bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cover crops improve early season natural enemy recruitment and pest management in cotton production
Authors: Bowers Carson , Toews Michael , Liu Yangxuan , Schmidt Jason M. 
Published: October 2019

AbstractA shift to more ecologically based farming practices would improve the sustainability and economic stability of agricultural systems. Habitat management in and around agricultural fields can provide stable environments that aid in the proliferation of natural enemy communities that moderate pest populations and injury. Winter cover crops offer a potentially cost-effective approach to improving habitat that supports natural enemy communities early in the growing season. We investigated the effects of winter cover crops including cereal rye (Secale cereal L.) and crimson clover (Trifolium incarnatum L.) on the abundance and diversity of natural enemies, key pest populations, biological control services, and cotton yield. Winter cover crops were established on 0.4 ha replicated field plots in the fall of 2017 and 2018. Suction sampling during each cotton development stage demonstrated that a rye cover crop promoted greater abundance and diversity of natural enemy communities in early cotton stages. Extensive leaf sampling of seedling cotton showed that cover crops significantly reduced thrips infestations. Furthermore, stink bug boll injury decreased on plots prepared with a rye cover compared to cotton lacking this additional habitat. Combining end of season yield results and management practices with an economic analysis of the costs of production, the value of cotton grown into a cover crop was cost competitive with conventional (no cover) cotton production. These results suggest that conventional growers utilizing cover crops could reduce insecticide inputs through natural reductions in pest pressure, and overall do not incur additional production costs.
Bacterial flagellar motor PL-ring disassembly Sub-complexes are widespread and ancient
Authors: Kaplan Mohammed , Sweredoski Michael J. , Rodrigues João P.G.L.M. , Tocheva Elitza I. , Chang Yi-Wei , Ortega Davi R. , Beeby Morgan , Jensen Grant J. 
Published: October 2019

AbstractThe bacterial flagellar motor is an amazing nanomachine. Understanding how such complex structures arose is crucial to our understanding of cellular evolution. We and others recently reported that in several Gammaproteobacterial species, a relic sub-complex comprising the decorated P- and L-rings persists in the outer membrane after flagellum disassembly. Imaging nine additional species with cryo-electron tomography, here we show that this sub-complex persists after flagellum disassembly in other phyla as well. Bioinformatic analyses fail to show evidence of any recent horizontal transfers of the P- and L-ring genes, suggesting that this sub-complex and its persistence is an ancient and conserved feature of the flagellar motor. We hypothesize that one function of the P- and L-rings is to seal the outer membrane after motor disassembly.
Population Dynamics and Biological Feasibility of Sustainable Harvesting as a Conservation Strategy for Tropical and Temperate Freshwater Turtles
Authors: Rachmansah Angga , Norris Darren , Gibbs James P. 
Published: October 2019

AbstractBackgroundConservation strategies are urgently needed for tropical turtles. Studies conducted exclusively in the temperate zone have revealed that the suite of life history traits that characterizes turtles and includes delayed sexual maturity and high adult survivorship makes sustainable harvest programs an unviable strategy for turtle conservation. However, most turtles are tropical in distribution and the tropics have higher, more constant and more extended ambient temperature regimes that, in general, are more favorable for population growth.MethodsTo estimate the capacity of freshwater turtle species from temperate and tropical regions to sustain harvest we synthesized life history traits from 165 freshwater turtle species in 12 families (Carettochelydae, Chelidae, Chelydridae, Dermatemydidae, Emydidae, Geoemydidae, Kinosternidae, Pelomedusidae, Platysternidae, Podocnemididae, Staurotypidae and Trionychidae). The influence of climate variables and latitude on freshwater turtle life history traits (clutch size, clutch frequency, age at sexual maturity, and annual adult survival) were examined using Generalized Additive Models. The biological feasibility of sustainable harvest in temperate and tropical species was evaluated using a sensitivity analysis of population growth rates obtained from stage structured matrix population models.ResultsTurtles at low latitudes (tropical zones) exhibit smaller clutch sizes, higher clutch frequency, and earlier age at sexual maturity than those at high latitudes (temperate zone). Adult survival increased weakly with latitude and declined significantly with increasing bioclimatic temperature (mean temperature of warmest quarter). A modeling synthesis of these data indicates that the interplay of life history traits does not create higher harvest opportunity in adults of tropical species. Yet we found potential for sustainable exploitation of eggs in tropical species.ConclusionsSustainable harvest as a conservation strategy for tropical turtles appears to be as biologically problematic as in temperature zones and likely only possible if the focus is on limited harvest of eggs. Further studies are urgently needed to understand how the predicted population surplus in early life stages can be most effectively incorporated into conservation programs for tropical turtles increasingly threatened by unsustainable exploitation, climate change and deforestation.
Deposition of Polycyclic Aromatic Hydrocarbons (PAHs) into Northern Ontario Lake Sediments
Authors: Colby Graham A. 
Published: October 2019

AbstractPolycyclic aromatic hydrocarbons (PAHs) are priority pollutants that are produced through incomplete combustion of modern biomass and fossil fuels. In aquatic systems PAHs are absorbed by suspended matter and ultimately deposited into sediments. PAH fluxes to sediments have been declining in North American since the mid 1960s. Improving technology and regulations were expected to contribute to declining PAH concentrations; however, in some urban sediment there are recent increases in deposition. Trends in concentrations of pyrogenic PAHs and perylene were determined in the sediment of two lakes, in central Ontario. Intact piston cores that preserve the depositional history were collected from each site, sliced into 1 cm intervals and analyzed using gas-chromatography/ mass-spectrometry. Pyrogenic PAH trends at each site displayed unique characteristics suggesting differing extents of influence from various atmospheric sources. The upper core profile (above 8.5 cm) in the more remote site had decreasing PAH concentrations consistent with observations from Siskitwit Lake. The more urban site (above 3.5 cm) had increasing PAH concentrations suggesting modern anthropogenic activities have a larger influence in this region. Perylene fluxes at both sites do not correlate with the observed PAH fluxes, increasing in concentration with depth, thus indicating separate sources for this PAH, likely diagenesis within the sediments. Both sites had PAH concentrations exceeding the interim sediment quality guidelines in the uppermost sediment deposits. This study provides insights into the differential atmospheric deposition in Ontario and may aid in establishing strategies for reducing or mitigating the production of PAHs.
A window into lysogeny: Revealing temperate phage biology with transcriptomics
Authors: Owen Siân V. , Canals Rocío , Wenner Nicolas , Hammarlöf Disa L. , Kröger Carsten , Hinton Jay C. D. 
Published: October 2019

ABSTRACTIntegrated phage elements, known as prophages, are a pervasive feature of bacterial genomes. Prophages can enhance the fitness of their bacterial hosts by conferring beneficial functions, such as virulence, stress tolerance or phage resistance, which are encoded by accessory loci. Whilst the majority of phage-encoded genes are repressed during lysogeny, accessory loci are often highly expressed. However, novel prophage accessory loci are challenging to identify based on DNA sequence data alone. Here, we use bacterial RNA-seq data to examine the transcriptional landscapes of five Salmonella prophages. We show that transcriptomic data can be used to heuristically enrich for prophage features that are highly expressed within bacterial cells and often represent functionally-important accessory loci. Using this approach we identify a novel anti-sense RNA species in prophage BTP1, STnc6030, which mediates superinfection exclusion of phage BTP1 and immunity to closely-related phages. Bacterial transcriptomic datasets are a powerful tool to explore the molecular biology of temperate phages.
Listeriaphages induce Cas9 degradation to protect lysogenic genomes
Authors: Osuna Beatriz A. , Karambelkar Shweta , Mahendra Caroline , Christie Kathleen A. , Garcia Bianca , Davidson Alan R. , Kleinstiver Benjamin P. , Kilcher Samuel , Bondy-Denomy Joseph 
Published: October 2019

SUMMARYBacterial CRISPR-Cas systems employ RNA-guided nucleases to destroy foreign DNA. Bacteriophages, in turn, have evolved diverse “anti-CRISPR” proteins (Acrs) to counteract acquired immunity. InListeria monocytogenes, prophages encode 2-3 distinct anti-Cas9 proteins, withacrIIA1always present; however, its mechanism is unknown. Here, we report that AcrIIA1 binds with high affinity to Cas9 via the catalytic HNH domain and, inListeria, triggers Cas9 degradation. AcrIIA1 displays broad-spectrum inhibition of Type II-A and II-C Cas9s, including an additional highly-divergedListeriaCas9. During lytic infection, AcrIIA1 is insufficient for rapid Cas9 inactivation, thus phages require an additional “partner” Acr that rapidly blocks Cas9-DNA-binding. The AcrIIA1 N-terminal domain (AcrIIA1NTD) is dispensable for anti-CRISPR activity; instead it is required for optimal phage replication through direct transcriptional repression of the anti-CRISPR locus. AcrIIA1NTDis widespread amongstFirmicutes, can repress anti-CRISPR deployment by other phages, and has been co-opted by hosts potentially as an “anti-anti-CRISPR.” In summary,Listeriaphages utilize narrow-spectrum inhibitors of DNA binding to rapidly inactivate Cas9 in lytic growth and the broad-spectrum AcrIIA1 to stimulate Cas9 degradation for protection of theListeriagenome in lysogeny.
Spatiotemporal patterns of neocortical activity around hippocampal sharp-wave ripples
Authors: Abadchi J. Karimi , Nazari-Ahangarkolaee M. , Gattas S. , Bermudez-Contreras E. , Luczak A. , McNaughton B.L. , Mohajerani M. H. 
Published: October 2019

AbstractA prevalent model is that sharp-wave ripples (SWR) arise ‘spontaneously’ in CA3 and propagate recent memory traces outward to the neocortex to facilitate memory consolidation there. Using voltage and extracellular glutamate transient recording over widespread regions of mice dorsal neocortex in relation to CA1 multiunit activity (MUA) and SWR, we find that the largest SWR-related modulation occurs in retrosplenial cortex; however, contrary to the unidirectional hypothesis, neocortical activation exhibited a continuum of activation timings relative to SWRs, varying from leading to lagging. Thus, contrary to the model in which SWRs arise ‘spontaneously’ in the hippocampus, neocortical activation often precedes SWRs and may thus constitute a trigger event in which neocortical information seeds associative reactivation of hippocampal ‘indices’. This timing continuum is consistent with a dynamics in which older, more consolidated memories may in fact initiate the hippocampal-neocortical dialog, whereas reactivation of newer memories may be initiated predominantly in the hippocampus.
Cell-specific targeting byClostridium perfringensβ-toxin unraveled: the role of CD31 as the toxin receptor
Authors: Bruggisser Julia , Tarek Basma , Wyder Marianne , Witz Guillaume , Enzmann Gaby , Deutsch Urban , Engelhardt Britta , Posthaus Horst 
Published: October 2019

SUMMARYClostridium perfringensβ-toxin (CPB) is a highly active hemolysin β-pore forming toxin and the essential virulence factor for a severe, necro-hemorrhagic enteritis in animals and humans.In vivoandin vitroit exerts a remarkable cell type specificity towards endothelial cells, platelets and some leucocytic cell lines. The target cell specificity of CPB is, however, poorly understood and a receptor explaining this selective toxicity has not been identified. This has hampered further research into the pathogenesis ofC. perfringenstype C induced enteritis. Here we identify Platelet Endothelial Cell Adhesion Molecule-1 (CD31 or PECAM-1) as the specific membrane receptor for CPB on endothelial cells. CD31 expression is essential for CPB toxicity in endothelial cells and lethality in mice and sufficient to render previously resistant cells highly susceptible to the toxin. We further demonstrate, that the extracellular membrane proximal Ig6 domain of CD31 is required for the interaction with CPB and that expression of CD31 corresponds with the specificity of the toxin towards cultured cell lines. Our results thus provide an explanation for the cell type specificity of CPB and can be linked to the characteristic lesions observed a devastating enteric disease in animals and humans.
Cardiac function modulates endocardial cell dynamics to shape the cardiac outflow tract
Authors: Sidhwani Pragya , Boezio Giulia L.M. , Yang Hongbo , Chi Neil C. , Roman Beth L. , Stainier Didier Y.R. , Yelon Deborah 
Published: October 2019

ABSTRACTPhysical forces are important participants in the cellular dynamics that shape developing organs. During heart formation, for example, contractility and blood flow generate biomechanical cues that influence patterns of cell behavior. Here, we address the interplay between function and form during the assembly of the cardiac outflow tract (OFT), a crucial connection between the heart and vasculature that develops while circulation is underway. In zebrafish, we find that the OFT expands via accrual of both endocardial and myocardial cells. However, when cardiac function is disrupted, OFT endocardial growth ceases, accompanied by reduced proliferation and reduced addition of cells from adjacent vessels. The TGFβ receptor Acvrl1 is required for addition of endocardial cells, but not for their proliferation, indicating distinct regulation of these essential cell behaviors. Together, our results suggest that cardiac function modulates OFT morphogenesis by triggering endocardial cell accumulation that induces OFT lumen expansion and shapes OFT dimensions.
TSUNAMI: Translational Bioinformatics Tool Suite For Network Analysis And Mining
Authors: Huang Zhi , Han Zhi , Wang Tongxin , Shao Wei , Xiang Shunian , Salama Paul , Rizkalla Maher , Huang Kun , Zhang Jie 
Published: October 2019

AbstractGene co-expression network (GCN) mining identifies gene modules with highly correlated expression profiles across samples/conditions. It helps to discover latent gene/molecular interactions, identify novel gene functions, and extract molecular features from certain disease/condition groups, thus help to identify disease biomarkers. However, there lacks an easy-to-use tool package for users to mine GCN modules that are relatively small in size with tightly connected genes that can be convenient for downstream Gene Ontology (GO) enrichment analysis, as well as modules that may share common members. To address this need, we develop a GCN mining tool package TSUNAMI (Tools SUite for Network Analysis and MIning) which incorporates our state-of-the-art lmQCM algorithm to mine GCN modules in public and user-input data (microarray, RNA-seq, or any other numerical omics data), then performs downstream GO and enrichment analysis based on the modules identified. It has several features and advantages: (i) user friendly interface and the real-time co-expression network mining through web server; (ii) direct access and search of GEO and TCGA databases as well as user-input expression matrix (microarray, RNA-seq, etc.) for GCN module mining; (iii) multiple co-expression analysis tools to choose with highly flexible of parameter selection options; (iv) identified GCN modules are summarized to eigengenes, which are convenient for user to check their correlation with other clinical traits; (v) integrated downstream Enrichr enrichment analysis and links to other GO tools; (vi) visualization of gene loci by Circos plot in any step. The web service is freely accessible through URL: http://spore.ph.iu.edu:3838/zhihuan/TSUNAMI/. Source code is available at https://github.com/huangzhii/TSUNAMI/.
HIGD2A is required for assembly of the COX3 module of human mitochondrial complex IV
Authors: Hock Daniella H. , Reljic Boris , Ang Ching-Seng , Mountford Hayley S. , Compton Alison G. , Ryan Michael T. , Thorburn David R. , Stroud David A. 
Published: October 2019

AbstractAssembly factors play a critical role in the biogenesis of mitochondrial respiratory chain complexes I-IV where they assist in the membrane insertion of subunits, attachment of co-factors, and stabilization of assembly intermediates. The major fraction of complexes I, III and IV are present together in large molecular structures known as respiratory chain supercomplexes. A number of assembly factors have been proposed as required for supercomplex assembly, including the hypoxia inducible gene 1 domain family member HIGD2A. Using gene-edited human cell lines and extensive steady state, translation and affinity enrichment proteomics techniques we show that loss of HIGD2A leads to defects in the de novo biogenesis of mtDNA-encoded COX3, subsequent accumulation of complex IV intermediates and turnover of COX3 partner proteins. Deletion of HIGD2A also leads to defective complex IV activity. The impact of HIGD2A loss on complex IV was not altered by growth under hypoxic conditions, consistent with its role being in basal complex IV assembly. While in the absence of HIGD2A we show that mitochondria do contain an altered supercomplex assembly, we demonstrate it to harbor a crippled complex IV lacking COX3. Our results redefine HIGD2A as a classical assembly factor required for building the COX3 module of complex IV.
A secreted LysM effector protects fungal hyphae through chitin-dependent homodimer polymerization
Authors: Sánchez-Vallet Andrea , Tian Hui , Rodriguez-Moreno Luis , Valkenburg Dirk-Jan , Saleem-Batcha Raspudin , Wawra Stephan , Kombrink Anja , Verhage Leonie , de Jonge Ronnie , van Esse H. Peter , Zuccaro Alga , Croll Daniel , Mesters Jeroen R. , Thomma Bart P.H.J. 
Published: October 2019

ABSTRACTPlants trigger immune responses upon recognition of fungal cell wall chitin, followed by the release of various antimicrobials, including chitinase enzymes that hydrolyze chitin. In turn, many fungal pathogens secrete LysM effectors that prevent chitin recognition by the host through scavenging of chitin oligomers. We previously showed that intrachain LysM dimerization of theCladosporium fulvumeffector Ecp6 confers an ultrahigh-affinity binding groove that competitively sequesters chitin oligomers from host immune receptors. Additionally, particular LysM effectors are found to protect fungal hyphae against chitinase hydrolysis during host colonization. However, the molecular basis for the protection of fungal cell walls against hydrolysis remained unclear. Here, we determined a crystal structure of the single LysM domain-containing effector Mg1LysM of the wheat pathogenZymoseptoria triticiand reveal that Mg1LysM is involved in the formation of two kinds of dimers; a chitin-dependent dimer as well as a chitin-independent homodimer. In this manner, Mg1LysM gains the capacity to form a supramolecular structure by chitin-induced oligomerization of chitin-independent Mg1LysM homodimers, a property that confers protection to fungal cell walls against host chitinases.
Electroacupuncture at Governor Vessel improves neurobehavioral function via reduction of complexin1
Authors: Xu Yang , Liu Jia , Zhao Xiaoming , Zhou Lei , Xiong Liuling , Li Cuiyun , Jiang Ya , Wang Yangyang , Wang Tinghua 
Published: October 2019

AbstractElectroacupuncture at Governor Vessel (GV), as a traditional chinese medicine, has been proved that it can reduce scar and promote axon regeneration. However, the underlying mechanism remains unclear. Herein, complexin1 (CPLX1), as a candidate protein, was found using protein chip. Therefore, using a CRISPR/Cas9 knockout approach, we deleted CPLX1 specifically in the SD rats to assess the role of CPLX1 in GV treatment. Additionally, eIF5A1 stimulate the translation of CPLX1 with PPG sequence, we attempt to uncover whether eIF5A1 play a role in the GV treatment. In fact, GV can reduce scar and promote axon regeneration after SCC. CPLX1−/+ SCC rats demonstrated that decreased CPLX1 improved the microenvironment of injured area via reducing the components of fibrotic scar and further enhanced the synaptic plasticity, which benefit the regeneration of axons. And eIF5A1 could regulate the expression of CPLX1 in the process of GV treatment. Therefore, GV contributes to axon regeneration and synapse plasticity via eIF5A1 regulating CPLX1 following SCC, providing a convincible mechanism for improving the therapeutic efficacy of GV for SCC.
Changes in the expression of interleukin-10 in myocardial infarction and its relationship with macrophage activation and cell apoptosis
Authors: Yang Wenqi , Li Shuming , Zhao Yang , Sun Ying , Huang Yuling , Diao Zengli , Xing Cainai , Yang Fang , Liu Wenbo , Zhao Xuan , Shang Xiaoming 
Published: October 2019

ABSTRACTCurrently, the role of IL-10 as an anti-inflammatory factor in the occurrence and development of heart disease is still unclear. This study aimed to observe the dynamic changes in the expression of IL-10 in serum and myocardial tissues, as well as to investigate the relationship of IL-10 expression with macrophage activation and cardiomyocyte apoptosis during the occurrence of myocardial infarction. Mice models with myocardial infarction were prepared by ligating anterior descending branch of the coronary artery. The animals were classified into sham operation group (the control group), as well as groups of myocardial infarction based on days 1, 7, 14 and 28. On days 7 and 14, the cells with positive IL-10 expression were largely distributed in the infarct areas, while cells with positive IL-10 expression were decreased on day 28. Serum IL-10 was significantly positively correlated with IL-10 protein expression in myocardial tissues. Moreover, Bcl-2 and Bax protein expression in myocardial tissues, as well as the ratio of Bcl-2/Bax proteins were gradually elevated with prolonged time of infarction. There were positive correlations between IL-10 and Arginase expressions, and between the expressions of Bcl-2 and Bax proteins. After the occurrence of myocardial infarction, the expression of IL-10 was firstly increased and then decreased in serum and myocardial tissues, and this might affect macrophage activation, phenotypic transformation and the occurrence of cardiomyocyte apoptosis.