bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multigranular exocytosis of Weibel-Palade bodies in vascular endothelial cells
Authors: Valentijn Karine M. , van Driel Linda F. , Mourik Marjon J. , Hendriks Gert-Jan , Arends Tom J. , Koster Abraham J. , Valentijn Jack A. 
Published: May 2010

AbstractRegulated exocytosis of Weibel-Palade bodies (WPBs) is a pivotal mechanism via which vascular endothelial cells initiate repair in response to injury and inflammation. Several pathways have been proposed to enable differential release of bioactive molecules from WPBs under different pathophysiologic conditions. Due to the complexity, many aspects of WPB biogenesis and exocytosis are still poorly understood. Herein, we have investigated the regulated exocytosis of the major WPB constituent, von Willebrand Factor (VWF), which upon its release forms strings of up to several millimeters long that capture circulating platelets and thereby initiate the formation of a haemostatic plug. Using correlative, fluorescence, and electron microscopic imaging techniques, we provide evidence that multigranular exocytosis is an important pathway for VWF release in secretagogue-challenged human umbilical vein endothelial cells. A novel membrane-delimited structure (secretory pod) was identified as the site of WPB coalescence and VWF exocytosis. Clathrin-coated profiles present on the secretory pods suggested remodeling via compensatory membrane retrieval. Small, 30- to 40-nm cytoplasmic vesicles (nanovesicles) mediated the fusion of WPBs with secretory pods. Multigranular exocytosis may facilitate VWF string formation by pooling the content of multiple WPBs. In addition, it may provide a novel mechanism for the differential release of WPB cargo.
Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data
Authors: Imamura Haruna , Yachie Nozomu , Saito Rintaro , Ishihama Yasushi , Tomita Masaru 
Published: May 2010

AbstractBackgroundPhosphorylation is a ubiquitous and fundamental regulatory mechanism that controls signal transduction in living cells. The number of identified phosphoproteins and their phosphosites is rapidly increasing as a result of recent mass spectrometry-based approaches.ResultsWe analyzed time-course phosphoproteome data obtained previously by liquid chromatography mass spectrometry with the stable isotope labeling using amino acids in cell culture (SILAC) method. This provides the relative phosphorylation activities of digested peptides at each of five time points after stimulating HeLa cells with epidermal growth factor (EGF). We initially calculated the correlations between the phosphorylation dynamics patterns of every pair of peptides and connected the strongly correlated pairs to construct a network. We found that peptides extracted from the same intracellular fraction (nucleus vs. cytoplasm) tended to be close together within this phosphorylation dynamics-based network. The network was then analyzed using graph theory and compared with five known signal-transduction pathways. The dynamics-based network was correlated with known signaling pathways in the NetPath and Phospho.ELM databases, and especially with the EGF receptor (EGFR) signaling pathway. Although the phosphorylation patterns of many proteins were drastically changed by the EGF stimulation, our results suggest that only EGFR signaling transduction was both strongly activated and precisely controlled.ConclusionsThe construction of a phosphorylation dynamics-based network provides a useful overview of condition-specific intracellular signal transduction using quantitative time-course phosphoproteome data under specific experimental conditions. Detailed prediction of signal transduction based on phosphoproteome dynamics remains challenging. However, since the phosphorylation profiles of kinase-substrate pairs on the specific pathway were localized in the dynamics-based network, our method will be a complementary strategy to explore new components of protein signaling pathways in combination with previous methods (including software) of predicting direct kinase-substrate relationships.
Identification of genetic modifiers of behavioral phenotypes in serotonin transporter knockout rats
Authors: Homberg Judith , Nijman Isaäc J , Kuijpers Sylvia , Cuppen Edwin 
Published: May 2010

Abstract

Background
Genetic variation in the regulatory region of the human serotonin transporter gene (SLC6A4) has been shown to affect brain functionality and personality. However, large heterogeneity in its biological effects is observed, which is at least partially due to genetic modifiers. To gain insight into serotonin transporter (SERT)-specific genetic modifiers, we studied an intercross between the Wistar SERT-/- rat and the behaviorally and genetically divergent Brown Norway rat, and performed a QTL analysis.

Results
In a cohort of >150 intercross SERT-/- and control (SERT+/+) rats we characterized 12 traits that were previously associated with SERT deficiency, including activity, exploratory pattern, cocaine-induced locomotor activity, and abdominal and subcutaneous fat. Using 325 genetic markers, 10 SERT-/--specific quantitative trait loci (QTLs) for parameters related to activity and exploratory pattern (Chr.1,9,11,14), and cocaine-induced anxiety and locomotor activity (Chr.5,8) were identified. No significant QTLs were found for fat parameters. Using in silico approaches we explored potential causal genes within modifier QTL regions and found interesting candidates, amongst others, the 5-HT1D receptor (Chr. 5), dopamine D2 receptor (Chr. 8), cannabinoid receptor 2 (Chr. 5), and genes involved in fetal development and plasticity (across chromosomes).

Conclusions
We anticipate that the SERT-/--specific QTLs may lead to the identification of new modulators of serotonergic signaling, which may be targets for pharmacogenetic and therapeutic approaches.
Internalin profiling and multilocus sequence typing suggest four Listeria innocua subgroups with different evolutionary distances from Listeria monocytogenes
Authors: Chen Jianshun , Chen Qiaomiao , Jiang Lingli , Cheng Changyong , Bai Fan , Wang Jun , Mo Fan , Fang Weihuan 
Published: May 2010

AbstractBackgroundEcological, biochemical and genetic resemblance as well as clear differences of virulence betweenL. monocytogenesandL. innocuamake this bacterial clade attractive as a model to examine evolution of pathogenicity. This study was attempted to examine the population structure ofL. innocuaand the microevolution in theL. innocua-L. monocytogenesclade via profiling of 37 internalin genes and multilocus sequence typing based on the sequences of 9 unlinked genesgyrB,sigB,dapE,hisJ,ribC,purM,gap,tufandbetL.ResultsL. innocuawas genetically monophyletic compared toL. monocytogenes, and comprised four subgroups. Subgroups A and B correlated with internalin types 1 and 3 (except the strain 0063 belonging to subgroup C) and internalin types 2 and 4 respectively. The majority ofL. innocuastrains belonged to these two subgroups. Subgroup A harbored a whole set ofL. monocytogenes-L. innocuacommon andL. innocua-specific internalin genes, and displayed higher recombination rates than those of subgroup B, including the relative frequency of occurrence of recombination versus mutation (ρ/θ) and the relative effect of recombination versus point mutation (r/m). Subgroup A also exhibited a significantly smaller exterior/interior branch length ratio than expected under the coalescent model, suggesting a recent expansion of its population size. The phylogram based on the analysis with correction for recombination revealed that the time to the most recent common ancestor (TMRCA) ofL. innocuasubgroups A and B were similar. Additionally, subgroup D, which correlated with internalin type 5, branched off from the other three subgroups. AllL. innocuastrains lacked seventeen virulence genes found inL. monocytogenes(except for the subgroup D strain L43 harboringinlJand two subgroup B strains bearingbsh) and were nonpathogenic to mice.ConclusionsL. innocuarepresents a young species descending fromL. monocytogenesand comprises four subgroups: two major subgroups A and B, and one atypical subgroup D serving as a link betweenL. monocytogenesandL. innocuain the evolutionary chain. Although subgroups A and B appeared at approximately the same time, subgroup A seems to have experienced a recent expansion of the population size with higher recombination frequency and effect than those of subgroup B, and might represent the possible evolutionary direction towards adaptation to enviroments. The evolutionary history in theL. monocytogenes-L. innocuaclade represents a rare example of evolution towards reduced virulence of pathogens.
Loss of phosphoinositide 3-kinase γ decreases migration and activation of phagocytes but not T cell activation in antigen-induced arthritis
Authors: Gruen Michael , Rose Christina , König Christian , Gajda Mieczyslaw , Wetzker Reinhard , Bräuer Rolf 
Published: May 2010

AbstractBackgroundPhosphoinositide 3-kinase γ (PI3Kγ) has been depicted as a major regulator of inflammatory processes, including leukocyte activation and migration towards several chemokines. This study aims to explore the role of PI3Kγ in the murine model of antigen-induced arthritis (AIA).MethodsDevelopment of AIA was investigated in wildtype and PI3Kγ-deficient mice as well as in mice treated with a specific inhibitor of PI3Kγ (AS-605240) in comparison to untreated animals. Inflammatory reactions of leukocytes, including macrophage and T cell activation, and macrophage migration, were studiedin vivoandin vitro.ResultsGenetic deletion or pharmacological inhibition of PI3Kγ induced a marked decrease of clinical symptoms in early AIA, together with a considerably diminished macrophage migration and activation (lower production of NO, IL-1β, IL-6). Also, macrophage and neutrophil infiltration into the knee joint were impairedin vivo. However, T cell functions, measured by cytokine production (TNFα, IFNγ, IL-2, IL-4, IL-5, IL-17)in vitroand DTH reactionin vivowere not altered, and accordingly, disease developed normally at later timepointsConclusionPI3Kγ specifically affects phagocyte function in the AIA model but has no impact on T cell activation.
Cadmium induces Wnt signaling to upregulate proliferation and survival genes in sub-confluent kidney proximal tubule cells
Authors: Chakraborty Prabir K , Lee Wing-Kee , Molitor Malte , Wolff Natascha A , Thévenod Frank 
Published: May 2010

Abstract

Background
The class 1 carcinogen cadmium (Cd2+) disrupts the E-cadherin/β-catenin complex of epithelial adherens junctions (AJs) and causes renal cancer. Deregulation of E-cadherin adhesion and changes in Wnt/β-catenin signaling are known to contribute to carcinogenesis.

Results
We investigated Wnt signaling after Cd2+-induced E-cadherin disruption in sub-confluent cultured kidney proximal tubule cells (PTC). Cd2+ (25 μM, 3-9 h) caused nuclear translocation of β-catenin and triggered a Wnt response measured by TOPflash reporter assays. Cd2+ reduced the interaction of β-catenin with AJ components (E-cadherin, α-catenin) and increased binding to the transcription factor TCF4 of the Wnt pathway, which was upregulated and translocated to the nucleus. While Wnt target genes (c-Myc, cyclin D1 and ABCB1) were up-regulated by Cd2+, electromobility shift assays showed increased TCF4 binding to cyclin D1 and ABCB1 promoter sequences with Cd2+. Overexpression of wild-type and mutant TCF4 confirmed Cd2+-induced Wnt signaling. Wnt signaling elicited by Cd2+ was not observed in confluent non-proliferating cells, which showed increased E-cadherin expression. Overexpression of E-cadherin reduced Wnt signaling, PTC proliferation and Cd2+ toxicity. Cd2+ also induced reactive oxygen species dependent expression of the pro-apoptotic ER stress marker and Wnt suppressor CHOP/GADD153 which, however, did not abolish Wnt response and cell viability.

Conclusions
Cd2+ induces Wnt signaling in PTC. Hence, Cd2+ may facilitate carcinogenesis of PTC by promoting Wnt pathway-mediated proliferation and survival of pre-neoplastic cells.
A high-throughput transient gene expression system for switchgrass (Panicum virgatum L.) seedlings
Authors: Chen Xinlu , Equi Raymie , Baxter Holly , Berk Kyle , Han Jin , Agarwal Sujata , Zale Janice 
Published: May 2010

Abstract

Background
Grasses are relatively recalcitrant to genetic transformation in comparison to certain dicotyledons, yet they constitute some of the most important biofuel crops. Genetic transformation of switchgrass (Panicum virgatum L.) has previously been reported after cocultivation of explants with Agrobacterium and biolistics of embryogenic calli. Experiments to increase transient gene expression in planta may lead to stable transformation methods with increased efficiency.

Results
A high-throughput Agrobacterium-mediated transient gene expression system has been developed for in planta inoculation of germinating switchgrass seedlings. Four different Agrobacterium strains were compared for their ability to infect switchgrass seedlings, and strain AGL1 was found to be the most infective. Wounding pretreatments such as sonication, mixing by vortex with carborundum, separation by centrifugation, vacuum infiltration, and high temperature shock significantly increased transient expression of a reporter gene (GUSPlus, a variation of the β-glucuronidase (GUS) gene). The addition of L-cysteine and dithiothreitol in the presence of acetosyringone significantly increased GUS expression compared with control treatments, whereas the addition of 0.1% surfactants such as Silwet L77 or Li700 decreased GUS expression. 4-Methylumbelliferyl beta-D-galactopyranoside (MUG) assays showed a peak of β-glucuronidase (GUS) enzyme activity 3 days after cocultivation with Agrobacterium harboring pCambia1305.2, whereas MUG assays showed a peak of enzyme activity 5 days after cocultivation with Agrobacterium harboring pCambia1305.1.

Conclusion

Agrobacterium strains C58, GV3101 and EHA105 are less able to deliver transfer DNA to switchgrass seedlings (cultivar Alamo) compared with strain AGL1. Transient expression was increased by double or triple wounding treatments such as mixing by vortex with carborundum, sonication, separation by centrifugation, and heat shock. The addition of thiol compounds such as L-cysteine and dithiothreitol in combination with acetosyringone during cocultivation also increased transient expression. The combination of multiple wounding treatments along with the addition of thiol compounds during cocultivation increased transient expression levels from 6% to 54%. There were differences in temporal GUS expression induced by pCambia1305.1 and pCambia1305.2.
Proton pump inhibitors as anti vacuolar-ATPases drugs: a novel anticancer strategy
Authors: Spugnini Enrico P , Citro Gennaro , Fais Stefano 
Published: May 2010

AbstractThe vacuolar ATPases are ATP-dependent proton pumps whose functions include the acidification of intracellular compartments and the extrusion of protons through the cell cytoplasmic membrane. These pumps play a pivotal role in the regulation of cell pH in normal cells and, to a much greater extent, in tumor cells. In fact, the glucose metabolism in hypoxic conditions by the neoplasms leads to an intercellular pH drift towards acidity. The acid microenvironment is modulated through the over-expression of H+transporters that are also involved in tumor progression, invasiveness, distant spread and chemoresistance. Several strategies to block/downmodulate the efficiency of these transporters are currently being investigated. Among them, proton pump inhibitors have shown to successfully block the H+transporters in vitro and in vivo, leading to apoptotic death. Furthermore, their action seems to synergize with conventional chemotherapy protocols, leading to chemosensitization and reversal of chemoresistance. Aim of this article is to critically revise the current knowledge of this cellular machinery and to summarize the therapeutic strategies developed to counter this mechanism.
Human adenosine deaminase 2 induces differentiation of monocytes into macrophages and stimulates proliferation of T helper cells and macrophages
Authors: Zavialov Andrey V , Gracia Eduard , Glaichenhaus Nicolas , Franco Rafael , Zavialov Anton V , Lauvau Grégoire 
Published: May 2010

Abstract
Discovery of the growth factor activity of ADA2.
ADAs play a pivotal role in regulating the level of adenosine, a signaling molecule controlling a variety of cellular responses by binding to and activating four ADRs. Two enzymes, ADA1 and ADA2, are known to possess ADA activity in humans. Although the structure of ADA1 and its role in lymphocytic activation have been known for a long time, the structure and function of ADA2, a member of ADGF, remain enigmatic. Here, we found that ADA2 is secreted by monocytes undergoing differentiation into macrophages or DCs and that it binds to the cell surface via proteoglycans and ADRs. We demonstrate that ADA1 and ADA2 increase the rate of proliferation of monocyte-activated CD4+ T cells independently of their catalytic activity. We also show that ADA2 induces T cell-dependent differentiation of monocytes into macrophages and stimulates macrophage proliferation. Our discovery of the growth factor-like activity of ADA2 explains clinical observations and suggests that this enzyme could be used as a drug candidate to modulate the immune responses during inflammation and cancer.
T cell immunoglobulin- and mucin-domain-containing molecule-4 attenuates concanavalin A-induced hepatitis by regulating macrophage
Authors: Xu Liyun , Qi Jianni , Zhao Peiqing , Liang Xiaohong , Ju Ying , Liu Peng , Liu Bing , Guo Chun , Zhang Lining , Ma Chunhong , Gao Lifen 
Published: May 2010

Abstract
Tim-4 plays an important role in preventing liver injury through inhibition of CD80, CD86, and MHC II expression and TNF-α secretion by macrophages.
Tim-4 is expressed primarily on APCs, including macrophages, and has been shown to play a critical role in T cell regulation. However, it remains unclear whether Tim-4 also plays a role in the regulation of macrophage functions. In the present study, we investigated the effects of Tim-4 on macrophage activity in Con A-induced hepatitis in mice. We found that high levels of Tim-4 expression were associated with a diminished serum level of ALT in Con A-induced hepatitis. In addition, adoptive transfer of T4-RAW cells resulted in a significant decrease in ALT levels and Con A-induced liver injuries in mice. Concurrently, T4-RAW cells transfer displayed, markedly decreased apoptosis in liver and depressed TNF-α secretion in serum, supporting the hypothesis that Tim-4 protects Con A-induced hepatitis by negatively regulating macrophages. Consistent with the in vivo findings, in vitro studies showed that Tim-4 overexpression in RAW264.7 cells was associated with decreased expression of CD80, CD86, and MHCII molecules and the production of TNF-α. Moreover, Tim-4 blockade promoted LPS-induced macrophage activation. In conclusion, these findings indicate that Tim-4 plays an important role in alleviating liver damage by inhibition of macrophage activity. Tim-4 pathway could be a potential target for the treatment of acute hepatitis.
Promethazine Prescribing Patterns in Pediatric Inpatients Younger than Two Years before and after the Product Black Box Warning
Authors: Kessler Tiffany L. , Harrison Donald L. , Hagemann Tracy M. 
Published: May 2010

Purpose A black box warning was added to promethazine's labeling in November 2004 related to reports of respiratory depression in children younger than 2 years. The objective of this study was to determine what effect the changes in product labeling had on prescribing practices for promethazine at a pediatric hospital 1 year before (2004), 1 year immediately after (2005), and 2 years after (2006). Methods A retrospective chart review of orders for promethazine in pediatric inpatients (2 years and younger) admitted between 2004 and 2006 was conducted. Information collected included patient demographics and specifics about orders for promethazine (dose in mg/kg, route, indication, and number of as-needed doses received). Results A total of 255 orders for promethazine met study criteria. Though the number of promethazine orders decreased each year, there was no significant difference in promethazine use observed between 2004 and 2005 ( P = 0.223). However, a significant decrease in promethazine use occurred between 2005 and 2006 ( P = 0.017), a full year after the initial black box warning was released. Conclusion The black box warning has affected the prescribing patterns at a pediatric institution, causing a decrease in promethazine use. The response to the warning was slow for some services, which indicates a need for better communication and dissemination of prescribing information to medical staff and health care professionals.
Confirmatory factor analysis and factorial invariance analysis of the adolescent self‐report Strengths and Difficulties Questionnaire: How important are method effects and minor factors?
Authors: van de Looij‐Jansen Petra M. , Goedhart Arnold W. , de Wilde Erik J. , Treffers Philip D. A. 
Published: May 2010

Objectives. This study examined the factor structure of the self‐report Strengths and Difficulties Questionnaire, paying special attention to the number of factors and to negative effects of reverse‐worded items and minor factors within the subscales on model fit. Furthermore, factorial invariance across gender, age, level of education, and ethnicity was investigated. Design. Data were obtained from the Youth Health Monitor Rotterdam, a community‐based health surveillance system. Methods. The sample consisted of 11,881 pupils of 11–16 years old. Next to the original five‐factor model, a factor model with the number of factors based on parallel analysis and scree test was investigated. Confirmatory factor analysis for ordered‐categorical measures was applied to examine the goodness‐of‐fit and factorial invariance of the factor models. Results. After allowing reverse‐worded items to cross‐load on the prosocial behaviour factor and adding error correlations, a good fit to the data was found for the original five‐factor model (emotional symptoms, conduct problems, hyperactivity–inattention, peer problems, prosocial behaviour) and a model with four factors (emotional symptoms and peer problems, conduct problems, hyperactivity–inattention, prosocial behaviour). Factorial invariance across gender, age, level of education, and ethnicity was found for the final five‐ and four‐factor model, except for the prosocial factor of the four‐factor model that showed partial invariance across gender. Conclusions. While support was found for both models, the final five‐factor model is theoretically more plausible and gained additional support as the original scales emotional problems and peer problems showed different relations with gender, educational level, and ethnicity.