bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toll-like receptor 3 activation increases voluntary alcohol intake in C57BL/6J male mice
Authors: Warden Anna S. , Azzam Moatasem M. , DaCosta Adriana , Mason Sonia , Blednov Yuri A. , Messing Robert O. , Mayfield R. Dayne , Harris R. Adron 
Published: November 2018

AbstractMany genes differentially expressed in brain tissue from human alcoholics and animals that have consumed large amounts of alcohol are components of the innate immune toll-like receptor (TLR) pathway. TLRs initiate inflammatory responses via two branches: (1) MyD88-dependent or (2) TRIF-dependent. All TLRs signal through MyD88 except TLR3. Prior work demonstrated a direct role for MyD88-dependent signaling in regulation of alcohol consumption. However, the role of TLR3 as a potential regulator of excessive alcohol drinking has not previously been investigated. To test the possibility TLR3 activation regulates alcohol consumption, we injected mice with the TLR3 agonist polyinosinic:polycytidylic acid (poly(I:C)) and tested alcohol consumption in an every-other-day two-bottle choice test. Poly(I:C) produced a persistent increase in alcohol intake that developed over several days. Repeated poly(I:C) and ethanol exposure altered innate immune transcript abundance; increased levels of TRIF-dependent pathway components correlated with increased alcohol consumption. Administration of poly(I:C) before exposure to alcohol did not alter alcohol intake, suggesting that poly(I:C) and ethanol must be present together to change drinking behavior. To determine which branch of TLR signaling mediates poly(I:C)-induced changes in drinking behavior, we tested either mice lacking MyD88 or mice administered a TLR3/dsRNA complex inhibitor. MyD88 null mutants showed poly(I:C)-induced increases in alcohol intake. In contrast, mice pretreated with a TLR3/dsRNA complex inhibitor reduced their alcohol intake, suggesting poly(I:C)-induced escalations in alcohol intake function are, at least partially, dependent on TLR3. Together, these results strongly suggest that TLR3-dependent signaling drives excessive alcohol drinking behavior.HighlightsActivation of TLR3viapoly(I:C) increased alcohol intake.Poly(I:C) and ethanol must be present together to change drinking behavior.Increased alcohol intake due to poly(I:C) is independent of MYD88.Increased alcohol intake due to poly(I:C) is dependent on TLR3.
Momo – Multi-Objective Metabolic mixed integer Optimization: application to yeast strain engineering
Authors: Andrade Ricardo , Doostmohammadi Mahdi , Santos João L. , Sagot Marie-France , Mira Nuno P. , Vinga Susana 
Published: November 2018

AbstractIn this paper, we explore the concept of multi-objective optimization in the field of metabolic engineering when both continuous and integer decision variables are involved in the model. In particular, we propose a multi-objective model that may be used to suggest reaction deletions that maximize and/or minimize several functions simultaneously. The applications may include, among others, the concurrent maximization of a bioproduct and of biomass, or maximization of a bioproduct while minimizing the formation of a given by-product, two common requirements in microbial metabolic engineering.Production of ethanol by the widely used cell factorySaccharomyces cerevisiaewas adopted as a case study to demonstrate the usefulness of the proposed approach in identifying genetic manipulations that improve productivity and yield of this economically highly relevant bioproduct. We did anin vivovalidation and we could show that some of the predicted deletions exhibit increased ethanol levels in comparison with the wild-type strain. The multi-objective programming framework we developed, called Momo, is open-source and uses PolySCIP‡as underlying multi-objective solver. Momo is available athttp://momo-sysbio.gforge.inria.fr
Genome-wide screening reveals a novel class of carbonic anhydrase-like inorganic carbon pumps in chemoautotrophic bacteria
Authors: Desmarais John J. , Flamholz Avi I. , Blikstad Cecilia , Dugan Eli J. , Laughlin Thomas G. , Oltrogge Luke M. , Chen Allen W. , Wetmore Kelly , Diamond Spencer , Wang Joy Y. , Savage David F. 
Published: November 2018

AbstractMany bacterial autotrophs rely on CO2concentrating mechanisms (CCMs) to assimilate carbon. Although many CCM proteins have been identified, including a 200+ MDa protein organelle called the carboxysome, a systematic screen of CCM components has not been carried out. Here, we performed a genome-wide barcoded transposon screen to identify essential and CCM-related genes in the ɣ-proteobacteriumH. neapolitanus. Our screen revealed an operon critical for CCM function which encodes a domain of unknown function (PFAM:PF10070) and putative cation transporter subunit (PFAM:PF00361). These two proteins, which we name DabA and DabB for “DABs accumulate bicarbonate,” function as a heterodimeric, energy-coupled inorganic carbon pump inE. coli. Furthermore, DabA binds zinc and has a an active site homologous to a β-carbonic anhydrase. Based on these results, we propose that DABs function as vectorial CAs coupled to cation gradients and serve as inorganic carbon pumps throughout prokaryotic phyla.
Kinesin-6 Klp9 plays motor-dependent and -independent roles in collaboration with Kinesin-5 Cut7 and the microtubule crosslinker Ase1 in fission yeast
Authors: Yukawa Masashi , Okazaki Masaki , Teratani Yasuhiro , Furuta Ken’ya , Toda Takashi 
Published: November 2018

ABSTRACTBipolar mitotic spindles play a critical part in accurate chromosome segregation. During late mitosis, spindle microtubules undergo drastic elongation towards the cell cortex in a process called anaphase B. Two kinesin motors, Kinesin-5 and Kinesin-6, are thought to generate outward forces to drive spindle elongation, and the microtubule crosslinker Ase1/PRC1 maintains structural integrity of antiparallel microtubules. However, how these three proteins orchestrate this process remains unknown. Here we explore the functional interplay among fission yeast Kinesin-5/Cut7, Kinesin-6/Klp9 and Ase1. Using total internal reflection fluorescence microscopy, we show that Klp9 is a processive plus end-directed motor. klp9Δase1Δ is synthetically lethal. Surprisingly, this lethality is not ascribable to the defective motor activity of Klp9; instead, it is dependent upon an NLS and coiled coil domains within the non-motor region. We isolated a cut7 mutant (cut7-122) that displays temperature sensitivity only in the absence of Klp9. Interestingly, cut7-122 is impaired specifically in late mitotic stages. cut7-122klp9Δ double mutant cells exhibit additive defects in spindle elongation. Together, we propose that Klp9 plays dual roles during anaphase B; one is motor-dependent that collaborates with Cut7 in force generation, while the other is motor-independent and ensures structural integrity of spindle microtubules together with Ase1.
A xylose-inducible expression system and a CRISPRi-plasmid for targeted knock-down of gene expression inClostridioides difficile
Authors: Müh Ute , Pannullo Anthony G. , Weiss David S. , Ellermeier Craig D. 
Published: November 2018

AbstractHere we introduce plasmids for xylose-regulated expression and repression of genes inClostridioides difficile. The xylose-inducible expression vector allows for ~100-fold induction of anmCherryOptreporter gene. Induction is titratable and uniform from cell-to-cell. The gene repression plasmid is a CRISPR-interference (CRISPRi) system based on a nuclease-defective, codon-optimized allele of theStreptococcus pyogenesCas9 protein (dCas9) that is targeted to a gene of interest by a constitutively-expressed single guide RNA (sgRNA). Expression ofdCas9is induced by xylose, allowing investigators to control the timing and extent of gene-silencing, as demonstrated here by dose-dependent repression of a chromosomal gene for a red fluorescent protein (maximum repression ~100-fold). To validate the utility of CRISPRi for deciphering gene function inC. difficile, we knocked-down expression of three genes involved in biogenesis of the cell envelope: the cell division geneftsZ, the S-layer protein geneslpAand the peptidoglycan synthase genepbp-0712. CRISPRi confirmed known or expected phenotypes associated with loss of FtsZ and SlpA, and revealed that the previously uncharacterized peptidoglycan synthase PBP-0712 is needed for proper elongation, cell division and protection against lysis.ImportanceClostridioides difficilehas become the leading cause of hospital-acquired diarrhea in developed countries. A better understanding of the basic biology of this devastating pathogen might lead to novel approaches for preventing or treatingC. difficileinfections. Here we introduce new plasmid vectors that allow for titratable induction (Pxyl) or knockdown (CRISPRi) of gene expression. The CRISPRi plasmid allows for easy depletion of target proteins inC. difficile. Besides bypassing the lengthy process of mutant construction, CRISPRi can be used to study the function of essential genes, which are particularly important targets for antibiotic development.
Pooled clone collections by multiplexed CRISPR-Cas12a-assisted gene tagging in yeast
Authors: Buchmuller Benjamin C. , Herbst Konrad , Meurer Matthias , Kirrmaier Daniel , Sass Ehud , Levy Emmanuel D. , Knop Michael 
Published: November 2018

AbstractClone collections of modified strains (‘libraries’) are a major resource for systematic studies with the yeast Saccharomyces cerevisiae. Construction of such libraries is time-consuming, costly and confined to the genetic background of a specific yeast strain. To overcome these limitations, we present CRISPR-Cas12a (Cpf1)-assisted tag library engineering (CASTLING) for multiplexed strain construction. CASTLING uses microarray-synthesized oligonucleotide pools and in vitro recombineering to program the genomic insertion of long DNA constructs via homologous recombination. One simple transformation yields pooled libraries with >90% of correctly tagged clones. Up to several hundred genes can be tagged in a single step and, on a genomic scale, approximately half of all genes are tagged with only ∼10-fold oversampling. We report several parameters that affect tagging success and provide a quantitative targeted next-generation sequencing method to analyze such pooled collections. Thus, CASTLING unlocks new avenues for increased throughput in functional genomics and cell biology research.
MiR-195 regulates mitochondrial function by targeting mitofusin-2 in breast cancer cells
Authors: Purohit Paresh Kumar , Edwards Ruairidh , Tokatlidis Kostas , Saini Neeru 
Published: November 2018

AbstractMitochondrial dynamics is a highly dysregulated process in cancer. Apoptosis and mitochondrial fission are two concurrent events wherein increased mitochondrial fragmentation serves as a hallmark of apoptosis. We have shown earlier that miR-195 exerts pro-apoptotic effects in breast cancer cells. Herein, we have demonstrated miR-195 as a modulator of mitochondrial dynamics and function. Imaging experiments upon miR-195 treatment have shown that mitochondria undergo extensive fission. We validated mitofusin2 as a potential target of miR-195. Which may provide a molecular explanation for the respiratory defects induced by miR-195 over-expression in breast cancer cells? Active, but not total, mitochondrial mass, was reduced with increasing levels of miR-195. We have further shown that miR-195 enhances mitochondrial SOD-2 expression but does not affect PINK1 levels in breast cancer cells. Collectively, we have revealed that miR-195 is a modulator of mitochondrial dynamics by targeting MFN2 thereby impairing mitochondrial function. Concomitantly, it enhances the scavenger of reactive oxygen species (SOD-2) to maintain moderate levels of oxidative stress. Our findings suggest a therapeutic potential of miR-195 in both ER-positive as well as ER-negative breast cancer cells.
Physiological regulation of bud burst in grapevine
Authors: Signorelli Santiago , Shaw Jeremy , Hermawaty Dina , Wang Zi , Verboven Pieter , Considine John A. , Considine Michael J. 
Published: November 2018

AbstractThe physiological constraints on bud burst in woody perennials, including the prerequisite for vascular development remain unresolved. Both light and tissue oxygen status have emerged as important cues for vascular development in other systems, however, light requirement appears to be facultative in grapevine, and the information related to the spatial variability of oxygen in buds is unclear. Here, we analysed apoplastic development at early stages of grapevine bud burst and combined molecular modelling with histochemical techniques to determine the pore size of cell walls in grapevine buds. The data demonstrate that quiescent grapevine buds were impermeable to apoplastic dyes (acid fuchsin and eosin Y) until after bud burst was established. The molecular exclusion size was calculated to be 2.1 nm, which would exclude most macromolecules except simple sugars and phytohormones.In vivoexperiments show that grapevine buds were able to resume growth even following excision from the cane, and that the outer scales of grapevine buds may participate in the biochemical repression of bud burst. Furthermore, we demonstrate that the tissue oxygen partial pressure data correlated well with structural heterogeneity within the bud and differences in tissue density. These data consolidate evidence that the meristematic core becomes rapidly oxygenated during bud burst. Taken together, and when put in the context of earlier studies, these data provide solid evidence that the physiological and biochemical events that initiate bud burst reside within the bud, and question the role of long distance signalling in this developmental transition.HighlightsThe apoplastic pore size between the grapevine bud and the mother vine is dynamically regulated in the transition to bud burst.The molecular exclusion size of the apoplastic connection between the bud and cane is calculated 2.1 nm prior to the initiation of bud burst.The structural heterogeneity of the bud explains the spatial variance in tissue oxygen status, and the meristematic core is oxygenated during the initiation of bud burst.Long distance maternal signals are not a requirement for bud burst.
Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems: Biocoenosis ofBotryococcusconsortia
Authors: Blifernez-Klassen Olga , Klassen Viktor , Wibberg Daniel , Cebeci Enis , Henke Christian , Rückert Christian , Chaudhari Swapnil , Rupp Oliver , Blom Jochen , Winkler Anika , Al-Dilaimi Arwa , Goesmann Alexander , Sczyrba Alexander , Kalinowski Jörn , Bräutigam Andrea , Kruse Olaf 
Published: November 2018

AbstractBacteria occupy all major ecosystems and maintain an intensive relationship to the eukaryotes, developing together into complex biomes (i.e., phycosphere and rhizosphere). Interactions between eukaryotes and bacteria range from cooperative to competitive, with the associated microorganisms affecting their host’s development, growth, health and disease. Since the advent of non-culture dependent analytical techniques such as metagenome sequencing, consortia have been described but owing to the complex interactions rarely functionally dissected. Multifaceted analysis of the microbial consortium of the ancient phytoplanktonBotryococcusas an attractive model food web revealed that its all abundant bacterial members belong to a distinct niche of biotin auxotrophs, essentially depending on the microalga. In addition, hydrocarbonoclastic bacteria without vitamin auxotrophies, which adversely affect the algal cell morphology, appear evidently decimated. Synthetic rearrangement of a minimal community consisting of alga, mutualistic and parasitic bacteria underpins the model of a eukaryote that domesticates its own mutualistic bacterial “zoo” to manipulate and control its surrounding biosphere. This model of domestication of mutualistic bacteria for the defense against destruents by a eukaryotic host could represent ecologically relevant interactions that cross species boundaries. Metabolic and system reconstruction disentangles the relationships and provide a blueprint for the construction of mutually beneficial synthetic ecosystems.
Cold-Inducible RNA-binding protein (CIRBP) adjusts clock gene expression and REM sleep recovery following sleep deprivation
Authors: Hoekstra Marieke MB , Emmenegger Yann , Franken Paul 
Published: November 2018

AbstractSleep depriving mice affects clock gene expression, suggesting that these genes partake in sleep homeostasis. The mechanisms linking wakefulness to clock gene expression are, however, not well understood. We propose CIRBP because its rhythmic expression is i) sleep-wake driven and ii) necessary for high-amplitude clock gene expressionin vitro. We therefore expectCirbpknock-out (KO) mice to exhibit attenuated sleep-deprivation (SD) induced changes in clock gene expression, and consequently to differ in their sleep homeostatic regulation. Lack of CIRBP indeed blunted the SD-incurred changes in cortical expression of the clock geneRev-erbαwhereas it amplified the changes inPer2andClock. Concerning sleep homeostasis, KO mice accrued only half the extra REM sleep wild-type (WT) littermates obtained during recovery. Unexpectedly, KO mice were more active during lights-off which was accompanied by an acceleration of theta oscillations. Thus, CIRBP adjusts cortical clock gene expression after SD and expedites REM sleep recovery.
The mouse Klf1 Nan variant impairs nuclear condensation and erythroid maturation
Authors: Cantú Ileana , Werken Harmen J.G. van de , Gillemans Nynke , Stadhouders Ralph , Heshusius Steven , Maas Alex , Ozgur Zeliha , van IJcken Wilfred F.J. , Grosveld Frank , von Lindern Marieke , Philipsen Sjaak , van Dijk Thamar B. 
Published: November 2018

ABSTRACTKrüppel-like factor 1 (KLF1) is an essential transcription factor for erythroid development, as demonstrated by Klf1 knockout mice which die around E14 due to severe anemia. In humans, >65 KLF1 variants, causing different erythroid phenotypes, have been described. The Klf1 Nan variant, a single amino acid substitution (p.E339D) in the DNA binding domain, causes hemolytic anemia and is dominant over wildtype KLF1. Here we describe the effects of the Nan variant during fetal development. We show that Nan embryos have defects in erythroid maturation. RNA-sequencing of the Nan fetal liver cells revealed that Exportin 7 (Xpo7) was among the ~780 deregulated genes. This nuclear exportin is implicated in terminal erythroid differentiation; in particular it is involved in nuclear condensation. Indeed, KLF1 Nan fetal liver cells had larger nuclei and reduced chromatin condensation. Knockdown of XPO7 in wildtype erythroid cells caused a similar phenotype. We conclude that reduced expression of XPO7 is partially responsible for the erythroid defects observed in Nan erythroid cells.
Astroglial dysfunctions drive aberrant synaptogenesis in developing brain with lengthy general anesthesia
Authors: Zhou Bin , Chen Lingmin , Liao Ping , Huang Lu , Chen Zhuo , Yu Guoqiang , Wang Li , Zhang Jianguo , Zuo Yunxia , Liu Jin , Jiang Ruotian 
Published: November 2018

AbstractLengthy use of general anesthetics (GAs) causes cognitive deficits in developing brain, which has raised significant clinical concerns such that FDA is warning on the use of GAs in children younger than 3 years. However, the molecular and cellular mechanisms for GAs-induced neurotoxicity remain largely unknown. Here we report that sevoflurane, a commonly used GA in pediatrics, causes compromised astrocyte morphogenesis, spatiotemporally correlated to the synaptic overgrowth with reduced synaptic function in developing cortex in a regional-, exposure-length- and age-specific manner. Sevoflurane disrupts astrocyte Ca2+ homeostasis both acutely and chronically, which leads to the down regulation of Ezrin, an actin-binding membrane protein, which we found is critically involved in astrocyte morphogenesis in vivo. Importantly, in normal developing brain, the genetic intervention of astrocyte morphogenesis is sufficient to produce the aberrant synaptic structure and function virtually identical to the ones induced by lengthy sevoflurane exposure. Our data uncover that astrocytes are unexpectedly central targets for GAs to exert toxic effects, and that astrocyte morphological integrity is crucial for synaptogenesis in the developing brain.
Small GTPase patterning: How to stabilise cluster coexistence
Authors: Jacobs Bas , Molenaar Jaap , Deinum Eva E. 
Published: November 2018

AbstractMany biological processes have to occur at specific locations on the cell membrane. These locations are often specified by the localised activity of small GTPase proteins. Some processes require the formation of a single cluster of active GTPase, also called unipolar polarisation (here “polarisation”), whereas others need multiple coexisting clusters. Moreover, sometimes the pattern of GTPase clusters is dynamically regulated after its formation. This raises the question how the same interacting protein components can produce such a rich variety of naturally occurring patterns. Most currently used models for GTPase-based patterning inherently yield polarisation. Such models may at best yield transient coexistence of at most a few clusters, and hence fail to explain several important biological phenomena. These existing models are all based on mass conservation of total GTPase and some form of direct or indirect positive feedback. Here, we show that either of two biologically plausible modifications can yield stable coexistence: including explicit GTPase turnover, i.e., breaking mass conservation, or negative feedback by activation of an inhibitor like a GAP. Since we start from two different polarising models our findings seem independent of the precise self-activation mechanism. By studying the net GTPase flows among clusters, we provide insight into how these mechanisms operate. Our coexistence models also allow for dynamical regulation of the final pattern, which we illustrate with examples of pollen tube growth and the branching of fungal hyphae. Together, these results provide a better understanding of how cells can tune a single system to generate a wide variety of biologically relevant patterns.Author summaryWhere to form a bud? Where to reinforce the cell wall? In which direction to move? These are all important decisions a cell may have to make. Proper patterning of the cell membrane is a critical part of such decisions. These patterns are often specified by the local activity of proteins called small GTPases. Mathematical models have been an important tool in understanding the mechanisms behind small GTPase-based patterning. Most of these models, however, only allow for the formation of a single cluster of active GTPase and thus cannot explain patterns of multiple coexisting GTPase clusters. A previously proposed mechanism for such coexistence can only explain a temporary, unstable coexistence, and fails to explain several key biological phenomena. In this manuscript, we investigate two mechanisms that can produce patterns of many stably coexisting GTPase clusters. Using a combination of modelling techniques, we show why these mechanisms work. We also show that these mechanisms allow for the addition of new clusters to an existing pattern, as is observed for example during the branching of fungal hyphae. With our results, we now have handles to explain the full range of naturally occurring small GTPase patterns.