bluuebunny/crossref_metadata_2025 huggingface dataset:
Sufficient versus optimal climatic stability during the Late Quaternary: using environmental quality to guide phylogeographic inferences in a Neotropical montane system
Authors: Soley-Guardia Mariano , Carnaval Ana Carolina , Anderson Robert P
Published: October 2019

Quaternary climatic oscillations affected species distributions worldwide, creating cycles of connectivity and isolation that impacted population demography and promoted lineage divergence. These effects have been well studied in temperate regions. Taxa inhabiting mesic montane habitats in tropical ecosystems show high levels of endemism and diversification in the distinct mountain ranges they inhabit; such a pattern has commonly been ascribed to past climatic oscillations, but few phylogeographic studies have tested this hypothesis. Here, we combine ecological niche models of species distributions with molecular data to study phylogeographic patterns in two rodents endemic to the highlands of Costa Rica and western Panama (Reithrodontomys creper and Nephelomys devius). In so doing, we apply a novel approach that incorporates a basic ecological principle: the expected positive relationship between environmental suitability and population abundance. Specifically, we use niche models to predict potential patterns of population connectivity and stability of different suitability levels during climatic extremes of the last glacial–interglacial cycle; we then test these predictions with population genetic analyses of a mitochondrial and a nuclear marker. The detailed predictions arising from the different levels of suitability were moderately to highly congruent with the molecular data depending on the species. Overall, results suggest that in these tropical montane ecosystems, cycles of population connectivity and isolation followed a pattern opposite to that typically described for temperate or lowland tropical ecosystems: namely, higher connectivity during the colder glacials, with isolation in montane refugia during the interglacials, including today. Nevertheless, the individualistic patterns for each species indicate a potentially wide gamut of phylogeographic histories reflecting particularities of their niches. Taken together, this study illustrates how phylogeographic inferences may benefit from niche model outputs that provide more detailed predictions of connectivity and finer characterizations of potential refugia through time.
How the Distance Between Drag-Cloth Checks Affects the Estimate of Adult and Nymphal Ixodes scapularis (Acari: Ixodidae) Density
Authors: Borgmann-Winter Ben , Allen David
Published: October 2019

Drag-cloth sampling is the most commonly used method to sample for ticks. A cloth is dragged along the ground and checked for ticks at regular intervals to count ticks before they drop off. The distance between drag-cloth checks differs between studies, which could result in lower density estimates for studies with greater distances between checks. Here, we measured this effect by 1) calculating the rate at which nymphal and adult Ixodes scapularis Say ticks drop off the cloth per meter dragged and 2) measuring tick density by drag-cloth sampling with three different drag-cloth check interval distances. We found a higher drop-off rate for adult ticks, 0.083/m, than nymphal ticks, 0.047/m. The estimated density of ticks decreased with increasing check interval distance. Our results not only highlight the importance of accounting for check interval distance when estimating tick density, but also provide the first estimate of nymphal I. scapularis drop-off rate.
Stoichiometry of leaf carbon, nitrogen, and phosphorus along a geographic, climatic, and soil gradients in temperate desert of Hexi Corridor, northwest China
Authors: Zhang Ke , Li Mengmeng , Su Yongzhong , Yang Rong
Published: October 2019

Aims

Understanding the regional pattern of leaf stoichiometry and its contributing variables are of importance for predicting plant responses to global change and modelling the productivity and nutrient fluxes of ecosystems. In this study, we investigated leaf stoichiometry of plants that sampled from Hexi Corridor, a typical arid region in China, and tried to explore the contribution variables on leaf stoichiometry along the geographic, climatic, and soil gradients.

Methods

In August 2012, 70 sites in Hexi Corridor were investigated. Plant leaves and soils from five equivalent plots within each site were sampled. C, N, and P contents of leaf and soil were measured.

Important findings

Compared with leaf N and P contents in regional and global scales, leaf N content in Hexi Corridor was close to them with the value of 20.19 mg g-1, while leaf P content was lower than them with the value of 1.34 mg g-1. Overall, leaf N:P value in Hexi Corridor was 15.70. Individually, leaf N:P values of shrubs and herbs were 16.81 and 14.80, respectively. Scaling exponents for leaf N vs. P of overall and shrubs in Hexi Corridor were 1.29, higher than the scaling exponent of herbs (1.08). Leaf stoichiometry of shrubs and herbs did not show significant latitudinal and longitudinal patterns, meanwhile, it has no significant correlation with mean annual precipitation (MAP), mean annual temperature (MAT), and soil elements. However, only leaf stoichiometry of herbs has significant correlation with altitude and aridity degree. These results indicate that plants in Hexi Corridor are possibly co-limited by N and P, while shrubs are mainly limited by soil P and herbs are limited by soil N. Scaling relationship reveals that leaf N vs. P of herbs is isometric. With increasing altitude, the quadratic regression for leaf C and N contents and the linear regression for leaf P content of herbs reflect the difference responses of the three elements on the variation of MAT along the altitude and it could be explained by plant physiology hypothesis and biogeochemical hypotheses. With decreasing aridity, leaf N and N:P of herbs increased significantly, inferring that herbs growth would be limited by P increasingly and strengthening the increasing nitrogen availability with increasing precipitation. In conclusion, different altitude and aridity patterns for leaf stoichiometry of herbs and shrubs reveal the plastic survive strategies of different xerophytes in Hexi Corridor. Moreover, leaf stoichiometry of herbs in Hexi Corridor could be as indicator of the changing environment that caused by aridity.
Quantifying biological effects of radiation from high-energy linear accelerators on lymphocytes
Authors: Farkas Gyöngyi , Kocsis Zsuzsa S , Székely Gábor , Mihály Dalma , Pesznyák Csilla , Pócza Tamás , Major Tibor , Polgár Csaba , Jurányi Zsolt
Published: October 2019

The aim of this study was to investigate the radiobiological effects of flattening filter (FF) and flattening filter-free (FFF) modes of linear electron accelerators and to understand whether there is any difference between the effects of these modes. We evaluated the number of chromosome aberrations following irradiation of lymphocytes from healthy volunteers with X-ray photons at two energy levels, 6 and 10 MV; the dose rate ranged between 5.50 and 23.08 Gy/min and absorbed doses ranged between 0.5 and 8 Gy. A 60Co curve was employed for comparison. Metaphases from the lymphocyte cultures were prepared using standard cytogenetic techniques and chromosome analysis was performed. Our results allow the performance of biodosimetry at higher energies and doses than the currently used reference dosimetry. We observed significant differences in aberration frequencies when different irradiation techniques were used. FFF mode has a higher radiobiological effect than the FF mode. Linear-quadratic dose response calibration curves were constructed and relative biological effectiveness (RBE) values were calculated. Average RBE values using 6 MV (5.50 Gy/min) as a reference radiation were 1.28 for 60Co γ irradiation, 1.11 for 6 FFF and 0.79–0.92 for 10 FFF. Since there are compelling differences between radiation modalities in cases of hypofractionation, these results may be even more important in a therapeutic situation. In case of an accidental overdose of a patient, use of the appropriate calibration curves for biodosimetry are also essential for quantifying the overdose.
Deletion of bem46 retards spore germination and may be related to the polar growth of Aspergillus fumigatus
Authors: Ma Yan , Ji Ying , Yang Jing , Li Wen , Li Jiajuan , Cen Wen , Wang Yan , Feng Wenli
Published: October 2019

Bud emergence 46 (BEM46), a member of the α/β hydrolase superfamily, has been reported to be essential for polarized growth in Neurospora crassa. However, the role of BEM46 in aspergillus fumigatus (A. fumigatus) remains unclear. In this study, we constructed an A. fumigatus strain expressing BEM46 fused with enhanced green fluorescent protein, and a Δbem46 mutant, to explore the localization and the role of growth of BEM46 in A. fumigatus, respectively. Confocal laser scanning microscopy revealed that BEM46 was dominantly expressed in the sites where hyphae germinated from conidia in A. fumigatus. When compared with the control strain, the Δbem46 mutant exhibited insignificant morphological changes but delayed germination. No significant changes were found regarding the radial growth of both strains in response to various antifungal agents. These results suggest that BEM46 plays an essential role in timely germination in A. fumigatus. From the observation of fluorescence localization, we infer that that BEM46 might be involved in polarized growth in A. fumigatus.
What information can we derive from historical Far Eastern guest stars for modern research on novae and cataclysmic variables?
Authors: Hoffmann Susanne M
Published: October 2019

Recently, there have been several studies on the evolution of binary systems using historical data that are treated as facts in the chain of argument. This paper discusses six case studies of modern dwarf novae with suggested historical counterparts from the historical point of view, as well as the derived consequences for the physics of close binary systems (the dwarf novae Z Cam and AT Cnc, the nebula in M22, and the possible Nova 101, Nova 483 and Nova 1437). I consider the historical Far Eastern reports and, after a careful re-reading of the text, map the given information on to the sky. In some cases, the positions given in modern lists of classical nova–guest star pairs turn out to be wrong, or they have to be considered highly approximate: the historical position should, in most cases, be transformed into areas of the celestial sphere and not into point coordinates. Based on the correct information, I consider the consequences concerning the evolution of close binary systems. The result is that none of the cases of cataclysmic variables suggested to have a historical counterpart can be (fully) supported. Because the identification of the historical record of observation with the cataclysmic variables known today turns out to be always uncertain, a potential historical observation alone cannot be relied on to draw conclusions on the evolution of binaries. Evolution scenarios should be derived from astrophysical observations and modelling only.
Scale-invariance of black hole accretion: modelling emission from a black hole X-ray binary with relativistic accretion flow simulations
Authors: Mościbrodzka M
Published: October 2019

We model the non-thermal emission spectrum of the extremely sub-Eddington X-ray binary system A0620-00. It is believed that this non-thermal emission is produced by radiatively inefficient ‘quiescent’ accretion on to a stellar-mass black hole present in the system. We post-process general relativistic magnetohydrodynamics (GRMHD) simulations with multiwavelength, fully polarized, relativistic radiative transfer calculations to predict broad-band spectra and emission polarization levels for a range of electron models and accretion rates. We find that a model with strong coupling of electrons and ions in the accretion disc and accretion rate of only $\dot{M}=3\times 10^{-13} \, \rm [M_\odot \, yr^{-1}]$ is able to recover the observed X-ray spectral slope, as well as the excess of linear polarization detected in the source in the near-infrared (NIR)/optical bands. Our models constrain the spectral properties of a putative relativistic jet produced in this system. In addition, we show that the magnetized winds from our hot accretion flow carry away a small fraction of the orbital angular momentum of the binary, which is unable to explain the observed rapid orbital decay of the system. GRMHD simulations similar to the present ones are often used to explain emission from sub-Eddington supermassive black holes in Sgr A* or M87; the present simulations allow us to test whether some aspects of quiescent black hole accretion are scale-invariant.
Black hole accretion in scalar–tensor–vector gravity
Authors: John Anslyn J
Published: October 2019

We examine the accretion of matter on to a black hole in scalar–tensor–vector gravity (STVG) also known as modified gravity (MOG). The gravitational constant is G = GN(1 + α) where α is a parameter taken to be constant for static black holes in the theory. The MOG black hole is spherically symmetric and characterized by two event horizons. The matter falling into the black hole obeys the polytrope equation of state and passes through two critical points before entering the outer horizon. We obtain analytical expressions for the mass accretion rate as well as for the outer critical point, critical velocity, and critical sound speed. Our results complement existing strong field tests like lensing and orbital motion and could be used in conjunction to determine observational constraints on MOG.
Photometric flaring fraction of M dwarf stars from the SkyMapper Southern Survey
Authors: Chang Seo-Won , Wolf Christian , Onken Christopher A
Published: October 2019

We present our search for flares from M dwarf stars in the SkyMapper Southern Survey DR1, which covers nearly the full Southern hemisphere with six-filter sequences that are repeatedly observed in the passbands uvgriz. This allows us to identify bona fide flares in single-epoch observations on time-scales of less than four minutes. Using a correlation-based outlier search algorithm we find 254 flare events in the amplitude range of Δu ∼ 0.1 to 5 mag. In agreement with previous work, we observe the flaring fraction of M dwarfs to increase from ∼30 to ∼1000 per million stars for spectral types M0 to M5. We also confirm the decrease in flare fraction with larger vertical distance from the Galactic plane which is expected from declining stellar activity with age. Based on precise distances from Gaia DR2, we find a steep decline in the flare fraction from the plane to 150 pc vertical distance and a significant flattening towards larger distances. We then reassess the strong type dependence in the flaring fraction with a volume-limited sample within a distance of 50 pc from the Sun: in this sample the trend disappears and we find instead a constant fraction of ∼1 650 per million stars for spectral types M1 to M5. Finally, large-amplitude flares with Δi > 1 mag are very rare with a fraction of ∼0.5 per million M dwarfs. Hence, we expect that M-dwarf flares will not confuse SkyMapper’s search for kilonovae from gravitational-wave events. proper references for those databases (or follow their guideline on citation).
Tidal flows with convection: frequency-dependence of the effective viscosity and evidence for anti-dissipation
Authors: Duguid Craig D , Barker Adrian J , Jones C A
Published: October 2019

Tidal interactions are important in driving spin and orbital evolution in planetary and stellar binary systems, but the fluid dynamical mechanisms responsible remain incompletely understood. One key mechanism is the interaction between tidal flows and convection. Turbulent convection is thought to act as an effective viscosity in damping large-scale tidal flows, but there is a long-standing controversy over the efficiency of this mechanism when the tidal frequency exceeds the turnover frequency of the dominant convective eddies. This high frequency regime is relevant for many applications, such as for tides in stars hosting hot Jupiters. We explore the interaction between tidal flows and convection using hydrodynamical simulations within a local Cartesian model of a small patch of a convection zone of a star or planet. We adopt the Boussinesq approximation and simulate Rayleigh-Bénard convection, modelling the tidal flow as a background oscillatory shear flow. We demonstrate that the effective viscosity of both laminar and turbulent convection is approximately frequency-independent for low frequencies. When the forcing frequency exceeds the dominant convective frequency, the effective viscosity scales inversely with the square of the tidal frequency. We also show that negative effective viscosities are possible, particularly for high frequency tidal forcing, suggesting the surprising possibility of tidal anti-dissipation. These results are supported by a complementary high-frequency asymptotic analysis that extends prior work by Ogilvie & Lesur. We discuss the implications of these results for interpreting the orbital decay of hot Jupiters, and for several other astrophysical problems.
GRB 171010A/SN 2017htp: a GRB-SN at z = 0.33
Authors: Melandri A , Malesani D B , Izzo L , Japelj J , Vergani S D , Schady P , Sagués Carracedo A , de Ugarte Postigo A , Anderson J P , Barbarino C , Bolmer J , Breeveld A , Calissendorff P , Campana S , Cano Z , Carini R , Covino S , D’Avanzo P , D’Elia V , della Valle M , De Pasquale M , Fynbo J P U , Gromadzki M , Hammer F , Hartmann D H , Heintz K E , Inserra C , Jakobsson P , Kann D A , Kotilainen J , Maguire K , Masetti N , Nicholl M , Olivares E F , Pugliese G , Rossi A , Salvaterra R , Sollerman J , Stone M B , Tagliaferri G , Tomasella L , Thöne C C , Xu D , Young D R
Published: October 2019

The number of supernovae known to be connected with long-duration gamma-ray bursts (GRBs) is increasing and the link between these events is no longer exclusively found at low redshift (z ≲ 0.3) but is well established also at larger distances. We present a new case of such a liaison at z = 0.33 between GRB 171010A and SN 2017htp. It is the second closest GRB with an associated supernova of only three events detected by Fermi-LAT. The supernova is one of the few higher redshift cases where spectroscopic observations were possible and shows spectral similarities with the well-studied SN 1998bw, having produced a similar Ni mass ($M_{\rm Ni}=0.33\pm 0.02 ~\rm {M_{\odot }}$) with slightly lower ejected mass ($M_{\rm ej}=4.1\pm 0.7~\rm {M_{\odot }}$) and kinetic energy ($E_{\rm K} = 8.1\pm 2.5 \times 10^{51} ~\rm {erg}$). The host-galaxy is bigger in size than typical GRB host galaxies, but the analysis of the region hosting the GRB revealed spectral properties typically observed in GRB hosts and showed that the progenitor of this event was located in a very bright H ii region of its face-on host galaxy, at a projected distance of ∼ 10 kpc from its galactic centre. The star-formation rate (SFRGRB ∼ 0.2 M⊙ yr−1) and metallicity (12  + log(O/H) ∼8.15 ± 0.10) of the GRB star-forming region are consistent with those of the host galaxies of previously studied GRB–SN systems.
ProteomicsDB: a multi-omics and multi-organism resource for life science research
Authors: Samaras Patroklos , Schmidt Tobias , Frejno Martin , Gessulat Siegfried , Reinecke Maria , Jarzab Anna , Zecha Jana , Mergner Julia , Giansanti Piero , Ehrlich Hans-Christian , Aiche Stephan , Rank Johannes , Kienegger Harald , Krcmar Helmut , Kuster Bernhard , Wilhelm Mathias
Published: October 2019

ProteomicsDB (https://www.ProteomicsDB.org) started as a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. The data types and contents grew over time to include RNA-Seq expression data, drug-target interactions and cell line viability data. In this manuscript, we summarize new developments since the previous update that was published in Nucleic Acids Research in 2017. Over the past two years, we have enriched the data content by additional datasets and extended the platform to support protein turnover data. Another important new addition is that ProteomicsDB now supports the storage and visualization of data collected from other organisms, exemplified by Arabidopsis thaliana. Due to the generic design of ProteomicsDB, all analytical features available for the original human resource seamlessly transfer to other organisms. Furthermore, we introduce a new service in ProteomicsDB which allows users to upload their own expression datasets and analyze them alongside with data stored in ProteomicsDB. Initially, users will be able to make use of this feature in the interactive heat map functionality as well as the drug sensitivity prediction, but ultimately will be able to use all analytical features of ProteomicsDB in this way.
MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems
Authors: Gumerov Vadim M , Ortega Davi R , Adebali Ogun , Ulrich Luke E , Zhulin Igor B
Published: October 2019

Bacteria and archaea employ dedicated signal transduction systems that modulate gene expression, second-messenger turnover, quorum sensing, biofilm formation, motility, host-pathogen and beneficial interactions. The updated MiST database provides a comprehensive classification of microbial signal transduction systems. This update is a result of a substantial scaling to accommodate constantly growing microbial genomic data. More than 125 000 genomes, 516 million genes and almost 100 million unique protein sequences are currently stored in the database. For each bacterial and archaeal genome, MiST 3.0 provides a complete signal transduction profile, thus facilitating theoretical and experimental studies on signal transduction and gene regulation. New software infrastructure and distributed pipeline implemented in MiST 3.0 enable regular genome updates based on the NCBI RefSeq database. A novel MiST feature is the integration of unique profile HMMs to link complex chemosensory systems with corresponding chemoreceptors in bacterial and archaeal genomes. The data can be explored online or via RESTful API (freely available at https://mistdb.com).
Plant Reactome: a knowledgebase and resource for comparative pathway analysis
Authors: Naithani Sushma , Gupta Parul , Preece Justin , D’Eustachio Peter , Elser Justin L , Garg Priyanka , Dikeman Daemon A , Kiff Jason , Cook Justin , Olson Andrew , Wei Sharon , Tello-Ruiz Marcela K , Mundo Antonio Fabregat , Munoz-Pomer Alfonso , Mohammed Suhaib , Cheng Tiejun , Bolton Evan , Papatheodorou Irene , Stein Lincoln , Ware Doreen , Jaiswal Pankaj
Published: October 2019

Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project. It uses Oryza sativa (rice) as a reference species for manual curation of pathways and extends pathway knowledge to another 82 plant species via gene-orthology projection using the Reactome data model and framework. It currently hosts 298 reference pathways, including metabolic and transport pathways, transcriptional networks, hormone signaling pathways, and plant developmental processes. In addition to browsing plant pathways, users can upload and analyze their omics data, such as the gene-expression data, and overlay curated or experimental gene-gene interaction data to extend pathway knowledge. The curation team actively engages researchers and students on gene and pathway curation by offering workshops and online tutorials. The Plant Reactome supports, implements and collaborates with the wider community to make data and tools related to genes, genomes, and pathways Findable, Accessible, Interoperable and Re-usable (FAIR).
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species
Authors: Shefchek Kent A , Harris Nomi L , Gargano Michael , Matentzoglu Nicolas , Unni Deepak , Brush Matthew , Keith Daniel , Conlin Tom , Vasilevsky Nicole , Zhang Xingmin Aaron , Balhoff James P , Babb Larry , Bello Susan M , Blau Hannah , Bradford Yvonne , Carbon Seth , Carmody Leigh , Chan Lauren E , Cipriani Valentina , Cuzick Alayne , Della Rocca Maria , Dunn Nathan , Essaid Shahim , Fey Petra , Grove Chris , Gourdine Jean-Phillipe , Hamosh Ada , Harris Midori , Helbig Ingo , Hoatlin Maureen , Joachimiak Marcin , Jupp Simon , Lett Kenneth B , Lewis Suzanna E , McNamara Craig , Pendlington Zoë M , Pilgrim Clare , Putman Tim , Ravanmehr Vida , Reese Justin , Riggs Erin , Robb Sofia , Roncaglia Paola , Seager James , Segerdell Erik , Similuk Morgan , Storm Andrea L , Thaxon Courtney , Thessen Anne , Jacobsen Julius O B , McMurry Julie A , Groza Tudor , Köhler Sebastian , Smedley Damian , Robinson Peter N , Mungall Christopher J , Haendel Melissa A , Munoz-Torres Monica C , Osumi-Sutherland David
Published: October 2019

In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven’t been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search. We develop many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases. Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research. Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies such as HPO and uPheno); user interface (a redesigned website); and community development. Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics.
The (PATAN)-CheY-Like Response Regulator PixE Interacts with the Motor ATPase PilB1 to Control Negative Phototaxis in the Cyanobacterium Synechocystis sp. PCC 6803
Authors: Jakob Annik , Nakamura Hiroshi , Kobayashi Atsuko , Sugimoto Yuki , Wilde Annegret , Masuda Shinji
Published: October 2019

The cyanobacterium Synechocystis sp. PCC 6803 can move directionally on a moist surface toward or away from a light source to reach optimal light conditions for its photosynthetic lifestyle. This behavior, called phototaxis, is mediated by type IV pili (T4P), which can pull a single cell into a certain direction. Several photoreceptors and their downstream signal transduction elements are involved in the control of phototaxis. However, the critical steps of local pilus assembly in positive and negative phototaxis remain elusive. One of the photoreceptors controlling negative phototaxis in Synechocystis is the blue-light sensor PixD. PixD forms a complex with the CheY-like response regulator PixE that dissociates upon illumination with blue light. In this study, we investigate the phototactic behavior of pixE deletion and overexpression mutants in response to unidirectional red light with or without additional blue-light irradiation. Furthermore, we show that PixD and PixE partly localize in spots close to the cytoplasmic membrane. Interaction studies of PixE with the motor ATPase PilB1, demonstrated by in vivo colocalization, yeast two-hybrid and coimmunoprecipitation analysis, suggest that the PixD–PixE signal transduction system targets the T4P directly, thereby controlling blue-light-dependent negative phototaxis. An intriguing feature of PixE is its distinctive structure with a PATAN (PatA N-terminus) domain. This domain is found in several other regulators, which are known to control directional phototaxis. As our PilB1 coimmunoprecipitation analysis revealed an enrichment of PATAN domain response regulators in the eluate, we suggest that multiple environmental signals can be integrated via these regulators to control pilus function.
Exploring the Pathogenicity of Pseudomonas brassicacearum Q8r1-96 and Other Strains of the Pseudomonas fluorescens Complex on Tomato
Authors: Yang Mingming , Mavrodi Dmitri V. , Mavrodi Olga V. , Thomashow Linda S. , Weller David M.
Published: October 2019

Pseudomonas brassicacearum and related species of the P. fluorescens complex have long been studied as biocontrol and growth-promoting rhizobacteria involved in suppression of soilborne pathogens. We report here that P. brassicacearum Q8r1-96 and other 2,4-diacetylphloroglucinol (DAPG)-producing fluorescent pseudomonads involved in take-all decline of wheat in the Pacific Northwest of the United States can also be pathogenic to other plant hosts. Strain Q8r1-96 caused necrosis when injected into tomato stems and immature tomato fruits, either attached or removed from the plant, but lesion development was dose dependent, with a minimum of 106 CFU ml−1 required to cause visible tissue damage. We explored the relative contribution of several known plant-microbe interaction traits to the pathogenicity of strain Q8r1-96. Type III secretion system (T3SS) mutants of Q8r1-96, injected at a concentration of 108 CFU ml−1, were significantly less virulent, but not consistently, as compared with the wild-type strain. However, a DAPG-deficient phlD mutant of Q8r1-96 was significantly and consistently less virulent as compared with the wild type. Strain Q8r1-96acc, engineered to over express ACC deaminase, caused a similar amount of necrosis as the wild type. Cell-free culture filtrates of strain Q8r1-96 and pure DAPG also cause necrosis in tomato fruits. Our results suggest that DAPG plays a significant role in the ability of Q8r1-96 to cause necrosis of tomato tissue, but other factors also contribute to the pathogenic properties of this organism.
Advances in Plant−Nematode Interactions with Emphasis on the Notorious Nematode Genus Meloidogyne
Authors: Kaloshian Isgouhi , Teixeira Marcella
Published: October 2019

Plant infections by plant-parasitic nematodes (PPNs) continue to be one of the major limitations in agricultural systems. Root-knot nematodes (RKNs), belonging to the genus Meloidogyne, are one of the most important groups of PPNs worldwide. Their wide host range combined with ubiquitous presence, continues to provide challenges for their control and breeding for resistance. Although resistance to RKNs has been identified, incorporation of these resistances into crops and durability of the resistance remains challenging. In addition, progress in cloning of RKN resistance genes has been dismal. Recent identification of pattern-triggered immunity in roots against nematodes, an ascaroside as a nematode-associated molecular pattern (NAMP) and the discovery of a NAMP plant receptor, provide tools and opportunities to develop durable host resistance against nematodes including RKNs.
Nitric Oxide in Post-cardiac Arrest Syndrome
Authors: Miyazaki Yusuke , Ichinose Fumito
Published: October 2019

Sudden cardiac arrest is a leading cause of death worldwide. Although the methods of cardiopulmonary resuscitation have been improved, mortality is still unacceptably high, and many survivors suffer from lasting neurological deficits due to the post-cardiac arrest syndrome (PCAS). Pathophysiologically, generalized vascular endothelial dysfunction accompanied by platelet activation and systemic inflammation has been implicated in the pathogenesis of PCAS. Because endothelial-derived nitric oxide (NO) plays a central role in maintaining vascular homeostasis, the role of NO-dependent signaling has been a focus of the intense investigation. Recent preclinical studies showed that therapeutic interventions that increase vascular NO bioavailability may improve outcomes after cardiac arrest complicated with PCAS. In particular, NO inhalation therapy has been shown to improve neurological outcomes and survival in multiple species. Clinical studies examining the safety and efficacy of inhaled NO in patients sustaining PCAS are warranted.
Exploring factors that impact uptake of risk-reducing bilateral salpingo-oophorectomy (RRBSO) in high-risk women
Authors: Hickey Martha , Rio Ines , Trainer Alison , Marino Jennifer L. , Wrede C. David , Peate Michelle
Published: October 2019

Objective:

Only risk-reducing bilateral salpingo-oophorectomy (RRBSO) has been shown to reduce ovarian cancer deaths in high-risk women. Uptake of RRBSO is, however, suboptimal and reasons are not well defined. More information is needed about the barriers to RRBSO and patient needs for information and care.

Methods:

Cross-sectional study including the Perception of Cancer Risk Scale, factors affecting decision-making about RRBSO, and unmet information needs were measured using a purpose-designed questionnaire.

Results:

Of the 193 high-risk women aged 30 to 50 approached, 60 (31%) agreed to participate. Respondents were either considering or had recently undergone premenopausal RRBSO. Most (49/60) had no personal history of cancer; 11/60 had previous breast cancer. Overall, responses did not differ between pre- and post-RRBSO participants. The main barriers to RRBSO were surgical menopause and loss of fertility. Other concerns included the impact on sexual function and bone health. Reduction in ovarian cancer risk and prolonged life expectancy were the main drivers for RRBSO. Participants understood that RRBSO reduced cancer risk, although most substantially overestimated their personal ovarian cancer risk. High-risk women wanted more information about how to manage the short- and long-term consequences of surgical menopause.

Conclusions:

Concerns about surgical menopause and loss of fertility are barriers to RRBSO for high-risk women despite understanding the benefits of reduced cancer risk. There is an unmet need for more information about effectively managing the noncancer consequences of RRBSO in premenopausal women.

Video Summary:
http://links.lww.com/MENO/A478.
SMOKING STATUS AND TREATMENT OUTCOMES OF VASCULAR ENDOTHELIAL GROWTH FACTOR INHIBITORS FOR NEOVASCULAR AGE-RELATED MACULAR DEGENERATION
Authors: Vittorio Alexander F. , Nguyen Vuong , Barthelmes Daniel , Arnold Jennifer J. , Cheung Chui M. G. , Murray Neil , Gillies Mark C. ,   the Fight Retinal Blindness! Study Group
Published: October 2019

Purpose:

To assess whether smoking status affects 1-year visual outcomes in eyes treated with vascular endothelial growth factor inhibitors for neovascular age-related macular degeneration.

Methods:

Retrospective analysis of data from a prospectively designed, multicenter, observational database. Nine hundred and eighty seven treatment-naive eyes of patients with neovascular age-related macular degeneration were tracked by the Fight Retinal Blindness! outcome registry in Australia, New Zealand, Singapore, and Switzerland who had documented smoking status at baseline and commenced vascular endothelial growth factor inhibitor therapy from January 2006 to December 2016. Generalized additive models were used to display visual acuity results.

Results:

There was a significant difference in mean improvement in visual acuity at 12 months between nonsmokers, ex-smokers, and current smokers (7.7 vs. 6.1 vs. 3.5 letters of change; P = 0.046) among patients who completed 12 months of treatment when adjusted for age, baseline visual acuity, and choroidal neovascular membrane lesion type and nested for practice. There was no significant difference in the median number of injections over 12 months of treatment by smoking status. Current smokers were a mean of 6.2 years younger than nonsmokers when they started treatment (P < 0.001).

Conclusion:

This study found inferior 12-month visual outcomes in patients who continued to smoke while receiving vascular endothelial growth factor inhibitor therapy for neovascular age-related macular degeneration.
Intraoperative methadone administration and postoperative pain control: a systematic review and meta-analysis
Authors: D'Souza Ryan S. , Gurrieri Carmelina , Johnson Rebecca L. , Warner Nafisseh , Wittwer Erica
Published: October 2019

Postoperative pain is not adequately managed in greater than 40% of surgical patients and is a high priority for perioperative research. In this meta-analysis, we examined studies comparing postoperative opioid consumption and pain scores in surgical patients who received methadone by any route vs those who received another opioid by any route. Studies were identified from PubMed, Cochrane, Web of Science, EMBASE, and Scopus from January 1966 to November 2018. Pooled odds ratios were calculated for a primary outcome of postoperative opioid consumption and secondary outcomes of time-to-extubation, time-to-first postoperative analgesia request, satisfaction, hospital length-of-stay, and complications. Postoperative pain scores were assessed qualitatively. Ten studies (617 patients) were included. Postoperative opioid consumption at 24 hours was lower in the methadone group vs control (mean difference = −15.22 mg oral morphine equivalents, 95% confidence interval −27.05 to −3.38; P = 0.01). Patients in the methadone group generally reported lower postoperative pain scores in 7 of 10 studies. Meta-analysis revealed greater satisfaction scores with analgesia in the methadone group vs control (0-100 visual analog scale; mean difference = 7.16, 95% confidence interval 2.30-12.01; P = 0.004). There was no difference in time-to-extubation, time-to-first analgesia request, hospital length-of-stay, or complications (nausea, sedation, respiratory depression, and hypoxemia). The results demonstrate that surgical patients who received intraoperative methadone had lower postoperative opioid consumption, generally reported lower pain scores and experienced better satisfaction with analgesia. However, these advantages need to be weighed carefully against dangerous risks with perioperative methadone, specifically respiratory depression and arrhythmia. Future studies should explore logistics, safety, and cost effectiveness.
The deubiquitinating enzymes UBP12 and UBP13 negatively regulate the activity of the ubiquitin-dependent peptidases DA1, DAR1 and DAR2
Authors: Vanhaeren Hannes , Chen Ying , Vermeersch Mattias , De Vleeschhauwer Valerie , Persiau Geert , Eeckhout Dominique , De Jaeger Geert , Gevaert Kris , Inzé Dirk
Published: October 2019

Protein ubiquitination is a very diverse post-translational modification leading to protein degradation or delocalization, or altering protein activity. InArabidopsis thaliana, two E3 ligases, BIG BROTHER (BB) and DA2, activate the latent peptidases DA1, DAR1 and DAR2 by mono-ubiquitination at multiple sites. Subsequently, these activated peptidases destabilize various positive regulators of growth. Here, we show that two ubiquitin-specific proteases, UBP12 and UBP13, deubiquitinate DA1, DAR1 and DAR2, hence reducing their peptidase activity. Overexpression ofUBP12orUBP13strongly decreased leaf size and cell area, and resulted in lower ploidy levels. Mutants in whichUBP12andUBP13were downregulated produced smaller leaves that contained fewer and smaller cells. Remarkably, neither UBP12 nor UBP13 were found to be cleavage substrates of the activated DA1. Our results therefore suggest that UBP12 and UBP13 work upstream of DA1, DAR1 and DAR2 to restrict their protease activity and hence fine-tune plant growth and development.
Metage2Metabo: metabolic complementarity applied to genomes of large-scale microbiotas for the identification of keystone species
Authors: Belcour Arnaud , Frioux Clémence , Aite Méziane , Bretaudeau Anthony , Siegel Anne
Published: October 2019

Capturing the functional diversity of microbiotas entails identifying metabolic functions and species of interest within hundreds or thousands. Starting from genomes, a way to functionally analyse genetic information is to build metabolic networks. Yet, no method enables a functional screening of such a large number of metabolic networks nor the identification of critical species with respect to metabolic cooperation.

Metage2Metabo (M2M) addresses scalability issues raised by metagenomics datasets to identify keystone, essential and alternative symbionts in large microbiotas communities with respect to individual metabolism and collective metabolic complementarity. Genome-scale metabolic networks for the community can be either provided by the user or very efficiently reconstructed from a large family of genomes thanks to a multi-processing solution to run the Pathway Tools software. The pipeline was applied to 1,520 genomes from the gut microbiota and 913 metagenome-assembled genomes of the rumen microbiota. Reconstruction of metabolic networks and subsequent metabolic analyses were performed in a reasonable time.

M2M identifies keystone, essential and alternative organisms by reducing the complexity of a large-scale microbiota into minimal communities with equivalent properties, suitable for further analyses.
Community Standards for Open Cell Migration Data
Authors: Gonzalez-Beltran Alejandra N. , Masuzzo Paola , Ampe Christophe , Bakker Gert-Jan , Besson Sébastien , Eibl Robert H. , Friedl Peter , Gunzer Matthias , Kittisopikul Mark , Le Dévédec Sylvia E. , Leo Simone , Moore Josh , Paran Yael , Prilusky Jaime , Rocca-Serra Philippe , Roudot Philippe , Schuster Marc , Sergeant Gwendolien , Strömblad Staffan , Swedlow Jason R. , van Erp Merijn , Troys Marleen Van , Zaritsky Assaf , Sansone Susanna-Assunta , Martens Lennart
Published: October 2019

Cell migration research has become a high-content field. However, the quantitative information encapsulated in these complex and high-dimensional datasets is not fully exploited due to the diversity of experimental protocols and non-standardised output formats. In addition, typically the datasets are not open for reuse. Making the data open and Findable, Accessible, Interoperable, and Reusable (FAIR) will enable meta-analysis, data integration, and data mining. Standardised data formats and controlled vocabularies are essential for building a suitable infrastructure for that purpose but are not available in the cell migration domain. We here present standardisation efforts by the Cell Migration Standardisation Organization, CMSO, an open community-driven organisation to facilitate the development of standards for cell migration data. This work will foster the development of improved algorithms and tools, and enable secondary analysis of public datasets, ultimately unlocking new knowledge of the complex biological process of cell migration.
T-Gene: Improved target gene prediction
Authors: O’Connor Timothy , Grant Charles E. , Bodén Mikael , Bailey Timothy L.
Published: October 2019

Motivation

Identifying the genes regulated by a given transcription factor (its “target genes”) is a key step in developing a comprehensive understanding of gene regulation. Previously we developed a method for predicting the target genes of a transcription factor (TF) based solely on the correlation between a histone modification at the TF’s binding site and the expression of the gene across a set of tissues. That approach is limited to organisms for which extensive histone and expression data is available, and does not explicitly incorporate the genomic distance between the TF and the gene.

Results

We present the T-Gene algorithm, which overcomes these limitations. T-Gene can be used to predict which genes are most likely to be regulated by a TF, and which of the TF’s binding sites are most likely involved in regulating particular genes. T-Gene calculates a novel score that combines distance and histone/expression correlation, and we show that this score accurately predicts when a regulatory element bound by a TF is in contact with a gene’s promoter, achieving median positive predictive value (PPV) above 50%. T-Gene is easy to use via its web server or as a command-line tool, and can also make accurate predictions (median PPV above 40%) based on distance alone when extensive histone/expression data is not available for the organism. T-Gene provides an estimate of the statistical significance of each of its predictions.

Availability

The T-Gene web server, source code, histone/expression data and genome annotation files are provided at http://meme-suite.org.

Contact

timothybailey@unr.edu
Biallelic mutations in M1AP are a frequent cause of meiotic arrest leading to male infertility
Authors: Wyrwoll Margot J. , Temel Şehime G. , Nagirnaja Liina , Oud Manon S. , Lopes Alexandra M. , van der Heijden Godfried W. , Rotte Nadja , Wistuba Joachim , Wöste Marius , Ledig Susanne , Krenz Henrike , Smits Roos M. , Carvalho Filipa , Gonçalves João , Fietz Daniela , Türkgenç Burcu , Ergören Mahmut C. , Çetinkaya Murat , Başar Murad , Kahraman Semra , Pilatz Adrian , Röpke Albrecht , Dugas Martin , Kliesch Sabine , Neuhaus Nina ,   GEMINI Consortium, Aston Kenneth I. , Conrad Donald F. , Veltman Joris A. , Friedrich Corinna , Tüttelmann Frank
Published: October 2019

Male infertility affects ∼7% of men in Western societies, but its causes remain poorly understood. The most clinically severe form of male infertility is non-obstructive azoospermia (NOA), which is, in part, caused by an arrest at meiosis, but so far only few genes have been reported to cause germ cell arrest in males. To address this gap, whole exome sequencing was performed in 60 German men with complete meiotic arrest, and we identified in three unrelated men the same homozygous frameshift variant c.676dup (p.Trp226LeufsTer4) in M1AP, encoding meiosis 1 arresting protein. Then, with collaborators from the International Male Infertility Genomics Consortium (IMIGC), we screened a Dutch cohort comprising 99 infertile men and detected the same homozygous variant c.676dup in a man with hypospermatogenesis predominantly displaying meiotic arrest. We also identified two Portuguese men with NOA carrying likely biallelic loss-of-function (LoF) and missense variants in M1AP among men screened by the Genetics of Male Infertility Initiative (GEMINI). Moreover, we discovered a homozygous missense variant p.(Pro389Leu) in M1AP in a consanguineous Turkish family comprising five infertile men. M1AP is predominantly expressed in human and mouse spermatogonia up to secondary spermatocytes and previous studies have shown that knockout male mice are infertile due to meiotic arrest. Collectively, these findings demonstrate that both LoF and missense M1AP variants that impair its protein cause autosomal-recessive meiotic arrest, non-obstructive azoospermia and male infertility. In view of the evidence from several independent groups and populations, M1AP should be included in the growing list of validated NOA genes.
Molecular mechanism of attenuation of heat shock transcription factor 1 activity
Authors: Kmiecik Szymon W. , Breton Laura Le , Mayer Matthias P.
Published: October 2019

The heat shock response is a universal transcriptional response to proteotoxic stress orchestrated by heat shock transcription factor Hsf1 in all eukaryotic cells. Despite over 40 years of intense research, the mechanism of HSF1 activity regulation remains poorly understood at a molecular level. In metazoa Hsf1 trimerizes upon heat shock through a leucin-zipper domain and binds to DNA. How Hsf1 is dislodged from DNA and monomerized remained enigmatic. Here, we demonstrate that trimeric Hsf1 is dissociated from DNA in vitro by Hsc70 and DnaJB1. Hsc70 acts at two distinct sites on Hsf1. Hsf1 trimers are monomerized by successive cycles of entropic pulling, unzipping the triple leucine-zipper. This process directly monitors the concentration of Hsc70 and DnaJB1. During heat shock adaptation Hsc70 first binds to the transactivation domain leading to partial attenuation of the response and subsequently, at higher concentrations, Hsc70 removes Hsf1 from DNA to restore the resting state.