bluuebunny/crossref_metadata_2025_split huggingface dataset:
Facets of diazotrophy in the OMZ off Peru revisited- what we couldn’t see from a single marker gene approach
Authors: Christiansen Christian Furbo , Löscher Carolin Regina 
Published: February 2019

AbstractBiological dinitrogen (N2) fixation is the pathway making the large pool of atmospheric N2available to marine life. Besides direct rate measurements, a common approach to explore the potential for N2fixation in the ocean is a mining based on molecular genetic methods targeting the key functional genenifH, coding for a subunit of the nitrogenase reductase. As novel sequencing and single cell techniques improved, our knowledge on the diversity of marine N2fixers grew exponentially. However, to date one aspect of N2fixation in the ocean is commonly left aside. This is the existence of two alternative types of nitrogenases, which are besides the Mo-Fe nitrogenaseNif, the Fe-Fe nitrogenaseAnf, and the V-Fe nitrogenaseVnf, which differ with regard to their metal co-enzymes, as well as regarding their operon structure and composition.nifH-based studies may thus be biased, and alternative nitrogenases could not be recovered. Here, we screened a set of 6 metagenomes and -transcriptomes from a sulfidic water patch from the oxygen minimum zone off Peru for genes involved in N2fixation. We identified genes related to all three nitrogenases, and generally increased diversity as compared to our previousnifH-based study from the same waters. While we could not confirm gene expression of the alternative nitrogenases from our transcriptomes, we detected additional diazotrophs involved in N2fixation. We suggest that alternative nitrogenases may not be used under conditions present in those waters, however, depending on trace metal limitation in the future they may become active.Significance statementThis study addresses the important process of N2fixation, based on a whole-metagenome and –transcriptome screening, reports an increased diversity of N2fixing microbes in the sulfidic shelf water off Peru, as compared to previous target-gene based studies from the same waters. In addition to a generally higher diversity, genes encoding for alternative nitrogenases, which were previously not subject of any study on N2fixation in oxygen minimum zones, were detected. The ecological meaning and evolutionary history of those alternative nitrogenases is subject of ongoing debates, however, their presence in OMZ waters would allow for N2fixation at extreme anoxia, which may become important in a future ocean challenged by progressive deoxygenation.
Cancer-Associated Fibroblasts Promote Prostate Cancer Malignancy via Metabolic Rewiring and Mitochondrial Transfer
Authors: Ippolito Luigi , Morandi Andrea , Taddei Maria Letizia , Parri Matteo , Comito Giuseppina , Iscaro Alessandra , Raspollini Maria Rosaria , Magherini Francesca , Rapizzi Elena , Masquelier Julien , Muccioli Giulio G. , Sonveaux Pierre , Chiarugi Paola , Giannoni Elisa 
Published: February 2019

ABSTRACTCancer-associated fibroblasts (CAFs) are the major cellular stromal component of many solid tumors. In prostate cancer (PCa), CAFs establish a metabolic symbiosis with PCa cells, contributing to cancer aggressiveness through lactate shuttle. In this study, we report that lactate uptake alters the NAD+/NADH ratio in the cancer cells, which culminates with SIRT1-dependent PGC-1α activation and subsequent enhancement of mitochondrial mass and activity. The high exploitation of mitochondria results in tricarboxylic acid cycle deregulation, accumulation of oncometabolites and in the altered expression of mitochondrial complexes, responsible for superoxide generation. Additionally, cancer cells hijack CAF-derived functional mitochondria through the formation of cellular bridges, a phenomenon that we observed in both in vitro and in vivo PCa models. Our work reveals a crucial function of tumor mitochondria as the energy sensors and transducers of CAF-dependent metabolic reprogramming and underscores the reliance of PCa cells on CAF catabolic activity and mitochondria trading.
High extracellular lactate increases reductive carboxylation in breast tissue cell lines grown under normoxic conditions
Authors: Brodsky Arthur Nathan , Odenwelder Daniel C. , Harcum Sarah W. 
Published: February 2019

AbstractIn cancer tumors, lactate accumulation was initially attributed to high glucose consumption associated with the Warburg Effect. Now it is evident that lactate can also serve as an energy source in cancer cell metabolism. Additionally, lactate has been shown to promote metastasis, generate gene expression patterns in cancer cells consistent with “cancer stem cell” phenotypes, and result in treatment resistant tumors. Therefore, the goal of this work was to quantify the impact of lactate on metabolism in three breast cell lines (one normal and two breast cancer cell lines – MCF 10A, MCF7, and MDA-MB-231), in order to better understand the role lactate may have in different disease cell types. Parallel labeling metabolic flux analysis (13C-MFA) was used to quantify the intracellular fluxes under normal and high extracellular lactate culture conditions. Additionally, high extracellular lactate cultures were labelled in parallel with [U-13C] lactate, which provided qualitative information regarding the lactate uptake and metabolism. The 13C-MFA model, which incorporated the measured extracellular fluxes and the parallel labeling mass isotopomer distributions (MIDs) for five glycolysis, four tricarboxylic acid cycle (TCA), and three intracellular amino acid metabolites, predicted lower glycolysis fluxes in the high lactate cultures. All three cell lines experienced increased reductive carboxylation of glutamine to citrate in the TCA cycle as a result of high extracellular lactate. Increased reductive carboxylation previously has been observed under hypoxia and other mitochondrial stresses, whereas these cultures were grown aerobically. In addition, this is the first study to investigate the intracellular metabolic responses of different stages of breast cancer progression to high lactate exposure. These results provide insight into the role lactate accumulation has on metabolic reaction distributions in the different disease cell types while the cells are still proliferating in lactate concentrations that do not significantly decrease exponential growth rates.
Tissue-specific mouse mRNA isoform networks
Authors: Kandoi Gaurav , Dickerson Julie A. 
Published: February 2019

AbstractAlternative Splicing produces multiple mRNA isoforms of genes which have important diverse roles such as regulation of gene expression, human heritable diseases, and response to environmental stresses. However, little has been done to assign functions at the mRNA isoform level. Functional networks, where the interactions are quantified by their probability of being involved in the same biological process are typically generated at the gene level. We use a diverse array of tissue-specific RNA-seq datasets and sequence information to train random forest models that predict the functional networks. Since there is no mRNA isoform-level gold standard, we use single isoform genes co-annotated to Gene Ontology biological process annotations, Kyoto Encyclopedia of Genes and Genomes pathways, BioCyc pathways and protein-protein interactions as functionally related (positive pair). To generate the non-functional pairs (negative pair), we use the Gene Ontology annotations tagged with “NOT” qualifier. We describe 17 Tissue-spEcific mrNa iSoform functIOnal Networks (TENSION) following a leave-one-tissue-out strategy in addition to an organism level reference functional network for mouse. We validate our predictions by comparing its performance with previous methods, randomized positive and negative class labels, updated Gene Ontology annotations, and by literature evidence. We demonstrate the ability of our networks to reveal tissue-specific functional differences of the isoforms of the same genes.
PAK4 regulates stemness and progression in endocrine resistant ER-positive metastatic breast cancer
Authors: Santiago-Gómez Angélica , Dragoni Ilaria , NicAmhlaoibh Roisin , Trivier Elisabeth , Sabin Verity , Simões Bruno M. , Gee Julia M. , Sims Andrew H. , Howell Sacha J. , Clarke Robert B. 
Published: February 2019

AbstractDespite the effectiveness of endocrine therapies to treat estrogen receptor-positive (ER+) breast tumours, two thirds of patients will eventually relapse due tode novoor acquired resistance to these agents. Cancer Stem-like Cells (CSCs), a rare cell population within the tumour, accumulate after anti-estrogen treatments and are likely to contribute to their failure. Here we studied the role of p21-activated kinase 4 (PAK4) as a promising target to overcome endocrine resistance and disease progression in ER+ breast cancers. PAK4 predicts for resistance to tamoxifen and poor prognosis in 2 independent cohorts of ER+ tumours. We observed that PAK4 strongly correlates with CSC activity in metastatic patient-derived samples irrespective of breast cancer subtype. However, PAK4-driven mammosphere-forming CSC activity increases alongside progression only in ER+ metastatic samples. PAK4 activity increases in ER+ models during acquired resistance to endocrine therapies. Targeting PAK4 with either CRT PAKi, a small molecule inhibitor of PAK4, or with specific siRNAs abrogates CSC activity/self-renewal in clinical samples and endocrine-resistant cells. Together, our findings establish that PAK4 regulates stemness during disease progression and that its inhibition reverses endocrine resistance in ER+ breast cancers.HighlightsPAK4 predicts for failure of endocrine therapies and poor prognosisPAK4 drives stemness and progression in ER+ metastatic breast cancerTargeting PAK4 abrogates breast CSC activity and restores sensitivity to endocrine treatmentsTargeting PAK4 will improve outcome of ER+ breast cancer patientsList of Abbreviations that appeared in abstractCancer Stem-like Cells (CSCs)p21-activated kinase 4 (PAK4)Estrogen Receptor (ER)
Cell-type specific mechanical response and myosin dynamics during retinal lens development in Drosophila
Authors: Blackie Laura , Walther Rhian F. , Staddon Michael F. , Banerjee Shiladitya , Pichaud Franck 
Published: February 2019

ABSTRACTDuring organogenesis, different cell types need to work together to induce functional multicellular structures. To study this process, we made use of the genetically tractable fly retina, with a focus on the mechanisms that coordinate morphogenesis between the different epithelial cell types that make up the optical lens. Our work shows that these epithelial cells present contractile apical-medial MyosinII meshworks, which control the apical area and junctional geometry of these cells during lens development. Our study also suggests that MyosinII meshworks drive cell shape changes in response to external forces, and thus they mediate part of the biomechanical coupling that takes place between these cells. Importantly, our work, including mathematical modelling of forces and material stiffness during lens development, raises the possibility that increased cell stiffness acts as a mechanism for limiting this mechanical coupling. We propose this might be required in complex tissues, where different cell types undergo concurrent morphogenesis and where averaging out of forces across cells could compromise individual cell apical geometry and thereby organ function.
Intrinsic checkpoint deficiency during cell cycle re-entry from quiescence
Authors: Matson Jacob Peter , House Amy M. , Grant Gavin D. , Wu Huaitong , Perez Joanna , Cook Jeanette Gowen 
Published: February 2019

SUMMARYThe authors find that human cells re-entering the cell cycle from quiescence have both an impaired p53-dependent DNA replication origin licensing checkpoint and slow origin licensing. This combination makes every first S phase underlicensed and hypersensitive to replication stress.ABSTRACTTo maintain tissue homeostasis, cells transition between cell cycle quiescence and proliferation. An essential G1 process is Minichromosome Maintenance complex (MCM) loading at DNA replication origins to prepare for S phase, known as origin licensing. A p53-dependent origin licensing checkpoint normally ensures sufficient MCM loading prior to S phase entry. We used quantitative flow cytometry and live cell imaging to compare MCM loading during the long first G1 upon cell cycle entry and the shorter G1 phases in the second and subsequent cycles. We discovered that despite the longer G1 phase, the first G1 after cell cycle re-entry is significantly underlicensed. As a result, the first S phase cells are hypersensitive to replication stress. This underlicensing is from a combination of slow MCM loading with a severely compromised origin licensing checkpoint. The hypersensitivity to replication stress increases over repeated rounds of quiescence. Thus, underlicensing after cell cycle re-entry from quiescence distinguishes a higher risk cell cycle that promotes genome instability.
Phosphoinositides regulate the TRPV1 channel via two functionally distinct binding sites
Authors: Yazici Aysenur Torun , Gianti Eleonora , Kasimova Marina A. , Carnevale Vincenzo , Rohacs Tibor 
Published: February 2019

AbstractRegulation of the heat- and capsaicin-activated Transient Receptor Potential Vanilloid 1 (TRPV1) channel by phosphoinositides is controversial. In a recent cryoEM structure, an endogenous phosphoinositide was detected in the vanilloid binding site, and phosphoinositides were proposed to act as competitive vanilloid antagonists. This model is difficult to reconcile with phosphatidylinositol 4,5- bisphosphate [PtdIns(4,5)P2] being a well established positive regulator of TRPV1. To resolve this controversy, we propose that phosphoinositides regulate TRPV1 via two functionally distinct binding sites. Our molecular dynamics simulations show that phosphatidylinositol (PtdIns) is more stable in the vanilloid binding site, whereas a distinct site responsible for activation is preferentially occupied by PtdIns(4,5)P2. Consistently, we show that in the presence of PtdIns(4,5)P2 in excised patches PtdIns partially inhibited TRPV1 activity induced by low, but not high capsaicin concentrations. In the absence of PtdIns(4,5)P2 on the other hand, PtdIns partially stimulated TRPV1 activity presumably by binding to the activating site. Overall, our data resolve a major controversy in the regulation of TRPV1.
Endocytosis against high turgor pressure is made easier by partial protein coating and a freely rotating base
Authors: Ma Rui , Berro Julien 
Published: February 2019

ABSTRACTDuring clathrin-mediated endocytosis, a patch of flat plasma membrane is deformed into a vesicle. In walled cells, such as plants and fungi, the turgor pressure is high and pushes the membrane against the cell wall, thus hindering membrane internalization. In this paper, we study how a patch of membrane is deformed against turgor pressure by force and by curvature-generating proteins. We show that a large amount of force is needed to merely start deforming the membrane and an even larger force is needed to pull a membrane tube. The magnitude of these forces strongly depends on how the base of the membrane is constrained and how the membrane is coated with curvature-generating proteins. In particular, these forces can be reduced by partially but not fully coating the membrane patch with curvature-generating proteins. Our theoretical results show excellent agreement with experimental data.SIGNIFICANCEYeast cells have been widely used as a model system to study clathrin-mediated endocytosis. The mechanics of membrane during endocytosis has been extensively studied mostly in low turgor pressure condition, which is relevant for mammalian cells but not for yeast cells. It has been suggested that as a result of high turgor pressure in yeast cells, a large amount of force is needed to drive the progress of the membrane invagination. In this paper, we investigated biologically relevant mechanisms to reduce the force requirement. We highlight the role of boundary conditions at the membrane base, which is a factor that has been largely ignored in previous studies. We also investigate the role of curvature-generating proteins and show that a large protein coat does not necessarily reduce the force barrier for endocytosis.
Gene-drive-mediated extinction is thwarted by evolution of sib mating
Authors: Bull James J , Remien Christopher H , Krone Stephen M 
Published: February 2019

AbstractGenetic engineering combined with CRISPR technology has developed to the point that gene drives can, in theory, be engineered to cause extinction in countless species. Success of extinction programs now rests on the possibility of resistance evolution, which is largely unknown. For CRISPR technology, resistance may take many forms, from mutations in the nuclease target sequence to specific types of non-random population structures that limit the drive. We develop mathematical models of various deviations from random mating to consider escapes from extinction-causing gene drives. We use a version of Maynard Smith’s haystack model to show that population structure can enable drive-free subpopulations to be maintained against gene drives. Our main emphasis, however, is sib mating in the face of recessive-lethal and Y-chromosome drives. Sib mating easily evolves in response to both kinds of gene drives and maintains mean fitness above 0, with equilibrium fitness depending on the level of inbreeding depression. Environmental determination of sib mating (as might stem from population density crashes) can also maintain mean fitness above 0. Translation of mean fitness into population size depends on ecological details, so understanding mean fitness evolution and dynamics is merely the first step in predicting extinction. Nonetheless, these results point to possible escapes from gene drive-mediated extinctions that lie beyond the control of genome engineering.
Phosphorylation of Nephrin induces phase separated domains that move through actomyosin contraction
Authors: Kim Soyeon , Kalappurakkal Joseph M. , Mayor Satyajit , Rosen Michael K. 
Published: February 2019

AbstractThe plasma membrane of eukaryotic cells is organized into lipid and protein microdomains, whose assembly mechanisms and functions are incompletely understood. We demonstrate that proteins in the Nephrin/Nck/N-WASP actin-regulatory pathway cluster into micron-scale domains at the basal plasma membrane upon triggered phosphorylation of transmembrane Nephrin. The domains are persistent but readily exchange components with their surroundings, and their formation is dependent on the number of Nck SH3 domains, suggesting they are phase separated polymers assembled through multivalent interactions among the three proteins. The domains form independent of the actin cytoskeleton, but acto-myosin contractility induces their rapid lateral movement. Nephrin phosphorylation induces larger clusters at the cell periphery, which are associated with extensive actin assembly and dense filopodia. Our studies illustrate how multivalent interactions between proteins at the plasma membrane can produce micron-scale organization of signaling molecules, and how the resulting clusters can both respond to and control the actin cytoskeleton.
High multiplex, digital spatial profiling of proteins and RNA in fixed tissue using genomic detection methods
Authors: Merritt Christopher R. , Ong Giang T. , Church Sarah , Barker Kristi , Geiss Gary , Hoang Margaret , Jung Jaemyeong , Liang Yan , McKay-Fleisch Jill , Nguyen Karen , Sorg Kristina , Sprague Isaac , Warren Charles , Warren Sarah , Zhou Zoey , Zollinger Daniel R. , Dunaway Dwayne L. , Mills Gordon B. , Beechem Joseph M. 
Published: February 2019

ABSTRACTWe have developed Digital Spatial Profiling (DSP), a non-destructive method for high-plex spatial profiling of proteins and RNA, using oligonucleotide detection technologies with unlimited multiplexing capability. The key breakthroughs underlying DSP are threefold: (1) multiplexed readout of proteins/RNA using oligo-tags; (2) oligo-tags attached to affinity reagents (antibodies/RNA probes) through a photocleavable (PC) linker; (3) photocleaving light projected onto the tissue sample to release PC-oligos in any spatial pattern. Here we show precise analyte reproducibility, validation, and cellular resolution using DSP. We also demonstrate biological proof-of-concept using lymphoid, colorectal tumor, and autoimmune tissue as models to profile immune cell populations, stroma, and cancer cells to identify factors specific for the diseased microenvironment. DSP utilizes the unlimited multiplexing capability of modern genomic approaches, while simultaneously providing spatial context of protein and RNA to examine biological questions based on analyte location and distribution.
12h-clock control of central dogma information flow by XBP1s
Authors: Pan Yinghong , Ballance Heather , Meng Huan , Gonzalez Naomi , Dacso Clifford C. , Chen Xi , Levy Oren , Coarfa Cristian , O’Malley Bert W , Zhu Bokai 
Published: February 2019

ABSTRACTOur group recently discovered a cell-autonomous mammalian 12h-clock regulating physiological unfolded protein response. Xbp1s ablation impairs 12h-transcript oscillations in vitro, and we now show liver-specific deletion of XBP1s globally impaired murine 12h-transcriptome, but not the circadian rhythms in vivo. XBP1s-dependent 12h-transcriptome is enriched for transcription, mRNA processing, ribosome biogenesis, translation, and protein ER-Golgi processing/sorting in a temporal order consistent with the progressive molecular processing sequence described by the central dogma information flow (CEDIF). The 12h-rhythms of CEDIF are cell-autonomous and evolutionarily conserved in circatidal marine animals. Mechanistically, we found the motif stringency of promoter XBP1s binding sites, but not necessarily XBP1s expression, dictates its ability to drive 12h-rhythms of transcription and further identified GABP as putative novel transcriptional regulator of 12h-clock. We hypothesize the 12h-rhythms of CEDIF allows rush hours’ gene expression and processing, with the particular genes processed at each rush hour regulated by circadian and/or tissue specific pathways.
Suppressing Random Response of a Regular Structure by an Inerter-Based Dynamic Vibration Absorber
Authors: Jin Xiaoling , Chen M. Z. Q. , Huang Zhilong 
Published: February 2019

AbstractThis paper concentrates on the random vibration suppression of a regular straight beam by using an inerter-based dynamic vibration absorber. For a wideband random point-driven straight beam with an inerter-based dynamic vibration absorber, the distribution of mean-square velocity response along the axis of the straight beam as well as the mean kinetic energy of the whole beam are first analytically derived through the classical linear random vibration theory. Two optimization objectives are established to determine the optimal design parameters: (1) minimizing the maximal mean-square velocity along the axis of the straight beam, which corresponds to the maximal mean kinetic energy density along the axis and (2) minimizing the mean kinetic energy of the whole beam. Numerical search gives the optimal location and the associated optimal parameters of the inerter-based dynamic vibration absorber. Numerical results for a simply supported straight beam illustrate the better performance of an inerter-based dynamic vibration absorber than a traditional dynamic vibration absorber. Parametric sensitivity studies for the robustness analysis of the beam response to deviations from the optimal parameters are conducted. The optimal location locates on the force-excited point, while the suboptimal location locates on its symmetry position. Furthermore, the optimal and suboptimal locations remain invariable regardless of the upper cutoff frequency of band-limited noise, which is fairly important to the location optimization of the inerter-based dynamic vibration absorber.