bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polymorphisms inBrucellaCarbonic anhydrase II mediate CO2dependence and fitnessin vivo
Authors: García-Lobo JM , Ortiz Y , González-Riancho C , Seoane A , Arellano-Reynoso B , Sangari FJ 
Published: October 2019

AbstractSomeBrucellaisolates are known to require an increased concentration of CO2for growth, especially in the case of primary cultures obtained directly from infected animals. Moreover, the differentBrucellaspecies and biovars show a characteristic pattern of CO2requirement, and this trait has been included among the routine typing tests used for species and biovar differentiation. By comparing the differences in gene content among different CO2-dependent and CO2-independentBrucellastrains we have confirmed that carbonic anhydrase II (CA II), is the enzyme responsible for this phenotype in all theBrucellastrains tested.Brucellaspecies contain two carbonic anhydrases of the β family, CA I and CA II; genetic polymorphisms exist for both of them in different isolates, but only those putatively affecting the activity of CA II correlate with the CO2requirement of the corresponding isolate. Analysis of these polymorphisms does not allow the determination of CA I functionality, while the polymorphisms in CA II consist of small deletions that cause a frameshift that changes the C-terminus of the protein, probably affecting its dimerization status, essential for the activity.CO2-independent mutants arise easilyin vitro, although with a low frequency ranging from 10−6to 10−10depending on the strain. These mutants carry compensatory mutations that produce a full length CA II. At the same time, no change was observed in the sequence coding for CA I. A competitive index assay designed to evaluate the fitness of a CO2-dependent strain compared to its corresponding CO2-independent strain revealed that while there is no significant difference when the bacteria are grown in culture plates, growthin vivoin a mouse model of infection provides a significant advantage to the CO2-dependent strain. This could explain why someBrucellaisolates are CO2-dependent in primary isolation. The polymorphism described here also allows thein silicodetermination of the CO2requirement status of anyBrucellastrain.
A novel major output target for pheromone-sensitive projection neurons in male moths
Authors: Chu Xi , Heinze Stanley , Ian Elena , Berg Bente G. 
Published: October 2019

AbstractThe male-specific macroglomerular complex (MGC) in the moth antennal lobe contains circuitry dedicated to pheromone processing. Output neurons from this region project along three parallel pathways, the medial, mediolateral, and lateral tracts. The MGC-neurons of the lateral tract are least described and their functional significance is unknown. We used mass-staining, calcium imaging, and intracellular recording/staining to characterize the morphological and physiological properties of these neurons in Helicoverpa armigera. All lateral-tract MGC neurons targeted the column, a small region within the superior intermediate neuropil. We identified this region as the major converging site for lateral-tract neurons responsive to pheromones and plant-odors. The lateral-tract MGC-neurons consistently responded with a faster onset than the well-described medial-tract neurons. Different from the medial-tract MGC neurons encoding odor quality important for signal identification, those in the lateral tract seem to convey a robust and rapid, but fixed signal – potentially important for fast control of hard-wired behavior.
Impaired renal gluconeogenesis is a major determinant of acute kidney injury associated mortality
Authors: Legouis David , Ricksten Sven-Erick , Faivre Anna , Gariani Karim , Galichon Pierre , Berchtold Lena , Feraille Eric , Koppitch Kari , Hertig Alexandre , Martin Pierre-Yves , Naesens Maarten , Pugin Jérôme , McMahon Andrew P , Cippà Pietro E , de Seigneux Sophie 
Published: October 2019

Nature letterAcute Kidney Injury (AKI) is strongly associated with adverse outcome and mortality independently of the cause of renal damage1-3. The mechanisms determining the deleterious systemic effects of AKI are poorly understood and specific interventions, including optimization of renal replacement therapy, had a marginal effect on AKI-associated mortality in clinical trials4-8. The kidney contributes to up to 40% of systemic glucose production by gluconeogenesis during fasting and stress conditions, mainly synthesized from lactate in the proximal tubule9-12, rendering this organ a major systemic lactate disposal13. Whether kidney gluconeogenesis is impaired during AKI and how this might influence systemic metabolism remains unknown. Here we demonstrate that glucose production and lactate clearance are impaired during human AKI using renal arteriovenous catheterization in patients. Using single cell transcriptomics in mice and RNA sequencing in human biopsies, we show that glycolytic and gluconeogenetic pathways are modified during AKI in the proximal tubule specifically, explaining the metabolic alterations. We further demonstrate that impaired renal gluconeogenesis and lactate clearance during AKI are major determinants of systemic glucose and lactate levels in critically ill patients. Most importantly, altered glucose metabolism in AKI emerged as a major determinant of AKI-associated mortality. Thiamine supplementation restored renal glucose metabolism and substantially reduced AKI-associated mortality in intensive care patients. This study highlights an unappreciated systemic role of renal glucose and lactate metabolism in stress conditions, delineates general mechanisms explaining AKI-associated mortality and introduces a potential therapeutic intervention for a highly prevalent clinical condition with limited therapeutic options.
Drug Combination Antagonism and Single Agent Dominance Result from Differences in Death Activation Kinetics
Authors: Richards Ryan , Schwartz Hannah R. , Stewart Mariah S. , Cruz-Gordillo Peter , Honeywell Megan E. , Joyce Anna J. , Landry Benjamin D. , Lee Michael J. 
Published: October 2019

ABSTRACTTherapeutic regimens for cancer generally involve drugs used in combinations. Most prior work has focused on identifying and understanding synergistic drug-drug interactions; however, understanding sources of antagonistic interactions remains an important and understudied issue. To enrich for antagonistic interactions and reveal common features of these drug combinations, we screened all pairwise combinations of drugs characterized as canonical activators of different forms of regulated cell death. We find that this network is strongly enriched for antagonistic interactions, and in particular, enriched for an extreme form of antagonism, which we call “single agent dominance”. Single agent dominance refers to antagonisms in which a two drug combination phenocopies one of the two agents. We find that dominance results from differences in the cell death onset time, with dominant drugs inducing death earlier and at faster rates than their suppressed counterparts. Finally, we explored the mechanisms by which parthanatotic agents dominate apoptotic agents, finding that dominance in this scenario is caused by mutually exclusive and conflicting use of PARP1. Taken together, our study reveals death activation kinetics as a predictive feature of antagonism, due to inhibitory crosstalk between cell death pathways.
Targeting endogenous K-RAS for degradation through the affinity-directed protein missile system
Authors: Röth Sascha , Macartney Thomas J. , Konopacka Agnieszka , Queisser Markus A. , Sapkota Gopal P. 
Published: October 2019

AbstractFor over three decades,K-RAShas been known as the holy grail of cancer targets, one of the most frequently mutated oncogenes in cancer. Because the development of conventional small molecule K-RAS inhibitors has been extremely challenging, K-RAS has been dubbed as an undruggable target, and only recently a mutation specific inhibitor has reached clinical trials. Targeted protein degradation has emerged as a new modality in drug discovery to tackle undruggable targets. However, no degrader for K-RAS has been described thus far. Our laboratory has developed an Affinity-directed PROtein Missile (AdPROM) system for targeted proteolysis of endogenous proteins through the ubiquitin proteasome system. Here, we show that we can achieve degradation of endogenous K-RAS and H-RAS in different cell lines in a targeted manner using our AdPROM system. Our findings imply that endogenous RAS proteins can be targeted for proteolysis, thereby offering tantalising possibilities for an alternative therapeutic approach to these so-called undruggable targets in cancer.
Cryo-electron microscopy structure of a nucleosome-bound SWI/SNF chromatin remodeling complex
Authors: Han Yan , Reyes Alexis A , Malik Sara , He Yuan 
Published: October 2019

AbstractThe multi-subunit chromatin remodeling complex SWI/SNF1–3 is highly conserved from yeast to humans and plays critical roles in various cellular processes including transcription and DNA damage repair4, 5. It uses the energy from ATP hydrolysis to remodel chromatin structure by sliding and evicting the histone octamer6–10, creating DNA regions that become accessible to other essential protein complexes. However, our mechanistic understanding of the chromatin remodeling activity is largely hindered by the lack of a high-resolution structure of any complex from this family. Here we report the first structure of SWI/SNF from the yeast S. cerevisiae bound to a nucleosome at near atomic resolution determined by cryo-electron microscopy (cryo-EM). In the structure, the Arp module is sandwiched between the ATPase and the Body module of the complex, with the Snf2 HSA domain connecting all modules. The HSA domain also extends into the Body and anchors at the opposite side of the complex. The Body contains an assembly scaffold composed of conserved subunits Snf12 (SMARCD/BAF60), Snf5 (SMARCB1/BAF47/ INI1) and an asymmetric dimer of Swi3 (SMARCC/BAF155/170). Another conserved subunit Swi1 (ARID1/BAF250) folds into an Armadillo (ARM) repeat domain that resides in the core of the SWI/SNF Body, acting as a molecular hub. In addition to the interaction between Snf2 and the nucleosome, we also observed interactions between the conserved Snf5 subunit and the histones at the acidic patch, which could serve as an anchor point during active DNA translocation. Our structure allows us to map and rationalize a subset of cancer-related mutations in the human SWI/SNF complex and propose a model of how SWI/SNF recognizes and remodels the +1 nucleosome to generate nucleosome-depleted regions during gene activation11–13.
Dynamic interactions and intracellular fate of label-free, thin graphene oxide sheets within mammalian cells: role of lateral sheet size
Authors: Chen Yingxian , Rivers-Auty Jack , Crică Livia Elena , Barr Katie , Rosano Vinicio , Arranz Adrian Esteban , Loret Thomas , Spiller David , Bussy Cyrill , Kostarelos Kostas , Vranic Sandra 
Published: October 2019

AbstractGraphene oxide (GO) holds great potential for biomedical applications, however fundamental understanding of the way it interacts with biological systems is still lacking even though it is essential for successful clinical translation. In this study, we exploit intrinsic fluorescent properties of thin GO sheets to establish the relationship between lateral dimensions of the material, its cellular uptake mechanisms and intracellular fate over time. Label-free GO with distinct lateral dimensions, small (s-GO) and ultra-small (us-GO) were thoroughly characterised both in water and in biologically relevant cell culture medium. Interactions of the material with a range of non-phagocytic mammalian cell lines (BEAS-2B, NIH/3T3, HaCaT, 293T) were studied using a combination of complementary analytical techniques (confocal microscopy, flow cytometry and TEM). The uptake mechanism was initially interrogated using a range of pharmaceutical inhibitors and validated using polystyrene beads of different diameters (0.1 and 1 μm). Subsequently, RNA-Seq was used to follow the changes in the uptake mechanism used to internalize s-GO flakes over time. Regardless of lateral dimensions, both types of GO were found to interact with the plasma membrane and to be internalized by a panel of cell lines studied. However, s-GO was internalized mainly via macropinocytosis while us-GO was mainly internalized via clathrin- and caveolae-mediated endocytosis. Importantly, we report the shift from macropinocytosis to clathrin-dependent endocytosis in the uptake of s-GO at 24 h, mediated by upregulation of mTORC1/2 pathway. Finally, we show that both s-GO and us-GO terminate in lysosomal compartments for up to 48 h. Our results offer an insight into the mechanism of interaction of GO with non-phagocytic cell lines over time that can be exploited for the design of biomedically-applicable 2D transport systems.
Classification of platelet aggregates by agonist type
Authors: Zhou Yuqi , Yasumoto Atsushi , Lei Cheng , Huang Chun-Jung , Kobayashi Hirofumi , Wu Yunzhao , Yan Sheng , Sun Chia-Wei , Yatomi Yutaka , Goda Keisuke 
Published: October 2019

SUMMARYPlatelets are anucleate cells in blood whose principal function is to stop bleeding by forming aggregates for hemostatic reactions. In addition to their participation in physiological hemostasis, platelet aggregates are also involved in pathological thrombosis and play an important role in inflammation, atherosclerosis, and cancer metastasis. The aggregation of platelets is elicited by various agonists, but these platelet aggregates have long been considered indistinguishable and impossible to classify. Here we present an intelligent method for classifying them by agonist type. It is based on a convolutional neural network trained by high-throughput imaging flow cytometry of blood cells to identify and differentiate subtle yet appreciable morphological features of platelet aggregates activated by different types of agonists. The method is a powerful tool for studying the underlying mechanism of platelet aggregation and is expected to open a window on an entirely new class of clinical diagnostics, pharmacometrics, and therapeutics.
A memory of RPS25 loss drives resistance phenotypes
Authors: Johnson Alex G. , Flynn Ryan A. , Lapointe Christopher P. , Ooi Yaw Shin , Zhao Michael L. , Richards Christopher M. , Qiao Wenjie , Yamada Shizuka B. , Couthouis Julien , Gitler Aaron D. , Carette Jan E. , Puglisi Joseph D. 
Published: October 2019

ABSTRACTIn order to maintain cellular protein homeostasis, ribosomes are safeguarded against dysregulation by myriad processes. Many cell types can nonetheless withstand genetic lesions of certain ribosomal protein genes, some of which are linked to diverse cellular phenotypes and human disease. However, the direct and indirect consequences from sustained alterations in ribosomal protein levels are poorly understood. To address this knowledge gap, we studied in vitro and cellular consequences that follow genetic knockout of the ribosomal proteins RPS25 or RACK1 in a human cell line, as both proteins are implicated in direct translational control. Prompted by the unexpected detection of an off-target ribosome alteration in the RPS25 knockout, we closely interrogated cellular phenotypes. We found that multiple RPS25 knockout clones display viral- and toxin-resistance phenotypes that cannot be rescued by functional cDNA expression, suggesting that RPS25 loss elicits a cell state transition. We characterized this state and found that it underlies pleiotropic phenotypes and has a common rewiring of gene expression. Rescuing RPS25 expression by genomic locus repair failed to correct for the phenotypic and expression hysteresis. Our findings illustrate how the elasticity of cells to a ribosome perturbation can drive specific phenotypic outcomes that are indirectly linked to translation.
In vivo imaging defines vascular interplay in the development of lymphocytic leukemia in zebrafish models
Authors: Revskoy Sergei , Blair Margaret E. , Powell Shaw M. , Hausman Elizabeth S. , Blackburn Jessica S. 
Published: October 2019

AbstractThe vascular microenvironment at the primary tumor site is represented by functionally diverse types of vessels that contribute to metabolic supply, trafficking/dissemination of tumor cells, and delivery of chemotherapeutics. However, the role of leukemia-associated vascular networks in leukemia progression remains poorly understood. We utilized a MYC-induced T cell leukemia model in zebrafish to assess the involvement of vascular endothelial growth factor A-dependent (VEGFR2+), VEGFA-independent vasculature (VEGFR2-), and lymphatics in the initial stages of leukemia cell dissemination using intravital microscopy. Leukemogenesis underwent sequential progression, from initial successive emigration of single leukemic cells from the thymus towards the kidney marrow, followed by collective migration in a dorsal-lateral direction with scattered migration from the ventral thymus towards the aortic arches, before streaming towards the rostral kidney area. Trafficking appeared independent of VEGFR2+ vasculature but was closely associated with VEGFR2-microvessels, and, interestingly, leukemic cells did not utilize lymphatics during initial dissemination. Overall, leukemic cells appeared to utilize the same routes as normal T cell progenitors during development but in a reverse order, and primarily recruited VEGFR2-microvessels during the initial stages of progression. Ultimately, interfering with leukemia cell migration by targeting vascular networks may represent a new therapeutic strategy to control leukemia progression.
Spatiotemporal control of gene expression boundaries using a feedforward loop
Authors: Bandodkar Prasad U. , Asafen Hadel Al , Reeves Gregory T. 
Published: October 2019

AbstractA feed forward loop (FFL) is commonly observed in several biological networks. The FFL network motif has been mostly been studied with respect to variation of the input signal in time, with only a few studies of FFL activity in a spatially distributed system such as morphogen-mediated tissue patterning. However, most morphogen gradients also evolve in time. We studied the spatiotemporal behavior of a coherent FFL in two contexts: (1) a generic, oscillating morphogen gradient and (2) the dorsal-ventral patterning of the earlyDrosophilaembryo by a gradient of the NF-κB homolog Dorsal with its early target Twist. In both models, we found features in the dynamics of the intermediate node – phase difference and noise filtering – that were largely independent of the parameterization of the models, and thus were functions of the structure of the FFL itself. In the Dorsal gradient model, we also found that the dynamics of Dorsal require maternal pioneering factor Zelda for proper target gene expression.
Exosomes transmit retroelement RNAs to drive inflammation and immunosuppression in Ewing Sarcoma
Authors: Evdokimova Valentina , Ruzanov Peter , Gassmann Hendrik , Zaidi Syed H. , Peltekova Vanya , Heisler Lawrence E. , McPherson John D. , Orlic-Milacic Marija , Specht Katja , Steiger Katja , Schober Sebastian J. , Thiel Uwe , McKee Trevor D. , Zaidi Mark , Spring Christopher M. , Lapouble Eve , Delattre Olivier , Burdach Stefan , Stein Lincoln D. , Sorensen Poul H. 
Published: October 2019

SUMMARYEwing sarcoma (EwS) is an aggressive childhood malignancy with a high propensity for metastasis. By analyzing cohorts of patients and age-matched healthy donors, we establish that EwS metastatic progression is accompanied by elevated plasma levels of multiple proinflammatory cytokines, interferons and extracellular vesicles (EVs). The latter were enriched with transcripts derived from LINE, SINE and ERV retroelements and from locus-specific pericentromeric regions, including HSAT2. We show that some of these RNAs, including HSAT2 and HERV-K, are selectively transmitted in EwS EVs and taken up by stromal fibroblasts and peripheral blood CD33+ myeloid cells and CD8+ T-cells, inducing immune exhaustion, immunosuppressive phenotypes and proinflammatory responses. Moreover, EwS EV-derived repeat RNAs were propagated and serially transmitted in recipient cell EVs, reminiscent of viral infection. As such, this study uncovers a novel mechanism driving cancer-associated inflammation, immunosuppression and metastatic progression.
Identification of peptides interfering the lrrk2/pp1 interaction
Authors: Dong Chang Zhi , Bruzzoni-Giovanell Heriberto , Yu Yanhua , Dorgham Karim , Parizot Christophe , Zini Jean Marc , Tuffery Pierre , Rebollo Angelita 
Published: October 2019

ABSTRACTSerine/threonine phosphatases are responsible for counteracting the effect of the protein kinases implicated in the development of several pathologies. Here we identified by PEP-scan approach the sequence of a fragment of LRRK2, a Parkinson’s disease associated protein, interacting with the phosphatase PP1. The fragment, that is located in a LRRK2 domain of undefined function, was associated in N-terminal to an optimized cell penetrating peptide in order to study their in vitro and in vivo biological activity. From this original sequence, we developed and studied five interfering peptides (IPs) and identified two peptides able to disrupt the LRRK2/PP1 interaction by in vitro competition in anti-LRRK2 immunoprecipitates. Using FITC-labelled peptides, we confirmed the internalization of the peptides in cell lines as well as in and primary human normal and pathological cells. Finally, we have confirmed by ELISA test the association of Mut3DPT-LRRK2-Long and Mut3DPT-LRRK2-Short peptides to purified PP1 protein in a selective manner. The shortest peptides, MuteDPT-LRRK2-5 to 8 with either N or C-terminal deletions are not able neither disrupt the association LRRK2/PP1 nor to associate to purified PP1 protein. The peptides Mut3DPT-LRRK2-Long and Mut3DPT-LRRK2-Short may be new tools to study the role of LRRK2/PP1 interaction in normal and pathological conditions.
Performance of agricultural cooperative banks in Japan
Authors: Harimaya Kozo , Kagitani Koichi 
Published: October 2019

Purpose
The purpose of this paper is to investigate the efficiency of the banking business of Japan’s agricultural cooperatives (JAs), which depend heavily on financial business with non-farmers, contradictory to cooperative principles.

Design/methodology/approach
The authors construct a panel data set over 2005–2016 from the financial statements of JAs’ prefectural-level federations and use the input distance stochastic frontier model with a time-variant inefficiency effect for analysis. Both the flow and stock measures of the banking output are used in identical models and the efficiency results are compared. The authors also investigate the determinants of efficiency by using the Tobit and ordinary least squares regression models.

Findings
There is strong evidence of significant prefectural differences in efficiency values. The ratio of lending to non-members to total loans is positively related to efficiency. In contrast, the higher reliance on a central organization and credit business leads to lower efficiency.

Research limitations/implications
Apart from banking, JAs provide mutual insurance business services. As the authors investigate only the efficiency of JAs’ banking business in this study, it would be necessary to investigate the efficiency of their insurance business as well when evaluating JAs’ overall financial business.

Originality/value
There are few studies that investigate the efficiency of JAs’ banking business and its determinants, although significant attention has been paid to their excessive dependence on the financial business.