bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Flow Cytometry-Based Phenotypic Screen To Identify Novel Endocytic Factors inSaccharomyces cerevisiae
Authors: Wrasman Kristie , Alioto Salvatore L , Zhang Yorke , Hoban Kyle , Khairy Marjon , Goode Bruce L , Wendland Beverly 
Published: March 2018

AbstractEndocytosis is a fundamental process for internalizing material from the plasma membrane, including many transmembrane proteins that are selectively internalized depending on environmental conditions. In most cells, the main route of entry is clathrin-mediated endocytosis (CME), a process that involves the coordinated activity of over 60 proteins; however, there are likely as-yet unidentified proteins involved in cargo selection and/or regulation of endocytosis. We performed a mutagenic screen to identify novel endocytic genes in Saccharomyces cerevisiae expressing the methionine permease Mup1 tagged with pHluorin (pHl), a pH-sensitive GFP variant whose fluorescence is quenched upon delivery to the acidic vacuole lumen. We used fluorescence-activated cell sorting to isolate mutagenized cells with elevated fluorescence, resulting from failure to traffic Mup1-pHl cargo to the vacuole, and further assessed subcellular localization of Mup1-pHl to characterize the endocytic defects in 256 mutants. A subset of mutant strains was classified as having general endocytic defects based on mislocalization of additional cargo proteins. Within this group, we identified mutations in four genes encoding proteins with known roles in endocytosis: the endocytic coat components SLA2, SLA1, and EDE1, and the ARP3 gene, whose product is involved in nucleating actin filaments to form branched networks. All four mutants demonstrated aberrant dynamics of the endocytic machinery at sites of CME; moreover, the arp3R346H mutation showed reduced actin nucleation activity in vitro. Finally, whole genome sequencing of two general endocytic mutants identified mutations in conserved genes not previously implicated in endocytosis, KRE33 and IQG1, demonstrating that our screening approach can be used to identify new components involved in endocytosis.
Identification of General Patterns of Sex-Biased Expression in Daphnia, a Genus with Environmental Sex Determination
Authors: Molinier Cécile , Reisser Céline M O , Fields Peter , Ségard Adeline , Galimov Yan , Haag Christoph R 
Published: March 2018

Abstract
Daphnia reproduce by cyclic-parthenogenesis, where phases of asexual reproduction are intermitted by sexual production of diapause stages. This life cycle, together with environmental sex determination, allow the comparison of gene expression between genetically identical males and females. We investigated gene expression differences between males and females in four genotypes of Daphnia magna and compared the results with published data on sex-biased gene expression in two other Daphnia species, each representing one of the major phylogenetic clades within the genus. We found that 42% of all annotated genes showed sex-biased expression in D. magna. This proportion is similar both to estimates from other Daphnia species as well as from species with genetic sex determination, suggesting that sex-biased expression is not reduced under environmental sex determination. Among 7453 single copy, one-to-one orthologs in the three Daphnia species, 707 consistently showed sex-biased expression and 675 were biased in the same direction in all three species. Hence these genes represent a core-set of genes with consistent sex-differential expression in the genus. A functional analysis identified that several of them are involved in known sex determination pathways. Moreover, 75% were overexpressed in females rather than males, a pattern that appears to be a general feature of sex-biased gene expression in Daphnia.
A Host-Pathogen Interaction Screen Identifies ada2 as a Mediator of Candida glabrata Defenses Against Reactive Oxygen Species
Authors: Kounatidis Ilias , Ames Lauren , Mistry Rupal , Ho Hsueh-lui , Haynes Ken , Ligoxygakis Petros 
Published: March 2018

Abstract
Candida glabrata (C. glabrata) forms part of the normal human gut microbiota but can cause life-threatening invasive infections in immune-compromised individuals. C. glabrata displays high resistance to common azole antifungals, which necessitates new treatments. In this investigation, we identified five C. glabrata deletion mutants (∆ada2, ∆bas1, ∆hir3, ∆ino2 and ∆met31) from a library of 196 transcription factor mutants that were unable to grow and activate an immune response in Drosophila larvae. This highlighted the importance of these transcription factors in C. glabrata infectivity. Further ex vivo investigation into these mutants revealed the requirement of C. glabrata ADA2 for oxidative stress tolerance. We confirmed this observation in vivo whereby growth of the C. glabrata Δada2 strain was permitted only in flies with suppressed production of reactive oxygen species (ROS). Conversely, overexpression of ADA2 promoted C. glabrata replication in infected wild type larvae resulting in larval killing. We propose that ADA2 orchestrates the response of C. glabrata against ROS-mediated immune defenses during infection. With the need to find alternative antifungal treatment for C. glabrata infections, genes required for survival in the host environment, such as ADA2, provide promising potential targets.
Evolution, growth and phenology of Phalaris minor biotypes resistant to ACCase-inhibiting herbicides in Mexico
Authors: Torres-García Jesús Rubén , Segura-León Obdulia , Uscanga-Mortera Ebandro , Trejo Carlos , Conde-Martínez Víctor , Kohashi-Shibata Josué , Martínez-Moreno David 
Published: March 2018

Background: Herbicide application to control weeds can promote a rapid selection of resistant phenotypes in small geographic areas. Also, in areas with a spatial heterogeneous management, resistance may evolve independently, promoting local adaptation in weeds. In the Mexican region known as “El Bajio,” 100,000 ha are cultivated with wheat, and the weed Phalaris minor , resistant to ACCase-inhibiting herbicides is present common.Question: We aim to identify the population structure of two genes in four different P. minor biotypes from “El Bajio” and to determine their association with phenology and plant growth differences (biomass and seed yield) that may contribute to survival in the agricultural environment.Studied species: Phalaris minor Retz . Study site and years of study:Methods: The diversity of the psbA gene and the sequence of two ACCase gene fragments as well as phenology, growth and biomass allocation were evaluated.Results: Results indicated different polymorphism levels for the two genes. There were no differences in the psbA gene between biotypes, although the ACCase gene exhibited high polymorphism level. In addition, each biotype showed differences in phenology, biomass accumulation and fecundity.Conclusions: The ACCase-inhibiting herbicide resistance in “El Bajio” region might be a resistance hotspot leading to the local adaptation of weeds.
Mobilization and synthesis of seed storage and LEA proteins during natural priming of Buddleja cordata and Opuntia tomentosa
Authors: Alvarado-López Sandra , Gómez-Maqueo Ximena , Soriano Diana , Orozco-Segovia Alma , Gamboa-de Buen Alicia 
Published: March 2018

Background: In crop plants, the induction of seed storage protein mobilization and synthesis of LEA family proteins has been extensively described.Question: Natural priming promotes mobilization and synthesis of seed storage and LEA proteins in wild plants?Species studied: Buddleja cordata and Opuntia tomentosa. Study site: Reserva Ecológica del Pedregal de San Angel (REPSA).Methods: Natural priming treatments were applied to B. cordata and O. tomentosa seeds during one and six months respectively. Phosphorylated proteins fractions were obtained by affinity chromatography from control and treated seeds. Differences in protein pattern between control and treated seeds were determined by electrophoresis and the treated seed proteins were identified by LS/LS/MALDITOF. Results: The phosphorylated fraction of B. cordata treated seeds presented two proteins that were absent in the control protein fraction. These two proteins were identified as two different 11S globulins. The phosphorylated fraction of O. tomentosa treated seeds also presented two proteins that were absent in the control protein fraction. These two proteins were identified as a 12S globulin and a LEA protein.Conclusion: Seeds are subjected to changes in soil water content during their permanence in soil; this natural priming process promotes mobilization and synthesis of storage and LEA proteins that are involved in stress resistance.
Temporary freshwater wetlands floristics in central Mexico highlands
Authors: Lobato-de Magalhães Tatiana , Martínez Mahinda 
Published: March 2018

Background: Mexico has a high diversity of aquatic and subaquatic plants that occur between 1,000 and 2,500 m of elevation, although a larger proportion of aquatic plants is concentrated at lower altitudes. Temporary wetlands harbor close to 73 % of the aquatic species in Mexico. These systems are under a strong anthropogenic pressure and suffer constant degradation.Questions: i) How many species grow in highland temporary wetlands? ii) Are they floristically similar? iii) Is there a latitudinal pattern of species richness?Studied groups: Charophyta, Pteridophyta, Angiosperms.Study site and years of study: Central Mexico (39 wetlands) from 2015 to 2016.Methods: We collected in 39 temporary wetlands for two years. We made a presence/absence list of species per locality, and calculated floristic similarities and correlations between wetlands. We include data characterizing life form, plant use, and conservation status.Results: We found 126 species belonging to 80 genera and 38 families. The richest families were Cyperaceae, Asteraceae, and Poaceae. As to genera, Eleocharis , Cyperus , and Juncus had more species. Species with the widest distributions were Persicaria mexicana , Marsilea mollis , Luziola fluitans , Heteranthera peduncularis , and Nymphoides fallax . We found five different life forms – all herbaceous, including 27 threatened species, 24 species with economic use, 48 endemic species, and 19 cosmopolitan species. In addition, we found 20 species recorded for the first time in some states included in our study, and two species of Eleocharis that might represent undescribed species. The richest wetland harbors 40 species, the poorest has only five. Wetlands were comparable to each other in species composition, and species richness increases towards the south.Conclusions: Temporary wetlands harbor a high floristic diversity and are similar to each other. Lower latitudes host higher numbers of species.
Öğretmen Adaylarının Protein Sentezine Yönelik Algıları: Öğrenme Güçlüğüne Karşı Önerilen Çözümler
Authors: Gül Şeyda , Özay Köse Esra 
Published: March 2018

Protein sentezi öğrenci ve
öğretmenler arasında öğrenme güçlüğü çekilen konular arasındadır. Bununla beraber bu konunun öğrenimi ve
öğretiminde karşılaşılan zorlukların nedeni ve doğasına yönelik detaylı bir
araştırmaya rastlanılmamıştır. Buradan hareketle bu çalışmanın amacı biyoloji
öğretmen adaylarının protein sentezi konusunda karşılaştıkları öğrenme
güçlüklerinin nedenleri ve önerilen çözümleri öğretmen adaylarının bakış
açısıyla saptamaktır. Çalışmanın örneklemi Türkiye'de Atatürk Üniversitesi,
Kazım Karabekir Eğitim Fakültesi, Biyoloji Eğitimi A.B.D.’ nda öğrenim gören 42
dördüncü sınıf öğretmen adayı oluşturmaktadır. Nitel araştırma yönteminin
kullanıldığı bu çalışmada öğretmen adaylarına iki açık uçlu soru sorulmuştur:
(1) Protein sentezini öğrenmenizde zorlanmanıza sebep olan faktörler
nelerdir? (2) Bu zorlukların üstesinden
gelmek için neler tavsiye edersiniz?. Elde edilen bulgulara göre öğretmen
adaylarının öğrenmede güçlük çekmesine sebep olan faktörler arasında sınıf
ortamı, ders kitabı, öğretmen, öğrenci ve konu yer almaktadır. Bununla beraber
öğretmen adaylarının bu sorunları gidermede önerdikleri çözümler içerisinde de
sınıf ortamı, ders kitabı, öğretmen ve öğretim sürecine ilişkin değişkenlerden
kaynaklanan sorunların düzeltilmesi ile mümkün olabileceğini belirtmişlerdir.
The use of doppler ultrasound in evaluation and follow-up of arteriovenous fistula patients
Authors: KAHRAMAN Nail , ÖZSİN Kadir Kaan 
Published: March 2018

Objectives:
The aim of the present study was to search the effect of preoperative Doppler
ultrasonography (DUS) of the concerning limb on AVF patency for arteriovenous
fistula (AVF) to be performed on the patients with end-stage renal disease. Methods: One hundred and three patients were enrolled into the study. The exclusion
criteria were previous central catheter procedure, history of thrombophlebitis
on the upper limb and previous surgery on the upper limb. Among the remaining
patients, those who fulfilled the physical examination criteria were included.
The patients were divided into two groups as the control, DUS (-) group and the
study group, DUS (+). The patients in the control group were taken into the
procedure after a physical examination only. Brescio-Cimino method was
preferred for all patients. Function of the AVF was controlled on the procedure
day, at day 10, months 1, 3 and 6 as well as year 1 after the procedure. The
results in both groups were statistically evaluated. Results: Twenty patients in the DUS (+) group (50% male, mean age: 57.25 ± 13.34 years)
and 20 patients in the DUS (-) group (45% male, mean age: 56.10 ± 12.35) were
recorded in the study. Cumulative primary patency rates between DUS (+) group
and DUS(-) group for 12 months were 95% and 65%, respectively (log-rank, p = 0.022). Conclusion: We believe that the DUS performed
before AVF procedure would increase the primary patency rates of AVF created
between the most convenient vessels and reduce the procedure failure.
Organic Phosphorus Can Make an Important Contribution to Phosphorus Loss from Riparian Buffers
Authors: Dodd Rosalind J. , Sharpley Andrew N. , Berry Lawrence G. 
Published: March 2018

Core Ideas
Forested and vegetative buffers can retain P runoff from adjacent fields.
High concentrations of molybdate unreactive P were detected in soil water extracts.
With time, these buffer soils can be a source of soluble inorganic and organic P.
High microbial activity in buffer soils suggests biologically mediated P release.
Vegetative buffer strips (VBS) and managed or unmanaged riparian zones between the edge of field and receiving watercourse are widely adopted conservation practices aimed at reducing nonpoint nutrient pollution. However, their effectiveness at decreasing phosphorus (P) loss has been mixed. This study investigated the effectiveness of a VBS and a forested riparian zone (FRZ) in decreasing P loss from pasture soils receiving swine manure and aimed to determine the potential factors controlling P release, using water extractable P (WEP) as a proxy for P loss. The inorganic WEP concentrations were significantly greater in the fertilized pasture zone soils than the VBS or FRZ soils. However, there was no significant difference between the field and riparian soils for total WEP due to increased contribution from organic WEP in these soils. Degree of P saturation, which is a function of soil test P, was a good predictor of inorganic WEP, but not organic WEP, where the variation in concentrations was better explained by variables involved in biotic P release.
Phosphorus Distribution in Soils Treated with Bioenergy Co‐product Materials following Corn Growth
Authors: Pagliari Paulo H. , Strock Jeffrey S. , Johnson Jane M. F. , Waldrip Heidi M. 
Published: March 2018

Core Ideas
Biochar changes chemical distribution of P in soils.Biochar changes the distribution of hydrolysable organic P in soils.No two biochar materials are alike.
This research was conducted to investigate the impact of corn cob gasification biochar (CCGB), switchgrass pyrolysis biochar (SPB), turkey manure ash (TMA), and triple superphosphate fertilizer (TSP) on soil phosphorus (P) distribution in three agricultural soils from Minnesota, USA. Understanding how biochar can change soil P distribution is crucial to develop best management practices for recycling biochar products. Phosphorus sources were incorporated at rates of 0, 28, 56, and 84 mg P2O5 kg−1 to 1.5 kg of each soil in 2‐L pots. Corn (Zea mays L.) plants were grown (2 plants pot−1) in treated soils for 56 d after emergence. After 56 d, plants were harvested and soil samples collected for sequential P fractionation (H2O, 0.5 mol L−1 NaHCO3, 0.1 mol L−1 NaOH, and 1.0 mol L−1 HCl) and enzymatic hydrolysis. The results of the sequential fractionation showed that CCGB and SPB were as effective as TSP and TMA at increasing total P extractable in water and HCl. In contrast, the increase in NaHCO3 and NaOH extractable total P was higher with TSP and TMA than with the CCGB and SPB. In most cases, the increase in inorganic P was similar between biochar and TSP, suggesting that biochar could supply equal amounts of plant available P as commercial fertilizer. The effects of biochar on enzymatically hydrolysable P were not consistent and varied by soil. In conclusion, the results of this study showed that biochar has potential to increase the available P pools in soils similar to commercial fertilizer.
Strip Tillage Implements for Single and Twin Row Peanut
Authors: Balkcom Kipling S. , Tubbs R. Scott , Balkcom Kris B. 
Published: March 2018

Core Ideas
Grower interest in conservation tillage and cover crops remains high for peanut.Twin rows improved yields and peanut grade compared to single rows.Peanut performance did not vary across strip tillage implements.Twin rows with strip tillage and a cover crop is a productive option for peanut.
Soil degradation and rising production costs have prompted grower interest in conservation tillage with cover crops for peanut (Arachis hypogaea L.). Our objective was to evaluate single and twin row peanut production across three different strip tillage implements (KMC, Orthman, Unverferth) with and without a rye (Secale cereale L.) cover crop in Headland, AL, and Tifton, GA, during 2012 to 2014. Surface residue cover following planting, plant populations, peanut yield, total sound mature kernels (TSMK), and soil penetration resistance (PR) for the cultivar Georgia 06G were compared across cover crop treatments, tillage implements, and row patterns. Surface residue exceeded 60% at both locations in the rye treatment. Plant populations were greater across the fallow treatment and the twin row pattern at both locations. Twin rows increased yield compared with single rows in Headland (360 kg ha−1) and Tifton (>1000 kg ha−1) and also improved grade (TSMK) at both locations. Strip tillage implements had no effect on peanut plant parameters. At planting, soil PR was greater with a cover crop only at Headland; whereas implements reduced soil PR in 2012 (Orthman) and 2014 (Unverferth). At harvest, soil PR differences were only observed in 2013. The KMC and Unverferth implements maintained less resistance compared with Orthman at Headland, whereas cover crop reduced PR at Tifton. Peanut performance did not differ in response to one strip tillage implement over the other; however, results show strip tillage with a cover crop and twin row management improves peanut production across the Southeast.
Air‐Filled Porosity as a Key to Reducing Dissolved Arsenic and Cadmium Concentrations in Paddy Soils
Authors: Nakamura Ken , Katou Hidetaka , Suzuki Katsuhiro , Honma Toshimitsu 
Published: March 2018

Simultaneous suppression of rice (Oryza sativa L.) uptake of As and Cd is challenging because these toxic elements are immobilized under contrasting redox conditions. Given the notion that oxygen diffusion governs redox conditions in temporarily drained paddy soil, we assume that the key to simultaneous suppression of dissolved As and Cd concentrations is air‐filled porosity (AFP) of soil. The objectives of this study were to reveal relationships between AFP and dissolved As and Cd concentrations in paddy soils and to identify the optimum water management, in terms of AFP, for simultaneous reduction of As and Cd. Dissolved As and Cd concentrations were determined in soil cores collected at different depths and times during rice growing seasons. Dissolved As concentrations were appreciable (>3 µg L−1) only when AFP was below a threshold value of 0.04 to 0.10 m3 m−3, suggesting that dissolved As was rapidly immobilized once AFP exceeded the threshold value on drainage. Dissolved Cd concentrations were roughly proportional to AFP, with higher concentrations associated with lower soil pH. Although dissolved As concentrations tended to be low in soil samples with high dissolved Cd concentrations and vice versa, both concentrations were low when AFP was slightly above the threshold value for As immobilization. The results suggest that dissolved As and Cd can be simultaneously kept at low levels by appropriate water management practices that produce AFP slightly above the threshold value for As immobilization.Core Ideas
Dissolved As and Cd in paddy soil respond to changes in air‐filled porosity (AFP).
Dissolved As was appreciable only when AFP was below a threshold value.
The increase in dissolved Cd with AFP upon drainage was a slowly continuing process.
Slightly above the threshold AFP, both dissolved As and Cd were at low levels.
AFP is easier to predict than Eh, serving as a guide to optimal water management.
Greenhouse Gas Emissions and Management Practices that Affect Emissions in US Rice Systems
Authors: Linquist Bruce A. , Marcos Mathias , Adviento‐Borbe M. Arlene , Anders Merle , Harrell Dustin , Linscombe Steve , Reba Michele L. , Runkle Benjamin R. K. , Tarpley Lee , Thomson Allison 
Published: March 2018

Previous reviews have quantified factors affecting greenhouse gas (GHG) emissions from Asian rice (Oryza sativa L.) systems, but not from rice systems typical for the United States, which often vary considerably particularly in practices (i.e., water and carbon management) that affect emissions. Using meta‐analytic and regression approaches, existing data from the United States were examined to quantify GHG emissions and major practices affecting emissions. Due to different production practices, major rice production regions were defined as the mid‐South (Arkansas, Texas, Louisiana, Mississippi, and Missouri) and California, with emissions being evaluated separately. Average growing season CH4 emissions for the mid‐South and California were 194 (95% confidence interval [CI] = 129–260) and 218 kg CH4 ha−1 season−1 (95% CI = 153–284), respectively. Growing season N2O emissions were similar between regions (0.14 kg N2O ha−1 season−1). Ratoon cropping (allowing an additional harvestable crop to grow from stubble after the initial harvest), common along the Gulf Coast of the mid‐South, had average CH4 emissions of 540 kg CH4 ha−1 season−1 (95% CI = 465–614). Water and residue management practices such as alternate wetting and drying, and stand establishment method (water vs. dry seeding), and the amount of residue from the previous crop had the largest effect on growing season CH4 emissions. However, soil texture, sulfate additions, and cultivar selection also affected growing season CH4 emissions. This analysis can be used for the development of tools to estimate and mitigate GHG emissions from US rice systems and other similarly mechanized systems in temperate regions.Core Ideas
Emissions of CH4 and N2O were quantified for US rice systems using a meta‐analysis.
Emissions were determined for both the growing and fallow seasons.
We assessed the major management practices affecting emissions.
Analysis can be used to develop a tool for quantifying emissions from rice fields.