bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Salmonella LysR family regulator, RipR, activates the SPI-13 encoded itaconate degradation cluster
Authors: Hersch Steven J. , Navarre William Wiley 
Published: May 2019

AbstractItaconate is a dicarboxylic acid that inhibits the isocitrate lyase enzyme of the bacterial glyoxylate shunt. Activated macrophages have been shown to produce itaconate, suggesting that these immune cells may employ this metabolite as a weapon against invading bacteria. Here we demonstrate that, in vitro, itaconate can exhibit bactericidal effects under acidic conditions similar to the pH of a macrophage phagosome. In parallel, successful pathogens including Salmonella have acquired a genetic operon encoding itaconate degradation proteins, which are induced heavily in macrophages. We characterize the regulation of this operon by the neighbouring gene, ripR, in specific response to itaconate. Moreover, we develop an itaconate biosensor based on the operon promoter that can detect itaconate in a semi-quantitative manner and, when combined with the ripR gene, is sufficient for itaconate-regulated expression in E. coli. Using this biosensor with fluorescence microscopy, we observe bacteria responding to itaconate in the phagosomes of macrophage and provide additional evidence that interferon-γ stimulates macrophage itaconate synthesis and that J774 mouse macrophages produce substantially more itaconate than the human THP-1 monocyte cell line. In summary, we examine the role of itaconate as an antibacterial metabolite in mouse and human macrophage, characterize the regulation of Salmonella’s defense against it, and develop it as a convenient itaconate biosensor and inducible promoter system.ImportanceIn response to invading bacteria, immune cells can produce a molecule called itaconate, which can inhibit microbial metabolism. Here we show that itaconate can also directly kill Salmonella when combined with moderate acidity, further supporting itaconate’s role as an antibacterial weapon. We also discover how Salmonella recognizes itaconate and activates a defense to degrade it, and we harness this response to make a biosensor that detects the presence of itaconate. This biosensor is versatile, working in Salmonella enterica or lab strains of Escherichia coli, and can detect itaconate quantitatively in the environment and in immune cells. By understanding how immune cells kill bacteria and how the microbes defend themselves, we can better develop novel antibiotics to inhibit pathogens such as Salmonella.
cfrB, cfrC, and a potential new cfr-like gene in Clostridium difficile strains recovered across Latin America
Authors: Stojković Vanja , Ulate María Fernanda , Hidalgo-Villeda Fanny , Aguilar Emmanuel , Monge-Cascante Camilo , Pizarro-Guajardo Marjorie , Tsai Kaitlyn , Tzoc Edgardo , Camorlinga Margarita , Paredes-Sabja Daniel , Quesada-Gómez Carlos , Fujimori Danica Galonić , Rodríguez César 
Published: May 2019

ABSTRACTCfr is a radical S-adenosyl-L-methionine (SAM) enzyme that confers cross-resistance to all antibiotics targeting the large ribosomal subunit through hypermethylation of nucleotide A2503 of 23S rRNA. Of the four known cfr genes known to date, cfr(B) and cfr(C) have been sporadically found in C. difficile, yet functional characterization of cfr(C) is still lacking. We identified genes for putative Cfr-like enzymes among clinical C. difficile strains from Mexico, Honduras, Costa Rica, and Chile. To confirm their identity and activity, we obtained minimum inhibitory concentrations for ribosome-targeting antibiotics, annotated whole genome sequences, and performed a functional characterization of Cfr(C). The seven representative isolates analyzed displayed different levels of resistance to PhLOPSA antibiotics in the absence of the ribosome protection factor OptrA, and mutations in genes for 23S rRNAs or the ribosomal proteins L3 and L4. cfr(B) was detected in four isolates as part of a Tn6218-like transposon or an un-described mobile genetic element. In turn, cfr(C) was found integrated into an ICE-element. One isolate harbored a putative cfr-like gene that shows only 51-58% of sequence identity to Cfr and known Cfr-like enzymes. Moreover, our in vitro assays confirmed that Cfr(C) methylates E. coli and C. difficile 23S rRNA fragments. These results indicate selection of cfr-like genes in C. difficile from Latin America, suggest that the diversity of cfr-like resistance genes is larger than anticipated, and provide the first assessment of the methylation activity of Cfr(C).
PI3K activation prevents Aβ42-induced synapse loss and favors insoluble amyloid deposits formation
Authors: Arnés Mercedes , Romero Ninovska , Casas-Tintó Sergio , Acebes Ángel , Ferrús Alberto 
Published: May 2019

AbstractAlzheimer’s disease is, to a large extent, a disease of the synapse triggered by the unbalanced amyloidogenic cleavage of the amyloid precursor protein APP. Excess of Aβ42 peptide in particular is considered a hallmark of the disease. Here we drive the expression of the human Aβ42 peptide to assay the neuroprotective effects of PI3K in adultDrosophila melanogaster. We show that the neuronal expression of the human peptide elicits progressive toxicity in the adult. The pathological traits include reduced axonal transport, synapse loss, defective climbing ability and olfactory perception, as well as life-span reduction. The Aβ42-dependent synapse decay does not involve transcriptional changes in the core synaptic protein encoding genes:bruchpilot,liprinandsynaptobrevin. All toxicity features, however, are suppressed by the co-expression of PI3K. Moreover, PI3K activation induces a significant increase of 6E10 and Thioflavin-positive amyloid deposits. Mechanistically, we suggest that Aβ42-Ser26 could be a candidate residue for direct or indirect phosphorylation by PI3K. Finally, along with thesein vivoexperiments we further analyze Aβ42 toxicity and its suppression by PI3K activation inin vitroassays with SH-SY5Y human neuroblastoma cell cultures, where Aβ42 aggregation into large insoluble deposits is reproduced. Taken together, these results uncover a potential novel pharmacological strategy against this disease with PI3K activation as a target.
Deep Lipidomics and Molecular Imaging of Unsaturated Lipid Isomers: A Universal Strategy Initiated by mCPBA Epoxidation
Authors: Kuo Ting-Hao , Chung Hsin-Hsiang , Chang Hsin-Yuan , Lin Chiao-Wei , Wang Ming-Yang , Shen Tang-Long , Hsu Cheng-Chih 
Published: May 2019

ABSTRACTCellular lipidome is highly regulated through lipogenesis, rendering diverse double-bond positional isomers (C=C isomer) of a given unsaturated lipid species. In recent years, there are increasing reports indicating the physiological roles of C=C isomer compositions associated with diseases, while the biochemistry has not been fully understood due to the challenge in characterizing lipid isomers inherent to conventional mass spectrometry-based lipidomics. To address this challenge, we reported a universal, user-friendly, derivatization-based strategy, MELDI (mCPBA Epoxidation for Lipid Double-bond Identification), which enables both large-scale identification and spatial mapping of biological C=C isomers using commercial mass spectrometers without any instrument modification. With the developed liquid-chromatography mass spectrometry (LC-MS) lipidomics workflow, we elucidated more than 100 isomers among mono- and poly-unsaturated fatty acids and glycerophospholipids in both human serum, where novel isomers of low abundance were unambiguously quantified for the first time. The capability of MELDI-LC-MS in lipidome analysis was further demonstrated using the differentiated 3T3-L1 adipocytes, providing an insight into the cellular lipid reprogramming upon stearoyl-coenzyme A desaturase 1 (SCD1) inhibition. Finally, we highlighted the versatility of MELDI coupled with mass spectrometry imaging to spatially resolve cancer-associated alteration of lipid isomers in a metastatic mouse tissue section. Our results suggested that MELDI will contribute to current lipidomics pipelines with a deeper level of structural information, allowing us to investigate underlying lipid biochemistry.
Seawater salt-trappedPseudomonas aeruginosasurvives for years and gets primed for salinity tolerance
Authors: Elabed Hamouda , González-Tortuero Enrique , Ibacache-Quiroga Claudia , Bakhrouf Amina , Johnston Paul , Gaddour Kamel , Blázquez Jesús , Rodríguez-Rojas Alexandro 
Published: May 2019

AbstractBackgroundIn nature, microorganisms have to adapt to long-term stressful conditions often with growth limitations. However, little is known about the evolution of the adaptability of new bacteria to such environments.Pseudomonas aeruginosa, an opportunistic pathogen, after natural evaporation of seawater, was shown to be trapped in laboratory-grown halite crystals and to remain viable after entrapment for years. However, how this bacterium persists and survives in such hypersaline conditions is not understood.ResultsIn this study, we aimed to understand the basis of survival, and to characterise the physiological changes required to develop salt tolerance usingP. aeruginosaas a model. Several clones ofP. aeruginosawere rescued after fourteen years in naturally evaporated marine salt crystals. Incubation of samples in nutrient-rich broth allowed re-growth and subsequent plating yielded observable colonies. Whole genome sequencing of theP. aeruginosaisolates confirmed the recovery of the original strain. The re-grown strains, however, showed a new phenotype consisting of an enhanced growth in growing salt concentration compared to the ancestor strain. The intracellular accumulation of K+was elicited by high concentration of Na+in the external medium to maintain the homeostasis. Whole transcriptomic analysis by microarray indicated that seventy-eight genes had differential expression between the parental strain and derivative clones. Sixty-one transcripts were up-regulated, while seventeen were down-regulated. Based on a collection of single-gene knockout mutants and gene ontology analysis, we suggest that the adaptive response inP. aeruginosato hyper-salinity relies on multiple gene product interactions.ConclusionsThe individual gene contributions build up the observed phenotype, but do not ease the identification of salinity-related metabolic pathways. The long-term inclusion ofP. aeruginosain salt crystals primes the bacteria, mediating a readjustment of the bacterial physiology to growth in higher salt concentrations. Our findings provide a starting point to understand howP. aeruginosa, a relevant environmental and pathogenic bacterium, survives to long-term salt stress.
Engineering bacteriocin-mediated resistance against plant pathogenic bacteria in plants
Authors: Rooney William M. , Grinter Rhys , Correia Annapaula , Parkhill Julian , Walker Daniel , Milner Joel J. 
Published: May 2019

ABSTRACTPseudomonas syringae(Ps) and related plant pathogenic bacteria are responsible for losses in diverse crops such as tomato, kiwifruit, pepper, olive and soybean. Current solutions, involving the use of chemicals and the introduction of resistance genes, have enjoyed only limited success and may have adverse environmental impacts. Consequently, there is a pressing need to develop alternative technologies to address the problem of bacterial disease in crops. An alternative strategy is to utilise the narrow spectrum protein antibiotics (bacteriocins) used by diverse bacteria for competition against closely related species. Here, we demonstrate that active putidacin L1 (PL1) can be expressed at high levelsin plantaand expression of PL1 provides effective resistance against diverse pathovars ofPs.Furthermore, we found that strains which evolve to become insensitive to PL1; lose their O-antigen, exhibit reduced motility and are less virulent in PL1 transgenic plants. Our results provide proof-of-principle that transgene-mediated expression of a bacteriocinin plantais an effective strategy for providing disease resistance against bacterial pathogens. Genetically modified (GM) crops expressing insecticidal proteins have proved extremely successful as a strategy for pest management; expressing bacteriocins to control bacterial disease may have a similar potential. Crucially, nearly all genera of bacteria, including many plant pathogenic species, produce bacteriocins, providing an extensive source of these antimicrobial agents.SIGNIFICANCEWith the global population to surpass 9 billion by 2050 there is a huge demand to make industrial farming as efficient as possible. A disadvantage of industrial farming is the lack of genetic diversity within crop monocultures, which make them highly susceptible to diseases caused by plant pathogenic bacteria likePseudomonas syringae. Bacteriocins are narrow spectrum protein antibiotics which are produced by all major bacterial lineages. Their main purpose is to eliminate competitor strains to establish dominance within a niche. By arming plants with bacteriocins we can increase the genetic toolbox used to engineer crops to be resistant to specific bacterial plant pathogens.
Learning may help pollinators find their host plants in polluted landscapes
Authors: Cook Brynn , Haverkamp Alexander , Hansson Bill S. , Roulston T’ai , Lerdau Manuel , Knaden Markus 
Published: May 2019

AbstractPollination strongly contributes to food production, and often relies on pollinating insects. However, atmospheric pollution may interfere with pollination by disrupting floral plumes that pollinators use to navigate to flowers.In this study, we examine the impacts of pollution-induced elevated ozone levels on the composition of a floral blend ofNicotiana alataand examine the response of innate and trainedManduca sextato the ozone-altered blend.Ozone exposure altered the floral blend ofN. alata, and disrupted the innate attraction of naïveM. sextato the altered blend. However, associative learning can offset this disruption in attraction. Moths that were enticed with visual cues to an artificial flower emitting an ozonated blend learned to associate this blend with a nectar reward after just one rewarded experience. More importantly, moths that were rewarded while experiencing the unozonated floral blend of their host subsequently found the ozonated floral blend of the same host attractive, most likely due to experience-based reinforcement of ozone-insensitive cues in the blend.The attraction of moths to both unaltered and ozonated plumes is critical for tolerating polluted landscapes. At the host plant, where moths feed, floral emissions are relatively pure. As floral odors travel away from the host, however, they become degraded by pollution. Therefore, targeting the flower requires recognizing both conditions of the odor. The ability to generalize between the pure and ozone-altered scents may enable pollinators likeM. sextato maintain communication with their flowers and reduce the impact anthropogenic oxidants may have on plant-pollinator systems.
Fine chromatin-driven mechanism of transcription interference by antisense noncoding transcription
Authors: Gill Jatinder Kaur , Maffioletti Andrea , García-Molinero Varinia , Stutz Françoise , Soudet Julien 
Published: May 2019

AbstractEukaryotic genomes are almost entirely transcribed by RNA polymerase II (RNAPII). Consequently, the transcription of long noncoding RNAs (lncRNAs) often overlaps with coding gene promoters triggering potential gene repression through a poorly characterized mechanism of transcription interference. In this study, we propose a global model of chromatin-based transcription interference in Saccharomyces cerevisiae (S. cerevisiae). By using a noncoding transcription inducible strain, we analyzed the relationship between antisense elongation and coding sense repression, nucleosome occupancy and transcription-associated histone modifications using near-base pair resolution techniques. We show that antisense noncoding transcription leads to the deaceylation of a subpopulation of −1/+1 nucleosomes associated with increased H3K36 trimethylation (H3K36me3). Reduced acetylation results in decreased binding of the RSC chromatin remodeler at −1/+1 nucleosomes and subsequent sliding into the Nucleosome-Depleted Region (NDR) hindering Pre-Initiation Complex (PIC) association. Finally, we extend our model by showing that natural antisense noncoding transcription significantly represses around 20% of S. cerevisiae genes through this chromatin-based transcription interference mechanism.HighlightsInduction of antisense noncoding transcription leads to −1/+1 nucleosome sliding that competes with sense transcription PIC deposition.Antisense induction leads to a subpopulation of H3K36me3 nucleosomes differently positioned compared to H3K18ac nucleosomes.RSC chromatin remodeler recruitment to −1/+1 nucleosomes is modulated by histone acetylation levels.20% of S. cerevisiae genes are significantly repressed by this antisense-dependent chromatin-based transcription interference mechanism.
An arbitrary-spectrum spatial visual stimulator for vision research
Authors: Franke Katrin , Chagas André Maia , Zhao Zhijian , Zimmermann Maxime J.Y. , Qiu Yongrong , Szatko Klaudia , Baden Tom , Euler Thomas 
Published: May 2019

AbstractVisual neuroscientists require accurate control of visual stimulation. However, few stimulator solutions simultaneously offer high spatio-temporal resolution and free control over the spectra of the light sources, because they rely on off-the-shelf technology developed for human trichromatic vision. Importantly, consumer displays fail to drive UV-shifted short wavelength-sensitive photoreceptors, which strongly contribute to visual behaviour in many animals, including mice, zebrafish and fruit flies. Moreover, many non-mammalian species feature more than three spectral photoreceptor types. Here, we present a flexible, spatial visual stimulator with up to 6 arbitrary spectrum chromatic channels. It combines a standard digital light processing engine with open source hard- and software that can be easily adapted to the experimentalist’s needs. We demonstrate the capability of this general visual stimulator experimentally in thein vitromouse retinal whole-mount and thein vivozebrafish. Hereby, we intend starting a community effort of sharing and developing a common stimulator design.
Differential sperm motility mediates the sex ratio drive shaping mouse sex chromosome evolution
Authors: Rathje CC , Johnson EEP , Drage D , Patinioti C , Silvestri G , Affara NA , Ialy-Radio C , Cocquet J , Skinner BM , Ellis PJI 
Published: May 2019

SummaryThe search for morphological or physiological differences between X- and Y-bearing mammalian sperm has provoked controversy for decades. Many potential differences have been proposed, but none validated, while accumulating understanding of syncytial sperm development has cast doubt on whether such differences are possible even in principle. We present the first ever mammalian experimental model to trace a direct link from a measurable physiological difference between X- and Y-bearing sperm to the resulting skewed sex ratio. We show that in mice with deletions on chromosome Yq, birth sex ratio distortion is due to a relatively greater motility of X-bearing sperm, and not to any aspect of sperm/egg interaction. Moreover, the morphological distortion caused by Yq deletion is more severe in Y-bearing sperm, providing a potential hydrodynamic basis for the altered motility. This reinforces a growing body of work indicating that sperm haploid selection is an important and underappreciated evolutionary force.
Chromosome organization by a conserved condensin-ParB system in the actinobacteriumCorynebacterium glutamicum
Authors: Böhm Kati , Giacomelli Giacomo , Schmidt Andreas , Imhof Axel , Koszul Romain , Marbouty Martial , Bramkamp Marc 
Published: May 2019

AbstractHigher-order chromosome folding and segregation is tightly regulated in all domains of life. In bacteria, details on nucleoid organization regulatory mechanisms and function remains poorly characterized, especially in non-model species. Here, we investigate the role of DNA partitioning protein ParB and condensin complexes, two key players in bacterial chromosome structuring, in the actinobacteriumCorynebacterium glutamicum. Chromosome conformation capture reveals SMC-mediated long-range interactions around ten centromere-likeparSsites clustered at the replication origin (oriC). At least oneoriC-proximalparSsite is necessary for a reliable chromosome segregation. Using a combination of chromatin immunoprecipitation and photoactivated single molecule localization microscopy evidences the formation of distinct ParB-nucleoprotein subclusters in dependence ofparSnumbers. We further identified and functionally characterized two condensin paralogs. Whereas SMC/ScpAB complexes are loaded via ParB atparSsites mediating chromosomal inter-arm contacts like inBacillus subtilis, the MukBEF-like SMC complex MksBEFG does not contribute to chromosomal DNA-folding. Rather, the MksBEFG complex is involved in plasmid maintenance and interacts with the polaroriC-tethering factor DivIVA. These data complement current models of ParB-SMC/ScpAB crosstalk, while showing that some condensin complexes evolved functions uncoupled from chromosome folding.
Loss of developmental diapause as a prerequisite for social evolution in bees
Authors: Santos Priscila Karla Ferreira , Arias Maria Cristina , Kapheim Karen M. 
Published: May 2019

AbstractDiapause is a physiological arrest of development ahead of adverse environmental conditions and is a critical phase of the life cycle of many insects. In bees, diapause has been reported in species from all seven taxonomic families. However, they exhibit a variety of diapause strategies. These different strategies are of particular interest since shifts in the phase of the insect life cycle in which diapause occurs has been hypothesized to promote the evolution of sociality. Here we provide a comprehensive evaluation of this hypothesis with phylogenetic analysis and ancestral state reconstruction of the ecological and evolutionary factors associated with diapause phase. We find that social lifestyle, latitude, and voltinism are significant predictors of the life stage in which diapause occurs. Ancestral state reconstruction revealed that the most recent common ancestor of all bees likely exhibited developmental diapause and shifts to adult or reproductive diapause have occurred in the ancestors of lineages in which social behavior has evolved. These results provide fresh insight regarding the role of diapause as a prerequisite for the evolution of sociality in bees.
Mechanisms of chromosome biorientation and bipolar spindle assembly analyzed by computational modeling
Authors: Edelmaier Christopher J. , Lamson Adam R. , Gergely Zachary R. , Ansari Saad , Blackwell Robert , McIntosh J. Richard , Glaser Matthew A. , Betterton Meredith D. 
Published: May 2019

AbstractThe essential functions required for mitotic spindle assembly and chromosome biorientation and segregation are not fully understood, despite extensive study. To illuminate the combinations of ingredients most important to align and segregate chromosomes and simultaneously assemble a bipolar spindle, we developed a computational model of fission-yeast mitosis. Robust chromosome biorientation requires progressive restriction of attachment geometry, destabilization of misaligned attachments, and attachment force dependence. Large spindle length fluctuations can occur when the kinetochore-microtubule attachment lifetime is long. The primary spindle force generators are kinesin-5 motors and crosslinkers in early mitosis, while interkinetochore stretch becomes important after biorientation. The same mechanisms that contribute to persistent biorientation lead to segregation of chromosomes to the poles after anaphase onset. This model therefore provides a framework to interrogate key requirements for robust chromosome biorientation, spindle length regulation, and force generation in the spindle.