bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climatic and land‐use drivers along a latitudinal gradient: species diversity in temperate grasslands on agricultural soils
Authors: Perelman Susana B. , Burkart Silvia E. , Oyarzabal Mariano , Bagnato Camilo , Batista William 
Published: September 2017

AbstractQuestionsDo remaining mesophytic grasslands on soils with agricultural potential respond to a latitudinal gradient? Are climatic or land‐use factors the principal drivers of regional and local diversity of these grasslands?LocationMesophytic grasslands, Argentine Pampas, Rio de la Plata grasslands.MethodsThe species presence and cover was recorded in each of 96 remnant grasslands on soils suitable for cropping, grouped into five sampling locations. In each region, CIs for γ‐diversity and for the slope of species/area curves were estimated. Unconstrained ordination was applied to detect the principal gradients in floristic composition and correlation analysis to identify their main drivers. Mantel test was used to evaluate the correlation between floristic similarity and geographic distance, and with Euclidean distance in fragmentation and climatic variables. To rank the climatic and land‐use factors that account for local species richness and percentge of exotics, we applied correlation analysis and regression models.ResultsCommunity composition (73% native species) was mainly related to climatic variables determined by latitude, with a slight influence of fragmentation variables. Regional species richness responded to latitude: γ‐diversity decreased linearly with increasing distance from the Equator, as did the rate of species accumulation with expanding area. Alpha‐diversity did not vary in a systematic way with latitude, being associated with landscape fragmentation and mean annual precipitation. Relative importance of C4 grasses and mean percentage exotics showed opposite latitudinal tendencies, the former decreasing and the latter increasing towards the south.ConclusionsLatitude was a strong determinant of regional diversity and community composition, but a partial driver for local species richness, mainly influenced by landscape fragmentation. While climatic and geographic drivers determined gradual latitudinal turnover in regional species pools, within regions land‐use history, stochastic processes and biotic interactions were also important. All these patterns need to be considered together when delimiting grassland nature reserves for conservation of the most diverse ecosystems of this region, currently threatened by agricultural expansion and intensification.
Job contenders: roles of the β‐barrel assembly machinery and the translocation and assembly module in autotransporter secretion
Authors: Albenne Cécile , Ieva Raffaele 
Published: September 2017

SummaryIn Gram‐negative bacteria, autotransporters secrete effector protein domains that are linked to virulence. Although they were once thought to be simple and autonomous secretion machines, mounting evidence reveals that multiple factors of the bacterial envelope are necessary for autotransporter assembly. Secretion across the outer membrane of their soluble effector “passenger domain” is promoted by the assembly of an outer membrane‐spanning “β‐barrel domain”. Both reactions require BamA, an essential component of the β‐barrel assembly machinery (BAM complex) that catalyzes the final reaction step by which outer membrane proteins are integrated into the lipid bilayer. A large amount of data generated in the last decade has shed key insights onto the mechanistic coordination of autotransporter β‐barrel domain assembly and passenger domain secretion. These results, together with the recently solved structures of the BAM complex, offer an unprecedented opportunity to discuss a detailed model of autotransporter assembly. Importantly, some autotransporters benefit from the presence of an additional machinery, the translocation and assembly module (TAM), a two‐membrane spanning complex, which contains a BamA‐homologous subunit. Although it remains unclear how the BAM complex and the TAM cooperate, it is evident that multiple preparatory steps are necessary for efficient autotransporter biogenesis.
Cassava brown streak disease: historical timeline, current knowledge and future prospects
Authors: Tomlinson Katie R. , Bailey Andy M. , Alicai Titus , Seal Sue , Foster Gary D. 
Published: September 2017

SummaryCassava is the second most important staple food crop in terms of per capita calories consumed in Africa and holds potential for climate change adaptation. Unfortunately, productivity in East and Central Africa is severely constrained by two viral diseases: cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). CBSD was first reported in 1936 from northeast Tanzania. For approximately 70 years, CBSD was restricted to coastal East Africa and so had a relatively low impact on food security compared with CMD. However, at the turn of the 21st century, CBSD re‐emerged further inland, in areas around Lake Victoria, and it has since spread through many East and Central African countries, causing high yield losses and jeopardizing the food security of subsistence farmers. This recent re‐emergence has attracted intense scientific interest, with studies shedding light on CBSD viral epidemiology, sequence diversity, host interactions and potential sources of resistance within the cassava genome. This review reflects on 80 years of CBSD research history (1936–2016) with a timeline of key events. We provide insights into current CBSD knowledge, management efforts and future prospects for improved understanding needed to underpin effective control and mitigation of impacts on food security.
Impact of climate change on vector transmission of Trypanosoma cruzi (Chagas, 1909) in North America
Authors: CARMONA‐CASTRO O. , MOO‐LLANES D. A. , RAMSEY J. M. 
Published: September 2017

AbstractClimate change can influence the geographical range of the ecological niche of pathogens by altering biotic interactions with vectors and reservoirs. The distributions of 20 epidemiologically important triatomine species in North America were modelled, comparing the genetic algorithm for rule‐set prediction (GARP) and maximum entropy (MaxEnt), with or without topographical variables. Potential shifts in transmission niche for Trypanosoma cruzi (Trypanosomatida: Trypanosomatidae) (Chagas, 1909) were analysed for 2050 and 2070 in Representative Concentration Pathway (RCP) 4.5 and RCP 8.5. There were no significant quantitative range differences between the GARP and MaxEnt models, but GARP models best represented known distributions for most species [partial‐receiver operating characteristic (ROC) > 1]; elevation was an important variable contributing to the ecological niche model (ENM). There was little difference between niche breadth projections for RCP 4.5 and RCP 8.5; the majority of species shifted significantly in both periods. Those species with the greatest current distribution range are expected to have the greatest shifts. Positional changes in the centroid, although reduced for most species, were associated with latitude. A significant increase or decrease in mean niche elevation is expected principally for Neotropical 1 species. The impact of climate change will be specific to each species, its biogeographical region and its latitude. North American triatomines with the greatest current distribution ranges (Nearctic 2 and Nearctic/Neotropical) will have the greatest future distribution shifts. Significant shifts (increases or decreases) in mean elevation over time are projected principally for the Neotropical species with the broadest current distributions. Changes in the vector exposure threat to the human population were significant for both future periods, with a 1.48% increase for urban populations and a 1.76% increase for rural populations in 2050.
Effects of temperature on germination of sporangia, infection and protein secretion by Phytophthora kernoviae
Authors: Shelley B. A. , Luster D. G. , Garrett W. M. , McMahon M. B. , Widmer T. L. 
Published: September 2017

Phytophthora kernoviae is a pathogen on a wide range of plants, but little is known of optimal infection conditions. Rhododendron ponticum leaves were inoculated with six different isolates of P. kernoviae sporangia and incubated at different temperatures from 10 to 28 °C. After 1 week, lesion development and pathogen recovery were only observed from all isolates at 15 and 20 °C and a few isolates at 10 °C. In an experiment with temperatures ranging from 20 to 25 °C, lesion development and pathogen recovery on R. ponticum, Magnolia stellata and Viburnum tinus occurred consistently at 20 and 21 °C, was limited at 22 °C, and did not occur at 23 °C and above. There was no difference in sporangia and zoospore germination at 20–25 °C. In a temperature fluctuation experiment, the necrotic area of inoculated R. ponticum leaves increased with longer incubation at 20 °C and decreased with longer incubation at 24 °C. Crude extracts of secreted proteins from P. kernoviae cultures grown at 20 and 24 °C were compared to determine any effects of temperature on pathogenicity. When spot tested on R. ponticum leaves, crude protein suspensions from cultures grown at 20 °C induced necrosis, while proteins from cultures grown at 24 °C did not. Proteomic analysis confirmed that a 10 kDa protein secreted at both 20 and 24 °C shared sequence homology to the conserved domains of known elicitins of other Phytophthora spp. The protein secreted at 20 °C that was responsible for necrosis has not been identified.
Introduction to the South African Revenue Service and National Treasury Firm‐Level Panel
Authors: Pieterse Duncan , Gavin Elizabeth , Kreuser C. Friedrich 
Published: September 2017

AbstractThe South African Revenue Service and National Treasury Firm‐Level Panel is an unbalanced panel data set created by merging several sources of administrative tax data received during 2015. The four data sources that constitute the panel are: (i) company income tax from registered firms who submit tax forms; (ii) employee data from employee income tax certificates submitted by employers; (iii) value‐added tax data from registered firms; and (iv) customs records from traders. These data sets constitute a significant and unique source for the study of firm‐level behaviour in post‐apartheid South Africa. We review the key data sources used to construct the panel, highlight some important questions that arise as a result of panel construction, discuss the biases in the resulting data, compare key aggregates in the panel to other data sources, and provide a descriptive overview of the tax records.
Mapping soil salinity in 3‐dimensions using an EM38 and EM4Soil inversion modelling at the reconnaissance scale in central Morocco
Authors: Dakak H. , Huang J. , Zouahri A. , Douaik A. , Triantafilis J. 
Published: September 2017

AbstractLarge areas of Morocco require irrigation and although good quality water is available in dams, farmers augment river water with poorer quality ground water, resulting in salt build‐up without a sufficient leaching fraction. Implementation of management plans requires baseline reconnaissance maps of salinity. We developed a method to map the distribution of salinity profiles by establishing a linear regression (LR) between calculated true electrical conductivity (σ, mS/m) and electrical conductivity of the saturated soil‐paste extract (ECe, dS/m). Estimates of σ were obtained by inverting the apparent electrical conductivity (ECa, mS/m) collected from a 500‐m grid survey using an EM38. Spherical variograms were developed to interpolate ECa data onto a 100 m grid using residual maximum likelihood. Inversion was carried out on kriged ECa data using a quasi‐3d model (EM4Soil software), selecting the cumulative function (CF) forward modelling and S2 inversion algorithm with a damping factor of 3.0. Using a ‘leave‐one‐out cross‐validation' (LOOCV), of one in 12 of the calibration sites, the use of the q‐3d model yielded a high accuracy (RMSE = 0.42 dS/m), small bias (ME = −0.02 dS/m) and Lin's concordance (0.91). Slightly worse results were obtained using individual LR established at each depth increment overall (i.e. RMSE = 0.45 dS/m; ME = 0.00 dS/m; Lin's = 0.89) with the raw EM38 ECa. Inversion required a single LR (ECe = 0.679 + 0.041 × σ), enabling efficiencies in estimating ECe at any depth across the irrigation district. Final maps of ECe, along with information on water used for irrigation (ECw) and the characterization of properties of the two main soil types, enabled better understanding of causes of secondary soil salinity. The approach can be applied to problematic saline areas with saline water tables.
Aminoglycoside Concentrations Required for Synergy with Carbapenems against Pseudomonas aeruginosa Determined via Mechanistic Studies and Modeling
Authors: Yadav Rajbharan , Bulitta Jürgen B. , Schneider Elena K. , Shin Beom Soo , Velkov Tony , Nation Roger L. , Landersdorfer Cornelia B. 
Published: September 2017

ABSTRACT

This study aimed to systematically identify the aminoglycoside concentrations required for synergy with a carbapenem and characterize the permeabilizing effect of aminoglycosides on the outer membrane of
Pseudomonas aeruginosa
. Monotherapies and combinations of four aminoglycosides and three carbapenems were studied for activity against
P. aeruginosa
strain AH298-GFP in 48-h static-concentration time-kill studies (SCTK) (inoculum: 10
7.6
CFU/ml). The outer membrane-permeabilizing effect of tobramycin alone and in combination with imipenem was characterized via electron microscopy, confocal imaging, and the nitrocefin assay. A mechanism-based model (MBM) was developed to simultaneously describe the time course of bacterial killing and prevention of regrowth by imipenem combined with each of the four aminoglycosides. Notably, 0.25 mg/liter of tobramycin, which was inactive in monotherapy, achieved synergy (i.e., ≥2-log
10
more killing than the most active monotherapy at 24 h) combined with imipenem. Electron micrographs, confocal image analyses, and the nitrocefin uptake data showed distinct outer membrane damage by tobramycin, which was more extensive for the combination with imipenem. The MBM indicated that aminoglycosides enhanced the imipenem target site concentration up to 4.27-fold. Tobramycin was the most potent aminoglycoside to permeabilize the outer membrane; tobramycin (0.216 mg/liter), gentamicin (0.739 mg/liter), amikacin (1.70 mg/liter), or streptomycin (5.19 mg/liter) was required for half-maximal permeabilization. In summary, our SCTK, mechanistic studies and MBM indicated that tobramycin was highly synergistic and displayed the maximum outer membrane disruption potential among the tested aminoglycosides. These findings support the optimization of highly promising antibiotic combination dosage regimens for critically ill patients.
Colistin Is Extensively Lost during Standard
In Vitro
Experimental Conditions
Authors: Karvanen Matti , Malmberg Christer , Lagerbäck Pernilla , Friberg Lena E. , Cars Otto 
Published: September 2017

ABSTRACT

Colistin adheres to a range of materials, including plastics in labware. The loss caused by adhesion influences an array of methods detrimentally, including MIC assays and
in vitro
time-kill experiments. The aim of this study was to characterize the extent and time course of colistin loss in different types of laboratory materials during a simulated time-kill experiment without bacteria or plasma proteins present. Three types of commonly used large test tubes, i.e., soda-lime glass, polypropylene, and polystyrene, were studied, as well as two different polystyrene microplates and low-protein-binding microtubes. The tested concentration range was 0.125 to 8 mg/liter colistin base. Exponential one-phase and two-phase functions were fitted to the data, and the adsorption of colistin to the materials was modeled with the Langmuir adsorption model. In the large test tubes, the measured start concentrations ranged between 44 and 102% of the expected values, and after 24 h, the concentrations ranged between 8 and 90%. The half-lives of colistin loss were 0.9 to 12 h. The maximum binding capacities of the three materials ranged between 0.4 and 1.1 μg/cm
2
, and the equilibrium constants ranged between 0.10 and 0.54 ml/μg. The low-protein-binding microtubes showed start concentrations between 63 and 99% and concentrations at 24 h of between 59 and 90%. In one of the microplates, the start concentrations were below the lower limit of quantification at worst. In conclusion, to minimize the effect of colistin loss due to adsorption, our study indicates that low-protein-binding polypropylene should be used when possible for measuring colistin concentrations in experimental settings, and the results discourage the use of polystyrene. Furthermore, when diluting colistin in protein-free media, the number of dilution steps should be minimized.
Inactivation of Human Norovirus Genogroups I and II and Surrogates by Free Chlorine in Postharvest Leafy Green Wash Water
Authors: Dunkin Nathan , Weng ShihChi , Jacangelo Joseph G. , Schwab Kellogg J. 
Published: September 2017

ABSTRACT

Human noroviruses (hNoVs) are a known public health concern associated with the consumption of leafy green vegetables. While a number of studies have investigated pathogen reduction on the surfaces of leafy greens during the postharvest washing process, there remains a paucity of data on the level of treatment needed to inactivate viruses in the wash water, which is critical for preventing cross-contamination. The objective of this study was to quantify the susceptibility of hNoV genotype I (GI), hNoV GII, murine norovirus (MNV), and bacteriophage MS2 to free chlorine in whole leaf, chopped romaine, and shredded iceberg lettuce industrial leafy green wash waters, each sampled three times over a 4-month period. A suite of kinetic inactivation models was fit to the viral reduction data to aid in quantification of concentration-time (CT) values. Results indicate that 3-log
10
infectivity reduction was achieved at CT values of less than 0.2 mg · min/liter for MNV and 2.5 mg · min/liter for MS2 in all wash water types. CT values for 2-log
10
molecular reduction of hNoV GI in whole leaf and chopped romaine wash waters were 1.5 and 0.9 mg · min/liter, respectively. For hNoV GII, CT values were 13.0 and 7.5 mg · min/liter, respectively. In shredded iceberg wash water, 3-log
10
molecular reduction was not observed for any virus over the time course of experiments. These findings demonstrate that noroviruses may exhibit genogroup-dependent resistance to free chlorine and emphasize the importance of distinguishing between genogroups in hNoV persistence studies.

IMPORTANCE
Postharvest washing of millions of pounds of leafy greens is performed daily in industrial processing facilities with the intention of removing dirt, debris, and pathogenic microorganisms prior to packaging. Modest inactivation of pathogenic microorganisms (less than 2 log
10
) is known to occur on the surfaces of leafy greens during washing. Therefore, the primary purpose of the sanitizing agent is to maintain microbial quality of postharvest processing water in order to limit cross-contamination. This study modeled viral inactivation data and quantified the free-chlorine CT values that processing facilities must meet in order to achieve the desired level of hNoV GI and GII reduction. Disinfection experiments were conducted in industrial leafy green wash water collected from a full-scale fresh produce processing facility in the United States, and hNoV GI and GII results were compared with surrogate molecular and infectivity data.
Glycolytic Functions Are Conserved in the Genome of the Wine Yeast Hanseniaspora uvarum, and Pyruvate Kinase Limits Its Capacity for Alcoholic Fermentation
Authors: Langenberg Anne-Kathrin , Bink Frauke J. , Wolff Lena , Walter Stefan , von Wallbrunn Christian , Grossmann Manfred , Heinisch Jürgen J. , Schmitz Hans-Peter 
Published: September 2017

ABSTRACT

Hanseniaspora uvarum
(anamorph
Kloeckera apiculata
) is a predominant yeast on wine grapes and other fruits and has a strong influence on wine quality, even when
Saccharomyces cerevisiae
starter cultures are employed. In this work, we sequenced and annotated approximately 93% of the
H. uvarum
genome. Southern and synteny analyses were employed to construct a map of the seven chromosomes present in a type strain. Comparative determinations of specific enzyme activities within the fermentative pathway in
H. uvarum
and
S. cerevisiae
indicated that the reduced capacity of the former yeast for ethanol production is caused primarily by an ∼10-fold-lower activity of the key glycolytic enzyme pyruvate kinase. The heterologous expression of the encoding gene,
H. uvarum
PYK1
(
HuPYK1
), and two genes encoding the phosphofructokinase subunits,
HuPFK1
and
HuPFK2
, in the respective deletion mutants of
S. cerevisiae
confirmed their functional homology.

IMPORTANCE
Hanseniaspora uvarum
is a predominant yeast species on grapes and other fruits. It contributes significantly to the production of desired as well as unfavorable aroma compounds and thus determines the quality of the final product, especially wine. Despite this obvious importance, knowledge on its genetics is scarce. As a basis for targeted metabolic modifications, here we provide the results of a genomic sequencing approach, including the annotation of 3,010 protein-encoding genes, e.g., those encoding the entire sugar fermentation pathway, key components of stress response signaling pathways, and enzymes catalyzing the production of aroma compounds. Comparative analyses suggest that the low fermentative capacity of
H. uvarum
compared to that of
Saccharomyces cerevisiae
can be attributed to low pyruvate kinase activity. The data reported here are expected to aid in establishing
H. uvarum
as a non-
Saccharomyces
yeast in starter cultures for wine and cider fermentations.
Flexibility-Rigidity Coordination of the Dense Exopolysaccharide Matrix in Terrestrial Cyanobacteria Acclimated to Periodic Desiccation
Authors: Liu Wen , Cui Lijuan , Xu Haiyan , Zhu Zhaoxia , Gao Xiang 
Published: September 2017

ABSTRACT

A dense exopolysaccharide (EPS) matrix is crucial for cyanobacterial survival in terrestrial xeric environments, in which cyanobacteria undergo frequent expansion and shrinkage processes during environmental desiccation-rehydration cycles. However, it is unclear how terrestrial cyanobacteria coordinate the structural dynamics of the EPS matrix upon expansion and shrinkage to avoid potential mechanical stress while benefiting from the matrix. In the present study, we sought to answer this question by investigating the gene expression, protein dynamics, enzymatic characteristics, and biological roles of WspA, an abundantly secreted protein, in the representative terrestrial cyanobacterium
Nostoc flagelliforme
. The results demonstrated that WspA is a novel β-galactosidase that facilitates softening of the EPS matrix by breaking the polysaccharide backbone under substantial moisture or facilitates the thickening and relinkage of the broken matrix during the drying process, and thus these regulations are well correlated with moisture availability or desiccation-rehydration cycles. This coordination of flexibility and rigidity of the cyanobacterial extracellular matrix may contribute to a favorable balance of cell growth and stress resistance in xeric environments.

IMPORTANCE
How the exopolysaccharide matrix is dynamically coordinated by exoproteins to cope with frequent expansion and shrinkage processes in terrestrial colonial cyanobacteria remains unclear. Here we elucidated the biochemical identity and biological roles of a dominant exoprotein in these regulation processes. Our study thus gained insight into this regulative mechanism in cyanobacteria to combat periodic desiccation. In addition, the filamentous drought-adapted cyanobacterium
Nostoc flagelliforme
serves as an ideal model for us to explore this issue in this study.