bluuebunny/crossref_metadata_2025_split huggingface dataset:
Splicing-related Retinitis Pigmentosa mutations mimicked in C. elegans allow the identification of disease modifiers and drug screens
Authors: Kukhtar Dmytro , Rubio-Peña Karinna , Serrat Xènia , Cerón Julián 
Published: August 2019

ABSTRACTCRISPR and the high conservation of the spliceosome components facilitate the mimicking of human pathological mutations in splicing factors of model organisms. The degenerative retinal disease Retinitis Pigmentosa (RP) is caused by mutations in distinct types of genes, including missense mutations in splicing factors that provoke RP in an autosomal dominant form (s-adRP). Using CRISPR in C. elegans, we generated mutant strains to mimic RP mutations reported in PRPF8 and SNRNP200. Whereas these inherited mutations are present in heterozygosis in patients, C. elegans allows the maintenance of these mutations in homozygosis, which is advantageous for genetic and drug screens. We found that snrp-200(cer23[V676L]) and prp-8(cer14[H2302del]) display pleiotropic phenotypes, including a reduced fertility. However, snrp-200(cer24[S1080L]) and prp-8(cer22[R2303G]) are weak alleles suitable for RNAi screens to identify genetic interactions, which would uncover potential disease modifiers. We screened a collection of RNAi clones for splicing-related genes and identified three splicing factors, isy-1/ISY1, cyn-15/PPWD1 and mog-2/SNRPA1 whose partial inactivation may modify the course of the disease. Interestingly, these three genes were acting as modifiers of prp-8(cer22) but no snrp-200(cer24).Finally, the strong allele prp-8(cer14) was used in a screen with FDA-approved drugs to find molecules capable of alleviating the phenotype. Instead, we detected drugs, as Dequalinium Chloride, which exacerbated the phenotype and therefore are potentially harmful for s-adRP patients since they may accelerate the progression of the disease.
High-resolution 3D imaging and topological mapping of the lymph node conduit system
Authors: Kelch Inken D. , Bogle Gib , Sands Gregory B. , Phillips Anthony R. J. , LeGrice Ian J. , Dunbar P. Rod 
Published: August 2019

AbstractThe conduit network is a hallmark of lymph node microanatomy, but lack of suitable imaging technology has prevented comprehensive investigation of its topology. We employed an extended-volume imaging system to capture the conduit network of an entire murine lymph node (≈280,000 segments). The extensive 3D images provide a comprehensive overview of the regions supplied by conduits including perivascular sleeves, and distinctive “follicular reservoirs” within B cell follicles, surrounding follicular dendritic cells. A 3D topology map of conduits within the T cell zone showed homogeneous branching, but conduit density was significantly higher in the superficial T cell zone compared to the deep zone, where distances between segments are sufficient for T cells to lose contact with fibroblastic reticular cells. This topological mapping of the conduit anatomy can now aid modeling of its roles in lymph node function, as we demonstrate by simulating T cell motility in the different T cell zones.
NRL- and CRX-guided gene network modulates photoreceptor presynapse size and positioning during retinal development
Authors: Whitaker D. Thad , Mondal Anupam K. , Fann Hannah , Hargrove Passley , Brooks Matthew J. , Chaitankar Vijender , Yu Wenhan , Wu Zhijian , Kim Soo-Young , Swaroop Anand 
Published: August 2019

AbstractUnique morphologies of rod and cone photoreceptor presynaptic terminals permit the formation of synapses onto interneurons during retina development. We integrated multiple “omics” datasets of developing rod and S-cone-like photoreceptors and identified 719 genes that are regulated by NRL and CRX, critical transcriptional regulators of rod differentiation, as candidates for controlling presynapse morphology. In vivo knockdown of 72 candidate genes in the developing retina uncovered 26 genes that alter size and/or positioning of rod spherules in the outer plexiform layer. Co-expression of seven cDNAs with their cognate shRNAs rescued the rod presynapse phenotype. Loss of function of four genes in germline or by an AAV-mediated CRISPR/Cas9 strategy validated RNAi screen findings. A protein interaction network analysis of the 26 positive effectors revealed additional candidates in the NRL/CRX-regulated presynapse morphology-associated gene network. Follow-up knockdowns of two novel candidates support the proposed network. Our studies demonstrate a requirement of multiple components in a modular network for rod presynapse morphogenesis and provide a functional genomic framework for deciphering genetic determinants of morphological specification during development.Author SummaryThe relationship between neuronal morphology and function has been recognized for over 100 years. However, we still have poor understanding of genes and proteins that control morphogenesis of a specific neuron. In the current study, we address this connection between gene expression and neural morphology by identifying and knocking down a subset of expressed genes in rod photoreceptors. We ascertained a number of candidate genes controlling photoreceptor pre-synaptic terminal morphology, which is necessary for its connection with second-order neurons in the retinal circuit. Furthermore, we have curated a more plausible network of genes, either identified in our study or predicted, that are enriched for processes underlying photoreceptor morphogenesis. We suggest that our work will provide a framework for dissecting genetic basis of neuronal architecture and assist in better design of cell replacement therapies for retinal degeneration.
Single cell transcriptome analysis reveals an essential role for Gata2b in hematopoietic lineage decisions in zebrafish
Authors: Gioacchino Emanuele , Koyunlar Cansu , de Looper Hans , de Jong Madelon , Dobrzycki Tomasz , Hoogenboezem Remco , Peulen Joke , Bosch Dennis , van Strien Paulette , van Royen Martin E , French Pim J , Bindels Eric , Monteiro Rui , Gussinklo Kirsten J , Touw Ivo P , de Pater Emma 
Published: September 2019

AbstractHematopoietic stem cells (HSCs) are tightly controlled to keep a balance between myeloid and lymphoid cell differentiation. Gata2 is a pivotal hematopoietic transcription factor required for HSC generation and maintenance. We generated a zebrafish mutant for the mammalianGata2orthologue,gata2b. We found that in adult zebrafish,gata2bis required for both neutrophilic- and monocytic lineage differentiation. Single cell transcriptome analysis revealed that the myeloid defect present in Gata2b deficient zebrafish arise in the most immature hematopoietic stem and progenitor cell (HSPC) compartment and that this population is instead committed towards the lymphoid and erythroid lineage. Taken together, we find that Gata2b is vital for the fate choice between the myeloid and lymphoid lineages.
Expression of heat shock protein 70 is insufficient to extendDrosophila melanogasterlongevity
Authors: Xiao Chengfeng , Hull Danna , Qiu Shuang , Yeung Joanna , Zheng Jie , Barwell Taylor , Robertson R Meldrum , Seroude Laurent 
Published: August 2019

AbstractIt has been known for over 20 years thatDrosophila melanogasterflies with twelve additional copies of thehsp70gene encoding the 70 kDa heat shock protein lives longer after a non-lethal heat treatment. Since the heat treatment also induces the expression of additional heat shock proteins, the biological effect can be due either to HSP70 acting alone or in combination. This study used the UAS/GAL4 system to determine whetherhsp70is sufficient to affect the longevity and the resistance to thermal, oxidative or desiccation stresses of the whole organism. We observed that HSP70 expression in the nervous system or muscles has no effect on longevity or stress resistance but ubiquitous expression reduces the life span of males. We also observed that the down-regulation ofHsp70using RNAi did not affect longevity.
Robustness and applicability of functional genomics tools on scRNA-seq data
Authors: Holland Christian H. , Tanevski Jovan , Gleixner Jan , Kumar Manu P. , Mereu Elisabetta , Perales-Patón Javier , Joughin Brian A. , Stegle Oliver , Lauffenburger Douglas A. , Heyn Holger , Szalai Bence , Saez-Rodriguez Julio 
Published: September 2019

AbstractMany tools have been developed to extract functional and mechanistic insight from bulk transcriptome profiling data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible to do such an analysis for single cells. However, scRNA-seq data has characteristics such as drop-out events, low library sizes and a comparatively large number of samples/cells. It is thus not clear if functional genomics tools established for bulk sequencing can be applied to scRNA-seq in a meaningful way. To address this question, we performed benchmark studies on in silico and in vitro single-cell RNA-seq data. We included the bulk-RNA tools PROGENy, GO enrichment and DoRothEA that estimate pathway and transcription factor (TF) activities, respectively, and compared them against the tools AUCell and metaVIPER, designed for scRNA-seq. For the in silico study we simulated single cells from TF/pathway perturbation bulk RNA-seq experiments. Our simulation strategy guarantees that the information of the original perturbation is preserved while resembling the characteristics of scRNA-seq data. We complemented the in silico data with in vitro scRNA-seq data upon CRISPR-mediated knock-out. Our benchmarks on both the simulated and real data revealed comparable performance to the original bulk data. Additionally, we showed that the TF and pathway activities preserve cell-type specific variability by analysing a mixture sample sequenced with 13 scRNA-seq different protocols. Our analyses suggest that bulk functional genomics tools can be applied to scRNA-seq data, outperforming dedicated single cell tools. Furthermore we provide a benchmark for further methods development by the community.
The Imposition of Value on Odor: Transient and Persistent Representations of Odor Value in Prefrontal Cortex
Authors: Wang Peter Y. , Boboila Cristian , Shamash Philip , Wu Zheng , Stein Nicole P , Abbott L.F. , Axel Richard 
Published: August 2019

SUMMARYThe representation of odor in olfactory cortex (piriform) is distributive and unstructured and can only be afforded behavioral significance upon learning. We performed 2-photon imaging to examine the representation of odors in piriform and in two downstream stations, the orbitofrontal cortex (OFC) and medial prefrontal cortex (mPFC), as mice learned olfactory associations. In piriform we observed minor changes in neural activity unrelated to learning. In OFC, 30% of the neurons acquired robust responses to conditioned stimuli (CS+) after learning, and these responses were gated by context and internal state. The representation in OFC, however, diminished after learning and persistent representations of CS+ and CS− odors emerged in mPFC. Optogenetic silencing indicates that these two brain structures function sequentially to consolidate the learning of appetitive associations. These data demonstrate the transformation of a representation of odor identity in piriform into transient and persistent representations of value in the prefrontal cortex.
The Developmental Transcriptome ofAe. albopictus,a Major Worldwide Human Disease Vector
Authors: Gamez Stephanie , Antoshechkin Igor , Mendez-Sanchez Stelia C. , Akbari Omar S. 
Published: September 2019

AbstractAedes albopictusmosquitoes are important vectors for a number of human pathogens including the Zika, dengue, and chikungunya viruses. Capable of displacingAedes aegyptipopulations, it adapts to cooler environments which increases its geographical range and transmission potential. There are limited control strategies forAedes albopictusmosquitoes which is likely attributed to the lack of comprehensive biological studies on this emerging vector. To fill this void, here using RNAseq we characterizedAedes albopictusmRNA expression profiles at 47 distinct time points throughout development providing the first high-resolution comprehensive view of the developmental transcriptome of this worldwide human disease vector. This enabled us to identify several patterns of shared gene expression among tissues as well as sex-specific expression patterns. Moreover, to illuminate the similarities and differences betweenAedes aegypti, a related human disease vector, we performed a comparative analysis using the two developmental transcriptomes. We identify life stages were the two species exhibited significant differential expression among orthologs. These findings provide insights into the similarities and differences betweenAedes albopictusandAedes aegyptimosquito biology. In summary, the results generated from this study should form the basis for future investigations on the biology ofAedes albopictusmosquitoes and provide a goldmine resource for the development of transgene-based vector control strategies.
Methods for broad-scale plant phenology assessments using citizen scientists’ photographs
Authors: Barve Vijay V. , Brenskelle Laura , Li Daijiang , Stucky Brian J. , Barve Narayani V. , Hantak Maggie M. , McLean Bryan S. , Paluh Daniel J. , Oswald Jessica A. , Belitz Michael , Folk Ryan , Guralnick Robert 
Published: September 2019

AbstractBroad-scale plant flowering phenology data has predominantly come from geographically and taxonomically restricted monitoring networks. However, platforms such as iNaturalist, where citizen scientists upload photographs and curate identifications, provide a promising new source of data. Here we develop a general set of best practices for scoring iNaturalist digital records supporting downstream re-use in phenology studies. We focus on a case study group, Yucca, because it has showy flowers and is well documented on iNaturalist. Additionally, drivers of Yucca phenology are not well-understood despite need for Yucca to synchronize flowering with obligate moth pollinators. Finally, evidence of anomalous flowering events have been recently reported, but the extent of those events is unknown. We use best-practices approach to annotate nearly 9,000 Yucca iNaturalist records, and compare the spatiotemporal coverage of this dataset with other broad-scale monitoring resources. Our findings demonstrate that iNaturalist provides unique phenology information, including delineation of extents of unusual flowering events. We also determine if unusual early flowering events impact later, typical flowering periods. Finally, we adapt a plant phenology global knowledge-store to integrate iNaturalist annotation results, supporting broadest reuse. Our approach has application to other plant groups, leveraging rapidly increasing data resources from iNaturalist to study phenology.
Identification of the main glutamine and glutamate transporters inStaphylococcus aureusand their impact on c-di-AMP production
Authors: Zeden Merve S. , Kviatkovski Igor , Schuster Christopher F. , Thomas Vinai C. , Fey Paul D. , Gründling Angelika 
Published: September 2019

SummaryAStaphylococcus aureusstrain deleted for the c-di-AMP cyclase genedacAis unable to survive in rich medium unless it acquires compensatory mutations. Previously identified mutations were inopuD, encoding the main glycine-betaine transporter, andalsT, encoding a predicted amino acid transporter. Here, we show that inactivation of OpuD restores the cell size of adacAmutant to near wild-type size, while inactivation of AlsT does not, suggesting two different mechanisms for the growth rescue. AlsT was identified as an efficient glutamine transporter, indicating that preventing glutamine uptake in rich medium rescues the growth of theS. aureus dacAmutant. In addition, GltS was identified as a glutamine transporter. By performing growth curves with WT,alsTandgltSmutant strains in defined medium supplemented with ammonium, glutamine or glutamate, we revealed that ammonium and glutamine, but not glutamate promote the growth ofS. aureus. This suggests that besides ammonium also glutamine can serve as a nitrogen source under these conditions. Ammonium and uptake of glutamine via AlsT inhibited c-di-AMP production, while glutamate uptake had no effect. These findings provide, besides the previously reported link between potassium and osmolyte uptake, a connection between nitrogen metabolism and c-di-AMP signalling inS. aureus.Graphical abstract
Cdc42 promotes Bgs1 recruitment for septum synthesis and glucanase localization for cell separation during cytokinesis in fission yeast
Authors: Onwubiko Udo N. , Robinson Julie , Mustaf Rose Albu , Das Maitreyi E. 
Published: September 2019

AbstractCytokinesis in fission yeast involves actomyosin ring constriction concurrent to septum synthesis followed by septum digestion resulting in cell separation. A recent report indicates that endocytosis is required for septum synthesis and cell separation. The conserved GTPase Cdc42 is required for membrane trafficking and promotes endocytosis. Cdc42 is activated by Guanine nucleotide exchange factors (GEFs). Cdc42 GEFs have been shown to promote timely initiation of septum synthesis and proper septum morphology. Here we show that Cdc42 promotes the recruitment of the major primary septum synthesizing enzyme Bgs1 and consequent ring constriction. Cdc42 is also required for proper localization of the septum digesting glucanases at the division site. Thus, Cdc42 is required to promote multiple steps during cytokinesis.
A G1 sizer mechanism coordinates growth and division in the mouse epidermis
Authors: Xie Shicong , Skotheim Jan M. 
Published: September 2019

SummaryCell size homeostasis is often achieved by coupling cell cycle progression to cell growth. Studies of cell size homeostasis in single-celled bacteria and yeast have observed several distinct phenomena. Growth can be coupled to division through a range of mechanisms, including a ‘sizer’, wherein cells of varying birth size divide at similar final sizes [1–3], and an ‘adder’, wherein cells increase in size a fixed amount per cell cycle [4–6]. Importantly, intermediate control mechanisms are observed, and even the same organism can exhibit distinct control phenomena depending on growth conditions [2,7,8]. While studying unicellular organisms in laboratory conditions may give insight into their growth control in the wild, this is less apparent for studies of mammalian cells growing outside the organism. Sizer, adder, and intermediate mechanisms have been observedin vitro[9–12], but it is unclear how these diverse size homeostasis phenomena relate to mammalian cell proliferationin vivo. To address this gap, we analyzed time-lapse images of the mouse epidermis taken over one week during normal tissue turnover [13]. We quantified the 3D volume growth and cell cycle progression of single cells within the mouse skin. In dividing epidermal stem cells, we found that cell growth is coupled to division through a sizer mechanism operating largely in the G1 phase. Thus, while the majority of tissue culture studies to-date identified adder mechanisms, our analysis demonstrates that sizer mechanisms are importantin vivoand highlights the need to determine their underlying molecular origin.
AKT but not MYC promotes reactive oxygen species-mediated cell death in oxidative culture
Authors: Zheng Dongqing , Sussman Jonathan H. , Jeon Matthew P. , Parrish Sydney T. , Delfarah Alireza , Graham Nicholas A. 
Published: September 2019

ABSTRACTOncogenes can generate metabolic vulnerabilities in cancer cells. Here, we tested how AKT and MYC affect the ability of cells to shift between respiration and glycolysis. Using immortalized mammary epithelial cells, we discovered that constitutively active AKT but not MYC induced cell death in galactose culture, where cells must rely on oxidative phosphorylation for energy generation. However, the negative effects of AKT were short-lived, and AKT-expressing cells recommenced growth after ~15 days in galactose. To identify the mechanisms regulating AKT-mediated cell death, we used metabolomics and found that AKT cells dying in galactose upregulated glutathione metabolism. Next, using proteomics, we discovered that AKT-expressing cells dying in galactose upregulated nonsense-mediated mRNA decay, a marker of sensitivity to oxidative stress. We therefore measured levels of reactive oxygen species (ROS) and discovered that galactose induced ROS in cells expressing AKT but not MYC. Additionally, ROS were required for the galactose-induced death of AKT-expressing cells. We then tested whether these findings could be replicated in breast cancer cell lines with constitutively active AKT signaling. Indeed, we found that galactose induced rapid cell death in breast cancer cell lines and that ROS were required for galactose-induced cell death. Together, our results demonstrate that AKT but not MYC induces a metabolic vulnerability in cancer cells, namely the restricted flexibility to use oxidative phosphorylation.ImplicationsThe discovery that AKT but not MYC restricts the ability to utilize oxidative phosphorylation highlights that therapeutics targeting tumor metabolism must be tailored to the individual genetic profile of tumors.
Sympatric wren-warblers partition acoustic signal space and song perch height
Authors: Chitnis Shivam S. , Rajan Samyuktha , Krishnan Anand 
Published: September 2019

AbstractBy evolving divergent acoustic signals, sympatric assemblages of animals may minimize potentially costly masking interference. Acoustic signal space may be multidimensional, with coexisting species also vocalizing from different regions of physical space. Here, we demonstrate acoustic signal space partitioning in four sympatric species of wren-warbler (Cisticolidae, Prinia), in an Indian dry deciduous scrub habitat. We find that the breeding songs of wren-warblers are divergent from each other in multivariate parameter space, with only minimal interspecific overlap. Partitioning of signal space exerts constraints on the intraspecific diversity of acoustic signals, and each species exhibits different strategies to overcome these constraints. Two species partition intraspecific signal space into multiple note types, whereas a third exhibits intraspecific variation in repetition rate, thus supporting song diversity within a constrained acoustic space. Finally, we find that the four species also partition song perch heights, thus exhibiting separation along multiple axes of acoustic signal space. We hypothesize that divergent song perch heights may be driven by competition for higher singing perches or other ecological factors rather than signal propagation. Acoustic signal partitioning along multiple axes may therefore, we propose, arise from a combination of diverse ecological processes.