bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rap-protein paralogs ofB. thuringiensis: a multifunctional and redundant regulatory repertoire for the control of collective functions
Authors: Gastélum Gabriela , de la Torre Mayra , Rocha Jorge 
Published: September 2019

AbstractQuorum Sensing (QS) are mechanisms of synthesis and detection of signaling molecules to regulate gene expression and coordinate behaviors in bacterial populations. InBacillus subtilis(Bs), multiple paralog Rap-Phr QS systems (receptor-signaling peptide) are highly redundant and multifunctional, interconnecting the regulation of differentiation processes such as sporulation and competence. However, their functions in theB. cereusgroup are largely unknown. We evaluated the diversification of Rap-Phr systems in theB. cereusgroup as well as their functions, usingBacillus thuringiensisBt8741 as model. Bt8741 codes for eight Rap-Phr systems; these were overexpressed to study their participation in sporulation, biofilm formation, extracellular proteolytic activity and spreading. Our results show that five Rap-Phr systems (RapC, K, F, I and RapLike) inhibit sporulation, two of which (RapK and RapF) probably dephosphorylate of Spo0F from the Spo0A phosphorelay; these two Rap proteins also inhibit biofilm formation. Five systems (RapC, F, F2, I1 and RapLike) decrease extracellular proteolytic activity; finally, four systems (RapC, F1, F2 and RapLike) participate in spreading inhibition. Our bioinformatic analyses showed that Rap proteins from theB. cereusgroup diversified into five pherogroups, and we foresee that functions performed by Rap proteins of Bt8741 could also be carried out by Rap homologs in other species within the group. These results indicate that Rap-Phr systems constitute a highly multifunctional and redundant regulatory repertoire that enables bacteria from theB. cereusgroup to efficiently regulate collective functions during the bacterial life cycle, in the face of changing environments.ImportanceTheBacillus cereusgroup of bacteria includes species of high economic, clinical, biological warfare and biotechnological interest, e.g.B. anthracisin bioterrorism,B. cereusin food intoxications andB. thuringiensisin biocontrol. Knowledge on the ecology of these bacteria is hindered due to our limited understanding about the regulatory circuits that control differentiation and specialization processes. Here, we uncover the participation of eight Rap quorum-sensing receptors in collective functions ofB. thuringiensis. These proteins are highly multifunctional and redundant in their functions, linking ecologically relevant processes such as sporulation, biofilm formation, extracellular proteolytic activity, spreading, and probably other additional functions in species from theB. cereusgroup.
Exome sequencing of bulked segregants identified a novel TaMKK3-A allele linked to the wheat ERA8 ABA-hypersensitive germination phenotype
Authors: Martinez Shantel A. , Shorinola Oluwayesi , Conselman Samantha , See Deven , Skinner Daniel Z. , Uauy Cristobal , Steber Camille M. 
Published: September 2019

AbstractPreharvest sprouting (PHS) is the germination of mature grain on the mother plant when it rains before harvest. The ENHANCED RESPONSE TO ABA8 (ERA8) mutant increases seed dormancy and, consequently, PHS tolerance in soft white wheat ‘Zak’. ERA8 was mapped to chromosome 4A in a Zak/‘ZakERA8’ backcross population using bulked segregant analysis of exome sequenced DNA (BSA-exome-seq). ERA8 was fine-mapped relative to mutagen-induced SNPs to a 4.6 Mb region containing 70 genes. In the backcross population, the ERA8 ABA hypersensitive phenotype was strongly linked to a missense mutation TaMKK3-A-G1093A (LOD 16.5), a gene associated with natural PHS tolerance in barley and wheat. The map position of ERA8 was confirmed in an ‘Otis’/ZakERA8 but not in a ‘Louise’/ZakERA8 mapping population. This is likely because Otis carries the same natural PHS susceptible MKK3-A-A660S allele as Zak, whereas Louise carries the PHS tolerant MKK3-A-C660R allele. Thus, the variation for grain dormancy and PHS tolerance in the Louise/ZakERA8 population likely resulted from segregation of other loci rather than segregation for PHS tolerance at the MKK3 locus. This inadvertent complementation test suggests that the MKK3-A-G1093A mutation causes the ERA8 phenotype. Moreover, MKK3 was a known ABA signaling gene in the 70-gene 4.6 Mb ERA8 interval. None of these 70 genes showed the differential regulation in wild-type Zak versus ERA8 expected of a promoter mutation. Thus, the working model is that the ERA8 phenotype results from the MKK3-A-G1093A mutation.Key MessageUsing bulked segregant analysis of exome sequence, we fine-mapped the ABA hypersensitive mutant ERA8 in a wheat backcross population to the TaMKK3-A locus of chromosome 4A.
Loss of cerebellar function selectively affects intrinsic rhythmicity of eupneic breathing
Authors: Liu Yu , Qi Shuhua , Thomas Fridtjof , Correia Brittany L. , Taylor Angela P. , Sillitoe Roy V. , Heck Detlef H. 
Published: September 2019

ABSTRACTRespiration is controlled by central pattern generating circuits in the brain stem, whose activity can be modulated by inputs from other brain areas to adapt respiration to autonomic and behavioral demands. The cerebellum is known to be part of the neuronal circuitry activated during respiratory challenges, such as hunger for air, but has not been found to be involved in the control of unobstructed breathing at rest (eupnea). Here we applied a measure of intrinsic rhythmicity, the CV2, which evaluates the similarity of subsequent intervals and is thus sensitive to changes in rhythmicity at the temporal resolution of individual respiratory intervals. The variability of intrinsic respiratory rhythmicity was reduced in a mouse model of cerebellar ataxia compared to their healthy littermates. Irrespective of that difference, the average respiratory rate and the average coefficient of variation (CV) were comparable between healthy and ataxic mice. We argue that these findings are consistent with a proposed role of the cerebellum in the coordination of respiration with other rhythmic orofacial movements, such as fluid licking and swallowing.
Analysis of spatiotemporal specificity of small RNAs regulating hPSC differentiation and beyond
Authors: Li Lu , Li Jin Feng , Cao Dan Dan , Papadopoulos Vassilios , Chan Wai Yee 
Published: September 2019

AbstractWe present a quantitative analysis of small RNA dynamics during the transition from hPSCs to the three germ layer lineages to identify spatiotemporal-specific small RNAs that may be involved in hPSC differentiation. To determine the degree of spatiotemporal specificity, we utilized two algorithms, namely normalized maximum timepoint specificity index (NMTSI) and across-tissue specificity index (ASI). NMTSI could identify spatiotemporal-specific small RNAs that go up or down at just one timepoint in a specific lineage. ASI could identify spatiotemporal-specific small RNAs that maintain high expression from intermediate timepoints to the terminal timepoint in a specific lineage. Beyond analyzing single small RNAs, we also quantified the spatiotemporal-specificity of microRNA families and observed their differential expression patterns in certain lineages. To clarify the regulatory effects of group miRNAs on cellular events during lineage differentiation, we performed a gene ontology (GO) analysis on the downstream targets of synergistically up-and downregulated microRNAs. To provide an integrated interface for researchers to access and browse our analysis results, we designed a web-based tool at https://keyminer.pythonanywhere.com/km/.
Architectural RNA is required for heterochromatin organization
Authors: Thakur Jitendra , Fang He , Llagas Trizia , Disteche Christine M. , Henikoff Steven 
Published: September 2019

AbstractIn addition to its known roles in protein synthesis and enzyme catalysis, RNA has been proposed to stabilize higher-order chromatin structure. To distinguish presumed architectural roles of RNA from other functions, we applied a ribonuclease digestion strategy to our CUT&RUN in situ chromatin profiling method (CUT&RUN.RNase). We find that depletion of RNA compromises association of the murine nucleolar protein Nucleophosmin with pericentric heterochromatin and alters the chromatin environment of CCCTC-binding factor (CTCF) bound regions. Strikingly, we find that RNA maintains the integrity of both constitutive (H3K9me3 marked) and facultative (H3K27me3 marked) heterochromatic regions as compact domains, but only moderately stabilizes euchromatin. To establish the specificity of heterochromatin stabilization by RNA, we performed CUT&RUN on cells deleted for the Firre long non-coding RNA and observed disruption of H3K27me3 domains on several chromosomes. We conclude that RNA maintains local and global chromatin organization by acting as a structural scaffold for heterochromatic domains.
A conserved regulatory switch controls phosphatase activity and specificity
Authors: Ho Kristin , Bradshaw Niels 
Published: September 2019

AbstractProtein phosphatases must be regulated and specific for their substrates; how this control is achieved is critical for signaling by reversible phosphorylation. We recently reported the discovery of a regulatory switch that controls the activity of the PP2C family serine/threonine phosphatase SpoIIE from the bacterium Bacillus subtilis. This regulatory switch activates SpoIIE during spore development by forming the catalytically essential metal-binding site that is conserved across the PP2C family. We hypothesized that this switch is a conserved platform for regulating other PP2C phosphatases. An orthologous phosphatase from B. subtilis, RsbU, is activated under stress conditions and responds to different signals and acts on a different phosphoprotein substrate than SpoIIE. Using a combination of biochemical and genetic approaches, we find that broad features of the regulatory mechanism are conserved between SpoIIE and RsbU but that each phosphatase has adapted its response to be most appropriate for the distinct biological outputs it controls. In both cases, the switch accomplishes this by integrating substrate binding and recognition with regulatory inputs to control metal cofactor binding and catalysis. Thus, the switch is a conserved and mechanistically flexible regulatory platform that controls phosphatase activity and substrate specificity.
Pseudomonas aeruginosaleucine aminopeptidase influences early biofilm composition and structure via vesicle-associated anti-biofilm activity
Authors: Esoda Caitlin N. , Kuehn Meta J. 
Published: September 2019

AbstractPseudomonas aeruginosa, known as one of the leading causes of disease in cystic fibrosis (CF) patients, secretes a variety of proteases. These enzymes contribute significantly toP. aeruginosapathogenesis and biofilm formation in the chronic colonization of CF patient lungs, as well as playing a role in infections of the cornea, burn wounds and chronic wounds. We previously characterized a secretedP. aeruginosapeptidase, PaAP, that is highly expressed in chronic CF isolates. This leucine aminopeptidase is highly expressed during infection and in biofilms, and it associates with bacterial outer membrane vesicles (OMVs), structures known to contribute to virulence mechanisms in a variety of Gram-negative species and one of the major components of the biofilm matrix. We hypothesized that PaAP may play a role inP. aeruginosabiofilm formation. Using a lung epithelial cell/bacterial biofilm coculture model, we show that PaAP deletion in a clinicalP. aeruginosabackground alters biofilm microcolony composition to increase cellular density, while decreasing matrix polysaccharide content, and that OMVs from PaAP expressing strains but not PaAP alone or in combination with PaAP deletion strain-derived OMVs could complement this phenotype. We additionally found that OMVs from PaAP expressing strains could cause protease-mediated biofilm detachment, leading to changes in matrix and colony composition. Finally, we showed that the OMVs could also mediate the detachment of biofilms formed by both non-selfP. aeruginosastrains andKlebsiella pneumoniae, another respiratory pathogen. Our findings represent novel roles for OMVs and the aminopeptidase in the modulation ofP. aeruginosabiofilm architecture.ImportanceBiofilm formation by the bacterial pathogenP. aeruginosais known to contribute to drug- resistance in nosocomial infections and chronic lung infections of cystic fibrosis patients. In order to treat these infections more successfully, the mechanisms of bacterial biofilm development must be elucidated. While both bacterially-secreted aminopeptidase and outer membrane vesicles have been shown to be abundant inP. aeruginosabiofilm matrices, the contributions of each of these factors to the steps in biofilm generation have not been well studied. This work provides new insight as to how these bacterial components mediate the formation of a robust, drug-resistant extracellular matrix and implicates outer membrane vesicles as active components of biofilm architecture, expanding our overall understanding ofP. aeruginosabiofilm biology.
The APL1 immune factor is encoded by a single ancestral gene in mostAnophelesspecies and expanded to three paralogs with distinct function in theAnopheles gambiaecomplex
Authors: Mitri Christian , Bischoff Emmanuel , Eiglmeier Karin , Holm Inge , Dieme Constentin , Brito-Fravallo Emma , Raz Abbasali , Zakeri Sedigheh , Nejad Mahdokht I. K. , Djadid Navid D. , Vernick Kenneth D. , Riehle Michelle M. 
Published: September 2019

ABSTRACTBackgroundThe recent reference genome assembly and annotation of the Asian malaria vectorAnopheles stephensirevealed only one gene encoding the leucine-rich repeat immune factor APL1, while inAnopheles gambiaeand siblingAnopheles coluzzii, APL1 factors are encoded by a family of three paralogs. The phylogeny and biological function of the unique APL1 gene inA. stephensihave not yet been specifically examined.MethodsThe APL1 locus was manually sequenced to confirm the computationally predicted single APL1 gene inA. stephensi, and APL1 evolution withinAnopheleswas explored by phylogenomic analysis. The single or paralogous APL1 genes were silenced inA. stephensiandA. coluzzii, respectively, followed by mosquito survival analysis, experimental infection withPlasmodium, and expression analysis.ResultsAPL1 is present as a single ancestral gene in mostAnophelesincludingA. stephensi, but has expanded to three paralogs in an African lineage that includes only the Gambiae species complex andAnopheles christyi. Silencing of the unique APL1 copy inA. stephensiresults in significant mosquito mortality. Elevated mortality of APL1-depletedA. stephensiis rescued by antibiotic treatment, suggesting that bacteria are the cause of mortality, and that the unique APL1 gene is essential for host survival. SuccessfulPlasmodiumdevelopment inA. stephensidepends upon APL1 activity for protection from high host mortality, probably caused by exposure to enteric bacteria when parasites cross the midgut epithelial barrier. In contrast, silencing of all three APL1 paralogs inA. coluzziidoes not result in elevated mortality, either with or withoutPlasmodiuminfection. Expression of the single APL1 gene is regulated by both the Imd and Toll immune pathways, while control by the two pathways is subdivided to different paralogs in the expanded APL1 locus.ConclusionsAPL1 underwent neofunctionalization with both loss and gain of functions concomitant with expansion from a single ancestral gene to three paralogs in one lineage of AfricanAnopheles. The evolution of an expanded APL1 gene family could be a factor contributing to the exceptional levels of malaria transmission mediated by human-feeding members of the Gambiae complex in Africa.
Prominin-1-Radixin Axis controls hepatic gluconeogenesis by regulating PKA activity
Authors: Lee Hyun , Yu Dong-Min , Park Jun Sub , Lee Hwayeon , Kim Jun-Seok , Koo Seung-Hoi , Lee Jae-Seon , Lee Sungsoo , Ko Young-Gyu 
Published: September 2019

AbstractProminin-1 (Prom1) is a major cell surface marker of cancer stem cells, but its physiological functions in the liver have not been elucidated. We analyzed the levels of mRNA transcripts in serum-starved primary Prom1+/+ and Prom1-/- mouse hepatocytes using RNA-sequencing (RNA-seq) data, and found that CREB target genes were down-regulated. This initial observation led us to determine that the Prom1 deficiency inhibited cAMP response element binding protein (CREB) activation and gluconeogenesis, but not cyclic AMP (cAMP) accumulation, in glucagon-, epinephrine-, or forskolin-treated liver tissues and primary hepatocytes, and mitigated glucagon-induced hyperglycemia. Because Prom1 interacted with radixin, the Prom1 deficiency prevented radixin from localizing to the plasma membrane. Moreover, systemic adenoviral knockdown of radixin inhibited CREB activation and gluconeogenesis in glucagon-treated liver tissues and primary hepatocytes, and mitigated glucagon-elicited hyperglycemia. Based on these results, we conclude that Prom1 regulates hepatic PKA signaling via radixin functioning as an A kinase-anchored protein (AKAP).
Large-scale network analysis captures biological features of bacterial plasmids
Authors: Acman Mislav , van Dorp Lucy , Santini Joanne M. , Balloux Francois 
Published: September 2019

AbstractMany bacteria can exchange genetic material through horizontal gene transfer (HGT) mediated by plasmids and plasmid-borne transposable elements. Here, we study the population structure and dynamics of over 10,000 bacterial plasmids, by quantifying their genetic similarities and reconstructing a network based on their shared k-mer content. We use a community detection algorithm to assign plasmids into cliques, which correlate with plasmid gene content, bacterial host range, GC content, and existing classifications based on replicon and mobility (MOB) types. Further analysis of plasmid population structure allows us to uncover candidates for yet undescribed replicon genes and to identify transposable elements as the main drivers of HGT at broad phylogenetic scales. Our work illustrates the potential of network-based analyses of the bacterial ‘mobilome’ and opens up the prospect of a natural, exhaustive classification framework for bacterial plasmids.
Clinical evaluation of postoperative analgesia and serum biochemical changes of paracetamol compared to meloxicam and carprofen in bitches undergoing ovariohysterectomy
Authors: Hernández-Avalos Ismael , Valverde Alexander , Ibancovichi-Camarillo José Antonio , Sánchez-Aparicio Pedro , Recillas-Morales Sergio , Osorio-Avalos Jorge , Rodríguez-Velázquez Desiderio , Miranda-Cortés Agatha Elisa 
Published: September 2019

AbstractBackgroundIn veterinary medicine, the administration of nonsteroidal anti-inflammatory analgesics (NSAIDs) for the control of postsurgical pain in dogs and cats is common given the anti-inflammatory, analgesic, and antipyretic effects of these drugs. This study compared the serum biochemical changes and postoperative analgesic effects of paracetamol, meloxicam, and carprofen in bitches submitted to an ovariohysterectomy using the Dynamic Interactive Visual Analog Scale (DIVAS) and Pain Scale of the University of Melbourne (UMPS) scoring systems.MethodsThirty bitches of different breeds underwent elective ovariohysterectomies and were randomly assigned to one of three treatment groups: a paracetamol group [15 mg kg-1intravenous (IV)], a carprofen group (4 mg kg-1IV), and a meloxicam group (0.2 mg kg-1IV). All treatments were administered 30 minutes prior to surgery. Paracetamol was administered every 8 hours postoperatively for 48 hours total, while carprofen and meloxicam were intravenously administered every 24 hours. An evaluation of post-surgical pain was done with the DIVAS and the UMPS. The first post-surgical pain measurement was performed 1 hour after surgery and then 2, 4, 6, 8, 12, 16, 20, 24, 36, and 48 hours after surgery.ResultsAll groups exhibited a gradual reduction in pain throughout the postoperative period in both scales; however, neither scale significantly differed between the three treatment groups (P> 0.05) during the 48 postoperative hours.ConclusionsParacetamol was as effective as meloxicam and carprofen for post-surgical analgesia in bitches subjected to elective ovariohysterectomy. The present study demonstrates that paracetamol may be considered a tool for the effective treatment of acute perioperative pain in dogs. Furthermore, this drug led to no adverse reactions or changes in the parameters assessed in the present study, indicating its safety.
Development of a simple method for differential delivery of volatile anaesthetics to the spinal cord of the rabbit
Authors: Zhang Peng , Li Yao , Xu Ting 
Published: September 2019

AbstractEmulsified volatile anaesthetics can be easily injected into the circulation and eliminated from blood to lungs. Taking advantage of this unique pharmacokinetics, we aimed to develop a less trauma model for preferential delivery of volatile anaesthetics to the spinal cord with an intact CNS and circulatory system in the rabbit. Sixteen New Zealand White rabbits were randomly assigned to the isoflurane and sevoflurane group. A catheter for delivering emulsified isoflurane (8mg/kg/h) or sevoflurane (12mg/kg/h) to the spinal cord was placed into the descending aorta in all rabbits. The concentration and partial pressure of isoflurane and sevoflurane in the jugular and femoral vein were measured. Our results showed that the partial pressure of isoflurane was 3.91±1.11 mmHg in the jugular vein and 12.61±1.60 mmHg (1.0MAC) in the femoral vein. The partial pressure of sevoflurane was 3.89±1.00 mmHg in the jugular vein and 19.92±1.84mmHg (1.0MAC) in the femoral vein. There was significant difference regarding the partial pressure of isoflurane and sevoflurane between jugular and femoral veins in two groups (both P<0.001). In conclusion, a simple method has been successfully developed to selectively deliver isoflurane and sevoflurane to the spinal cord in the rabbit. Before acting on the brain, 69% isoflurane and 81% sevoflurane were removed from body via lungs. This method can be used to investigate the pharmacological properties of volatile anesthetics.