bluuebunny/crossref_metadata_2025 huggingface dataset:
SVM-based prediction of linear B-cell epitopes using Bayes Feature Extraction
Authors: Wee Lawrence JK , Simarmata Diane , Kam Yiu-Wing , Ng Lisa FP , Tong Joo Chuan
Published: December 2010

Backgound

The identification of B-cell epitopes on antigens has been a subject of intense research as the knowledge of these markers has great implications for the development of peptide-based diagnostics, therapeutics and vaccines. As experimental approaches are often laborious and time consuming, in silico methods for prediction of these immunogenic regions are critical. Such efforts, however, have been significantly hindered by high variability in the length and composition of the epitope sequences, making naïve modeling methods difficult to apply.

Results

We analyzed two benchmark datasets and found that linear B-cell epitopes possess distinctive residue conservation and position-specific residue propensities which could be exploited for epitope discrimination in silico. We developed a support vector machines (SVM) prediction model employing Bayes Feature Extraction to predict linear B-cell epitopes of diverse lengths (12- to 20-mers). The best SVM classifier achieved an accuracy of 74.50% and AROC of 0.84 on an independent test set and was shown to outperform existing linear B-cell epitope prediction algorithms. In addition, we applied our model to a dataset of antigenic proteins with experimentally-verified epitopes and found it to be generally effective for discriminating the epitopes from non-epitopes.

Conclusion

We developed a SVM prediction model utilizing Bayes Feature Extraction and showed that it was effective in discriminating epitopes from non-epitopes in benchmark datasets and annotated antigenic proteins. A web server for predicting linear B-cell epitopes was developed and is available, together with supplementary materials, at http://www.immunopred.org/bayesb/index.html.
Algorithms and semantic infrastructure for mutation impact extraction and grounding
Authors: Laurila Jonas B , Naderi Nona , Witte René , Riazanov Alexandre , Kouznetsov Alexandre , Baker Christopher JO
Published: December 2010

Background

Mutation impact extraction is a hitherto unaccomplished task in state of the art mutation extraction systems. Protein mutations and their impacts on protein properties are hidden in scientific literature, making them poorly accessible for protein engineers and inaccessible for phenotype-prediction systems that currently depend on manually curated genomic variation databases.

Results

We present the first rule-based approach for the extraction of mutation impacts on protein properties, categorizing their directionality as positive, negative or neutral. Furthermore protein and mutation mentions are grounded to their respective UniProtKB IDs and selected protein properties, namely protein functions to concepts found in the Gene Ontology. The extracted entities are populated to an OWL-DL Mutation Impact ontology facilitating complex querying for mutation impacts using SPARQL. We illustrate retrieval of proteins and mutant sequences for a given direction of impact on specific protein properties. Moreover we provide programmatic access to the data through semantic web services using the SADI (Semantic Automated Discovery and Integration) framework.

Conclusion

We address the problem of access to legacy mutation data in unstructured form through the creation of novel mutation impact extraction methods which are evaluated on a corpus of full-text articles on haloalkane dehalogenases, tagged by domain experts. Our approaches show state of the art levels of precision and recall for Mutation Grounding and respectable level of precision but lower recall for the task of Mutant-Impact relation extraction. The system is deployed using text mining and semantic web technologies with the goal of publishing to a broad spectrum of consumers.
TSCC: Two-Stage Combinatorial Clustering for virtual screening using protein-ligand interactions and physicochemical features
Authors: Clinciu Daniel L , Chen Yen-Fu , Ko Cheng-Neng , Lo Chi-Chun , Yang Jinn-Moon
Published: December 2010

Background

The increasing numbers of 3D compounds and protein complexes stored in databases contribute greatly to current advances in biotechnology, being employed in several pharmaceutical and industrial applications. However, screening and retrieving appropriate candidates as well as handling false positives presents a challenge for all post-screening analysis methods employed in retrieving therapeutic and industrial targets.

Results

Using the TSCC method, virtually screened compounds were clustered based on their protein-ligand interactions, followed by structure clustering employing physicochemical features, to retrieve the final compounds. Based on the protein-ligand interaction profile (first stage), docked compounds can be clustered into groups with distinct binding interactions. Structure clustering (second stage) grouped similar compounds obtained from the first stage into clusters of similar structures; the lowest energy compound from each cluster being selected as a final candidate.

Conclusion

By representing interactions at the atomic-level and including measures of interaction strength, better descriptions of protein-ligand interactions and a more specific analysis of virtual screening was achieved. The two-stage clustering approach enhanced our post-screening analysis resulting in accurate performances in clustering, mining and visualizing compound candidates, thus, improving virtual screening enrichment.
Improving protein secondary structure prediction based on short subsequences with local structure similarity
Authors: Lin Hsin-Nan , Sung Ting-Yi , Ho Shinn-Ying , Hsu Wen-Lian
Published: December 2010

Background

When characterizing the structural topology of proteins, protein secondary structure (PSS) plays an important role in analyzing and modeling protein structures because it represents the local conformation of amino acids into regular structures. Although PSS prediction has been studied for decades, the prediction accuracy reaches a bottleneck at around 80%, and further improvement is very difficult.

Results

In this paper, we present an improved dictionary-based PSS prediction method called SymPred, and a meta-predictor called SymPsiPred. We adopt the concept behind natural language processing techniques and propose synonymous words to capture local sequence similarities in a group of similar proteins. A synonymous word is an n- gram pattern of amino acids that reflects the sequence variation in a protein’s evolution. We generate a protein-dependent synonymous dictionary from a set of protein sequences for PSS prediction.

On a large non-redundant dataset of 8,297 protein chains (DsspNr-25), the average Q
3 of SymPred and SymPsiPred are 81.0% and 83.9% respectively. On the two latest independent test sets (EVA Set_1 and EVA_Set2), the average Q
3 of SymPred is 78.8% and 79.2% respectively. SymPred outperforms other existing methods by 1.4% to 5.4%. We study two factors that may affect the performance of SymPred and find that it is very sensitive to the number of proteins of both known and unknown structures. This finding implies that SymPred and SymPsiPred have the potential to achieve higher accuracy as the number of protein sequences in the NCBInr and PDB databases increases.

Conclusions

Our experiment results show that local similarities in protein sequences typically exhibit conserved structures, which can be used to improve the accuracy of secondary structure prediction. For the application of synonymous words, we demonstrate an example of a sequence alignment which is generated by the distribution of shared synonymous words of a pair of protein sequences. We can align the two sequences nearly perfectly which are very dissimilar at the sequence level but very similar at the structural level. The SymPred and SymPsiPred prediction servers are available at http://bio-cluster.iis.sinica.edu.tw/SymPred/.
UPS 2.0: unique probe selector for probe design and oligonucleotide microarrays at the pangenomic/ genomic level
Authors: Chen Shu-Hwa , Lo Chen-Zen , Su Sheng-Yao , Kuo Bao-Han , Hsiung Chao A , Lin Chung-Yen
Published: December 2010

Background

Nucleic acid hybridization is an extensively adopted principle in biomedical research, in which the performance of any hybridization-based method depends on the specificity of probes to their targets. To determine the optimal probe(s) for detecting target(s) from a sample cocktail, we developed a novel algorithm, which has been implemented into a web platform for probe designing. This probe design workflow is now upgraded to satisfy experiments that require a probe designing tool to take the increasing volume of sequence datasets.

Results

Algorithms and probe parameters applied in UPS 2.0 include GC content, the secondary structure, melting temperature (Tm), the stability of the probe-target duplex estimated by the thermodynamic model, sequence complexity, similarity of probes to non-target sequences, and other empirical parameters used in the laboratory. Several probe background options,
Unique probe within a group

,

Unique probe in a specific Unigene set

,

Unique probe based onthe pangenomic level

, and
Unique Probe in the user-defined genome/transcriptome

, are available to meet the scenarios that the experiments will be conducted. Parameters, such as salt concentration and the lower-bound Tm of probes, are available for users to optimize their probe design query. Output files are available for download on the result page. Probes designed by the UPS algorithm are suitable for generating microarrays, and the performance of UPS-designed probes has been validated by experiments.

Conclusions

The UPS 2.0 evaluates probe-to-target hybridization under a user-defined condition to ensure high-performance hybridization with minimal chance of non-specific binding at the pangenomic and genomic levels. The UPS algorithm mimics the target/non-target mixture in an experiment and is very useful in developing diagnostic kits and microarrays. The UPS 2.0 website has had more than 1,300 visits and 360,000 sequences performed the probe designing task in the last 30 months. It is freely accessible at http://array.iis.sinica.edu.tw/ups/.

Screen cast: http://array.iis.sinica.edu.tw/ups/demo/demo.htm
NGSQC: cross-platform quality analysis pipeline for deep sequencing data
Authors: Dai Manhong , Thompson Robert C , Maher Christopher , Contreras-Galindo Rafael , Kaplan Mark H , Markovitz David M , Omenn Gil , Meng Fan
Published: December 2010

Background

While the accuracy and precision of deep sequencing data is significantly better than those obtained by the earlier generation of hybridization-based high throughput technologies, the digital nature of deep sequencing output often leads to unwarranted confidence in their reliability.

Results

The NGSQC (N ext G eneration S equencing Q uality C ontrol) pipeline provides a set of novel quality control measures for quickly detecting a wide variety of quality issues in deep sequencing data derived from two dimensional surfaces, regardless of the assay technology used. It also enables researchers to determine whether sequencing data related to their most interesting biological discoveries are caused by sequencing quality issues.

Conclusions

Next generation sequencing platforms have their own share of quality issues and there can be significant lab-to-lab, batch-to-batch and even within chip/slide variations. NGSQC can help to ensure that biological conclusions, in particular those based on relatively rare sequence alterations, are not caused by low quality sequencing.
Discovery and characterization of medaka miRNA genes by next generation sequencing platform
Authors: Li Sung-Chou , Chan Wen-Ching , Ho Meng-Ru , Tsai Kuo-Wang , Hu Ling-Yueh , Lai Chun-Hung , Hsu Chun-Nan , Hwang Pung-Pung , Lin Wen-chang
Published: December 2010

Background

MicroRNAs (miRNAs) are endogenous non-protein-coding RNA genes which exist in a wide variety of organisms, including animals, plants, virus and even unicellular organisms. Medaka (Oryzias latipes) is a useful model organism among vertebrate animals. However, no medaka miRNAs have been investigated systematically. It is beneficial to conduct a genome-wide miRNA discovery study using the next generation sequencing (NGS) technology, which has emerged as a powerful sequencing tool for high-throughput analysis.

Results

In this study, we adopted ABI SOLiD platform to generate small RNA sequence reads from medaka tissues, followed by mapping these sequence reads back to medaka genome. The mapped genomic loci were considered as candidate miRNAs and further processed by a support vector machine (SVM) classifier. As result, we identified 599 novel medaka pre-miRNAs, many of which were found to encode more than one isomiRs. Besides, additional minor miRNAs (also called miRNA star) can be also detected with the improvement of sequencing depth. These quantifiable isomiRs and minor miRNAs enable us to further characterize medaka miRNA genes in many aspects. First of all, many medaka candidate pre-miRNAs position close to each other, forming many miRNA clusters, some of which are also conserved across other vertebrate animals. Secondly, during miRNA maturation, there is an arm selection preference of mature miRNAs within precursors. We observed the differences on arm selection preference between our candidate pre-miRNAs and their orthologous ones. We classified these differences into three categories based on the distribution of NGS reads. Finally, we also investigated the relationship between conservation status and expression level of miRNA genes. We concluded that the evolutionally conserved miRNAs were usually the most abundant ones.

Conclusions

Medaka is a widely used model animal and usually involved in many biomedical studies, including the ones on development biology. Identifying and characterizing medaka miRNA genes would benefit the studies using medaka as a model organism.
Circulating cytokines, chemokines and adhesion molecules in normal pregnancy and preeclampsia determined by multiplex suspension array
Authors: Szarka András , Rigó János , Lázár Levente , Bekő Gabriella , Molvarec Attila
Published: December 2010

Background

Preeclampsia is a severe complication of pregnancy characterized by an excessive maternal systemic inflammatory response with activation of both the innate and adaptive arms of the immune system. Cytokines, chemokines and adhesion molecules are central to innate and adaptive immune processes. The purpose of this study was to determine circulating levels of cytokines, chemokines and adhesion molecules in normal pregnancy and preeclampsia in a comprehensive manner, and to investigate their relationship to the clinical features and laboratory parameters of the study participants, including markers of overall inflammation (C-reactive protein), endothelial activation (von Willebrand factor antigen) and endothelial injury (fibronectin), oxidative stress (malondialdehyde) and trophoblast debris (cell-free fetal DNA).

Results

Serum levels of interleukin (IL)-1beta, IL-1 receptor antagonist (IL-1ra), IL-2, IL-4, IL-6, IL-8, IL-10, IL-12p40, IL-12p70, IL-18, interferon (IFN)-gamma, tumor necrosis factor (TNF)-alpha, transforming growth factor (TGF)-beta1, interferon-gamma-inducible protein (IP)-10, monocyte chemotactic protein (MCP)-1, intercellular adhesion molecule (ICAM)-1 and vascular cell adhesion molecule (VCAM)-1 were measured in 60 preeclamptic patients, 60 healthy pregnant women and 59 healthy non-pregnant women by multiplex suspension array and ELISA. In normal pregnancy, the relative abundance of circulating IL-18 over IL-12p70 and the relative deficiency of the bioactive IL-12p70 in relation to IL-12p40 might favour Th2-type immunity. Although decreased IL-1ra, TNF-alpha and MCP-1 concentrations of healthy pregnant relative to non-pregnant women reflect anti-inflammatory changes in circulating cytokine profile, their decreased serum IL-10 and increased IP-10 levels might drive pro-inflammatory responses. In addition to a shift towards Th1-type immunity (expressed by the increased IL-2/IL-4 and IFN-gamma/IL-4 ratios), circulating levels of the pro-inflammatory cytokines IL-6 and TNF-alpha, the chemokines IL-8, IP-10 and MCP-1, as well as the adhesion molecules ICAM-1 and VCAM-1, were raised in preeclampsia compared with healthy pregnancy, resulting in an overall pro-inflammatory systemic environment. Increased IP-10, MCP-1, ICAM-1 and VCAM-1 concentrations of preeclamptic patients showed significant correlations with blood pressure values, renal and liver function parameters, as well as with CRP, malondialdehyde, von Willebrand factor antigen and fibronectin levels.

Conclusions

According to our findings, preeclampsia was associated with an overall pro-inflammatory systemic environment. Elevated amounts of pro-inflammatory cytokines, chemokines and adhesion molecules in the maternal circulation might play a central role in the excessive systemic inflammatory response, as well as in the generalized endothelial dysfunction characteristics of the maternal syndrome of preeclampsia.
Merging transcriptomics and metabolomics - advances in breast cancer profiling
Authors: Borgan Eldrid , Sitter Beathe , Lingjærde Ole Christian , Johnsen Hilde , Lundgren Steinar , Bathen Tone F , Sørlie Therese , Børresen-Dale Anne-Lise , Gribbestad Ingrid S
Published: December 2010

Background

Combining gene expression microarrays and high resolution magic angle spinning magnetic resonance spectroscopy (HR MAS MRS) of the same tissue samples enables comparison of the transcriptional and metabolic profiles of breast cancer. The aim of this study was to explore the potential of combining these two different types of information.

Methods

Breast cancer tissue from 46 patients was analyzed by HR MAS MRS followed by gene expression microarrays. Two strategies were used to combine the gene expression and metabolic data; first using multivariate analyses to identify different groups based on gene expression and metabolic data; second correlating levels of specific metabolites to transcripts to suggest new hypotheses of connections between metabolite levels and the underlying biological processes. A parallel study was designed to address experimental issues of combining microarrays and HR MAS MRS.

Results

In the first strategy, using the microarray data and previously reported molecular classification methods, the majority of samples were classified as luminal A. Three subgroups of luminal A tumors were identified based on hierarchical clustering of the HR MAS MR spectra. The samples in one of the subgroups, designated A2, showed significantly lower glucose and higher alanine levels than the other luminal A samples, suggesting a higher glycolytic activity in these tumors. This group was also enriched for genes annotated with Gene Ontology (GO) terms related to cell cycle and DNA repair. In the second strategy, the correlations between concentrations of myo-inositol, glycine, taurine, glycerophosphocholine, phosphocholine, choline and creatine and all transcripts in the filtered microarray data were investigated. GO-terms related to the extracellular matrix were enriched among the genes that correlated the most to myo-inositol and taurine, while cell cycle related GO-terms were enriched for the genes that correlated the most to choline. Additionally, a subset of transcripts was identified to have slightly altered expression after HR MAS MRS and was therefore removed from all other analyses.

Conclusions

Combining transcriptional and metabolic data from the same breast carcinoma sample is feasible and may contribute to a more refined subclassification of breast cancers as well as reveal relations between metabolic and transcriptional levels.

See Commentary: http://www.biomedcentral.com/1741-7015/8/73
Boron neutron capture therapy induces apoptosis of glioma cells through Bcl-2/Bax
Authors: Wang Peng , Zhen Haining , Jiang Xinbiao , Zhang Wei , Cheng Xin , Guo Geng , Mao Xinggang , Zhang Xiang
Published: December 2010

Background

Boron neutron capture therapy (BNCT) is an alternative treatment modality for patients with glioma. The aim of this study was to determine whether induction of apoptosis contributes to the main therapeutic efficacy of BNCT and to compare the relative biological effect (RBE) of BNCT, γ-ray and reactor neutron irradiation.

Methods

The neutron beam was obtained from the Xi'an Pulsed Reactor (XAPR) and γ-rays were obtained from [60Co] γ source of the Fourth Military Medical University (FMMU) in China. Human glioma cells (the U87, U251, and SHG44 cell lines) were irradiated by neutron beams at the XAPR or [60Co] γ-rays at the FMMU with different protocols: Group A included control nonirradiated cells; Group B included cells treated with 4 Gy of [60Co] γ-rays; Group C included cells treated with 8 Gy of [60Co] γ-rays; Group D included cells treated with 4 Gy BPA (p-borono-phenylalanine)-BNCT; Group E included cells treated with 8 Gy BPA-BNCT; Group F included cells irradiated in the reactor for the same treatment period as used for Group D; Group G included cells irradiated in the reactor for the same treatment period as used for Group E; Group H included cells irradiated with 4 Gy in the reactor; and Group I included cells irradiated with 8 Gy in the reactor. Cell survival was determined using the 3-(4,5-dimethylthiazol-2-yl-2,5-diphenyltetrazolium (MTT) cytotoxicity assay. The morphology of cells was detected by Hoechst33342 staining and transmission electron microscope (TEM). The apoptosis rate was detected by flow cytometer (FCM). The level of Bcl-2 and Bax protein was measured by western blot analysis.

Results

Proliferation of U87, U251, and SHG44 cells was much more strongly inhibited by BPA-BNCT than by irradiation with [60Co] γ-rays (P < 0.01). Nuclear condensation was determined using both a fluorescence technique and electron microscopy in all cell lines treated with BPA-BNCT. Furthermore, the cellular apoptotic rates in Group D and Group E treated with BPA-BNCT were significantly higher than those in Group B and Group C irradiated by [60Co] γ-rays (P < 0.01). The clonogenicity of glioma cells was reduced by BPA-BNCT compared with cells treated in the reactor (Group F, G, H, I), and with the control cells (P < 0.01). Upon BPA-BNCT treatment, the Bax level increased in glioma cells, whereas Bcl-2 expression decreased.

Conclusions

Compared with γ-ray and reactor neutron irradiation, a higher RBE can be achieved upon treatment of glioma cells with BNCT. Glioma cell apoptosis induced by BNCT may be related to activation of Bax and downregulation of Bcl-2.
Specific genomic aberrations in primary colorectal cancer are associated with liver metastases
Authors: Bruin Sjoerd C , Klijn Christiaan , Liefers Gerrit-Jan , Braaf Linde M , Joosse Simon A , van Beers Eric H , Verwaal Victor J , Morreau Hans , Wessels Lodewyk F , van Velthuysen Marie-Louise F , Tollenaar Rob AEM , van't Veer Laura J
Published: December 2010

Background

Accurate staging of colorectal cancer (CRC) with clinicopathological parameters is important for predicting prognosis and guiding treatment but provides no information about organ site of metastases. Patterns of genomic aberrations in primary colorectal tumors may reveal a chromosomal signature for organ specific metastases.

Methods

Array Comparative Genomic Hybridization (aCGH) was employed to asses DNA copy number changes in primary colorectal tumors of three distinctive patient groups. This included formalin-fixed, paraffin-embedded tissue of patients who developed liver metastases (LM; n = 36), metastases (PM; n = 37) and a group that remained metastases-free (M0; n = 25).

A novel statistical method for identifying recurrent copy number changes, KC-SMART, was used to find specific locations of genomic aberrations specific for various groups. We created a classifier for organ specific metastases based on the aCGH data using Prediction Analysis for Microarrays (PAM).

Results

Specifically in the tumors of primary CRC patients who subsequently developed liver metastasis, KC-SMART analysis identified genomic aberrations on chromosome 20q. LM-PAM, a shrunken centroids classifier for liver metastases occurrence, was able to distinguish the LM group from the other groups (M0&PM) with 80% accuracy (78% sensitivity and 86% specificity). The classification is predominantly based on chromosome 20q aberrations.

Conclusion

Liver specific CRC metastases may be predicted with a high accuracy based on specific genomic aberrations in the primary CRC tumor. The ability to predict the site of metastases is important for improvement of personalized patient management.
The first three years of screening for medium chain acyl-CoA dehydrogenase deficiency (MCADD) by newborn screening ontario
Authors: Kennedy Shelley , Potter Beth K , Wilson Kumanan , Fisher Lawrence , Geraghty Michael , Milburn Jennifer , Chakraborty Pranesh
Published: December 2010

Background

Medium chain acyl-CoA dehydrogenase deficiency (MCADD) is a disorder of mitochondrial fatty acid oxidation and is one of the most common inborn errors of metabolism. Identification of MCADD via newborn screening permits the introduction of interventions that can significantly reduce associated morbidity and mortality. This study reports on the first three years of newborn screening for MCADD in Ontario, Canada.

Methods

Newborn Screening Ontario began screening for MCADD in April 2006, by quantification of acylcarnitines (primarily octanoylcarnitine, C8) in dried blood spots using tandem mass spectrometry. Babies with positive screening results were referred to physicians at one of five regional Newborn Screening Treatment Centres, who were responsible for diagnostic evaluation and follow-up care.

Results

From April 2006 through March 2009, approximately 439 000 infants were screened for MCADD in Ontario. Seventy-four infants screened positive, with a median C8 level of 0.68 uM (range 0.33-30.41 uM). Thirty-one of the screen positive infants have been confirmed to have MCADD, while 36 have been confirmed to be unaffected. Screening C8 levels were higher among infants with MCADD (median 8.93 uM) compared to those with false positive results (median 0.47 uM). Molecular testing was available for 29 confirmed cases of MCADD, 15 of whom were homozygous for the common c.985A > G mutation. Infants homozygous for the common mutation tended to have higher C8 levels (median 12.13 uM) relative to compound heterozygotes for c.985A > G and a second detectable mutation (median 2.01 uM). Eight confirmed mutation carriers were identified among infants in the false positive group. The positive predictive value of a screen positive for MCADD was 46%. The estimated birth prevalence of MCADD in Ontario is approximately 1 in 14 000.

Conclusions

The birth prevalence of MCADD and positive predictive value of the screening test were similar to those identified by other newborn screening programs internationally. We observed some evidence of correlation between genotype and biochemical phenotype (C8 levels), and between C8 screening levels and eventual diagnosis. Current research priorities include further examining the relationships among genotype, biochemical phenotype, and clinical phenotype, with the ultimate goal of improving clinical risk prediction in order to provide tailored disease management advice and genetic counselling to families.
Signal transducer and activator of transcription 3 activation up-regulates interleukin-6 autocrine production: a biochemical and genetic study of established cancer cell lines and clinical isolated human cancer cells
Authors: Huang Wei-Lun , Yeh Hsuan-Heng , Lin Chien-Chung , Lai Wu-Wei , Chang Jang-Yang , Chang Wen-Tsan , Su Wu-Chou
Published: December 2010

Background

Spontaneous interleukin-6 (IL-6) production has been observed in various tumors and implicated in the pathogenesis, progression and drug resistance in cancer. However, the regulation of IL-6 autocrine production in cancer cells is not fully understood. IL-6 is auto-regulated in many types of cell. Two of the three major downstream pathways of IL-6, MEK/extracellular signal-related kinase (Erk) pathway and phosphatidylinositol 3-kinase (PI3-K)/Akt pathway, have been shown to regulate IL-6 expression through the activation of AP-1 and NF-κB. However, it is not clear what the role of Janus kinase (Jak) 2/signal transducer and activator of transcription (Stat) 3 pathway. This study was designed to determine the role of Jak2/Stat3 pathway in the regulation of IL-6 autocrine production in cancer cells.

Results

Inhibitors of Jak2/Stat3, MEK/Erk and PI3-K/Akt pathways down-regulated IL-6 secretion in the lung adenocarcinoma PC14PE6/AS2 (AS2) cells, which spontaneously secreted IL-6 and possessed constitutively activated Stat3. Transfection with dominant-negative Stat3, Stat3 siRNA, or Stat3 shRNA decreased IL-6 expression in AS2 cells. Conversely, transfection with constitutively-activated Stat3 increased the production of IL-6. In AS2 derived cells, resistance to paclitaxel was positively correlated with Stat3 activation status and the expression of IL-6, which is commonly secreted in drug resistant cancer cells. The pharmacological inhibition of NF-κB, PI3-K/Akt and MEK/Erk and the pharmacological inhibition and genetic inhibition (Stat3 siRNA) of Jak2/Stat3 pathway decreased IL-6 autocrine production in various drug resistant cancer cell lines and similarly decreased IL-6 autocrine production in clinically isolated lung cancer cells.

Conclusions

This study is the first to directly address the role Stat3 plays on the autocrine production of IL-6, which occurs through a positive-feedback loop. Our biochemical and genetic studies clearly demonstrated that Jak2/Stat3, in combination with other IL-6 downstream pathways, contributed frequently and substantially to IL-6 autocrine production in a broad spectrum of cancer cell lines as well as in clinical cancer samples. Our findings suggest that Stat3 could potentially be regulated to suppress IL-6 autocrine production in cancer cells to inhibit the progression of cancer and reduce drug resistance.
Expression of hepatocytic- and biliary-specific transcription factors in regenerating bile ducts during hepatocyte-to-biliary epithelial cell transdifferentiation
Authors: Limaye Pallavi B , Bowen William C , Orr Anne , Apte Udayan M , Michalopoulos George K
Published: December 2010

Background

Under compromised biliary regeneration, transdifferentiation of hepatocytes into biliary epithelial cells (BEC) has been previously observed in rats, upon exposure to BEC-specific toxicant methylene dianiline (DAPM) followed by bile duct ligation (BDL), and in patients with chronic biliary liver disease. However, mechanisms promoting such transdifferentiation are not fully understood. In the present study, acquisition of biliary specific transcription factors by hepatocytes leading to reprogramming of BEC-specific cellular profile was investigated as a potential mechanism of transdifferentiation in two different models of compromised biliary regeneration in rats.

Results

In addition to previously examined DAPM + BDL model, an experimental model resembling chronic biliary damage was established by repeated administration of DAPM. Hepatocyte to BEC transdifferentiation was tracked using dipetidyl dipeptidase IV (DDPIV) chimeric rats that normally carry DPPIV only in hepatocytes. Following DAPM treatment, ~20% BEC population turned DPPIV-positive, indicating that they are derived from DPPIV-positive hepatocytes. New ductules emerging after DAPM + BDL and repeated DAPM exposure expressed hepatocyte-associated transcription factor hepatocyte nuclear factor (HNF) 4α and biliary specific transcription factor HNF1β. In addition, periportal hepatocytes expressed biliary marker CK19 suggesting periportal hepatocytes as a potential source of transdifferentiating cells. Although TGFβ1 was induced, there was no considerable reduction in periportal HNF6 expression, as observed during embryonic biliary development.

Conclusions

Taken together, these findings indicate that gradual loss of HNF4α and acquisition of HNF1β by hepatocytes, as well as increase in TGFβ1 expression in periportal region, appear to be the underlying mechanisms of hepatocyte-to-BEC transdifferentiation.
The G Protein regulators EGL-10 and EAT-16, the Giα GOA-1 and the Gqα EGL-30 modulate the response of the C. elegansASH polymodal nociceptive sensory neurons to repellents
Authors: Esposito Giovanni , Amoroso Maria R , Bergamasco Carmela , Di Schiavi Elia , Bazzicalupo Paolo
Published: December 2010

Background

Polymodal, nociceptive sensory neurons are key cellular elements of the way animals sense aversive and painful stimuli. In Caenorhabditis elegans, the polymodal nociceptive ASH sensory neurons detect aversive stimuli and release glutamate to generate avoidance responses. They are thus useful models for the nociceptive neurons of mammals. While several molecules affecting signal generation and transduction in ASH have been identified, less is known about transmission of the signal from ASH to downstream neurons and about the molecules involved in its modulation.

Results

We discovered that the regulator of G protein signalling (RGS) protein, EGL-10, is required for appropriate avoidance responses to noxious stimuli sensed by ASH. As it does for other behaviours in which it is also involved, egl-10 interacts genetically with the Go/iα protein GOA-1, the Gqα protein EGL-30 and the RGS EAT-16. Genetic, behavioural and Ca2+ imaging analyses of ASH neurons in live animals demonstrate that, within ASH, EGL-10 and GOA-1 act downstream of stimulus-evoked signal transduction and of the main transduction channel OSM-9. EGL-30 instead appears to act upstream by regulating Ca2+ transients in response to aversive stimuli. Analysis of the delay in the avoidance response, of the frequency of spontaneous inversions and of the genetic interaction with the diacylglycerol kinase gene, dgk-1, indicate that EGL-10 and GOA-1 do not affect signal transduction and neuronal depolarization in response to aversive stimuli but act in ASH to modulate downstream transmission of the signal.

Conclusions

The ASH polymodal nociceptive sensory neurons can be modulated not only in their capacity to detect stimuli but also in the efficiency with which they respond to them. The Gα and RGS molecules studied in this work are conserved in evolution and, for each of them, mammalian orthologs can be identified. The discovery of their role in the modulation of signal transduction and signal transmission of nociceptors may help us to understand how pain is generated and how its control can go astray (such as chronic pain) and may suggest new pain control therapies.
Detection of porcine parvovirus using a taqman-based real-time pcr with primers and probe designed for the NS1 gene
Authors: Song Cuiping , Zhu Chao , Zhang Chaofan , Cui Shangjin
Published: December 2010

A TaqMan-based real-time polymerase chain reaction (PCR) assay was devised for the detection of porcine parvovirus (PPV). Two primers and a TaqMan probe for the non-structural protein NS1 gene were designed. The detection limit was 1 × 102 DNA copies/μL, and the assay was linear in the range of 1 × 102 to 1 × 109 copies/μL. There was no cross-reaction with porcine circovirus 2 (PCV2), porcine reproductive and respiratory syndrome virus (PRRSV), pseudorabies virus (PRV), classical swine fever virus (CSFV), or Japanese encephalitis virus (JEV). The assay was specific and reproducible. In 41 clinical samples, PPV was detected in 32 samples with the real-time PCR assay and in only 11 samples with a conventional PCR assay. The real-time assay using the TaqMan-system can therefore be practically used for studying the epidemiology and management of PPV.
The variability of naturally occurring magnetic field levels: 10 Hz to 8 kHz
Authors: Sternberg Ben K.
Published: December 2010

The variability of naturally occurring magnetic fields in the frequency range from [Formula: see text] over a period of one year was studied. Contour plots for the [Formula: see text], [Formula: see text], and [Formula: see text] components and for frequencies of 10, 100, 1000, 2000, and 8000 Hz were produced. Average, minimum, maximum, and the standard deviations of these fields were also calculated for 12 distinctive time intervals. In the 1– to 8–kHz frequency range, the noise levels are typically higher at night. In the 10- to 100-Hz frequency range, the noise levels are typically higher during the day. During mid- to late-summer, there is frequent thunderstorm activity, known in the southwest United States as the monsoon season. The magnetic field levels are often very high during this time period. These variability ranges can be used to estimate the lowest levels of noise that may be encountered during field surveys, which iswhat the authors are looking for when running controlled-source electrical method surveys. These variability ranges can also be used to estimate the highest levels that may be encountered, which is what the authors are looking for when running natural-source electrical methods surveys, such as audio frequency magnetotelluric (AMT) surveys. These measurements of magnetic field strength variability show that better data for controlled-source electrical measurements can be obtained using the minimum noise level measurements, as opposed to using signal integration or signal averaging with all of the data. The minimum noise level is found by using frequency bins adjacent to the signal-frequency bin. Likewise, if one is interested in measuring the naturally occurring magnetic field data, using the maximum values during each time interval makes AMT measurements possible when the natural signal level is very low, particularly in the AMT dead zone around [Formula: see text].
Velocity estimation by image-focusing analysis
Authors: Biondi Biondo
Published: December 2010

Migration velocity can be estimated from seismic data by analyzing, focusing, and defocusing of residual-migrated images. The accuracy of these velocity estimates is limited by the inherent ambiguity between velocity and reflector curvature. However, velocity resolution improves when reflectors with different curvatures are present. Image focusing is measured by evaluating coherency across structural dips, in addition to coherency across aperture/azimuth angles. The inherent ambiguity between velocity and reflector curvature is directly tackled by introducing a curvature correction into the computation of the semblance functional that estimates image coherency. The resulting velocity estimator provides velocity estimates that are (1) unbiased by reflector curvature and (2) consistent with the velocity information that is routinely obtained by measuring coherency over aperture/azimuth angles. Applications to a 2D synthetic prestack data set and a 2D field prestack data set confirm that the proposed method provides consistent and unbiased velocity information. They also suggest that velocity estimates based on the new image-focusing semblance may be more robust and have higher resolution than estimates based on conventional semblance functionals. Applying the proposed method to zero-offset field data recorded in New York Harbor yields a velocity function that is consistent with available geologic information and clearly improves the focusing of the reflectors.
Treatment of Obstructive Sleep Apnea Improves Cardiometabolic Function in Young Obese Women with Polycystic Ovary Syndrome
Authors: Tasali Esra , Chapotot Florian , Leproult Rachel , Whitmore Harry , Ehrmann David A.
Published: December 2010

abstract

Context:

Women with polycystic ovary syndrome (PCOS) are insulin resistant and have a high risk of early-onset diabetes and cardiovascular disease. Obstructive sleep apnea (OSA) has adverse cardiometabolic consequences and is highly prevalent in women with PCOS. We sought to determine whether continuous positive airway pressure (CPAP) treatment of OSA has beneficial effects on cardiometabolic function in PCOS.

Methods:

Laboratory polysomnography and cardiometabolic measurements including insulin sensitivity and secretion (iv glucose tolerance test); 24-h profiles of plasma catecholamines, cortisol, and leptin; and daytime profiles of blood pressure and cardiac autonomic activity (heart rate variability) were obtained at baseline and again after 8 wk of home CPAP treatment with daily usage monitoring.

Results:

CPAP treatment modestly improved insulin sensitivity after controlling for body mass index (P = 0.013). The change in insulin sensitivity correlated positively with CPAP use (adjusted P = 0.027) and negatively with body mass index (adjusted P = 0.003). Daytime and nighttime norepinephrine levels were decreased after CPAP (P = 0.002), and the reductions were greater with increased CPAP use (P = 0.03). Epinephrine, cortisol, and leptin levels were not changed significantly. Daytime diastolic blood pressure decreased by an average of 2.3 mm Hg after CPAP (P = 0.035). Cardiac sympathovagal balance was 44% lower (P = 0.007) after CPAP, reflecting a shift toward lower sympathetic activity.

Conclusions:

In young obese women with PCOS, successful treatment of OSA improves insulin sensitivity, decreases sympathetic output, and reduces diastolic blood pressure. The magnitude of these beneficial effects is modulated by the hours of CPAP use and the degree of obesity.
Liver Fat But Not Other Adiposity Measures Influence Circulating FGF21 Levels in Healthy Young Adult Twins
Authors: Tyynismaa Henna , Raivio Taneli , Hakkarainen Antti , Ortega-Alonso Alfredo , Lundbom Nina , Kaprio Jaakko , Rissanen Aila , Suomalainen Anu , Pietiläinen Kirsi H.
Published: December 2010

abstract

Context:

Emerging as an important metabolic regulator, fibroblast growth factor 21 (FGF21) has gained considerable interest in diabetes and obesity research. The circulating FGF21 concentration is fairly low in normal individuals, but elevated hormone levels may associate with obesity. The determining factors of FGF21 levels in humans are not clear.

Objective:

Our objective was to study the influence of genetic and acquired components to serum FGF21 variability in healthy young adult twins.

Design and Participants:

Fasting serum FGF21, lipids, body fat, and oral glucose tolerance test were investigated in 46 monozygotic (MZ) and 75 dizygotic twin pairs aged 22.8–33.1 yr. Subcutaneous, intraabdominal, and liver fat content were measured by magnetic resonance imaging/spectroscopy in a subsample of 24 MZ pairs.

Results:

Genetic factors contributed moderately (heritability 40%) to circulating serum FGF21 levels. Subjects with high FGF21 concentrations (≥ 250 pg/ml, n = 30) had higher fasting triglycerides, insulin, homeostasis model assessment index, and area under the curve glucose and lower high-density lipoprotein cholesterol but similar measures of overall adiposity (body mass index, body fat percent) than subjects with lower FGF21 (<100 pg/ml, n = 148). Importantly, in the MZ subsample, higher liver fat but not sc or intraabdominal fat content was found in subjects with high FGF21. Furthermore, in analyses controlling for genetic/familial effects in twin pairs, within-pair differences in liver fat (MZ) and triglycerides (dizygotic pairs) were the major acquired factors that correlated with differences in FGF21 concentrations.

Conclusions:

Genetic factors influence serum FGF21 levels. Of the acquired components, high liver fat and triglycerides rather than overall adiposity associate with high FGF21 levels.
MMP9 is protective against lethal inflammatory mass lesions in the mouse colon
Authors: Hald Andreas , Rønø Birgitte , Melander Maria C. , Ding Ming , Holck Susanne , Lund Leif R.
Published: December 2010

The family of matrix metalloproteinases (MMPs) is responsible for extracellular matrix degradation during physiological and pathophysiological tissue remodeling processes such as embryogenesis, tissue repair and cancer progression. Despite these important roles of MMPs, inhibition or ablation of individual members of the MMP family in animal models have been shown to have little effect. It has been speculated that this results from a functional overlap between individual MMPs and (as-yet-unclassified) functional overlaps between MMPs and other protease systems. We here present genetic data showing that concomitant ablation of MMP9 (gelatinase B) and the serine protease plasmin results in lethal inflammatory mass lesions in the colon. These lesions possessed several histological attributes that are characteristic of mucosal prolapse seen in humans, and they were found to be associated with splenomegaly, enlarged mesenteric lymph nodes, decreased thymus size and altered populations of circulating immune cells. A time-course study provided evidence that the massive lymphoid hyperplasia and reactive changes were secondary to discrete fibrinous lesions also observed in mice only deficient for plasminogen (Plg), the zymogen for plasmin. These data demonstrate a non-appreciated vital protective role for MMP9 in the absence of Plg.
Degeneration and regeneration of the intervertebral disc: lessons from development
Authors: Smith Lachlan J. , Nerurkar Nandan L. , Choi Kyung-Suk , Harfe Brian D. , Elliott Dawn M.
Published: December 2010

Degeneration of the intervertebral discs, a process characterized by a cascade of cellular, biochemical, structural and functional changes, is strongly implicated as a cause of low back pain. Current treatment strategies for disc degeneration typically address the symptoms of low back pain without treating the underlying cause or restoring mechanical function. A more in-depth understanding of disc degeneration, as well as opportunities for therapeutic intervention, can be obtained by considering aspects of intervertebral disc development. Development of the intervertebral disc involves the coalescence of several different cell types through highly orchestrated and complex molecular interactions. The resulting structures must function synergistically in an environment that is subjected to continuous mechanical perturbation throughout the life of an individual. Early postnatal changes, including altered cellularity, vascular regression and altered extracellular matrix composition, might set the disc on a slow course towards symptomatic degeneration. In this Perspective, we review the pathogenesis and treatment of intervertebral disc degeneration in the context of disc development. Within this scope, we examine how model systems have advanced our understanding of embryonic morphogenesis and associated molecular signaling pathways, in addition to the postnatal changes to the cellular, nutritional and mechanical microenvironment. We also discuss the current status of biological therapeutic strategies that promote disc regeneration and repair, and how lessons from development might provide clues for their refinement.