bluuebunny/crossref_metadata_2025 huggingface dataset:
Vitamin C: Overview and Update
Authors: Schlueter Amanda K. , Johnston Carol S.
Published: March 2011

Vitamin C functions in enzyme activation, oxidative stress reduction, and immune function. There is considerable evidence that vitamin C protects against respiratory tract infections and reduces risk for cardiovascular disease and some cancers. Current trials are examining the efficacy of intravenous vitamin C as cancer therapy. Many experts believe that the recommended intakes for vitamin C (45 to 90 mg daily) are several orders of magnitude too low to support optimal vitamin C functionality. Also, there is a misperception that vitamin C deficiency disease (scurvy) is largely historical and rarely observed in developed nations. Physical symptoms of scurvy include swelling of the lower extremities, bleeding gums, fatigue, and hemorrhaging, as well as psychological problems, including depression, hysteria, and social introversion. The long-term safety of vitamin C supplementation seems evident as large investigations have noted reduced risk of mortality in vitamin C supplementing populations and in those with elevated plasma vitamin C concentrations.
The Role of Vitamin D in Human Health: A Paradigm Shift
Authors: Lappe Joan M.
Published: March 2011

Vitamin D deficiency is pandemic, spanning many continents and including all ages, genders and racial/ethnic groups. Currently, world-wide attention is focused on the importance of vitamin D in optimizing health and preventing disease. This focus is largely the result of the scientific discovery that vitamin D receptors are present in nearly every tissue and cell in the body and that adequate vitamin D status is essential for optimal functioning of these tissues and cells. An impressive body of research has accumulated over the past two decades providing new information about the role of vitamin D in prevention of a broad range of diseases. The purpose of this paper is to provide a review of this new information.
Does Mediatization Change MP-Media Interaction and MP Attitudes toward the Media? Evidence from a Longitudinal Study of Danish MPs
Authors: Elmelund-Præstekær Christian , Hopmann David Nicolas , Nørgaard Asbjørn Sonne
Published: March 2011

Mass media have become more important in political communication in western democracies in recent decades. Parliamentarians need to pay attention to the norms and demands of the media and conform to the ‘media logic’. Politicians allegedly lose communicative autonomy in their interaction with the media and the literature suggests that they regret this development. The consequences of this mediatization process are rarely studied empirically, however. Using two elite surveys this article studies Danish MPs’ interaction with and attitudes toward the media in 1980 and 2000. As expected, the evidence shows that MPs appear more often in the media in 2000 than in 1980, and that they have come to perceive the media as a more autonomous political actor. Contrary to expectations, MPs have not become more critical toward the media in general and they have become even more satisfied with the media coverage of their own activities as MPs. On the individual level, the increased satisfaction is correlated with media appearances which again correlate with seniority, position, and party affiliation. The evidence suggests that parliamentarians are not puppets of the media-at least some of them are in a position to take advantage of the mediatization of politics.
A 3-bp deletion in the HBS1L-MYB intergenic region on chromosome 6q23 is associated with HbF expression
Authors: Farrell John J. , Sherva Richard M. , Chen Zhi-yi , Luo Hong-yuan , Chu Benjamin F. , Ha Shau Yin , Li Chi Kong , Lee Anselm C. W. , Li Rever C. H. , Li Chi Keung , Yuen Hui Leung , So Jason C. C. , Ma Edmond S. K. , Chan Li Chong , Chan Vivian , Sebastiani Paola , Farrer Lindsay A. , Baldwin Clinton T. , Steinberg Martin H. , Chui David H. K.
Published: March 2011

Fetal hemoglobin (HbF) is regulated as a multigenic trait. By genome-wide association study, we confirmed that HBS1L-MYB intergenic polymorphisms (HMIP) and BCL11A polymorphisms are highly associated with HbF in Chinese β-thalassemia heterozygotes. In this population, the variance in HbF resulting from the HMIP is 13.5%; that resulting from the BCL11A polymorphism is 6.4%. To identify the functional variant in HMIP, we used 1000 Genomes Project data, single nucleotide polymorphism imputation, comparisons of association results across populations, potential transcription factor binding sites, and analysis of phylogenetic conservation. Based on these studies, a hitherto unreported association between HbF expression and a 3-bp deletion, between 135 460 326 and 135 460 328 bp on chromosome 6q23 was found. This 3-bp deletion is in complete linkage disequilibrium with rs9399137, which is the single nucleotide polymorphism in HMIP most significantly associated with HbF among Chinese, Europeans, and Africans. Chromatin immunoprecipitation assays confirmed erythropoiesis-related transcription factors binding to this region in K562 cells. Based on transient expression of a luciferase reporter plasmid, the DNA fragment encompassing the 3-bp deletion polymorphism has enhancer-like activity that is further augmented by the introduction of the 3-bp deletion. This 3-bp deletion polymorphism is probably the most significant functional motif accounting for HMIP modulation of HbF in all 3 populations.
A novel adoptive transfer model of chronic lymphocytic leukemia suggests a key role for T lymphocytes in the disease
Authors: Bagnara Davide , Kaufman Matthew S. , Calissano Carlo , Marsilio Sonia , Patten Piers E. M. , Simone Rita , Chum Philip , Yan Xiao-Jie , Allen Steven L. , Kolitz Jonathan E. , Baskar Sivasubramanian , Rader Christoph , Mellstedt Hakan , Rabbani Hodjattallah , Lee Annette , Gregersen Peter K. , Rai Kanti R. , Chiorazzi Nicholas
Published: March 2011

Chronic lymphocytic leukemia (CLL) is an incurable adult disease of unknown etiology. Understanding the biology of CLL cells, particularly cell maturation and growth in vivo, has been impeded by lack of a reproducible adoptive transfer model. We report a simple, reproducible system in which primary CLL cells proliferate in nonobese diabetes/severe combined immunodeficiency/γcnull mice under the influence of activated CLL-derived T lymphocytes. By cotransferring autologous T lymphocytes, activated in vivo by alloantigens, the survival and growth of primary CFSE-labeled CLL cells in vivo is achieved and quantified. Using this approach, we have identified key roles for CD4+ T cells in CLL expansion, a direct link between CD38 expression by leukemic B cells and their activation, and support for CLL cells preferentially proliferating in secondary lymphoid tissues. The model should simplify analyzing kinetics of CLL cells in vivo, deciphering involvement of nonleukemic elements and nongenetic factors promoting CLL cell growth, identifying and characterizing potential leukemic stem cells, and permitting preclinical studies of novel therapeutics. Because autologous activated T lymphocytes are 2-edged swords, generating unwanted graph-versus-host and possibly autologous antitumor reactions, the model may also facilitate analyses of T-cell populations involved in immune surveillance relevant to hematopoietic transplantation and tumor cytoxicity.
Combination of melphalan and dexamethasone for patients with newly diagnosed POEMS syndrome
Authors: Li Jian , Zhang Wei , Jiao Li , Duan Ming-Hui , Guan Hong-Zhi , Zhu Wei-Guo , Tian Zhuang , Zhou Dao-Bin
Published: March 2011

POEMS syndrome is a rare clonal plasma cell disorder without standard treatment. Based on the efficacy and low toxicity of a combination of melphalan and dexamethasone (MDex) for light chain amyloidosis, we conducted a prospective study of MDex treatment for patients with newly diagnosed POEMS syndrome. Thirty-one patients (19 men) were enrolled and the median age at the time of diagnosis was 44 years (range, 32-68 years). All patients received 12 cycles of MDex treatment. Twenty-five patients (80.6%) achieved hematologic response including 12 (38.7%) complete remission and 13 (41.9%) partial remission. Of all 31 patients, the neurologic response rate was 100%, assessed by overall neuropathy limitation scale (ONLS). The initial neurologic response was observed in 24 patients (77.4%) at 3 months after treatment and the median time to maximal neurologic response was 12 months (range, 3-15 months). Moreover, MDex substantially improved the level of serum vascular endothelial growth factor and relieved organomegaly, extravascular volume overload, and pulmonary hypertension. Only 6 patients (19.3%) suffered from grade 3 adverse events during treatment. All patients are alive and free of neurologic relapse after the median follow-up time of 21 months. Therefore, MDex is an effective and well-tolerated treatment option for patients with newly diagnosed POEMS syndrome.
Novel computational analysis of protein binding array data identifies direct targets of Nkx2.2 in the pancreas
Authors: Hill Jonathon T , Anderson Keith R , Mastracci Teresa L , Kaestner Klaus H , Sussel Lori
Published: March 2011

Background

The creation of a complete genome-wide map of transcription factor binding sites is essential for understanding gene regulatory networks in vivo. However, current prediction methods generally rely on statistical models that imperfectly model transcription factor binding. Generation of new prediction methods that are based on protein binding data, but do not rely on these models may improve prediction sensitivity and specificity.

Results

We propose a method for predicting transcription factor binding sites in the genome by directly mapping data generated from protein binding microarrays (PBM) to the genome and calculating a moving average of several overlapping octamers. Using this unique algorithm, we predicted binding sites for the essential pancreatic islet transcription factor Nkx2.2 in the mouse genome and confirmed >90% of the tested sites by EMSA and ChIP. Scores generated from this method more accurately predicted relative binding affinity than PWM based methods. We have also identified an alternative core sequence recognized by the Nkx2.2 homeodomain. Furthermore, we have shown that this method correctly identified binding sites in the promoters of two critical pancreatic islet β-cell genes, NeuroD1 and insulin2, that were not predicted by traditional methods. Finally, we show evidence that the algorithm can also be applied to predict binding sites for the nuclear receptor Hnf4α.

Conclusions

PBM-mapping is an accurate method for predicting Nkx2.2 binding sites and may be widely applicable for the creation of genome-wide maps of transcription factor binding sites.
Carbon monoxide prevents hepatic mitochondrial membrane permeabilization
Authors: Queiroga Cláudia SF , Almeida Ana S , Alves Paula M , Brenner Catherine , Vieira Helena LA
Published: March 2011

Background

Low concentrations of carbon monoxide (CO) protect hepatocytes against apoptosis and confers cytoprotection in several models of liver. Mitochondria are key organelles in cell death control via their membrane permeabilization and the release of pro-apoptotic factors.

Results

Herein, we show that CO prevents mitochondrial membrane permeabilization (MMP) in liver isolated mitochondria. Direct and indirect approaches were used to evaluate MMP inhibition by CO: mitochondrial swelling, mitochondrial depolarization and inner membrane permeabilization. Additionally, CO increases mitochondrial reactive oxygen species (ROS) generation, and their scavenging, by ß-carotene addition, decreases CO protection, which reveals the key role of ROS. Interestingly, cytochrome c oxidase transiently responds to low concentrations of CO by decreasing its activity in the first 5 min, later on there is an increase of cytochrome c oxidase activity, which were detected up to 30 min.

Conclusion

CO directly prevents mitochondrial membrane permeabilization, which might be implicated in the hepatic apoptosis inhibition by this gaseoustransmitter.
ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis
Authors: Ho Joshua WK , Bishop Eric , Karchenko Peter V , Nègre Nicolas , White Kevin P , Park Peter J
Published: March 2011

Background

Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone modifications. Previous reports only compared a small number of profiles, and little has been done to compare histone modification profiles generated by the two technologies or to assess the impact of input DNA libraries in ChIP-seq analysis. Here, we performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip/ChIP-seq profiles of the coactivator CBP, RNA polymerase II (RNA PolII), and six histone modifications across four developmental stages of Drosophila melanogaster.

Results

Both technologies produce highly reproducible profiles within each platform, ChIP-seq generally produces profiles with a better signal-to-noise ratio, and allows detection of more peaks and narrower peaks. The set of peaks identified by the two technologies can be significantly different, but the extent to which they differ varies depending on the factor and the analysis algorithm. Importantly, we found that there is a significant variation among multiple sequencing profiles of input DNA libraries and that this variation most likely arises from both differences in experimental condition and sequencing depth. We further show that using an inappropriate input DNA profile can impact the average signal profiles around genomic features and peak calling results, highlighting the importance of having high quality input DNA data for normalization in ChIP-seq analysis.

Conclusions

Our findings highlight the biases present in each of the platforms, show the variability that can arise from both technology and analysis methods, and emphasize the importance of obtaining high quality and deeply sequenced input DNA libraries for ChIP-seq analysis.
Transcriptional profiling identifies differentially expressed genes in developing turkey skeletal muscle
Authors: Sporer Kelly RB , Tempelman Robert J , Ernst Catherine W , Reed Kent M , Velleman Sandra G , Strasburg Gale M
Published: March 2011

Background

Skeletal muscle growth and development from embryo to adult consists of a series of carefully regulated changes in gene expression. Understanding these developmental changes in agriculturally important species is essential to the production of high quality meat products. For example, consumer demand for lean, inexpensive meat products has driven the turkey industry to unprecedented production through intensive genetic selection. However, achievements of increased body weight and muscle mass have been countered by an increased incidence of myopathies and meat quality defects. In a previous study, we developed and validated a turkey skeletal muscle-specific microarray as a tool for functional genomics studies. The goals of the current study were to utilize this microarray to elucidate functional pathways of genes responsible for key events in turkey skeletal muscle development and to compare differences in gene expression between two genetic lines of turkeys. To achieve these goals, skeletal muscle samples were collected at three critical stages in muscle development: 18d embryo (hyperplasia), 1d post-hatch (shift from myoblast-mediated growth to satellite cell-modulated growth by hypertrophy), and 16wk (market age) from two genetic lines: a randombred control line (RBC2) maintained without selection pressure, and a line (F) selected from the RBC2 line for increased 16wk body weight. Array hybridizations were performed in two experiments: Experiment 1 directly compared the developmental stages within genetic line, while Experiment 2 directly compared the two lines within each developmental stage.

Results

A total of 3474 genes were differentially expressed (false discovery rate; FDR < 0.001) by overall effect of development, while 16 genes were differentially expressed (FDR < 0.10) by overall effect of genetic line. Ingenuity Pathways Analysis was used to group annotated genes into networks, functions, and canonical pathways. The expression of 28 genes involved in extracellular matrix regulation, cell death/apoptosis, and calcium signaling/muscle function, as well as genes with miscellaneous function was confirmed by qPCR.

Conclusions

The current study identified gene pathways and uncovered novel genes important in turkey muscle growth and development. Future experiments will focus further on several of these candidate genes and the expression and mechanism of action of their protein products.
Proteomic assessment of a cell model of spinal muscular atrophy
Authors: Wu Chia-Yen , Whye Dosh , Glazewski Lisa , Choe Leila , Kerr Douglas , Lee Kelvin H , Mason Robert W , Wang Wenlan
Published: March 2011

Background

Deletion or mutation(s) of the survival motor neuron 1 (SMN1) gene causes spinal muscular atrophy (SMA), a neuromuscular disease characterized by spinal motor neuron death and muscle paralysis. Complete loss of the SMN protein is embryonically lethal, yet reduced levels of this protein result in selective death of motor neurons. Why motor neurons are specifically targeted by SMN deficiency remains to be determined. In this study, embryonic stem (ES) cells derived from a severe SMA mouse model were differentiated into motor neurons in vitro by addition of retinoic acid and sonic hedgehog agonist. Proteomic and western blot analyses were used to probe protein expression alterations in this cell-culture model of SMA that could be relevant to the disease.

Results

When ES cells were primed with Noggin/fibroblast growth factors (bFGF and FGF-8) in a more robust neural differentiation medium for 2 days before differentiation induction, the efficiency of in vitro motor neuron differentiation was improved from ~25% to ~50%. The differentiated ES cells expressed a pan-neuronal marker (neurofilament) and motor neuron markers (Hb9, Islet-1, and ChAT). Even though SMN-deficient ES cells had marked reduced levels of SMN (~20% of that in control ES cells), the morphology and differentiation efficiency for these cells are comparable to those for control samples. However, proteomics in conjunction with western blot analyses revealed 6 down-regulated and 14 up-regulated proteins with most of them involved in energy metabolism, cell stress-response, protein degradation, and cytoskeleton stability. Some of these activated cellular pathways showed specificity for either undifferentiated or differentiated cells. Increased p21 protein expression indicated that SMA ES cells were responding to cellular stress. Up-regulation of p21 was confirmed in spinal cord tissues from the same SMA mouse model from which the ES cells were derived.

Conclusion

SMN-deficient ES cells provide a cell-culture model for SMA. SMN deficiency activates cellular stress pathways, causing a dysregulation of energy metabolism, protein degradation, and cytoskeleton stability.
Causes and consequences of cerebral small vessel disease. The RUN DMC study: a prospective cohort study. Study rationale and protocol
Authors: van Norden Anouk GW , de Laat Karlijn F , Gons Rob AR , van Uden Inge WM , van Dijk Ewoud J , van Oudheusden Lucas JB , Esselink Rianne AJ , Bloem Bastiaan R , van Engelen Baziel GM , Zwarts Machiel J , Tendolkar Indira , Olde-Rikkert Marcel G , van der Vlugt Maureen J , Zwiers Marcel P , Norris David G , de Leeuw Frank-Erik
Published: March 2011

Background

Cerebral small vessel disease (SVD) is a frequent finding on CT and MRI scans of elderly people and is related to vascular risk factors and cognitive and motor impairment, ultimately leading to dementia or parkinsonism in some. In general, the relations are weak, and not all subjects with SVD become demented or get parkinsonism. This might be explained by the diversity of underlying pathology of both white matter lesions (WML) and the normal appearing white matter (NAWM). Both cannot be properly appreciated with conventional MRI. Diffusion tensor imaging (DTI) provides alternative information on microstructural white matter integrity. The association between SVD, its microstructural integrity, and incident dementia and parkinsonism has never been investigated.

Methods/Design

The RUN DMC study is a prospective cohort study on the risk factors and cognitive and motor consequences of brain changes among 503 non-demented elderly, aged between 50-85 years, with cerebral SVD. First follow up is being prepared for July 2011. Participants alive will be included and invited to the research centre to undergo a structured questionnaire on demographics and vascular risk factors, and a cognitive, and motor, assessment, followed by a MRI protocol including conventional MRI, DTI and resting state fMRI.

Discussion

The follow up of the RUN DMC study has the potential to further unravel the causes and possibly better predict the consequences of changes in white matter integrity in elderly with SVD by using relatively new imaging techniques. When proven, these changes might function as a surrogate endpoint for cognitive and motor function in future therapeutic trials. Our data could furthermore provide a better understanding of the pathophysiology of cognitive and motor disturbances in elderly with SVD. The execution and completion of the follow up of our study might ultimately unravel the role of SVD on the microstructural integrity of the white matter in the transition from "normal" aging to cognitive and motor decline and impairment and eventually to incident dementia and parkinsonism.
Reliability and validity of psychosocial and environmental correlates measures of physical activity and screen-based behaviors among Chinese children in Hong Kong
Authors: Huang Ya-Jun , Wong Stephen H , Salmon Jo , Hui Stanley S
Published: March 2011

Background

Insufficient participation in physical activity and excessive screen time have been observed among Chinese children. The role of social and environmental factors in shaping physical activity and sedentary behaviors among Chinese children is under-investigated. The purpose of the present study was to assess the reliability and validity of a questionnaire to measure child- and parent-reported psychosocial and environmental correlates of physical activity and screen-based behaviors among Chinese children in Hong Kong.

Methods

A total of 303 schoolchildren aged 9-14 years and their parents volunteered to participate in this study and 160 of them completed the questionnaire twice within an interval of 10 days. Intraclass correlation coefficients (ICCs), kappa statistics, and percent agreement were performed to evaluate test-retest reliability of the continuous and categorical variables, respectively. Exploratory factor analyses (EFAs) were conducted to assess convergent validity of the emergent scales. Cronbach's alpha and ICCs were performed to assess internal and test-retest reliability of the emergent scales. Criterion validity was assessed by correlating psychosocial and environmental measures with self-reported physical activity and screen-based behaviors, measured by a validated questionnaire.

Results

Reliability statistics for both child- and parent-reported continuous variables showed acceptable consistency for all of the ICC values greater than 0.70. Kappa statistics showed fair to perfect test-retest reliability for the categorical items. Adequate internal consistency and test-retest reliability were observed in most of the emergent scales. Criterion validity assessed by correlating psychosocial and environmental measures with child-reported physical activity found associations with physical activity in the self-efficacy scale (r = 0.25, P < 0.05), the peer support for physical activity scale (r = 0.25, P < 0.05) and home physical activity environmental (r = 0.14, P < 0.05). Children's screen-based behaviors were associated with the family support for physical activity scale (r = -0.22, P < 0.05) and parental role modeling of TV (r = 0.12, P = 0.053).

Conclusions

The findings provide psychometric support for using this questionnaire for examining psychosocial and environmental correlates of physical activity and screen-based behaviors among Chinese children in Hong Kong. Further research is needed to develop more robust measures based on the current questionnaire, especially for peer influence on physical activity and parental rules on screen-based behaviors.
Effect of thermal treatment on the growth, structure and luminescence of nitride-passivated silicon nanoclusters
Authors: Wilson Patrick RJ , Roschuk Tyler , Dunn Kayne , Normand Elise N , Chelomentsev Evgueni , Zalloum Othman HY , Wojcik Jacek , Mascher Peter
Published: March 2011

Silicon nanoclusters (Si-ncs) embedded in silicon nitride films have been studied to determine the effects that deposition and processing parameters have on their growth, luminescent properties, and electronic structure. Luminescence was observed from Si-ncs formed in silicon-rich silicon nitride films with a broad range of compositions and grown using three different types of chemical vapour deposition systems. Photoluminescence (PL) experiments revealed broad, tunable emissions with peaks ranging from the near-infrared across the full visible spectrum. The emission energy was highly dependent on the film composition and changed only slightly with annealing temperature and time, which primarily affected the emission intensity. The PL spectra from films annealed for duration of times ranging from 2 s to 2 h at 600 and 800°C indicated a fast initial formation and growth of nanoclusters in the first few seconds of annealing followed by a slow, but steady growth as annealing time was further increased. X-ray absorption near edge structure at the Si K- and L3,2-edges exhibited composition-dependent phase separation and structural re-ordering of the Si-ncs and silicon nitride host matrix under different post-deposition annealing conditions and generally supported the trends observed in the PL spectra.
Expression and cellular localization of cyclooxygenases and prostaglandin E synthases in the hemorrhagic brain
Authors: Wu Tao , Wu He , Wang Jessica , Wang Jian
Published: March 2011

Background

Although cyclooxygenases (COX) and prostaglandin E synthases (PGES) have been implicated in ischemic stroke injury, little is known about their role in intracerebral hemorrhage (ICH)-induced brain damage. This study examines the expression and cellular localization of COX-1, COX-2, microsomal PGES-1 (mPGES-1), mPGES-2, and cytosolic PGES (cPGES) in mice that have undergone hemorrhagic brain injury.

Methods

ICH was induced in C57BL/6 mice by intrastriatal injection of collagenase. Expression and cellular localization of COX-1, COX-2, mPGES-1, mPGES-2, and cPGES were examined by immunofluorescence staining.

Results

In the hemorrhagic brain, COX-1, mPGES-2, and cPGES were expressed constitutively in neurons; COX-1 was also constitutively expressed in microglia. The immunoreactivity of COX-2 was increased in neurons and astrocytes surrounding blood vessels at 5 h and then tended to decrease in neurons and increase in astrocytes at 1 day. At 3 days after ICH, COX-2 was observed primarily in astrocytes but was absent in neurons. Interestingly, the immunoreactivity of mPGES-1 was increased in neurons in the ipsilateral cortex and astrocytes in the ipsilateral striatum at 1 day post-ICH; the immunoreactivity of astrocytic mPGES-1 further increased at 3 days.

Conclusion

Our data suggest that microglial COX-1, neuronal COX-2, and astrocytic COX-2 and mPGES-1 may work sequentially to affect ICH outcomes. These findings have implications for efforts to develop anti-inflammatory strategies that target COX/PGES pathways to reduce ICH-induced secondary brain damage.
The preparation of an infectious full-length cDNA clone of Saffold virus
Authors: Himeda Toshiki , Hosomi Takushi , Asif Naeem , Shimizu Hiroyuki , Okuwa Takako , Muraki Yasushi , Ohara Yoshiro
Published: March 2011

The pathogenicity of Saffold virus (SAFV) among humans still remains unclear, although it was identified as a novel human cardiovirus in 2007. In order to encourage the molecular pathogenetic studies of SAFV, we generated an infectious cDNA clone of SAFV type 3 (SAFV-3). The present study demonstrated that the synthesis of the full-length infectious RNA by T7 RNA polymerase was terminated by a homologous sequence motif with the human preproparathyroid hormone (PTH) signal in the SAFV-3 genome. To obtain the infectious RNA using T7 promoter, a variant of T7 RNA polymerase, which fails to recognize the PTH signal, was useful. This study will provide a valuable technical insight into the reverse genetics of SAFV.
In vitro study on human cytomegalovirus affecting early pregnancy villous EVT's invasion function
Authors: Tao Liu , Suhua Chen , Juanjuan Chen , Zongzhi Yin , Juan Xiao , Dandan Zhang
Published: March 2011

Background

Human cytomegalovirus (HCMV) is the most common pathogen in uterus during pregnancy, which may lead to some serious results such as miscarriage, stillbirth, cerebellar malformation, fetus developmental retardation, but its pathogenesis has not been fully explained. The hypofunction of extravillous cytotrophoblast (EVT) invasion is the essential pathologic base of some complications of pregnancy. c-erbB-2 is a kind of oncogene protein and closely linked with embryogenesis, tissue repair and regeneration. Matrix metalloproteinase (MMP) is one of the key enzymes which affect EVT migration and invasion function. The expression level changes of c-erbB-2, MMP-2 and MMP-9 can reflect the changes of EVT invasion function.

Results

To explore the influence of HCMV on the invasion function of EVT, we tested the protein expression level changes of c-erbB-2, MMP-2 and MMP-9 in villous explant cultured in vitro infected by HCMV, with the use of immunohistochemistry SP method and western blot. We confirmed that HCMV can reproduce and spread in early pregnancy villus; c-erbB-2 protein mainly expressed in normal early pregnancy villous syncytiotrophoblast (ST) remote plasma membrane and EVT, especially remote EVT cell membrane in villous stem cell column, little expressed in ST proximal end cell membrane and interstitial cells; MMP-2 protein primarily expressed in early pregnancy villous EVT endochylema and rarely in villous trophoblast (VT), ST and interstitial cells; MMP-9 protein largely expressed in early pregnancy villous mesenchyme, EVT and VT endochylema. Compared with control group, the three kinds of protein expression level in early pregnancy villus of virus group significantly decreased (P < 0.05).

Conclusion

HCMV can infect villus in vitro and cause the decrease of early pregnancy villous EVT's invasion function.
Activity-dependent brain-derived neurotrophic factor expression regulates cortistatin-interneurons and sleep behavior
Authors: Martinowich Keri , Schloesser Robert J , Jimenez Dennisse V , Weinberger Daniel R , Lu Bai
Published: March 2011

Background

Sleep homeostasis is characterized by a positive correlation between sleep length and intensity with the duration of the prior waking period. A causal role for brain-derived neurotrophic factor (BDNF) in sleep homeostasis has been suggested, but the underlying mechanisms remain unclear. Cortistatin, a neuropeptide expressed primarily in a subset of cortical GABAergic interneurons, is another molecule implicated in sleep homeostasis.

Results

We confirmed that sleep deprivation leads to an increase in cortical cortistatin mRNA expression. Disruption of activity-dependent BDNF expression in a genetically modified mouse line impairs both baseline levels of cortistatin mRNA as well as its levels following sleep deprivation. Disruption of activity-dependent BDNF also leads to a decrease in sleep time during the active (dark) phase.

Conclusion

Our studies suggest that regulation of cortistatin-expressing interneurons by activity-dependent BDNF expression may contribute to regulation of sleep behavior.
Granulocyte-macrophage colony-stimulating factor (GM-CSF): a chemoattractive agent for murine leukocytes in vivo
Authors: Khajah Maitham , Millen Brandie , Cara Denise Carmona , Waterhouse Christopher , McCafferty Donna-Marie
Published: March 2011

GM-CSF is well recognized as a proliferative agent for hematopoietic cells and exerts a priming function on neutrophils. The aim of this study was to determine if GM-CSF has a role as a neutrophil chemoattractant in vivo and if it can contribute to recruitment during intestinal inflammation. Initial studies in vitro, using the under-agarose gel assay, determined that GM-CSF can induce neutrophil migration at a much lower molar concentration than the fMLP-like peptide WKYMVm (33.5–134 nM vs. 1–10 μM). GM-CSF-induced neutrophil migration was ablated (<95%) using neutrophils derived from GMCSFRβ−/− mice and significantly attenuated by 42% in PI3Kγ−/−neutrophils. In vivo, a significant increase in leukocyte recruitment was observed using intravital microscopy 4 h post-GM-CSF (10 μg/kg) injection, which was comparable with leukocyte recruitment induced by KC (40 μg/kg). GM-CSF-induced recruitment was abolished, and KC-induced recruitment was maintained in GMCSFRβ−/− mice. Furthermore, in vivo migration of extravascular leukocytes was observed toward a gel containing GM-CSF in WT but not GMCSFRβ−/− mice. Finally, in a model of intestinal inflammation (TNBS-induced colitis), colonic neutrophil recruitment, assessed using the MPO assay, was attenuated significantly in anti-GM-CSF-treated mice or GMCSFRβ−/− mice. These data demonstrate that GM-CSF is a potent chemoattractant in vitro and can recruit neutrophils from the microvasculature and induce extravascular migration in vivo in a β subunit-dependent manner. This property of GM-CSF may contribute significantly to recruitment during intestinal inflammation.
SorLA regulates the activity of lipoprotein lipase by intracellular trafficking
Authors: Klinger Stine C. , Glerup Simon , Raarup Merete K. , Mari Muriel C. , Nyegaard Mette , Koster Gerbrand , Prabakaran Thaneas , Nilsson Stefan K. , Kjaergaard Maj M. , Bakke Oddmund , Nykjær Anders , Olivecrona Gunilla , Petersen Claus Munck , Nielsen Morten S.
Published: March 2011

Many different tissues and cell types exhibit regulated secretion of lipoprotein lipase (LPL). However, the sorting of LPL in the trans Golgi network has not, hitherto, been understood in detail. Here, we characterize the role of SorLA (officially known as SorLA-1 or sortilin-related receptor) in the intracellular trafficking of LPL. We found that LPL bound to SorLA under neutral and acidic conditions, and in cells this binding mainly occurred in vesicular structures. SorLA expression changed the subcellular distribution of LPL so it became more concentrated in endosomes. From the endosomes, LPL was further routed to the lysosomes, which resulted in a degradation of newly synthesized LPL. Consequently, an 80% reduction of LPL activity was observed in cells that expressed SorLA. By analogy, SorLA regulated the vesicle-like localization of LPL in primary neuronal cells. Thus, LPL binds to SorLA in the biosynthetic pathway and is subsequently transported to endosomes. As a result of this SorLA mediated-transport, newly synthesized LPL can be routed into specialized vesicles and eventually sent to degradation, and its activity thereby regulated.
Phosphorylation of kinesin light chain 1 at serine 460 modulates binding and trafficking of calsyntenin-1
Authors: Vagnoni Alessio , Rodriguez Lilia , Manser Catherine , De Vos Kurt J. , Miller Christopher C. J.
Published: March 2011

Kinesin light chain 1 (KLC1) binds to the intracellular cytoplasmic domain of the type-1 membrane-spanning protein calsyntenin-1 (also known as alcadein-α) to mediate transport of a subset of vesicles. Here, we identify serine 460 in KLC1 (KLC1ser460) as a phosphorylation site and show that mutation of KLC1ser460 influences the binding of KLC1 to calsyntenin-1. Mutation of KLC1ser460 to an alanine residue, to preclude phosphorylation, increased the binding of calsyntenin-1, whereas mutation to an aspartate residue, to mimic permanent phosphorylation, reduced the binding. Mutation of KLC1ser460 did not affect the interaction of KLC1 with four other known binding partners: huntingtin-associated protein 1 isoform A (HAP1A), collapsin response mediator protein-2 (CRMP2), c-Jun N-terminal kinase-interacting protein-1 (JIP1) and kinase-D-interacting substrate of 220 kDa (Kidins220). KLC1ser460 is a predicted mitogen-activated protein kinase (MAPK) target site, and we show that extracellular-signal-regulated kinase (ERK) phosphorylates this residue in vitro. We also demonstrate that inhibition of ERK promotes binding of calsyntenin-1 to KLC1. Finally, we show that expression of the KLC1ser460 mutant proteins influences calsyntenin-1 distribution and transport in cultured cells. Thus, phosphorylation of KLC1ser460 represents a mechanism for selectively regulating the binding and trafficking of calsyntenin-1.
Experimental analysis of the blood-sucking mechanism of female mosquitoes
Authors: Kim Bo Heum , Kim Hae Koo , Lee Sang Joon
Published: March 2011

Pioneering studies have been conducted to reveal the functional characteristics of the two-pump system of the female mosquito. Mosquitoes are equipped with two pumping organs located in the head: the cibarial (CP) and the pharyngeal (PP) pumps. To analyze the functional relationship of these pumps during the blood-sucking process, micro-particle image velocimetry (PIV) and synchrotron X-ray micro-imaging were employed. The two pumps were found to be well coordinated with a phase shift (α) and time shift (β) but to have distinct functions in the liquid-sucking process. The first pump (CP) starts to expand first, and then the second pump (PP) expands in advance with a time shift (β) before the first pump (CP) begins to contract, playing a key role in improving pumping performance. The systaltic motion of the two pumps works systematically in a well-coordinated manner. In addition, the pumping performance of blood-sucking female mosquitoes is demonstrated to be superior to that of nectar-eating male mosquitoes. Intake flow rate is maximized by reducing the relaxation time of the CP and increasing the pumping frequency.
High duty cycle echolocation and prey detection by bats
Authors: Lazure Louis , Fenton M. Brock
Published: March 2011

There are two very different approaches to laryngeal echolocation in bats. Although most bats separate pulse and echo in time by signalling at low duty cycles (LDCs), almost 20% of species produce calls at high duty cycles (HDCs) and separate pulse and echo in frequency. HDC echolocators are sensitive to Doppler shifts. HDC echolocation is well suited to detecting fluttering targets such as flying insects against a cluttered background. We used two complementary experiments to evaluate the relative effectiveness of LDC and HDC echolocation for detecting fluttering prey. We measured echoes from fluttering targets by broadcasting artificial bat calls, and found that echo amplitude was greatest for sounds similar to those used in HDC echolocation. We also collected field recordings of syntopic LDC and HDC bats approaching an insect-like fluttering target and found that HDC bats approached the target more often (18.6% of passes) than LDC bats (1.2% of passes). Our results suggest that some echolocation call characteristics, particularly duty cycle and pulse duration, translate into improved ability to detect fluttering targets in clutter, and that HDC echolocation confers a superior ability to detect fluttering prey in the forest understory compared with LDC echolocation. The prevalence of moths in the diets of HDC bats, which is often used as support for the allotonic frequency hypothesis, can therefore be partly explained by the better flutter detection ability of HDC bats.
Biochemical integration of blood redox state in captive zebra finches (Taeniopygia guttata)
Authors: Costantini David , Monaghan Pat , Metcalfe Neil B.
Published: March 2011

Integration is a property of biological systems that refers to the extent to which their components are correlated through functional, structural, developmental or evolutionary interdependency. This study examined patterns of functional integration among different molecular components of the blood redox system (both plasma and red blood cells) in zebra finches (Taeniopygia guttata). Our results show a two cluster organization of the six measured variables: one cluster includes glutathione peroxidase in both red blood cells and plasma, thiol concentration in red blood cells and plasma hydroperoxides; the other cluster comprises a measure of the non-enzymatic antioxidant capacity in red blood cells and plasma. The interaction network amongst these variables shows (i) a strong positive connectivity among hydroperoxides, glutathione peroxidase and thiols, and (ii) negative connectivity between non-enzymatic and enzymatic antioxidants. Overall, our results also suggest strong and significant integration between the oxidative state of red blood cells and plasma.
Development of Multivalent Ion Conducting Solid Electrolytes
Authors: Imanaka Nobuhito , Tamura Shinji
Published: March 2011

Trivalent cation conduction has been successfully demonstrated by two strategies. One is crystal structure selection, and the other is the selection of the constituent ions in solids. Since the trivalent cations possess certain ionic volume, a suitable mobile ion pathway should appear in the structure. One candidate structure we selected is a two-dimensional layered structure and the other is a three-dimensional network crystal structure. The selection of the constituent ions in solids is performed by considering the electrostatic interaction between cations and anions in the structure.
Computational Testing of a Separation Procedure for the Knapsack Set with a Single Continuous Variable
Authors: Avella Pasquale , Boccia Maurizio , Vasilyev Igor
Published: March 2011

We study an exact separation procedure—SEP-MK—for the knapsack set with a single continuous variable XMK. Then, we address the question of whether SEP-MK can be of practical use in tightening mixed-integer programming (MIP) formulations when using standard (floating-point) MIP solvers. To this purpose, we present a separation procedure for MIP problems—SEP-MIPMK—where we derive knapsack sets of the form XMK by aggregating the continuous variables in the mixed knapsack inequalities of the formulation. Then, we use SEP-MK to generate cutting planes. Before the continuous variables are aggregated, the mixed knapsack inequalities are modified through the use of a bound substitution procedure to take into account fixed and variable bounds on the continuous variables. Bound substitution is made according to some heuristic rules, so even if its basic component SEP-MK is “exact,” the overall separation procedure for MIP problems, SEP-MIPMK, is heuristic. We perform a computational study on a wide set of mixed-integer programming instances from the MIPLIB 2003 [Achterberg, T., T. Koch, A. Martin. 2006. Mixed Integer Problem Library (MIPLIB) 2003. Konrad-Zuse-Zentrum für Informationstechnik Berlin, Berlin. http://miplib.zib.de] and Mittelmann [Mittelmann, H. 2010. MILP testcases. http://plato.asu.edu/ftp/milp] benchmark sets. Computational experiments confirm that lifted cover and mixed-integer rounding (MIR) inequalities are effective from a computational viewpoint. Nevertheless, there are several instances where SEP-MIPMK is able to significantly raise the lower bounds given by lifted cover and MIR inequalities.
An Algorithm for Fitting Heavy-Tailed Distributions via Generalized Hyperexponentials
Authors: Yu Kaiqi , Huang Mei-Ling , Brill Percy H.
Published: March 2011

In this paper, we propose an algorithm to fit heavy-tailed (HT) distribution functions by generalized hyperexponential (GH) distribution functions. A discussion of the steps, usage, and accuracy of the GH algorithm is given. Several examples in this paper show that the proposed method can be applied to fit HT distributions with a completely monotone probability density function (pdf) very well, like the Pareto distribution and the Weibull distribution with the shape parameter less than one, as well as HT distributions whose pdf is not completely monotone, like the lognormal distribution. In addition, we provide an example that shows that the proposed method can be applied to density estimation of real data presenting a heavy tail.
Highlight: Mechanisms of RNA-mediated regulation
Authors: Klostermeier Dagmar
Published: March 2011

No abstract available
Solution NMR studies of periplasmic binding proteins and their interaction partners
Authors: Pistolesi Sara , Tjandra Nico , Bermejo Guillermo A.
Published: March 2011

Periplasmic binding proteins (PBPs) are a crucial part of ATP-binding cassette import systems in Gram-negative bacteria. Central to their function is the ability to undergo a large-scale conformational rearrangement from open-unliganded to closed-liganded, which signals the presence of substrate and starts its translocation. Over the years, PBPs have been extensively studied not only owing to their essential role in nutrient uptake but also because they serve as excellent models for both practical applications (e.g., biosensor technology) and basic research (e.g., allosteric mechanisms). Although much of our knowledge at atomic level has been inferred from the detailed, static pictures afforded by crystallographic studies, nuclear magnetic resonance (NMR) has been able to fill certain gaps in such body of work, particularly with regard to dynamic processes. Here, we review NMR studies on PBPs, and their unique insights on conformation, dynamics, energetics, substrate binding, and interactions with related transport proteins. Based on the analysis of recent paramagnetic NMR results, as well as crystallographic and functional observations, we propose a mechanism that could explain the ability of certain PBPs to achieve a closed conformation in absence of ligand while others seem to remain open until ligand-mediated closure.
Increased urinary neutrophil gelatinase associated lipocalin in urinary tract infections and leukocyturia
Authors: Decavele An-Sofie C. , Dhondt Lien , De Buyzere Marc L. , Delanghe Joris R.
Published: March 2011

Background: Neutrophil gelatinase associated lipocalin (NGAL) is a protein present in neutrophils. NGAL is a promising biomarker for acute kidney injury. In urinary tract infections, urinary neutrophils can be a potential source of urinary NGAL. We investigated the effects of urinary tract infection and urinary neutrophil counts on urinary NGAL values.

Methods: NGAL was assayed using an immunoassay (ARCHITECT). Urine flowcytometry was performed with the UF-1000i (Sysmex).

Results: A correlation between the urinary white blood cell (WBC) count and NGAL concentrations was observed: log(Y) (NGAL, μg/L)=1.284+0.439 log(X) (urinary WBC, 109 cells/L); r=0.518. Similarly, the bacterial count correlated weakly with NGAL: log(Y) (NGAL, μg/L)=1.796+0.124 log(X) (bacterial count, 109 cells/L); r=0.243. Albuminuria correlated moderately with NGAL values: log(Y) (NGAL, μg/L)=1.557+0.339 log(X) (albuminuria, mg/L); r=0.368; α1-microglobulin (a1M) correlated weakly with NGAL: log(Y) (NGAL, μg/L)=1.631+0.360 log(X) (a1M, mg/L); r=0.381.

Conclusions: Leukocyte contributions to urinary NGAL concentrations can be important. In leukocyturia or tubular damage (e.g., intensive care patients), using a fixed cut-off value for interpreting urinary NGAL data can lead to false positive results. Therefore, we suggest a mathematical correction in cases with pyuria (>100×109 cells/L) and urinary NGAL concentration >100 μg/L: corrected NGAL (μg/L)=NGAL–0.12 (urinary WBC, 109 cells/L).