OR expression are well studied, and involve a massive cross-chromosomal enhancer interaction network. Trace amine-associated receptors (TAARs) form a distinct family of olfactory receptors, and here we find that mechanisms regulatingTaargene choice display many unique features. The epigenetic signature ofTaargenes in TAAR OSNs is different from that in OR OSNs. We further identify that two TAAR enhancers conserved across placental mammals are absolutely required for expression of the entireTaargene repertoire. Deletion of either enhancer dramatically decreases the expression probabilities of differentTaargenes, while deletion of both enhancers completely eliminates the TAAR OSN populations. In addition, both of the enhancers are sufficient to drive transgene expression in the partially overlapped TAAR OSNs. We also show that the TAAR enhancers operate incisto regulateTaargene expression. Our findings reveal a coordinated control ofTaargene choice in OSNs by two remote enhancers, and provide an excellent model to study molecular mechanisms underlying formation of an olfactory subsystem.
Quantification and demonstration of the constriction-by-rachet mechanism in the dynamin molecular motor
Authors: Ganichkin Oleg , Vancraenenbroeck Renee , Rosenblum Gabriel , Hofmann Hagen , Mikhailov Alexander S. , Daumke Oliver , Noel Jeffrey K.
Published: September 2020

Dynamin oligomerizes into helical filaments on tubular membrane templates and, through constriction, cleaves them in a GTPase-driven way. Structural observations of GTP-dependent cross-bridges between neighboring filament turns have led to the suggestion that dynamin operates as a molecular ratchet motor. However, the proof of such mechanism remains absent. Particularly, it is not known whether a powerful enough stroke is produced and how the motor modules would cooperate in the constriction process. Here, we characterized the dynamin motor modules by single molecule (sm) FRET and found strong nucleotide-dependent conformational changes. Integrating smFRET with molecular dynamics simulations allowed us to determine the forces generated in a power stroke. Subsequently, the quantitative force data and the measured kinetics of the GT-Pase cycle were incorporated into a model including both a dynamin filament, with explicit motor cross-bridges, and a realistic deformable membrane template. In our simulations, collective constriction of the membrane by dynamin motor modules, based on the ratchet mechanism, is directly reproduced and analyzed. Functional parallels between the dynamin system and actomyosin in the muscle are seen. Through concerted action of the motors, tight membrane constriction to the hemifission radius can be reached. Our experimental and computational study provides an example of how collective motor action in megadalton molecular assemblies can be approached and explicitly resolved.
Heterogeneous aggregation of amyloid-β 42 from single-molecule spectroscopy
Authors: Meng Fanjie , Yoo Janghyun , Chung Hoi Sung
Published: September 2020

Protein aggregation is implicated as the cause of pathology in various diseases such as Alzheimer’s and Parkinson’s disease. Polymorphism in the structure of fibrils formed by aggregation suggests the existence of many different assembly pathways and therefore a heterogeneous ensemble of soluble oligomers. Characterization of this heterogeneity is the key to understanding the aggregation mechanism and toxicity of specific oligomers, but in practice it is extremely difficult because oligomers cannot be readily separated. Here, we investigate highly heterogeneous oligomerization and fibril formation of the 42-residue amyloid-β peptide (Aβ42). We developed and used new single-molecule fluorescence spectroscopic and fluorescence lifetime imaging methods, combined with deep learning for image analysis. We found that the concentration of oligomers, including dimers, is extremely low and that the dimer is conformationally diverse. Aggregation to form fibrils is also highly heterogeneous in terms of the number of strands in a fibril and the elongation speed and conformation of fibrils. This heterogeneity in all stages of aggregation explains diverse and sometimes irreproducible results of experimental studies of amyloid-β. Based on our observations and analysis, we propose a new model for aggregation of Aβ42.
Phosphodiesterase Type 4 anchoring regulates cAMP signaling to Popeye domain-containing proteins
Authors: Tibbo Amy J , Dobi Sara , McFall Aisling , Tejeda Gonzalo S , Blair Connor , MacLeod Ruth , MacQuaide Niall , Gök Caglar , Fuller William , Smith Brian O , Smith Godfrey L , Brand Thomas , Baillie George S
Published: September 2020

Cyclic AMP is a ubiquitous second messenger used to transduce intracellular signals from a variety of Gs-coupled receptors. Compartmentalisation of protein intermediates within the cAMP signaling pathway underpins receptor-specific responses. The cAMP effector proteins protein-kinase A and EPAC are found in complexes that also contain phosphodiesterases whose presence ensures a coordinated cellular response to receptor activation events. Popeye proteins are the most recent class of cAMP effectors to be identified and have crucial roles in cardiac pacemaking and conduction. We report the first observation that Popeye proteins exist in complexes with members of the PDE4 family in cardiac myocytes thus restricting cAMP signaling. We show that POPDC1 preferentially binds the PDE4A sub-family via a specificity motif in the PDE4 UCR1 region and that PDE4s bind to the Popeye domain of POPDC1 in a region known to be susceptible to a mutation that causes human disease. Using a cell-permeable disruptor peptide that displaces the POPDC1-PDE4 complex we show that PDE4 activity localized to POPDC1 is essential to maintain action potential duration in beating cardiac myocytes.
The atypical Rho GTPase Rnd2 is critical for dentate granule neuron development and anxiety-like behavior during adult but not neonatal neurogenesis
Authors: Kerloch Thomas , Farrugia Fanny , Maître Marlène , Terral Geoffrey , Koehl Muriel , Heng Julian Ik-Tsen , Blanchard Mylène , Doat Hélène , Leste-Lasserre Thierry , Goron Adeline , Gonzales Delphine , Guillemot François , Abrous Djoher Nora , Pacary Emilie
Published: September 2020

Despite the central role of Rho GTPases in neuronal development, their functions in adult hippocampal neurogenesis remain poorly explored. Here, by using a retrovirus-based loss-of-function approachin vivo, we show that the atypical Rho GTPase Rnd2 is crucial for the survival, positioning, somatodendritic morphogenesis and functional maturation of adult-born dentate granule neurons. Interestingly, most of these functions are specific to granule neurons generated during adulthood since the deletion ofRnd2in neonatally-born granule neurons only affects dendritogenesis. In addition, suppression ofRnd2in adult-born dentate granule neurons increases anxiety-like behaviour whereas its deletion in pups has no such effect, a finding supporting the adult neurogenesis hypothesis of anxiety disorders. Thus, our results provide mechanistic insight into the differential regulation of hippocampal neurogenesis during development and adulthood, and establishes a causal relationship between Rnd2 expression and anxiety.
Genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs
Authors: Flutre Timothée , Le Cunff Loïc , Fodor Agota , Launay Amandine , Romieu Charles , Berger Gilles , Bertrand Yves , Terrier Nancy , Beccavin Isabelle , Bouckenooghe Virginie , Roques Maryline , Pinasseau Lucie , Verbaere Arnaud , Sommerer Nicolas , Cheynier Véronique , Bacilieri Roberto , Boursiquot Jean-Michel , Lacombe Thierry , Laucou Valérie , This Patrice , Péros Jean-Pierre , Doligez Agnès
Published: September 2020

To cope with the challenges faced by agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennials such as grapevine, but requires understanding the genetic architecture of target traits. To go beyond the mapping of quantitative trait locus (QTL) in bi-parental crosses, we exploited a diverse panel of 279Vitis viniferaL. cultivars. This panel planted in five blocks in the vineyard was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. The panel was genotyped for 63k single nucleotide polymorphisms (SNPs) by combining an 18K microarray and genotyping-by-sequencing (GBS). The experimental design allowed to reliably assess the genotypic values for most traits. Marker densification via GBS markedly increased the proportion of genetic variance explained by SNPs, and two multi-SNP models identified QTLs not found by a SNP-by-SNP model. Overall, 489 reliable QTLs were detected for 41% more response variables than by a SNP-by-SNP model with microarray-only SNPs, many new ones compared to the results from bi-parental crosses. Prediction accuracy higher than 0.42 was obtained for 50% of the response variables. Our overall approach as well as QTL and prediction results provide insights into the genetic architecture of target traits. New candidate genes and the application in breeding are discussed.
The inhibitory activity of glycine transporter 2 targeting bioactive lipid analgesics are influenced by formation of a deep lipid cavity
Authors: Wilson Katie A. , Mostyn Shannon N. , Frangos Zachary J. , Shimmon Susan , Rawling Tristan , Vandenberg Robert J. , O’Mara Megan L.
Published: September 2020

The human glycine transporter 2 (GlyT2 or SLC6A5) has emerged as a promising drug target for the development of new analgesics to manage chronic pain. N-acyl amino acids inhibit GlyT2 through binding to an allosteric binding site to produce analgesia in vivo with minimal overt side effects. In this paper we use a combination of medicinal chemistry, electrophysiology, and computational modelling to explore the molecular basis of GlyT2 inhibition at the allosteric site. We show how N-acyl amino acid head group stereochemistry, tail length and double bond position promote enhanced inhibition by deep penetration into the binding pocket. This work provides new insights into the interaction of lipids with transport proteins and will aid in future rational design of novel GlyT2 inhibitors.
Wheat developmental traits as affected by the interaction betweenEps-7Dand temperature under contrasting photoperiods with insensitivePpd-D1background
Authors: Basavaraddi Priyanka A. , Savin Roxana , Griffiths Simon , Slafer Gustavo A.
Published: September 2020

Earlinessper se(Eps) genes are important to fine tune adaptation, and studying their probable pleiotropic effect on wheat yield traits is worthwhile. In addition, it has been shown that some Eps genes interact with temperature. We studied two NILs differing in the newly identifiedEps-7Dbut carrying insensitivePpd-D1 in the background under three temperature regimes (9, 15 and 18 °C) and two photoperiods (12 h and 24 h).Eps-7Daffected time to anthesis as expected and theEps-7D-lateallele extended both the period before and after terminal spikelet. The interaction effect ofEps-7D× temperature was significant but not cross-over: the magnitude and level of significance of the difference between NILs with thelateorearlyallele was affected by the growing temperature (i.e. difference was least at 18 °C and largest at 9 °C), and differences in temperature sensitivity was influenced by photoperiod. Rate of leaf initiation was faster in NIL withEps-7D-earlythan with thelateallele which compensated for the shorter duration of leaf initiation resulting in similar final leaf number between two NILs.Eps-7D-late consistently increased spike fertility through improving floret primordia survival as a consequence of extending the late reproductive phase.
Decreased calmodulin recruitment triggers PMCA4 dysfunction and pancreatic injury in cystic fibrosis
Authors: Madácsy Tamara , Varga Árpad , Papp Noémi , Deák Barnabás , Tél Bálint , Pallagi Petra , Szabó Viktória , Fanczal Júlia , Rakonczay Zoltan , Rázga Zsolt , Hohwieler Meike , Kleger Alexander , Gray Mike , Hegyi Péter , Maléth József
Published: September 2020

Exocrine pancreatic damage is a common complication of cystic fibrosis (CF), which can significantly debilitate the quality of life and life expectancy of CF patients. The cystic fibrosis transmembrane conductance regulator (CFTR) has a major role in pancreatic ductal ion secretion, however, it presumably has an influence on intracellular signaling as well. Here we describe in multiple model systems, including iPSC-derived human pancreatic organoids from CF patients, that the activity of PMCA4 is impaired by the decreased expression of CFTR in ductal cells. The regulation of PMCA4, which colocalizes and physically interacts with CFTR on the apical membrane of the ductal cells, is dependent on the calmodulin binding ability of CFTR. Moreover, CFTR seems to be involved in the process of the apical recruitment of calmodulin, which enhances its role in calcium signaling and homeostasis. Sustained intracellular Ca2+ elevation in CFTR KO cells undermined the mitochondrial function and increased apoptosis. Based on these, the prevention of sustained intracellular Ca2+ overload may improve the exocrine pancreatic function and may have a potential therapeutic aspect in CF.
Neural representations of task context and temporal order during action sequence execution
Authors: Shahnazian Danesh , Senoussi Mehdi , Krebs Ruth M. , Verguts Tom , Holroyd Clay B.
Published: September 2020

Since routine action sequences can share a great deal of similarity in terms of their stimulus response mappings, their correct execution relies crucially on the ability to preserve contextual and temporal information (Lashley, 1951). However, there are few empirical studies on the neural mechanism and the brain areas maintaining such information. To address this gap in the literature, we recently recorded the blood-oxygen level dependent (BOLD) response in a newly developed coffee-tea making task (Holroyd et al., 2018). The task involves the execution of 4 action sequences that each feature 6 decision states. Here we report a reanalysis of this dataset using a data-driven approach, namely multivariate pattern analysis (MVPA), that examines context-dependent neural activity across several predefined regions of interest. Results highlight involvement of the inferior-temporal gyrus and lateral prefrontal cortex in maintaining temporal and contextual information for the execution of hierarchically-organized action sequences. Furthermore, temporal information seems to be more strongly encoded in areas over the left hemisphere.
CycleFlow quantifies cell-cycle heterogeneityin vivo
Authors: Jolly Adrien , Fanti Ann-Kathrin , Gräßer Ines , Becker Nils B. , Höfer Thomas
Published: September 2020

While the average cell-cycle length in a cell population can be derived from pulse-chase experiments, proliferative heterogeneity has been difficult to quantify. Here we describe CycleFlow, a broadly applicable method that applies Bayesian inference to combined measurements of EdU incorporation and DNA content. CycleFlowaccurately quantifies the fraction of proliferating versus quiescent cells and the durations of cell-cycle phases of the proliferating cellsin vitroandin vivo.