bluuebunny/crossref_metadata_2025_split huggingface dataset:
QTL‐seq for rapid identification of candidate genes for 100‐seed weight and root/total plant dry weight ratio under rainfed conditions in chickpea
Authors: Singh Vikas K. , Khan Aamir W. , Jaganathan Deepa , Thudi Mahendar , Roorkiwal Manish , Takagi Hiroki , Garg Vanika , Kumar Vinay , Chitikineni Annapurna , Gaur Pooran M. , Sutton Tim , Terauchi Ryohei , Varshney Rajeev K. 
Published: April 2016

SummaryTerminal drought is a major constraint to chickpea productivity. Two component traits responsible for reduction in yield under drought stress include reduction in seeds size and root length/root density. QTL‐seq approach, therefore, was used to identify candidate genomic regions for 100‐seed weight (100SDW) and total dry root weight to total plant dry weight ratio (RTR) under rainfed conditions. Genomewide SNP profiling of extreme phenotypic bulks from the ICC 4958 × ICC 1882 population identified two significant genomic regions, one on CaLG01 (1.08 Mb) and another on CaLG04 (2.7 Mb) linkage groups for 100SDW. Similarly, one significant genomic region on CaLG04 (1.10 Mb) was identified for RTR. Comprehensive analysis revealed four and five putative candidate genes associated with 100SDW and RTR, respectively. Subsequently, two genes (Ca_04364 and Ca_04607) for 100SDW and one gene (Ca_04586) for RTR were validated using CAPS/dCAPS markers. Identified candidate genomic regions and genes may be useful for molecular breeding for chickpea improvement.
The OsmiR396c‐OsGRF4‐OsGIF1 regulatory module determines grain size and yield in rice
Authors: Li Shuangcheng , Gao Fengyan , Xie Kailong , Zeng Xiuhong , Cao Ye , Zeng Jing , He Zhongshan , Ren Yun , Li Wenbo , Deng Qiming , Wang Shiquan , Zheng Aiping , Zhu Jun , Liu Huainian , Wang Lingxia , Li Ping 
Published: April 2016

SummaryGrain weight is the most important component of rice yield and is mainly determined by grain size, which is generally controlled by quantitative trait loci (QTLs). Although numerous QTLs that regulate grain weight have been identified, the genetic network that controls grain size remains unclear. Herein, we report the cloning and functional analysis of a dominant QTL, grain length and width 2 (GLW2), which positively regulates grain weight by simultaneously increasing grain length and width. The GLW2 locus encodes OsGRF4 (growth‐regulating factor 4) and is regulated by the microRNA miR396c in vivo. The mutation in OsGRF4 perturbs the OsmiR396 target regulation of OsGRF4, generating a larger grain size and enhanced grain yield. We also demonstrate that OsGIF1 (GRF‐interacting factors 1) directly interacts with OsGRF4, and increasing its expression improves grain size. Our results suggest that the miR396c‐OsGRF4‐OsGIF1 regulatory module plays an important role in grain size determination and holds implications for rice yield improvement.
TGF‐β induces SOX2 expression in a time‐dependent manner in human melanoma cells
Authors: Weina Kasia , Wu Huizi , Knappe Nathalie , Orouji Elias , Novak Daniel , Bernhardt Mathias , Hüser Laura , Larribère Lionel , Umansky Viktor , Gebhardt Christoffer , Utikal Jochen 
Published: April 2016

SummaryThe sry‐related high‐mobility box (SOX)‐2 protein has recently been proven to play a significant role in progression, metastasis, and clinical prognosis spanning several cancer types. Research on the role of SOX2 in melanoma is limited and currently little is known about the mechanistic function of this gene in this context. Here, we observed high expression of SOX2 in both human melanoma cell lines and primary melanomas in contrast to melanocytic nevi. This overexpression in melanoma can, in part, be explained by extra gene copy numbers of SOX2 in primary samples. Interestingly, we were able to induce SOX2 expression, mediated by SOX4, via TGF‐β1 stimulation in a time‐dependent manner. Moreover, the knockdown of SOX2 impaired TGF‐β‐induced invasiveness. This phenotype switch can be explained by SOX2‐mediated cross talk between TGF‐β and non‐canonical Wnt signaling. Thus, we propose that SOX2 is involved in the critical TGF‐β signaling pathway, which has been shown to correlate with melanoma aggressiveness and metastasis. In conclusion, we have identified a novel downstream factor of TGF‐β signaling in melanoma, which may have further implications in the clinic.
Resolution of Graves’ disease after renal transplantation
Authors: Lee Yvonne , Butani Lavjay , Glaser Nicole , Nguyen Stephanie 
Published: April 2016

AbstractWe report a case of an adolescent boy with Down's syndrome and ESRD on hemodialysis who developed mild Graves’ disease that was not amenable to radioablation, surgery, or ATDs. After 14 months of observation without resolution of Graves’ disease, he successfully received a DDRT with a steroid minimization protocol. Thymoglobulin and a three‐day course of steroids were used for induction and he was started on tacrolimus, MMF, and pravastatin for maintenance transplant immunosuppression. One month after transplantation, all biochemical markers and antibody profiling for Graves’ disease had resolved and remain normal one yr later.
Theoretical Guarantees for Approximate Sampling from Smooth and Log-Concave Densities
Authors: Dalalyan Arnak S. 
Published: April 2016

Summary
Sampling from various kinds of distribution is an issue of paramount importance in statistics since it is often the key ingredient for constructing estimators, test procedures or confidence intervals. In many situations, exact sampling from a given distribution is impossible or computationally expensive and, therefore, one needs to resort to approximate sampling strategies. However, there is no well-developed theory providing meaningful non-asymptotic guarantees for the approximate sampling procedures, especially in high dimensional problems. The paper makes some progress in this direction by considering the problem of sampling from a distribution having a smooth and log-concave density defined on Rp, for some integer p &gt; 0. We establish non-asymptotic bounds for the error of approximating the target distribution by the distribution obtained by the Langevin Monte Carlo method and its variants. We illustrate the effectiveness of the established guarantees with various experiments. Underlying our analysis are insights from the theory of continuous time diffusion processes, which may be of interest beyond the framework of log-concave densities that are considered in the present work.
No association between donor age and recipient outcomes: transfusion of plasma in patients undergoing coronary artery bypass grafting surgery
Authors: Guinn Nicole R. , Waldron Nathan H. , Cooter Mary L. , Goldberg Corinne L. , Kertai Miklos D. , Raghunathan Karthik , Bandarenko Nicholas , Hoffman Maureane , Bennett‐Guerrero Elliott 
Published: April 2016

BACKGROUNDRecent animal studies suggest that transfusion of plasma from young donors reverses age‐related neurologic and cardiac changes in older recipients. Associations between age of blood product donors and corresponding outcomes in recipients have not been studied in humans. Therefore, our primary objective was to examine this relationship between donor age and recipient outcomes among patients that received plasma during and after coronary artery bypass grafting (CABG) surgery.STUDY DESIGN AND METHODSThis retrospective cohort included patients undergoing CABG surgery who received plasma during or after surgery. All plasma units transfused were evenly divided into tertiles based on the plasma donor age (17‐37, 38‐50, and 51‐86 years), and CABG patients receiving all perioperative plasma within a single donor tertile were studied. Patient demographics and outcomes including mortality, length of stay (LOS), and acute kidney injury (AKI) were measured.RESULTSOverall, 1306 patients (24% of 5339) received American Red Cross plasma perioperatively, with a median dose of 2 units. In a multivariate model of 1‐year mortality, transfusion of a greater number of plasma units (p = 0.0007) and EuroSCORE (p < 0.0001) were significantly associated with patient mortality while donor age was not. There was no difference in mortality between patients receiving plasma from donors in the youngest, middle, or oldest age tertile (10.2 and 8.1% vs. 7.8%, respectively, p = 0.76). Other outcomes, including rates of AKI or LOS, were also independent of plasma donor age.CONCLUSIONSWe did not observe an association between donor age and recipient outcomes among patients who received plasma perioperatively while undergoing CABG surgery.
Phrenic motor outputs in response to bronchopulmonary C‐fibre activation following chronic cervical spinal cord injury
Authors: Lee Kun‐Ze 
Published: April 2016

Key points
Activation of bronchopulmonary C‐fibres, the main chemosensitive afferents in the lung, can induce pulmonary chemoreflexes to modulate respiratory activity.
Following chronic cervical spinal cord injury, bronchopulmonary C‐fibre activation‐induced inhibition of phrenic activity was exaggerated.
Supersensitivity of phrenic motor outputs to the inhibitory effect of bronchopulmonary C‐fibre activation is due to a shift of phrenic motoneuron types and slow recovery of phrenic motoneuron discharge in cervical spinal cord‐injured animals.
These data suggest that activation of bronchopulmonary C‐fibres may retard phrenic output recovery following cervical spinal cord injury.
The alteration of phenotype and discharge pattern of phrenic motoneuron enables us to understand the impact of spinal cord injury on spinal respiratory activity.
AbstractCervical spinal injury interrupts bulbospinal pathways and results in cessation of phrenic bursting ipsilateral to the lesion. The ipsilateral phrenic activity can partially recover over weeks to months following injury due to the activation of latent crossed spinal pathways and exhibits a greater capacity to increase activity during respiratory challenges than the contralateral phrenic nerve. However, whether the bilateral phrenic nerves demonstrate differential responses to respiratory inhibitory inputs is unclear. Accordingly, the present study examined bilateral phrenic bursting in response to capsaicin‐induced pulmonary chemoreflexes, a robust respiratory inhibitory stimulus. Bilateral phrenic nerve activity was recorded in anaesthetized and mechanically ventilated adult rats at 8–9 weeks after C2 hemisection (C2Hx) or C2 laminectomy. Intra‐jugular capsaicin (1.5 μg kg−1) injection was performed to activate the bronchopulmonary C‐fibres to evoke pulmonary chemoreflexes. The present results indicate that capsaicin‐induced prolongation of expiratory duration was significantly attenuated in C2Hx animals. However, ipsilateral phrenic activity was robustly reduced after capsaicin treatment compared to uninjured animals. Single phrenic fibre recording experiments demonstrated that C2Hx animals had a higher proportion of late‐inspiratory phrenic motoneurons that were relatively sensitive to capsaicin treatment compared to early‐inspiratory phrenic motoneurons. Moreover, late‐inspiratory phrenic motoneurons in C2Hx animals had a weaker discharge frequency and slower recovery time than uninjured animals. These results suggest bilateral phrenic nerves differentially respond to bronchopulmonary C‐fibre activation following unilateral cervical hemisection, and the severe inhibition of phrenic bursting is due to a shift in the discharge pattern of phrenic motoneurons.
Enumeration of Parasitic Chytrid Zoospores in the Columbia River via Quantitative PCR
Authors: Maier Michelle A. , Peterson Tawnya D. 
Published: April 2016

ABSTRACT

Through lethal infection, fungal parasites of phytoplankton (“chytrids”) repackage organic material from the large, effectively inedible, colonial diatoms they infect into much smaller zoospores, which are easier for zooplankton to consume. However, their small size and lack of distinguishing morphological features render it difficult to distinguish zoospores from other small flagellates in mixed assemblages in the natural environment. In this study, we developed and tested a method to quantify chytrid zoospores in field studies using quantitative PCR (qPCR) targeting the internal transcribed spacer 2 (ITS2) region within the rRNA gene cluster. To achieve accurate quantification, the assay was designed to be highly specific for a parasite (
Rhizophydium planktonicum
) of the diatom
Asterionella formosa
; however, the approach is applicable to additional host-parasite systems. Parasitic zoospores were detected and quantified in the freshwater reaches of the lower Columbia River, as well as in the salt-influenced estuary and river plume. The coincidence between zoospore abundances and a prevalence of small zooplankton during blooms of large, colonial diatoms in the spring suggests that Columbia River zooplankton may be poised to benefit nutritionally from chytrid zoospores, thus providing a mechanism to retain organic carbon within the system and reduce losses to downstream export. We estimate that ∼15% of the carbon biomass tied up in blooms of the dominant diatom species is transformed into zoospores through the parasitic shunt during spring.

IMPORTANCE
The small size of the parasitic fungi that infect phytoplankton makes it difficult to identify and quantify them in natural systems. We developed and tested a method to quantify these organisms (chytrid zoospores) using a molecular technique that targets the internal transcribed spacer region within the rRNA gene cluster. Using this method, we quantified the abundance of the motile stage of a specific parasite in the freshwater and saltwater-influenced regions of the Columbia River in the U.S. Pacific Northwest. Parasitic chytrid zoospores were found to be present throughout the year and at higher abundances during the spring, when phytoplankton blooms occur. The presence of these organisms indicates not only that they may be responsible for the death of host phytoplankton cells but that they may also provide a readily available food source to small consumers (zooplankton) in the food web of the Columbia River.
Evaluation of Daphnid Grazing on Microscopic Zoosporic Fungi by Using Comparative Threshold Cycle Quantitative PCR
Authors: Maier Michelle A. , Uchii Kimiko , Peterson Tawnya D. , Kagami Maiko 
Published: April 2016

ABSTRACT

Lethal parasitism of large phytoplankton by chytrids (microscopic zoosporic fungi) may play an important role in organic matter and nutrient cycling in aquatic environments by shunting carbon away from hosts and into much smaller zoospores, which are more readily consumed by zooplankton. This pathway provides a mechanism to more efficiently retain carbon within food webs and reduce export losses. However, challenges in accurate identification and quantification of chytrids have prevented a robust assessment of the relative importance of parasitism for carbon and energy flows within aquatic systems. The use of molecular techniques has greatly advanced our ability to detect small, nondescript microorganisms in aquatic environments in recent years, including chytrids. We used quantitative PCR (qPCR) to quantify the consumption of zoospores by
Daphnia
in laboratory experiments using a culture-based comparative threshold cycle (

C
T

) method. We successfully quantified the reduction of zoospores in water samples during
Daphnia
grazing and confirmed the presence of chytrid DNA inside the daphnid gut. We demonstrate that comparative

C
T

qPCR is a robust and effective method to quantify zoospores and evaluate zoospore grazing by zooplankton and will aid in better understanding how chytrids contribute to organic matter cycling and trophic energy transfer within food webs.

IMPORTANCE
The study of aquatic fungi is often complicated by the fact that they possess complex life cycles that include a variety of morphological forms. Studies that rely on morphological characteristics to quantify the abundances of all stages of the fungal life cycle face the challenge of correctly identifying and enumerating the nondescript zoospores. These zoospores, however, provide an important trophic link between large colonial phytoplankton and zooplankton: that is, once the carbon is liberated from phytoplankton into the parasitic zoospores, the latter are consumed by zooplankton and carbon is retained in the aquatic food web rather than exported from the system. This study provides a tool to quantify zoospores and evaluate the consumption of zoospores by zooplankton in order to further our understanding of their role in food web dynamics.
Molecular Profiling of Shiga Toxin-Producing Escherichia coli and Enteropathogenic E. coli Strains Isolated from French Coastal Environments
Authors: Balière C. , Rincé A. , Delannoy S. , Fach P. , Gourmelon M. 
Published: April 2016

ABSTRACT

Shiga toxin-producing
Escherichia coli
(STEC) and enteropathogenic
E. coli
(EPEC) strains may be responsible for food-borne infections in humans. Twenty-eight STEC and 75 EPEC strains previously isolated from French shellfish-harvesting areas and their watersheds and belonging to 68 distinguishable serotypes were characterized in this study. High-throughput real-time PCR was used to search for the presence of 75
E. coli
virulence-associated gene targets, and genes encoding Shiga toxin (
stx
) and intimin (
eae
) were subtyped using PCR tests and DNA sequencing, respectively. The results showed a high level of diversity between strains, with 17 unique virulence gene profiles for STEC and 56 for EPEC. Seven STEC and 15 EPEC strains were found to display a large number or a particular combination of genetic markers of virulence and the presence of
stx
and/or
eae
variants, suggesting their potential pathogenicity for humans. Among these, an O26:H11
stx
1a
eae
-β1 strain was associated with a large number of virulence-associated genes (
n
= 47), including genes carried on the locus of enterocyte effacement (LEE) or other pathogenicity islands, such as OI-122, OI-71, OI-43/48, OI-50, OI-57, and the high-pathogenicity island (HPI). One O91:H21 STEC strain containing 4
stx
variants (
stx
1a
,
stx
2a
,
stx
2c
, and
stx
2d
) was found to possess genes associated with pathogenicity islands OI-122, OI-43/48, and OI-15. Among EPEC strains harboring a large number of virulence genes (
n
, 34 to 50), eight belonged to serotype O26:H11, O103:H2, O103:H25, O145:H28, O157:H7, or O153:H2.

IMPORTANCE
The species
E. coli
includes a wide variety of strains, some of which may be responsible for severe infections. This study, a molecular risk assessment study of
E. coli
strains isolated from the coastal environment, was conducted to evaluate the potential risk for shellfish consumers. This report describes the characterization of virulence gene profiles and
stx
/
eae
polymorphisms of
E. coli
isolates and clearly highlights the finding that the majority of strains isolated from coastal environment are potentially weakly pathogenic, while some are likely to be more pathogenic.
Strain-Specific Features of Extracellular Polysaccharides and Their Impact on Lactobacillus plantarum-Host Interactions
Authors: Lee I-Chiao , Caggianiello Graziano , van Swam Iris I. , Taverne Nico , Meijerink Marjolein , Bron Peter A. , Spano Giuseppe , Kleerebezem Michiel 
Published: April 2016

ABSTRACT

Lactobacilli are found in diverse environments and are widely applied as probiotic, health-promoting food supplements. Polysaccharides are ubiquitously present on the cell surface of lactobacilli and are considered to contribute to the species- and strain-specific probiotic effects that are typically observed. Two
Lactobacillus plantarum
strains, SF2A35B and Lp90, have an obvious ropy phenotype, implying high extracellular polysaccharide (EPS) production levels. In this work, we set out to identify the genes involved in EPS production in these
L. plantarum
strains and to demonstrate their role in EPS production by gene deletion analysis. A model
L. plantarum
strain, WCFS1, and its previously constructed derivative that produced reduced levels of EPS were included as reference strains. The constructed EPS-reduced derivatives were analyzed for the abundance and sugar compositions of their EPS, revealing
cps2
-like gene clusters in SF2A35B and Lp90 responsible for major EPS production. Moreover, these mutant strains were tested for phenotypic characteristics that are of relevance for their capacity to interact with the host epithelium in the intestinal tract, including bacterial surface properties as well as survival under the stress conditions encountered in the gastrointestinal tract (acid and bile stress). In addition, the Toll-like receptor 2 (TLR2) signaling and immunomodulatory capacities of the EPS-negative derivatives and their respective wild-type strains were compared, revealing strain-specific impacts of EPS on the immunomodulatory properties. Taken together, these experiments illustrate the importance of EPS in
L. plantarum
strains as a strain-specific determinant in host interaction.

IMPORTANCE
This study evaluates the role of extracellular polysaccharides that are produced by different strains of
Lactobacillus plantarum
in the determination of the cell surface properties of these bacteria and their capacity to interact with their environment, including their signaling to human host cells. The results clearly show that the consequences of removal of these polysaccharides are very strain specific, illustrating the diverse and unpredictable roles of these polysaccharides in the environmental interactions of these bacterial strains. In the context of the use of lactobacilli as health-promoting probiotic organisms, this study exemplifies the importance of strain specificity.