bluuebunny/crossref_metadata_2025_split huggingface dataset:
An analysis and optimization of growth condition requirements of the fast-growing bacteriumVibrio natriegens
Authors: Örencik Celine , Müller Sara , Kirner Thomas , Amann Egon 
Published: September 2019

ABSTRACTThe fast-growing Gram-negative bacteriumVibrio natriegensis an attractive host for a range of applications in molecular biology and biotechnology. Moreover, the remarkable speed of growth ofVibrio natriegensposes fundamental questions on bacterial physiology and metabolism, energy production, DNA replication and protein synthesis, besides others. In order to address such questions, a solid understanding of the physiological and physical/chemical basis of growth requirements is essential. Here we report a systematic analysis of i) various growth media composition, ii) incubation temperature, iii) pH dependence, and iv) salt concentration requirements for optimal growth ofV. natriegensstrain DSMZ 759. As a result of the studies, the following optimal conditions were Established: LB medium with 2.5 % NaCl, pH 7.0 – 8.5 and incubation at 37°C under aerobic conditions. Incubation temperatures above 37 °C slows growth significantly. Incubation temperatures below 37 °C slows growth, but at a lower rate. Incubation at or below 28 °C should be avoided. Under such optimized, standard laboratory conditions, a doubling time of td= 13.6 minutes was observed forV. natriegensmeasured in mid-log growth phase. The optimized conditions presented here for the growth ofV. natriegenscan be easily applied in any standardly equipped laboratory. For comparison, identical growth conditions forEscherichia coliwere analyzed and are presented as well.IMPORTANCEGoal of this study was to understand the physiological growths requirements ofV. natriegensin routine microbiology and molecular biology laboratory settings. The result is a standardized protocol for the optimized growth of the naturally isolated (wild type)V. natriegensstrain DSMZ 759. This protocol can be employed for routine application ofV. natriegensfor any kind of biochemical, molecular biology and genomic studies and utilization under normal laboratory conditions used by many routinely equipped laboratories.
Forging new antibiotic combinations under iron-limiting conditions
Authors: Chan Derek C. K. , Guo Irene , Burrows Lori L. 
Published: September 2019

ABSTRACTPseudomonas aeruginosais a multidrug-resistant nosocomial pathogen. We showed previously that thiostrepton (TS), a gram-positive thiopeptide antibiotic, was imported via pyoverdine receptors and synergized with iron chelator deferasirox (DSX) to inhibit the growth ofP. aeruginosaandAcinetobacter baumanniiclinical isolates. A small number ofP. aeruginosaandA. baumanniiisolates were resistant to the combination, prompting us to search for other compounds that could synergize with TS against those strains. From literature surveys we selected 14 compounds reported to have iron-chelating activity, plus one iron analogue, and tested them for synergy with TS. Doxycycline (DOXY), ciclopirox olamine (CO), tropolone (TRO), clioquinol (CLI), and gallium nitrate (GN) synergized with TS. Individual compounds were bacteriostatic but the combinations were bactericidal. Our spectrophotometric data and chrome azurol S agar assay confirmed that the chelators potentate TS activity through iron sequestration rather than through their innate antimicrobial activities. A triple combination of TS + DSX + DOXY had the most potent activity againstP. aeruginosaandA. baumanniiisolates. OneP. aeruginosaclinical isolate was resistant to the triple combination, but susceptible to a triple combination containing higher concentrations of CLI, CO, or DOXY. AllA. baumanniiisolates were susceptible to the triple combinations. Our data reveal a diverse set of compounds with dual activity as antibacterial agents and TS adjuvants, allowing combinations to be tailored for resistant clinical isolates.
Optimal response to quorum-sensing signals varies in different host environments with different pathogen group size
Authors: Zhou Liqin , Slamti Leyla , Lereclus Didier , Raymond Ben 
Published: September 2019

AbstractThe persistence of genetic variation in master regulators of gene expression, such as quorum-sensing systems, is hard to explain. Here, we investigated two alternative hypotheses for the prevalence of polymorphic quorum-sensing in Gram-positive bacteria,i.e. the use of different signal / receptor pairs (‘pherotypes’) to regulate the same functions. First, social interactions between pherotypes or ‘facultative cheating’ may favour rare variants that exploit the signals of others. Second, different pherotypes may increase fitness in different environments. We evaluated these hypotheses in the invertebrate pathogenBacillus thuringiensis, using three pherotypes expressed in a common genetic background. Facultative cheating occurred in homogenized hosts, in contrast, rare pherotypes had reduced fitness in naturalistic infections. There was clear support for environment-dependent fitness: pherotypes varied in responsiveness to signals and in mean competitive fitness. Notably, competitive fitness varied with group size: the pherotype with highest responsiveness to signals performed best in smaller hosts where infections have a lower pathogen group size. Less responsive pherotypes performed best in larger hosts. Results using homogenized insect media fit with the expectation of facultative cheating and social evolution theory, but results from naturalist oral infections do not fit many of the predictions from this body of theory. In this system, low signal abundance appears to limit fitness in hosts while the optimal level of response to signals varies in different host environments.ImportanceQuorum sensing describes the ability of microbes to alter gene regulation according to their local population size. Some successful theory suggests that this is a form of cooperation: investment in shared products is only worthwhile if there are sufficient bacteria making the same product. This theory can explain the genetic diversity in these signaling systems in Gram-positive bacteria such asBacillusandStaphylococcus. The possible advantages gained by rare genotypes (which can exploit the products of their more common neighbours) could explain why different genotypes can coexist. We show that while these social interactions can occur in simple laboratory experiments they do not occur in naturalistic infections using an invertabrate pathogen,Bacillus thuringiensis. Instead our results suggest that different genotypes are adapted to different-sized hosts. Overall, social models are not easily applied to this system implying that a new explanation for this form of quorum sensing is required.
Dual UTR-A novel 5′ untranslated region design for synthetic biology applications
Authors: Le Simone Balzer , Onsager Ingerid , Lorentzen Jon Andreas , Lale Rahmi 
Published: September 2019

ABSTRACTBacterial 5′ untranslated regions of mRNA (UTR) involve in a complex regulation of gene expression; however, the exact sequence features contributing to gene regulation are not yet fully understood. In this study, we report the design of a novel 5′ UTR, dual UTR, utilising the transcriptional and translational characteristics of 5′ UTRs in a single expression cassette. The dual UTR consists of two 5′ UTRs, each separately leading to either increase in transcription or translation of the reporter, that are separated by a spacer region, enabling de novo translation initiation. We rationally create dual UTRs with a wide range of expression profiles and demonstrate the functionality of the novel design concept in Escherichia coli and in Pseudomonas putida using different promoter systems and coding sequences. Overall, we demonstrate the application potential of dual UTR design concept in various synthetic biology applications ranging from fine-tuning of gene expression to maximisation of protein production.
Programmed Cell Death in the Developing Brachypodium distachyon Grain
Authors: Saada Safia , Solomon Charles Ugochukwu , Drea Sinéad 
Published: September 2019

SummaryThe normal developmental sequence in a grass grain entails the death of several maternal and filial tissues in a genetically regulated process termed programmed cell death (PCD). The progression and molecular aspects of PCD in developing grain have been reported for domesticated species like barley, rice, maize and wheat. Here, we report a detailed investigation of PCD in the developing grain of a wild model species, Brachypodium distachyon.We detected PCD in developing Brachypodium grains using molecular and histological approaches. We also identified and surveyed the expression of Brachypodium orthologs of protease genes known to contribute to grain PCD.We found that Brachypodium nucellus degenerates by PCD in a centrifugal pattern following anthesis, although at a slower rate compared to cultivated cereals. Mesocarp PCD was not coordinated with endosperm development. Brachypodium lacks an expansion of vacuolar processing enzymes known for their roles in nucellar PCD.Combined with existing knowledge on grain PCD, our study suggests the importance of rapid nucellar PCD for grain size and that the pattern of mesocarp PCD affects grain shape.
Mechanistic macroecology: exploring the drivers of latitudinal variation in terrestrial body size in a General Ecosystem Model
Authors: Harfoot Michael Brian James , Abraham Andrew , Tittensor Derek P , Costa Gabriel C , Faurby Søren , Feldman Anat , Itescu Yuval , Meiri Shai , Morales-Castilla Ignacio , Oliveira Brunno F , Purves Drew 
Published: September 2019

ABSTRACTMany mechanisms have been hypothesized to explain Bergmann’s rule - the correlation of body size with latitude. However, it is not feasible to assess the contribution of hypothesised mechanisms by experimental manipulation or statistical correlation. Here, we evaluate two of the principal hypothesised mechanisms, related to thermoregulation and resource availability, using structured experiments in a mechanistic global ecosystem model. We simulated the broad structure of assemblages and ecosystems using the Madingley model, a mechanistic General Ecosystem Model (GEM). We compared emergent modelled biogeographic patterns in body mass to empirical patterns for mammals and birds. We then explored the relative contribution of thermoregulation and resource availability to body mass clines by manipulating the model’s environmental gradients. Madingley produces body size gradients that are in broad agreement with empirical estimates. Thermoregulation and resource availability were both important controls on body mass for endotherms, but only temperature for ectotherms. Our results suggest that seasonality explains animal body mass patterns through a complex set of mechanisms. Process-based GEMs generate broadly realistic biogeographic body mass patterns. Ecologists can use them in novel ways: to explore causality, or for generating and testing hypotheses for large-scale, emergent ecological patterns. At the same time, macroecological patterns are useful for evaluating mechanistic models. Iteratively developing GEMs, and evaluating them against macroecological patterns, could generate new insights into the complex causes of such patterns.
OTULIN protects the liver against cell death, inflammation, fibrosis, and cancer
Authors: Damgaard Rune Busk , Jolin Helen E. , Allison Michael E.D. , Davies Susan E. , McKenzie Andrew N.J. , Komander David 
Published: September 2019

SummaryThe deubiquitinase OTULIN removes methionine-1 (M1)-linked polyubiquitin chains to regulate TNF-mediated inflammation and cell death, but the physiological role of OTULIN outside the immune system is poorly understood. Here, we identify OTULIN as a liver tumour suppressor in mice. Hepatocyte-specific OTULIN deletion causes spontaneous steatohepatitis, extensive fibrosis, and pre-malignant tumours by eight weeks of age, which progresses to hepatocellular carcinoma by 7-12 months. OTULIN deficiency triggers apoptosis and inflammation in the liver, but surprisingly, steatohepatitis and pre-malignant growth is independent of TNFR1 signalling. Instead, the pathology in OTULIN-deficient livers is associated with increased mTOR activation, and mTOR inhibition with rapamycin reduces fibrosis and pre-malignant growth. This demonstrates that OTULIN is critical for maintaining liver homeostasis and preventing mTOR-driven liver disease.
Responses to heartbeats in ventromedial prefrontal cortex contribute to subjective preference-based decisions
Authors: Azzalini Damiano , Buot Anne , Palminteri Stefano , Tallon-Baudry Catherine 
Published: September 2019

AbstractForrest Gump or Matrix? Preference-based decisions are subjective and entail self-reflection. However, these self-related features are unaccounted for by known neural mechanisms of valuation and choice. Self-related processes have been linked to a basic interoceptive biological mechanism, the neural monitoring of heartbeats, in particular in ventromedial prefrontal cortex (vmPFC), a region also involved in value encoding. We thus hypothesized a functional coupling between the neural monitoring of heartbeats and the precision of value encoding in vmPFC. Human participants were presented with pairs of movie titles. They indicated either which movie they preferred, or performed a control objective visual discrimination that did not require self-reflection. Using magnetoencephalography, we measured heartbeat-evoked responses (HERs) before option presentation, and confirmed that HERs in vmPFC were larger when preparing to the subjective, self-related task. We retrieved the expected cortical value network during choice with time-resolved statistical modeling. Crucially, we show that larger HERs before option presentation are followed by stronger value encoding during choice in vmPFC. This effect is independent of the overall vmPFC baseline activity. The neural interaction between HERs and value encoding predicted preference-based choice consistency over time, accounting for both inter-individual differences and trial-to-trial fluctuations within individuals. Neither cardiac activity nor arousal fluctuations could account for any of the effects. HERs did not interact with the encoding of perceptual evidence in the discrimination task. Our results show that the self-reflection underlying preference-based decisions involves the integration of HERs to subjective value encoding in vmPFC, and that this integration contributes to preference stability.Significance statementDeciding whether you prefer Forrest Gump or Matrix is based on subjective values, which only you, the decision-maker, can estimate and compare, by asking yourself. Yet, how self-reflection is biologically implemented and its contribution to subjective valuation are not known. We show that in ventromedial prefrontal cortex, the neural response to heartbeats, an interoceptive self-related process, influences the cortical representation of subjective value. The neural interaction between the cortical monitoring of heartbeats and value encoding predicts choice consistency, i.e. whether you consistently prefer Forrest Gump over Matrix over time. Our results pave the way for the quantification of self-related process in decision making and may shed new light on the relationship between maladaptive decisions and impaired interoception.
A sex chromosome inversion is associated with copy number variation of mitochondrial DNA in zebra finch sperm
Authors: Knief Ulrich , Forstmeier Wolfgang , Kempenaers Bart , Wolf Jochen B. W. 
Published: September 2019

AbstractPropulsion of sperm cells via movement of the flagellum is of vital importance for successful fertilization. Presumably, the energy for this movement comes from the mitochondria in the sperm midpiece. Larger midpieces may contain more mitochondria, which should enhance the energetic capacity and hence promote mobility. Due to an inversion polymorphism on their sex chromosome TguZ, zebra finches (Taeniopygia guttata castanotis) exhibit large within-species variation in sperm midpiece length, and those sperm with the longest midpieces swim the fastest. Here, we test through quantitative real-time PCR in zebra finch ejaculates whether the inversion genotype has an effect on the copy number of mitochondrial DNA. Taking the inversion genotype as a proxy for midpiece length, we find that zebra finches with longer midpieces indeed have more copies of the mitochondrial DNA in their ejaculates than those with shorter midpieces, with potential downstream effects on the rate of ATP production and sperm swimming speed. This study sheds light on the proximate cause of a fitness-relevant genetic polymorphism, suggesting the involvement of central components of gamete energy metabolism.Data availabilitySupplementary data file
Structural Basis of Protein Arginine Methyltransferase Activation by a Catalytically Dead Homolog (Prozyme)
Authors: Hashimoto Hideharu , Kafková Lucie , Raczkowski Ashleigh , Jordan Kelsey , Read Laurie K. , Debler Erik W. 
Published: September 2019

AbstractProzymes are pseudoenzymes that stimulate the function of weakly active enzymes through complex formation. The majorTrypanosoma bruceiprotein arginine methyltransferase,TbPRMT1 enzyme (ENZ), requiresTbPRMT1 prozyme (PRO) to form an active heterotetrameric complex. Here we present the x-ray crystal structure of the ENZ-Δ52PRO tetrameric complex with the cofactor product S-adenosyl-L-homocysteine (AdoHcy) at 2.4 Å resolution. The individual ENZ and PRO units adopt the highly-conserved PRMT domain architecture and form an antiparallel heterodimer that corresponds to the canonical homodimer observed in all previously reported PRMTs. In turn, two such heterodimers assemble into a tetramer both in the crystal and in solution with twofold rotational symmetry. ENZ is unstable in absence of PRO and incapable of forming a homodimer due to a steric clash of a non-conserved tyrosine within the dimerization arm, rationalizing why PRO is required to complement ENZ to form a PRMT dimer that is necessary, but not sufficient for PRMT activity. The PRO structure deviates from other, active PRTMs in that it lacks the conserved η2 310-helix within the Rossmann fold, abolishing co-factor binding. In addition to its chaperone function for ENZ, PRO substantially contributes to substrate binding. Heterotetramerization is required for catalysis, since heterodimeric ENZ-PRO mutants lack binding affinity and methyltransferase activity towards the substrate proteinTbRGG1. Together, we provide a structural basis for PRMT1 ENZ activation by PRO heterotetramer formation, which is conserved across all kinetoplastids, and describe a chaperone function of the PRMT1 prozyme, which represents a novel mode of PRMT regulation.Graphical AbstractHighlightsThe crystal structure ofTrypanosoma bruceiprotein arginine methyltransferase 1 (PRMT1) is reportedTwo enzyme-prozyme heterodimers form a stable heterotetramer essential for catalysisThe catalytically dead prozyme lacks elements essential for AdoMet bindingThe enzyme alone is unstable and cannot form a canonical dimer due to steric clashesT. bruceiPRMT1 prozyme adopts a chaperone function conserved across kinetoplastids
Minimally disruptive optical control of protein tyrosine phosphatase 1B
Authors: Hongdusit Akarawin , Zwart Peter H. , Sankaran Banumathi , Fox Jerome M. 
Published: September 2019

ABSTRACTProtein tyrosine phosphatases regulate a myriad of essential subcellular signaling events, yet they remain difficult to study in their native biophysical context. Here we develop a minimally disruptive optical approach to control protein tyrosine phosphatase 1B (PTP1B)—an important regulator of receptor tyrosine kinases and a therapeutic target for the treatment of diabetes, obesity, and cancer—and we use that approach to probe the intracellular function of this enzyme. Our conservative architecture for photocontrol, which consists of a protein-based light switch fused to an allosteric regulatory element, preserves the native structure, activity, and subcellular localization of PTP1B, affords changes in activity that match those elicited by post-translational modifications inside the cell, and permits experimental analyses of the molecular basis of optical modulation. Findings indicate, most strikingly, that small changes in the activity of PTP1B can cause large shifts in the phosphorylation states of its regulatory targets.
Robust effects of corticothalamic feedback and behavioral state on movie responses in mouse dLGN
Authors: Spacek Martin A. , Crombie Davide , Bauer Yannik , Born Gregory , Liu Xinyu , Katzner Steffen , Busse Laura 
Published: September 2019

AbstractNeurons in the dorsolateral geniculate nucleus (dLGN) of the thalamus receive a substantial proportion of modulatory inputs from corticothalamic (CT) feedback and brain stem nuclei. Hypothesizing that these modulatory influences might be differentially engaged depending on the visual stimulus and behavioral state, we performed in vivo extracellular recordings from mouse dLGN while optogenetically suppressing CT feedback and monitoring behavioral state by locomotion and pupil dilation. For naturalistic movie clips, we found CT feedback to consistently increase dLGN response gain and promote tonic firing. In contrast, for gratings, CT feedback effects on firing rates were mixed. For both stimulus types, the neural signatures of CT feedback closely resembled those of behavioral state, yet effects of behavioral state on responses to movies persisted even when CT feedback was suppressed. We conclude that CT feedback modulates visual information on its way to cortex in a stimulus-dependent manner, but largely independently of behavioral state.