bluuebunny/crossref_metadata_2025_split huggingface dataset:
Composition dependent phase separation underlies directional flux through the nucleolus
Authors: Riback Joshua A. , Zhu Lian , Ferrolino Mylene C. , Tolbert Michele , Mitrea Diana M. , Sanders David W. , Wei Ming-Tzo , Kriwacki Richard W. , Brangwynne Clifford P. 
Published: October 2019

AbstractIntracellular bodies such as nucleoli, Cajal bodies, and various signaling assemblies, represent membraneless organelles, or condensates, that form via liquid-liquid phase separation (LLPS)1,2. Biomolecular interactions, particularly homotypic interactions mediated by self-associating intrinsically disordered protein regions (IDRs), are thought to underlie the thermodynamic driving forces for LLPS, forming condensates that can facilitate the assembly and processing of biochemically active complexes, such as ribosomal subunits within the nucleolus. Simplified model systems3–6have led to the concept that a single fixed saturation concentration (Csat) is a defining feature of endogenous LLPS7–9, and has been suggested as a mechanism for intracellular concentration buffering2,7,8,10. However, the assumption of a fixed Csatremains largely untested within living cells, where the richly multicomponent nature of condensates could complicate this simple picture. Here we show that heterotypic multicomponent interactions dominate endogenous LLPS, and give rise to nucleoli and other condensates that do not exhibit a fixed Csat. As the concentration of individual components is varied, their partition coefficients change, in a manner that can be used to extract thermodynamic interaction energies, that we interpret within a framework we term polyphasic interaction thermodynamic analysis (PITA). We find that heterotypic interactions between protein and RNA components stabilize a variety of archetypal intracellular condensates, including the nucleolus, Cajal bodies, stress granules, and P bodies. These findings imply that the composition of condensates is finely tuned by the thermodynamics of the underlying biomolecular interaction network. In the context of RNA processing condensates such as the nucleolus, this stoichiometric self-tuning manifests in selective exclusion of fully-assembled RNP complexes, providing a thermodynamic basis for vectorial ribosomal RNA (rRNA) flux out of the nucleolus. The PITA methodology is conceptually straightforward and readily implemented, and it can be broadly utilized to extract thermodynamic parameters from microscopy images. These approaches pave the way for a deep understanding of the thermodynamics of multi-component intracellular phase behavior and its interplay with nonequilibrium activity characteristic of endogenous condensates.
Insights into the desert living skin microbiome: geography, soil depth, and crust type affect biocrust microbial communities and networks in Mojave Desert, USA
Authors: Pombubpa Nuttapon , Pietrasiak Nicole , De Ley Paul , Stajich Jason E 
Published: October 2019

AbstractBiocrusts are the living skin of drylands, comprising diverse microbial communities that are essential to desert ecosystems. Although we have extensive knowledge on biocrust ecosystem function and what drives biodiversity in lichen and moss dominated biocrusts, much less is understood about the impacts of diversity among microbial communities. Moreover, most biocrust microbial composition studies have primarily focused on bacteria. We used amplicon-based metabarcode sequencing to explore composition of both fungal and bacterial communities in biocrusts. Specifically we tested how geography, soil depth, and crust type structured biocrust microbial communities or fungal-bacterial networks. Microbial communities were surveyed from biocrust surface and subsurface soils collected from Joshua Tree National Park, Granite Mountain, Kelso Dunes, and Cima volcanic flows located within the Mojave Desert, USA. Five biocrust types were examined: Light-algal, Cyano-lichen, Green-algal lichen, Smooth moss, and Rough moss crust types. We found the primary characteristics structuring biocrust microbial diversity were 1) geography, as central and southern Mojave sites displayed different community signatures, 2) presence of plant associated fungi (plant pathogens and wood saprotrophs), indicator, and endemic species were identified at each site, 3) soil depth patterns, as surface and subsurface microbial communities were distinctly structured, and 4) the crust type, which predicted distinct microbial compositions. Network analysis showed that Cyanobacteria and Dothideomycetes (Pleosporales) were the major hubs of overall biocrust microbial community. Such hierarchical spatial organization of biocrust communities and their associated biotic networks can have pronounced impacts to ecosystem functions. Our findings provide crucial insights for dryland restoration and sustainable management.
Inhibition of Sting rescues lupus disease by the regulation of Lyn-mediated dendritic cell differentiation
Authors: Thim-uam Arthid , Prabakaran Thaneas , Tansakul Mookmanee , Makjaroen Jiradej , Wongkongkathep Piriya , Chantaravisoot Naphat , Saethang Thammakorn , Leelahavanichkul Asada , Benjachat Thitima , Paludan Søren , Pisitkun Trairak , Pisitkun Prapaporn 
Published: October 2019

AbstractSLE (systemic lupus erythematosus) is an autoimmune disease that causes chronic inflammation and leads to fatality if left untreated. Immune complex-mediated inflammation and type I IFN signaling pathways are one of the mechanisms initiating lupus disease. Signaling through stimulator of interferon genes (STING) leads to the production of type I IFN and inflammatory cytokines. However, the role of STING in lupus mouse models is controversy. Here we demonstrated the mechanisms of STING involving in SLE pathogenesis at the molecular level. The disruption of STING signaling rescued lupus disease inFcgr2b-deficient mice. STING activated DC facilitated T cell proliferation, which depended on intrinsic expression of STING on DC but not on T cells. Upon STING activation, LYN was recruited and co-localized with STING in bone marrow-derived dendritic cells (BMDC). STING signaling induced phosphorylated LYN and AKT. The inhibition of LYN prohibited STING-induced DC differentiation. Adoptive transfer of STING-activated BMDC into the FCGR2B and STING double-deficiency mice restored lupus phenotypes. These findings provide the proof of concept that inhibition of STING signaling is a promising therapeutic approach for SLE patients.
The brain of a nocturnal migratory insect, the Australian Bogong moth
Authors: Adden Andrea , Wibrand Sara , Pfeiffer Keram , Warrant Eric , Heinze Stanley 
Published: October 2019

AbstractEvery year, millions of Australian Bogong moths (Agrotis infusa) complete an astonishing journey: in spring, they migrate over 1000 km from their breeding grounds to the alpine regions of the Snowy Mountains, where they endure the hot summer in the cool climate of alpine caves. In autumn, the moths return to their breeding grounds, where they mate, lay eggs and die. These moths can use visual cues in combination with the geomagnetic field to guide their flight, but how these cues are processed and integrated in the brain to drive migratory behavior is unknown. To generate an access point for functional studies, we provide a detailed description of the Bogong moth’s brain. Based on immunohistochemical stainings against synapsin and serotonin (5HT), we describe the overall layout as well as the fine structure of all major neuropils, including the regions that have previously been implicated in compass-based navigation. The resulting average brain atlas consists of 3D reconstructions of 25 separate neuropils, comprising the most detailed account of a moth brain to date. Our results show that the Bogong moth brain follows the typical lepidopteran ground pattern, with no major specializations that can be attributed to their spectacular migratory lifestyle. These findings suggest that migratory behavior does not require widespread modifications of brain structure, but might be achievable via small adjustments of neural circuitry in key brain areas. Locating these subtle changes will be a challenging task for the future, for which our study provides an essential anatomical framework.
High-throughput, temporal and dose dependent, effect of vitamins and minerals on chondrogenesis
Authors: Dennis James E. , Splawn Taylor , Kean Thomas J. 
Published: October 2019

AbstractTissue engineered hyaline cartilage is plagued by poor mechanical properties largely due to inadequate type II collagen expression. Of note, commonly used defined chondrogenic media lack 14 vitamins and minerals, some of which are implicated in chondrogenesis. Type II collagen promoter-drivenGaussialuciferase was transfected into ATDC5 cells to create a chondrogenic cell with a secreted-reporter. The reporter cells were used in an aggregate-based chondrogenic culture model to develop a high-throughput analytic platform. This high-throughput platform was used to assess the effect of vitamins and minerals, alone and in combination with TGFβ1, on type II collagen expression. Significant combinatorial effects between vitamins, minerals and TGFβ1 in terms of type II collagen expression and metabolism were discovered. An ‘optimal’ continual supplement of copper and vitamin K in the presence of TGFβ1 gave a 2.5-fold increase in collagen expression over TGFβ1 supplemented media alone.SummaryCurrent defined chondrogenic culture media lack several vitamins and minerals. Type II collagen is the quintessential marker of articular hyaline cartilage, and is commonly deficient in engineered tissue. A type II collagen promoter driven secreted luciferase construct has been transduced into ATDC5 cells and used to assess vitamin and mineral effects on chondrogenesis in a high-throughput format.
Network analyses implicate a role for PHYTOCHROME-mediated light signaling in the regulation of cuticle development in plant leaves
Authors: Qiao Pengfei , Bourgault Richard , Mohammadi Marc , Smith Laurie G. , Gore Michael A. , Molina Isabel , Scanlon Michael J. 
Published: October 2019

AbstractPlant cuticles are composed of wax and cutin, and evolved in the land plants as a hydrophobic boundary that reduces water loss from the plant epidermis. The expanding maize adult leaf displays a dynamic, proximodistal gradient of cuticle development, from the leaf base to the tip. Laser microdissection RNA Sequencing (LM-RNAseq) was performed along this proximodistal gradient, and complementary network analyses identified potential regulators of cuticle biosynthesis and deposition. Correlations between cuticle development and cell wall biosynthesis processes were identified, as well as evidence of roles for auxin and brassinosteroids. In addition, our network analyses suggested a previously undescribed function for PHYTOCHROME-mediated light signaling during cuticular wax deposition. Genetic analyses reveal that the phyB1 phyB2 double mutant of maize exhibits abnormal cuticle composition, supporting predictions of our coexpression analyses. Reverse genetic analyses also show that phy mutants of the moss Physcomitrella patens exhibit abnormal cuticle composition, suggesting a role for light-stimulated development of cuticular waxes during plant evolution.
Nuclear organisation and replication timing are coupled through RIF1-PP1 interaction
Authors: Gnan Stefano , Flyamer Ilya M. , Klein Kyle N. , Castelli Eleonora , Rapp Alexander , Maiser Andreas , Chen Naiming , Weber Patrick , Enervald Elin , Cardoso M. Cristina , Bickmore Wendy A. , Gilbert David M. , Buonomo Sara C. B. 
Published: October 2019

AbstractThree-dimensional genome organisation and replication timing are known to be correlated, however, it remains unknown whether nuclear architecture overall plays an instructive role in the replication-timing program and, if so, how. Here we demonstrate that RIF1 is a molecular hub that co-regulates both processes. Both nuclear organisation and replication timing depend upon the interaction between RIF1 and PP1. However, whereas nuclear architecture requires the full complement of RIF1 and its interaction with PP1, replication timing is not sensitive to RIF1 dosage. RIF1’s role in replication timing also extends beyond its interaction with PP1. Availing of this separation-of-function approach, we have therefore identified in RIF1 dual function the molecular bases of the co-dependency of the replication-timing program and nuclear architecture.
A novel method to detect intracellular metabolite alterations in MCF-7 cells by doxorubicin induced cell death
Authors: Kumar Ajay , Patel Sheetal , Bhatkar Devyani , Sharma Nilesh Kumar 
Published: October 2019

ABSTRACTMetabolic reprogramming within cancer cells is suggested as a potential barrier to chemotherapy. Additionally, metabolic tumor heterogeneity is one of factor behind discernible hallmarks such as drug resistance, relapse of tumor and the formation of secondary tumors. In this paper, cell based assays including PI/annexin V staining and immunoblot assay were performed to show the apoptotic cell death in MCF-7 cells treated with DOX. Further, MCF-7 cells were lysed in hypotonic buffer and whole cell lysate was purified by a novel and specifically designed metabolite (100 to 1000 Da) fractionation system as vertical tube gel electrophoresis (VTGE). Further, purified intracellular metabolites were subjected to identification by LC-HRMS technique. The authors show the presence of cleaved PARP 1 in MCF-7 cells treated with DOX. Concomitantly, data show the absence of active caspase 3 in MCF-7 cells. Novel findings are to identify key intracellular metabolites assisted by VTGE system that include lipid (CDP-DG, phytosphingosine, dodecanamide), non-lipid (N-acetyl-D-glucosamine, N1-acetylspermidine and gamma-L-glutamyl-L-cysteine) and tripeptide metabolites in MCF-7 cells treated by DOX. Interestingly, the authors report a first evidence of doxorubicinone, an aglycone form of DOX in MCF-7 cells that is potentially linked to the mechanism of cell death in MCF-7 cells. This paper reports on novel methods and processes that involve VTGE system based purification of hypotonically lysed novel intracellular metabolites of MCF-7 cells treated by DOX. Here, these identified intracellular metabolites corroborate to caspase 3 independent and mitochondria induced apoptotic cell death in MCF-7 cells.SIGNIFICANCE STATEMENTMetabolic reprogramming in cancer cells is implicated in various tumor hallmarks. Interestingly, thousands of research have addressed the molecular basis of drug treatment and resistance in chemotherapy. But, there is a significant gap in the precise methodologies and approaches in addressing intracellular metabolite alterations. This paper reports on a novel approach that helped reveal new findings on intracellular metabolite changes in case of doxorubicin (DOX) induced cell death in MCF-7 cells. This paper highlights the additional insights on debatable findings available in literature in the contexts of DOX induced cell death mechanisms. In this paper, novel and specifically designed vertical tube gel electrophoresis (VTGE) system is claimed to purify intracellular metabolites and this method is compatible with other biological system.
Establishment of the trans-resveratrol-induced mouse pulmonary fibrosis model and its comparison with the bleomycin-induced model
Authors: Yiwen Chen , Chenzhong Zong , Chunrui Sheng , Hongsheng Chang , Shuyan Wang , Hongzhao Zhao , Shanshan Liu , qiaohui Zhang , Ruijuan Dong , Dongyu Ge , Xue Yu , Lina Li 
Published: October 2019

ABSTRACTPulmonary fibrosis (PF) is a progressive, fatal disease, and its pathogenic mechanism has not yet been identified. The bleomycin (BLM)-induced animal model has several shortcomings that cannot be overcome. We accidentally found that the continuous oral administration of trans-resveratrol (TR) at levels above the prescribed dose can induce PF within a certain period of time, and this model can be successfully replicated in mice, as indicated by the hydroxyproline (HYP) test and pathological analysis. The TR model requires no anesthesia or surgery and thus causes less damage to mice than the BLM model. The progress of fibrosis in the TR model was slow but progressed steadily compared with the BLM model, and the TR model was more comparable to human PF. Although the pathogenesis is not understood, the TR-induced PF model indicated that there may be a close relationship between PF and tumors and antitumor drugs, which requires further exploration.
A novel toolkit for the efficient delivery of Cas9/sgRNA complexes to chromosomes in cells
Authors: Indikova Ivana , Indik Stanislav 
Published: October 2019

Introductory paragraphThe application of gene editing technology is currently limited by the lack of safe and efficient methods to deliver RNA-guided endonucleases to target cells. We engineered lentivirus-based nanoparticles to copackage the U6-sgRNA template and the CRISPR-associated protein 9 (Cas9) fused with a virion-targeted protein Vpr (Vpr.Prot.Cas9), for simultaneous delivery to cells. In addition to Vpr, equal spatiotemporal control of thevpr.prot.cas9andgag/polgene expression of was required for efficient packaging of the fusion protein into virus particles. Transduction of the unconcentrated, Vpr.Prot.Cas9-containing vectors resulted in >98% disruption of theEGFPgene in reporter HEK293-EGFP cells with minimal cytotoxicity. Furthermore, we detected indels in the targeted endogenous loci at frequencies of up to 100% in cell lines derived from lymphocytes and monocytes and up to 15% in primary CD4+ T cells by high-throughput sequencing. This approach may provide a platform for the efficient, safe and selective delivery of genome editing enzymes to cells and it may be suitable for simultaneous gene disruption and transgene delivery.
Adaptation by copy number variation increases insecticide resistance in fall armyworms
Authors: Nam Kiwoong , Gimenez Sylvie , Hilliou Frederique , Blanco Carlos A. , Hänniger Sabine , Bretaudeau Anthony , Legeai Fabrice , Nègre Nicolas , d’Alençon Emmanuelle 
Published: October 2019

AbstractInsecticide resistance is a major main challenge in pest control, and understanding its genetic basis is a key topic in agricultural ecology. Detoxification genes are well-known genetic elements that play a key role in adaptation to xenobiotics. The adaptive evolution of detoxification genes by copy number variations has been interpreted as a cause of insecticide resistance. However, the same pattern can be generated by the adaptation to host-plant defense toxins as well. In this study, we tested in fall armyworms (Lepidoptera Spodoptera frugiperda) if adaptation by copy number variation is the cause of the increased level of insecticide resistance from two geographic populations with different levels of resistance and two strains with different host plants. Following the generation of an assembly with chromosome-sized scaffolds (N50 = 13.2Mb), we observed that these two populations show a significant allelic differentiation of copy number variations, which is not observed between strains. In particular, a locus with almost complete allelic differentiation (Fst > 0.8) includes a cluster of P450 genes, which are well-known key players in detoxification. Detoxification genes are overrepresented in the genes with copy number variations, and the observed copy number variation appears to have beneficial effects in general. From this result, we concluded that copy number variation of detoxification genes in fall armyworms plays a key role in the insecticide resistance but not in the adaptation to host-plants, suggesting that the evolution of insecticide resistance may occur independently from host-plant adaptation.
mTORC1-Plin3 pathway is essential to activate lipophagy and protects against hepatosteatosis
Authors: Garcia-Macia Marina , Santos-Ledo Adrián , Leslie Jack , Paish Hanna , Watson Abigail , Borthwick Lee , Mann Jelena , Oakley Fiona , Korolchuk Viktor I. , Mann Derek A. 
Published: October 2019

ABSTRACTDuring postprandial state, the liver is exposed to high levels of dietary fatty acids (FAs) and carbohydrates. FAs are re-esterified into triglycerides, which can be stored in lipid droplets (LDs) in the liver. Aberrant accumulation of LDs can lead to diseases such as alcoholic liver disease and non-alcoholic fatty liver disease, the latter being the most common liver pathology in western countries. Improved understanding of LD biology has potential to unlock new treatments for these liver diseases. The Perilipin (Plin) family is the group of proteins that coat LDs, controlling their biogenesis, stabilization, and preventing their degradation. Recent studies have revealed that autophagy is involved in LD degradation and, therefore, may be crucial to avoid lipid accumulation. Here, we show that a phosphorylated form of Plin3 is required for selective degradation of LDs in fibroblasts, primary hepatocytes and human liver slices. We demonstrate that oleic acid treatment induces the recruitment of the autophagy machinery to the surface of LDs. When Plin3 is silenced, this recruitment is suppressed resulting in accumulation of lipid. Plin3 pulldowns revealed interactions with the autophagy initiator proteins Fip200 and Atg16L indicating that Plin3 may function as a docking protein involved in lipophagy activation. Of particular importance, we define Plin3 as a substrate for mTORC1-dependent phosphorylation and show that this event is decisive for lipophagy. Our study therefore reveals that Plin3, and its phosphorylation by mTORC1, is crucial for degradation of LDs by autophagy. We propose that stimulating this pathway to enhance LD autophagy in hepatocytes will help protect the liver from lipid-mediated toxicity thus offering new therapeutic opportunities in human steatotic liver diseases.
Distinct CASK domains control cardiac sodium channel membrane expression and focal adhesion anchoring
Authors: Beuriot Adeline , Eichel Catherine A. , Dilanian Gilles , Louault Florent , Melgari Dario , Doisne Nicolas , Coulombe Alain , Hatem Stéphane N. , Balse Elise 
Published: October 2019

ABSTRACTMembrane-associated guanylate kinase (MAGUK) proteins function as adaptor proteins to mediate the recruitment and scaffolding of ion channels in the plasma membrane in various cell types. In the heart, the protein CASK (Calcium/CAlmodulin-dependent Serine protein Kinase) negatively regulates the main cardiac sodium channel, NaV1.5, which carries the sodium current (INa) by preventing its anterograde trafficking. CASK is also a new member of the dystrophin-glycoprotein complex, and like syntrophin, binds to the C-terminal domain of the channel. Here we show that both L27B and GUK domains are required for the negative regulatory effect of CASK on INa and NaV1.5 surface expression and that the HOOK domain is essential for interaction with the cell adhesion dystrophin-glycoprotein complex. Thus, the multi-modular structure of CASK potentially provides the ability to control channel delivery at adhesion points in cardiomyocyte.SUMMARYSequential functional domain deletion approach identifies three critical domains of CASK in cardiomyocytes. CASK binds the cell adhesion dystrophin-glycoprotein complex through HOOK domain and inhibits NaV1.5 channel membrane expression by impeding trafficking through L27B and GUK domains.