bluuebunny/crossref_metadata_2025 huggingface dataset:
Fish-on-a-chip: a sensitive detection microfluidic system for alzheimer's disease
Authors: Devadhasan Jasmine P , Kim Sanghyo , An Jeongho
Published: May 2011

Microfluidics has become an important tool in diagnosing many diseases, including neurological and genetic disorders. Alzheimer's disease (AD) is a neurodegenerative disease that irreversibly and progressively destroys memory, language ability, and thinking skills. Commonly, detection of AD is expensive and complex. Fluorescence in situ hybridization (FISH)-based microfluidic chip platform is capable of diagnosing AD at an early stage and they are effective tools for the diagnosis with low cost, high speed, and high sensitivity. In this review, we tried to provide basic information on the diagnosis of AD via FISH-based microfluidics. Different sample preparations using a microfluidic chip for diagnosis of AD are highlighted. Moreover, rapid innovations in nanotechnology for diagnosis are explained. This review will provide information on dynamic quantification methods for the diagnosis and treatment of AD. The knowledge provided in this review will help develop new integration diagnostic techniques based on FISH and microfluidics.
Binding of ATP to vascular endothelial growth factor isoform VEGF-A165 is essential for inducing proliferation of human umbilical vein endothelial cells
Authors: Gast Ronald E , König Simone , Rose Karsten , Ferenz Katja B , Krieglstein Josef
Published: May 2011

Background

ATP binding is essential for the bioactivity of several growth factors including nerve growth factor, fibroblast growth factor-2 and brain-derived neurotrophic factor. Vascular endothelial growth factor isoform 165 (VEGF-A165) induces the proliferation of human umbilical vein endothelial cells, however a dependence on ATP-binding is currently unknown. The aim of the present study was to determine if ATP binding is essential for the bioactivity of VEGF-A165.

Results

We found evidence that ATP binding toVEGF-A165induced a conformational change in the secondary structure of the growth factor. This binding appears to be significant at the biological level, as we found evidence that nanomolar levels of ATP (4-8 nm) are required for the VEGF-A165-induced proliferation of human umbilical vein endothelial cells. At these levels, purinergic signaling by ATPviaP2 receptors can be excluded. Addition of alkaline phosphate to cell culture lowered the ATP concentration in the cell culture medium to 1.8 nM and inhibited cell proliferation.

Conclusions

We propose that proliferation of endothelial cells is induced by a VEGF-A165-ATP complex, rather than VEGF-A165alone.
Structator: fast index-based search for RNA sequence-structure patterns
Authors: Meyer Fernando , Kurtz Stefan , Backofen Rolf , Will Sebastian , Beckstette Michael
Published: May 2011

Background

The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence-structure patterns. Unfortunately, current tools for this task have, in the best case, a running time that is only linear in the size of sequence databases. Furthermore, established index data structures for fast sequence matching, like suffix trees or arrays, cannot benefit from the complementarity constraints introduced by the secondary structure of RNAs.

Results

We present a novel method and readily applicable software for time efficient matching of RNA sequence-structure patterns in sequence databases. Our approach is based on affix arrays, a recently introduced index data structure, preprocessed from the target database. Affix arrays support bidirectional pattern search, which is required for efficiently handling the structural constraints of the pattern. Structural patterns like stem-loops can be matched inside out, such that the loop region is matched first and then the pairing bases on the boundaries are matched consecutively. This allows to exploit base pairing information for search space reduction and leads to an expected running time that is sublinear in the size of the sequence database. The incorporation of a new chaining approach in the search of RNA sequence-structure patterns enables the description of molecules folding into complex secondary structures with multiple ordered patterns. The chaining approach removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our method runs up to two orders of magnitude faster than previous methods.

Conclusions

The presented method's sublinear expected running time makes it well suited for RNA sequence-structure pattern matching in large sequence databases. RNA molecules containing several stem-loop substructures can be described by multiple sequence-structure patterns and their matches are efficiently handled by a novel chaining method. Beyond our algorithmic contributions, we provide with Structator a complete and robust open-source software solution for index-based search of RNA sequence-structure patterns. The Structator software is available at http://www.zbh.uni-hamburg.de/Structator.
A Beta-mixture model for dimensionality reduction, sample classification and analysis
Authors: Laurila Kirsti , Oster Bodil , Andersen Claus L , Lamy Philippe , Orntoft Torben , Yli-Harja Olli , Wiuf Carsten
Published: May 2011

Background

Patterns of genome-wide methylation vary between tissue types. For example, cancer tissue shows markedly different patterns from those of normal tissue. In this paper we propose a beta-mixture model to describe genome-wide methylation patterns based on probe data from methylation microarrays. The model takes dependencies between neighbour probe pairs into account and assumes three broad categories of methylation, low, medium and high. The model is described by 37 parameters, which reduces the dimensionality of a typical methylation microarray significantly. We used methylation microarray data from 42 colon cancer samples to assess the model.

Results

Based on data from colon cancer samples we show that our model captures genome-wide characteristics of methylation patterns. We estimate the parameters of the model and show that they vary between different tissue types. Further, for each methylation probe the posterior probability of a methylation state (low, medium or high) is calculated and the probability that the state is correctly predicted is assessed. We demonstrate that the model can be applied to classify cancer tissue types accurately and that the model provides accessible and easily interpretable data summaries.

Conclusions

We have developed a beta-mixture model for methylation microarray data. The model substantially reduces the dimensionality of the data. It can be used for further analysis, such as sample classification or to detect changes in methylation status between different samples and tissues.
miRFam: an effective automatic miRNA classification method based on n-grams and a multiclass SVM
Authors: Ding Jiandong , Zhou Shuigeng , Guan Jihong
Published: May 2011

Background

MicroRNAs (miRNAs) are ~22 nt long integral elements responsible for post-transcriptional control of gene expressions. After the identification of thousands of miRNAs, the challenge is now to explore their specific biological functions. To this end, it will be greatly helpful to construct a reasonable organization of these miRNAs according to their homologous relationships. Given an established miRNA family system (e.g. the miRBase family organization), this paper addresses the problem of automatically and accurately classifying newly found miRNAs to their corresponding families by supervised learning techniques. Concretely, we propose an effective method, miRFam, which uses only primary information of pre-miRNAs or mature miRNAs and a multiclass SVM, to automatically classify miRNA genes.

Results

An existing miRNA family system prepared by miRBase was downloaded online. We first employed n-grams to extract features from known precursor sequences, and then trained a multiclass SVM classifier to classify new miRNAs (i.e. their families are unknown). Comparing with miRBase's sequence alignment and manual modification, our study shows that the application of machine learning techniques to miRNA family classification is a general and more effective approach. When the testing dataset contains more than 300 families (each of which holds no less than 5 members), the classification accuracy is around 98%. Even with the entire miRBase15 (1056 families and more than 650 of them hold less than 5 samples), the accuracy surprisingly reaches 90%.

Conclusions

Based on experimental results, we argue that miRFam is suitable for application as an automated method of family classification, and it is an important supplementary tool to the existing alignment-based small non-coding RNA (sncRNA) classification methods, since it only requires primary sequence information.

Availability

The source code of miRFam, written in C++, is freely and publicly available at: http://admis.fudan.edu.cn/projects/miRFam.htm.
The evolutionary history of the SAL1 gene family in eutherian mammals
Authors: Meslin Camille , Brimau Fanny , Meillour Patricia Nagnan-Le , Callebaut Isabelle , Pascal Géraldine , Monget Philippe
Published: May 2011

Background

SAL1 (salivary lipocalin) is a member of the OBP (Odorant Binding Protein) family and is involved in chemical sexual communication in pig. SAL1 and its relatives may be involved in pheromone and olfactory receptor binding and in pre-mating behaviour. The evolutionary history and the selective pressures acting on SAL1 and its orthologous genes have not yet been exhaustively described. The aim of the present work was to study the evolution of these genes, to elucidate the role of selective pressures in their evolution and the consequences for their functions.

Results

Here, we present the evolutionary history of SAL1 gene and its orthologous genes in mammals. We found that (1) SAL1 and its related genes arose in eutherian mammals with lineage-specific duplications in rodents, horse and cow and are lost in human, mouse lemur, bushbaby and orangutan, (2) the evolution of duplicated genes of horse, rat, mouse and guinea pig is driven by concerted evolution with extensive gene conversion events in mouse and guinea pig and by positive selection mainly acting on paralogous genes in horse and guinea pig, (3) positive selection was detected for amino acids involved in pheromone binding and amino acids putatively involved in olfactory receptor binding, (4) positive selection was also found for lineage, indicating a species-specific strategy for amino acid selection.

Conclusions

This work provides new insights into the evolutionary history of SAL1 and its orthologs. On one hand, some genes are subject to concerted evolution and to an increase in dosage, suggesting the need for homogeneity of sequence and function in certain species. On the other hand, positive selection plays a role in the diversification of the functions of the family and in lineage, suggesting adaptive evolution, with possible consequences for speciation and for the reinforcement of prezygotic barriers.
Molecular evolution of the vertebrate TLR1 gene family - a complex history of gene duplication, gene conversion, positive selection and co-evolution
Authors: Huang Yinhua , Temperley Nicholas D , Ren Liming , Smith Jacqueline , Li Ning , Burt David W
Published: May 2011

Background

The Toll-like receptors represent a large superfamily of type I transmembrane glycoproteins, some common to a wide range of species and others are more restricted in their distribution. Most members of the Toll-like receptor superfamily have few paralogues; the exception is the TLR1 gene family with four closely related genes in mammals TLR1, TLR2, TLR6 and TLR10, and four in birds TLR1A, TLR1B, TLR2A and TLR2B. These genes were previously thought to have arisen by a series of independent gene duplications. To understand the evolutionary pattern of the TLR1 gene family in vertebrates further, we cloned the sequences of TLR1A, TLR1B, TLR2A and TLR2B in duck and turkey, constructed phylogenetic trees, predicted codons under positive selection and identified co-evolutionary amino acid pairs within the TLR1 gene family using sequences from 4 birds, 28 mammals, an amphibian and a fish.

Results

This detailed phylogenetic analysis not only clarifies the gene gains and losses within the TLR1 gene family of birds and mammals, but also defines orthologues between these vertebrates. In mammals, we predict amino acid sites under positive selection in TLR1, TLR2 and TLR6 but not TLR10. We detect co-evolution between amino acid residues in TLR2 and the other members of this gene family predicted to maintain their ability to form functional heterodimers. In birds, we predict positive selection in the TLR2A and TLR2B genes at functionally significant amino acid residues. We demonstrate that the TLR1 gene family has mostly been subject to purifying selection but has also responded to directional selection at a few sites, possibly in response to pathogen challenge.

Conclusions

Our phylogenetic and structural analyses of the vertebrate TLR1 family have clarified their evolutionary origins and predict amino acid residues likely to be important in the host's defense against invading pathogens.
Cytoplasm affects grain weight and filled-grain ratio in indica rice
Authors: Tao Dayun , Xu Peng , Zhou Jiawu , Deng Xianneng , Li Jing , Deng Wei , Yang Jiangyi , Yang Guifeng , Li Qiong , Hu Fengyi
Published: June 2011

Background

Cytoplasmic effects on agronomic traits -involving cytoplasmic and nuclear genomes of either different species or different cultivars - are well documented in wheat but have seldom been demonstrated in rice (Oryza sativa L.). To detect cytoplasmic effects, we introgressed the nuclear genomes of three indica cultivars - Guichao 2, Jiangchengkugu, and Dianrui 449 - into the cytoplasms of six indica cultivars - Dijiaowujian, Shenglixian, Zhuzhan, Nantehao, Aizizhan, and Peta. These 18 nuclear substitution lines were evaluated during the winter season of 2005 in Sanya, Hainan, China, and during the summer season of 2006 in Kunming, Yunnan, China. The effects of 6 cytoplasm sources, 3 nucleus sources, 2 locations and their interactions were estimated for plant height, panicle length, panicle number per plant, spikelet number per panicle, grain weight, filled-grain ratio, and yield per plot.

Results

For five of the seven traits, analysis of variance showed that there were no significant cytoplasmic effects or interactions involving cytoplasmic effects. The effect of cytoplasm on 1000-grain weight was highly significant. Mean 1000-grain weight over the two locations in four of the six cytoplasms clustered close to the overall mean, whereas plants with Nantehao cytoplasm had a high, and those with Peta cytoplasm a low mean grain weight. There was a highly significant three-way interaction affecting filled-grain ratio. At Sanya, cytoplasms varied in very narrow ranges within nuclear backgrounds. Strong cytoplasmic effects were observed only at Kunming and in only two of the three nuclear backgrounds; in the Jianchenkugu nuclear background, there was no evidence of strong cytoplasmic effects at either location. In the Dianrui 449 and Guichao 2 nuclear background evaluated at Kunming, filled-grain ratios of the six cytoplasms showed striking rank shifts

Conclusions

We detected cytoplasmic variation for two agronomically important traits in indica rice. The cytoplasm source had a significant effect on grain weight across the two experimental locations. There was also a significant cytoplasmic effect on filled-grain ratio, but only in two of three nuclear background and at one of the two locations. The results extend our previous findings with japonica rice, suggesting that the selection of appropriate cytoplasmic germplasm is broadly important in rice breeding, and that cytoplasmic effects on some traits, such as filled-grain ratio, cannot be generalized; effects should be evaluated in the nuclear backgrounds of interest and at multiple locations.
The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation
Authors: Portnoy Thomas , Margeot Antoine , Linke Rita , Atanasova Lea , Fekete Erzsébet , Sándor Erzsébet , Hartl Lukas , Karaffa Levente , Druzhinina Irina S , Seiboth Bernhard , Le Crom Stéphane , Kubicek Christian P
Published: May 2011

Background

The identification and characterization of the transcriptional regulatory networks governing the physiology and adaptation of microbial cells is a key step in understanding their behaviour. One such wide-domain regulatory circuit, essential to all cells, is carbon catabolite repression (CCR): it allows the cell to prefer some carbon sources, whose assimilation is of high nutritional value, over less profitable ones. In lower multicellular fungi, the C2H2 zinc finger CreA/CRE1 protein has been shown to act as the transcriptional repressor in this process. However, the complete list of its gene targets is not known.

Results

Here, we deciphered the CRE1 regulatory range in the model cellulose and hemicellulose-degrading fungus Trichoderma reesei (anamorph of Hypocrea jecorina) by profiling transcription in a wild-type and a delta-cre1 mutant strain on glucose at constant growth rates known to repress and de-repress CCR-affected genes. Analysis of genome-wide microarrays reveals 2.8% of transcripts whose expression was regulated in at least one of the four experimental conditions: 47.3% of which were repressed by CRE1, whereas 29.0% were actually induced by CRE1, and 17.2% only affected by the growth rate but CRE1 independent. Among CRE1 repressed transcripts, genes encoding unknown proteins and transport proteins were overrepresented. In addition, we found CRE1-repression of nitrogenous substances uptake, components of chromatin remodeling and the transcriptional mediator complex, as well as developmental processes.

Conclusions

Our study provides the first global insight into the molecular physiological response of a multicellular fungus to carbon catabolite regulation and identifies several not yet known targets in a growth-controlled environment.
Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding
Authors: Pitts R Jason , Rinker David C , Jones Patrick L , Rokas Antonis , Zwiebel Laurence J
Published: May 2011

Background

Chemosensory signal transduction guides the behavior of many insects, includingAnopheles gambiae, the major vector for human malaria in sub-Saharan Africa. To better understand the molecular basis of mosquito chemosensation we have used whole transcriptome RNA sequencing (RNA-seq) to compare transcript expression profiles between the two major chemosensory tissues, the antennae and maxillary palps, of adult female and maleAn. gambiae.

Results

We compared chemosensory tissue transcriptomes to whole body transcriptomes of each sex to identify chemosensory enhanced genes. In the six data sets analyzed, we detected expression of nearly all known chemosensory genes and found them to be highly enriched in both olfactory tissues of males and females. While the maxillary palps of both sexes demonstrated strict chemosensory gene expression overlap, we observed acute differences in sensory specialization between male and female antennae. The relatively high expression levels of chemosensory genes in the female antennae reveal its role as an organ predominately assigned to chemosensation. Remarkably, the expression of these genes was highly conserved in the male antennae, but at much lower relative levels. Alternatively, consistent with a role in mating, the male antennae displayed significant enhancement of genes involved in audition, while the female enhancement of these genes was observed, but to a lesser degree.

Conclusions

These findings suggest that the chemoreceptive spectrum, as defined by gene expression profiles, is largely similar in female and maleAn. gambiae. However, assuming sensory receptor expression levels are correlated with sensitivity in each case, we posit that male and female antennae are perceptive to the same stimuli, but possess inverse receptive prioritizations and sensitivities. Here we have demonstrated the use of RNA-seq to characterize the sensory specializations of an important disease vector and grounded future studies investigating chemosensory processes.
Retraction Note MicroRNA expression profiling during the life cycle of the silkworm (Bombyx mori)
Authors: Liu Shiping , Zhang Liang , Li Qibin , Zhao Ping , Duan Jun , Cheng Daojun , Xiang Zhonghuai , Xia Qingyou
Published: June 2011

Retraction article
Site-Specific Mobilization of Vinyl Chloride Respiration Islands by a Mechanism Common in Dehalococcoides
Authors: McMurdie Paul J , Hug Laura A , Edwards Elizabeth A , Holmes Susan , Spormann Alfred M
Published: June 2011

Background

Vinyl chloride is a widespread groundwater pollutant and Group 1 carcinogen. A previous comparative genomic analysis revealed that the vinyl chloride reductase operon, vcrABC, of Dehalococcoides sp. strain VS is embedded in a horizontally-acquired genomic island that integrated at the single-copy tmRNA gene, ssrA.

Results

We targeted conserved positions in available genomic islands to amplify and sequence four additional vcrABC -containing genomic islands from previously-unsequenced vinyl chloride respiring Dehalococcoides enrichments. We identified a total of 31 ssrA-specific genomic islands from Dehalococcoides genomic data, accounting for 47 reductive dehalogenase homologous genes and many other non-core genes. Sixteen of these genomic islands contain a syntenic module of integration-associated genes located adjacent to the predicted site of integration, and among these islands, eight contain vcrABC as genetic 'cargo'. These eight vcrABC -containing genomic islands are syntenic across their ~12 kbp length, but have two phylogenetically discordant segments that unambiguously differentiate the integration module from the vcrABC cargo. Using available Dehalococcoides phylogenomic data we estimate that these ssrA-specific genomic islands are at least as old as the Dehalococcoides group itself, which in turn is much older than human civilization.

Conclusions

The vcrABC -containing genomic islands are a recently-acquired subset of a diverse collection of ssrA-specific mobile elements that are a major contributor to strain-level diversity in Dehalococcoides, and may have been throughout its evolution. The high similarity between vcrABC sequences is quantitatively consistent with recent horizontal acquisition driven by ~100 years of industrial pollution with chlorinated ethenes.
LabKey Server NAb: A tool for analyzing, visualizing and sharing results from neutralizing antibody assays
Authors: Piehler Britt , Nelson Elizabeth K , Eckels Josh , Ramsay Sarah , Lum Karl , Wood Blake , Greene Kelli M , Gao Hongmei , Seaman Michael S , Montefiori David C , Igra Mark
Published: May 2011

Background

Multiple types of assays allow sensitive detection of virus-specific neutralizing antibodies. For example, the extent of antibody neutralization of HIV-1, SIV and SHIV can be measured in the TZM-bl cell line through the degree of luciferase reporter gene expression after infection. In the past, neutralization curves and titers for this standard assay have been calculated using an Excel macro. Updating all instances of such a macro with new techniques can be unwieldy and introduce non-uniformity across multi-lab teams. Using Excel also poses challenges in centrally storing, sharing and associating raw data files and results.

Results

We present LabKey Server's NAb tool for organizing, analyzing and securely sharing data, files and results for neutralizing antibody (NAb) assays, including the luciferase-based TZM-bl NAb assay. The customizable tool supports high-throughput experiments and includes a graphical plate template designer, allowing researchers to quickly adapt calculations to new plate layouts. The tool calculates the percent neutralization for each serum dilution based on luminescence measurements, fits a range of neutralization curves to titration results and uses these curves to estimate the neutralizing antibody titers for benchmark dilutions. Results, curve visualizations and raw data files are stored in a database and shared through a secure, web-based interface. NAb results can be integrated with other data sources based on sample identifiers. It is simple to make results public after publication by updating folder security settings.

Conclusions

Standardized tools for analyzing, archiving and sharing assay results can improve the reproducibility, comparability and reliability of results obtained across many labs. LabKey Server and its NAb tool are freely available as open source software at http://www.labkey.com under the Apache 2.0 license. Many members of the HIV research community can also access the LabKey Server NAb tool without installing the software by using the Atlas Science Portal (https://atlas.scharp.org). Atlas is an installation of LabKey Server.
Study of the IgG endoglycosidase EndoS in group A streptococcal phagocyte resistance and virulence
Authors: Sjögren Jonathan , Okumura Cheryl YM , Collin Mattias , Nizet Victor , Hollands Andrew
Published: May 2011

Background

The secreted enzyme EndoS, an endoglycosidase from Streptococcus pyogenes, hydrolyzes the N-linked glycan of the constant region of immunoglobulin G (IgG) heavy chain and renders the antibody unable to interact with Fc receptors and elicit effector functions. In this study we couple targeted allelic replacement mutagenesis and heterologous expression to elucidate the contribution of EndoS to group A Streptococcus (GAS) phagocyte resistance and pathogenicity in vitro and in vivo.

Results

Knocking out the EndoS gene in GAS M1T1 background revealed no significant differences in bacterial survival in immune cell killing assays or in a systemic mouse model of infection. However, exogenous addition and heterologous expression of EndoS was found to increase GAS resistance to killing by neutrophils and monocytes in vitro. Additionally, heterologous expression of EndoS in M49 GAS increased mouse virulence in vivo.

Conclusions

We conclude that in a highly virulent M1T1 background, EndoS has no significant impact on GAS phagocyte resistance and pathogenicity. However, local accumulation or high levels of expression of EndoS in certain GAS strains may contribute to virulence.
Helicobacter pylori with stronger intensity of CagA phosphorylation lead to an increased risk of gastric intestinal metaplasia and cancer
Authors: Chuang Chiao-Hsiung , Yang Hsiao-Bai , Sheu Shew-Meei , Hung Kuei-Hsiang , Wu Jiunn-Jong , Cheng Hsiu-Chi , Chang Wei-Lun , Sheu Bor-Shyang
Published: May 2011

Background

Nearly all Taiwanese H. pylori stains are cagA-genopositive and encode CagA protein. In this study, we evaluated whether different intensity of tyrosine phosphorylated-CagA (p-CagA) had an impact on the clinical diseases and histological outcomes in this area.

Results

We enrolled 469 dyspeptic patients and prospectively obtained the gastric biopsy specimens and the H. pylori isolates. These patients were categorized according to the clinical diseases, such as duodenal ulcer, gastric ulcer, gastric cancer, and gastritis with or without intestinal metaplasia. Their gastric specimens were reviewed by the updated Sydney's system. Furthermore, a total of 146 patients were randomly selected from each clinical category for evaluation of their isolates' p-CagA intensity by in vitro AGS cells co-culture. The p-CagA was sparse in 30 (20.5%), weak in 59 (40.5%), and strong in 57 (39%) isolates. The isolates from the patients of gastric cancer or gastritis with intestinal metaplasia had stronger p-CagA intensity than those of gastritis without intestinal metaplasia (p ≤ 0.002). Moreover, the patients infected with isolates with strong or weak p-CagA intensity had a higher risk of gastric intestinal metaplasia (p < 0.05, odds ratio 3.09~15.26) than those infected with sparse p-CagA isolates.

Conclusions

Infection with H. pylori stains with stronger p-CagA intensity may lead to an increased risk of gastric intestinal metaplasia and cancer.
Synthesis of 86 species of 1,5-diaryl-3-oxo-1,4-pentadienes analogs of curcumin can yield a good lead in vivo
Authors: Kudo Chieko , Yamakoshi Hiroyuki , Sato Atsuko , Nanjo Hiroshi , Ohori Hisatsugu , Ishioka Chikashi , Iwabuchi Yoshiharu , Shibata Hiroyuki
Published: May 2011

Background

Curcumin is known to possess many anti-tumor properties such as inhibition of tumor growth and induction of apotosis. However, limited bioavailability of curcumin prevents its clinical application. A synthesized curcumin analog, 1,5-diaryl-3-oxo-1,4-pentadiene such as GO-Y030, has the improved anti-tumor potentialin vitroas well as in mouse model of colorectal carcinogenesis.

Results

These compounds were divided into two groups; one is the higher anti-proliferative group, in which 79.7% of 1,5-diaryl-3-oxo-1,4-pentadienes were clustered. One of the 1,5-diaryl-3-oxo-1,4-pentadiene analogs, GO-Y078 has the most enhanced growth inhibition, and its solubility was improved, compared with curcumin. GO-Y078 inhibits NF-κB transactivation, as well as expression of TP53 and DR5 more effectively than curcumin. In a mouse model, GO-Y078 presented 1.4 fold more survival elongation that was not achieved by curcumin and GO-Y030.

Conclusions

The 1,5-diaryl-3-oxo-1,4-pentadiene analogs can yield good lead compounds for cancer chemotherapy, to overcome low bioavailability of curcumin.
Non-leisure time physical activity is an independent predictor of longevity for a Taiwanese elderly population: an eight-year follow-up study
Authors: Lin Yu-Pei , Huang Ying-Hsiang , Lu Feng-Hwa , Wu Jin-Shang , Chang Chih-Jen , Yang Yi-Ching
Published: June 2011

Background

The aim of this study is to determine the relationship between leisure time physical activity (LTPA) and non-leisure time physical activity (NLTPA) on mortality among the elderly in Taiwan.

Methods

This is a prospective observational cohort study. We analyzed the mortality data from a cohort of 876 non-institutionalized community-dwelling men and women aged 65 years or over, who were recruited by stratified clustering random sampling from Tainan city and participated in the 1996 Elderly Medication Survey. Information about activities and other variables were collected by structured interviews at baseline in the participants' home. The Cox proportional hazards model and crude death rate were applied to estimate mortality risk.

Results

Among the 876 participants, 312 died during the follow-up period (1996-2004). In the unadjusted Cox regression model, subjects aged over 75, having difficulty in carrying out activities of daily living (ADLs), a BMI less than 18.5, a history of diabetes mellitus or stroke, without LTPA or being inactive in NLTPA, were found to have a higher risk of eight-year mortality. With the adjustment for age, gender, education level, habitual smoking and drinking, living status, BMI and medical history, the mortality was found to be higher among the sedentary subjects, either defined by lack of LTPA or NLTPA, with the hazard ratio of 1.27 (95% confidence interval [CI] = 0.97-1.66) and 1.45 (95% CI = 1.07-1.97), respectively. Furthermore, when both LTPA and NLTPA were put into the model simultaneously, NLTPA (HR = 1.40; 95% CI = 1.03-1.91) but not LTPA (HR = 1.21, 95% CI = 0.92-1.59) significantly predicted mortality during eight-year follow-up. In addition, subjects who were actively engaged in NLTPA had a lower mortality risk especially in subjects without performing LTPA.

Conclusions

NLTPA is an independent predictor of longevity among older people in Taiwan. A physically active lifestyle, especially engaged in NLTPA, is associated with lower mortality risk in the elderly population. We thus suggest that encouraging older people to keep on engaging in customary NLTPA is good for their health.
A miRNA expression signature that separates between normal and malignant prostate tissues
Authors: Carlsson Jessica , Davidsson Sabina , Helenius Gisela , Karlsson Mats , Lubovac Zelmina , Andrén Ove , Olsson Björn , Klinga-Levan Karin
Published: May 2011

Background

MicroRNAs (miRNAs) constitute a class of small non-coding RNAs that post-transcriptionally regulate genes involved in several key biological processes and thus are involved in various diseases, including cancer. In this study we aimed to identify a miRNA expression signature that could be used to separate between normal and malignant prostate tissues.

Results

Nine miRNAs were found to be differentially expressed (p<0.00001). With the exception of two samples, this expression signature could be used to separate between the normal and malignant tissues. A cross-validation procedure confirmed the generality of this expression signature. We also identified 16 miRNAs that possibly could be used as a complement to current methods for grading of prostate tumor tissues.

Conclusions

We found an expression signature based on nine differentially expressed miRNAs that with high accuracy (85%) could classify the normal and malignant prostate tissues in patients from the Swedish Watchful Waiting cohort. The results show that there are significant differences in miRNA expression between normal and malignant prostate tissue, indicating that these small RNA molecules might be important in the biogenesis of prostate cancer and potentially useful for clinical diagnosis of the disease.
Minichromosome Maintenance Protein 7 is a potential therapeutic target in human cancer and a novel prognostic marker of non-small cell lung cancer
Authors: Toyokawa Gouji , Masuda Ken , Daigo Yataro , Cho Hyun-Soo , Yoshimatsu Masanori , Takawa Masashi , Hayami Shinya , Maejima Kazuhiro , Chino Makoto , Field Helen I , Neal David E , Tsuchiya Eiju , Ponder Bruce AJ , Maehara Yoshihiko , Nakamura Yusuke , Hamamoto Ryuji
Published: May 2011

Background

The research emphasis in anti-cancer drug discovery has always been to search for a drug with the greatest antitumor potential but fewest side effects. This can only be achieved if the drug used is against a specific target located in the tumor cells. In this study, we evaluated Minichromosome Maintenance Protein 7 (MCM7) as a novel therapeutic target in cancer.

Results

Immunohistochemical analysis showed that MCM7 was positively stained in 196 of 331 non-small cell lung cancer (NSCLC), 21 of 29 bladder tumor and 25 of 70 liver tumor cases whereas no significant staining was observed in various normal tissues. We also found an elevated expression of MCM7 to be associated with poor prognosis for patients with NSCLC (P= 0.0055). qRT-PCR revealed a higher expression ofMCM7in clinical bladder cancer tissues than in corresponding non-neoplastic tissues (P< 0.0001), and we confirmed that a wide range of cancers also overexpressedMCM7by cDNA microarray analysis. Suppression of MCM7 using specific siRNAs inhibited incorporation of BrdU in lung and bladder cancer cells overexpressing MCM7, and suppressed the growth of those cells more efficiently than that of normal cell strains expressing lower levels of MCM7.

Conclusions

Since MCM7 expression was generally low in a number of normal tissues we examined, MCM7 has the characteristics of an ideal candidate for molecular targeted cancer therapy in various tumors and also as a good prognostic biomarker for NSCLC patients.
Ribosomal Protein S6 Kinase (RSK)-2 as a central effector molecule in RON receptor tyrosine kinase mediated epithelial to mesenchymal transition induced by macrophage-stimulating protein
Authors: Ma Qi , Guin Sunny , Padhye Snehal S , Zhou Yong-Qing , Zhang Rui-Wen , Wang Ming-Hai
Published: May 2011

Background

Epithelial to mesenchymal transition (EMT) occurs during cancer cell invasion and malignant metastasis. Features of EMT include spindle-like cell morphology, loss of epithelial cellular markers and gain of mesenchymal phenotype. Activation of the RON receptor tyrosine kinase by macrophage-stimulating protein (MSP) has been implicated in cellular EMT program; however, the major signaling determinant(s) responsible for MSP-induced EMT is unknown.

Results

The study presented here demonstrates that RSK2, a downstream signaling protein of the Ras-Erk1/2 pathway, is the principal molecule that links MSP-activated RON signaling to complete EMT. Using MDCK cells expressing RON as a model, a spindle-shape based screen was conducted, which identifies RSK2 among various intracellular proteins as a potential signaling molecule responsible for MSP-induced EMT. MSP stimulation dissociated RSK2 with Erk1/2 and promoted RSK2 nuclear translocation. MSP strongly induced RSK2 phosphorylation in a dose-dependent manner. These effects relied on RON and Erk1/2 phosphorylation, which is significantly potentiated by transforming growth factor (TGF)-β1, an EMT-inducing cytokine. Specific RSK inhibitor SL0101 completely prevented MSP-induced RSK phosphorylation, which results in inhibition of MSP-induced spindle-like morphology and suppression of cell migration associated with EMT. In HT-29 cancer cells that barely express RSK2, forced RSK2 expression results in EMT-like phenotype upon MSP stimulation. Moreover, specific siRNA-mediated silencing of RSK2 but not RSK1 in L3.6pl pancreatic cancer cells significantly inhibited MSP-induced EMT-like phenotype and cell migration.

Conclusions

MSP-induced RSK2 activation is a critical determinant linking RON signaling to cellular EMT program. Inhibition of RSK2 activity may provide a therapeutic opportunity for blocking RON-mediated cancer cell migration and subsequent invasion.
Immunohistochemical localization of hepatopancreatic phospholipase A2 in Hexaplex Trunculus digestive cells
Authors: Zarai Zied , Boulais Nicholas , Karray Aida , Misery Laurent , Bezzine Sofiane , Rebai Tarek , Gargouri Youssef , Mejdoub Hafedh
Published: June 2011

Background

Mammalian sPLA2-IB localization cell are well characterized. In contrast, much less is known about aquatic primitive ones. The aquatic world contains a wide variety of living species and, hence represents a great potential for discovering new lipolytic enzymes and the mode of digestion of lipid food.

Results

The marine snail digestive phospholipase A2 (mSDPLA2) has been previously purified from snail hepatopancreas. The specific polyclonal antibodies were prepared and used for immunohistochimical and immunofluorescence analysis in order to determine the cellular location of mSDPLA2. Our results showed essentially that mSDPLA2 was detected inside in specific vesicles tentatively named (mSDPLA2+) granules of the digestive cells. No immunolabelling was observed in secretory zymogene-like cells. This immunocytolocalization indicates that lipid digestion in the snail might occur in specific granules inside the digestive cells.

Conclusion

The cellular location of mSDPLA2 suggests that intracellular phospholipids digestion, like other food components digestion of snail diet, occurs in these digestive cells. The hepatopancreas of H. trunculus has been pointed out as the main region for digestion, absorption and storage of lipids.
The clinical implications of adult-onset henoch-schonelin purpura
Authors: Jithpratuck Warit , Elshenawy Yasmin , Saleh Hana , Youngberg George , Chi David S , Krishnaswamy Guha
Published: May 2011

Henoch-Schonlein Purpura (HSP) is a small vessel vasculitis mediated by IgA-immune complex deposition. It is characterized by the clinical tetrad of non-thrombocytopenic palpable purpura, abdominal pain, arthritis and renal involvement. Pathologically, it can be considered a form of immune complex-mediated leukocytoclastic vasculitis (LCV) involving the skin and other organs. Though it primarily affects children (over 90% of cases), the occurrence in adults has been rarely reported. Management often involves the use of immunomodulatory or immune-suppressive regimens.
Consumer purchasing patterns in response to calorie labeling legislation in New York City
Authors: Vadiveloo Maya K , Dixon L Beth , Elbel Brian
Published: May 2011

Background

Obesity is a major public health threat and policies aimed at curbing this epidemic are emerging. National calorie labeling legislation is forthcoming and requires rigorous evaluation to examine its impact on consumers. The purpose of this study was to examine whether point-of-purchase calorie labels in New York City (NYC) chain restaurants affected food purchasing patterns in a sample of lower income adults in NYC and Newark, NJ.

Methods

This study utilized a difference-in-difference design to survey 1,170 adult patrons of four popular chain restaurants in NYC and Newark, NJ (which did not introduce labeling) before and after calorie labeling was implemented in NYC. Receipt data were collected and analyzed to examine food and beverage purchases and frequency of fast food consumption. Descriptive statistics were generated, and linear and logistic regression, difference-in-difference analysis, and predicted probabilities were used to analyze the data.

Results

A difference-in-difference analysis revealed no significant favorable differences and some unfavorable differences in food purchasing patterns and frequency of fast food consumption between adult patrons of fast food restaurants in NYC and Newark, NJ. Adults in NYC who reported noticing and using the calorie labels consumed fast food less frequently compared to adults who did not notice the labels (4.9 vs. 6.6 meals per week, p <0.05).

Conclusion

While no favorable differences in purchasing as a result of labeling were noted, self-reported use of calorie labels was associated with some favorable behavioral patterns in a subset of adults in NYC. However, overall impact of the legislation may be limited. More research is needed to understand the most effective way to deliver calorie information to consumers.
A large, consistent plasma proteomics data set from prospectively collected breast cancer patient and healthy volunteer samples
Authors: Riley Catherine P , Zhang Xiang , Nakshatri Harikrishna , Schneider Bryan , Regnier Fred E , Adamec Jiri , Buck Charles
Published: May 2011

Background

Variability of plasma sample collection and of proteomics technology platforms has been detrimental to generation of large proteomic profile datasets from human biospecimens.

Methods

We carried out a clinical trial-like protocol to standardize collection of plasma from 204 healthy and 216 breast cancer patient volunteers. The breast cancer patients provided follow up samples at 3 month intervals. We generated proteomics profiles from these samples with a stable and reproducible platform for differential proteomics that employs a highly consistent nanofabricated ChipCube™ chromatography system for peptide detection and quantification with fast, single dimension mass spectrometry (LC-MS). Protein identification is achieved with subsequent LC-MS/MS analysis employing the same ChipCube™ chromatography system.

Results

With this consistent platform, over 800 LC-MS plasma proteomic profiles from prospectively collected samples of 420 individuals were obtained. Using a web-based data analysis pipeline for LC-MS profiling data, analyses of all peptide peaks from these plasma LC-MS profiles reveals an average coefficient of variability of less than 15%. Protein identification of peptide peaks of interest has been achieved with subsequent LC-MS/MS analyses and by referring to a spectral library created from about 150 discrete LC-MS/MS runs. Verification of peptide quantity and identity is demonstrated with several Multiple Reaction Monitoring analyses. These plasma proteomic profiles are publicly available through ProteomeCommons.

Conclusion

From a large prospective cohort of healthy and breast cancer patient volunteers and using a nano-fabricated chromatography system, a consistent LC-MS proteomics dataset has been generated that includes more than 800 discrete human plasma profiles. This large proteomics dataset provides an important resource in support of breast cancer biomarker discovery and validation efforts.
Immunological abnormalities as potential biomarkers in Chronic Fatigue Syndrome/Myalgic Encephalomyelitis
Authors: Brenu Ekua W , van Driel Mieke L , Staines Don R , Ashton Kevin J , Ramos Sandra B , Keane James , Klimas Nancy G , Marshall-Gradisnik Sonya M
Published: May 2011

Background

Chronic Fatigue Syndrome/Myalgic Encephalomyelitis (CFS/ME) is characterised by severe prolonged fatigue, and decreases in cognition and other physiological functions, resulting in severe loss of quality of life, difficult clinical management and high costs to the health care system. To date there is no proven pathomechanism to satisfactorily explain this disorder. Studies have identified abnormalities in immune function but these data are inconsistent. We investigated the profile of markers of immune function (including novel markers) in CFS/ME patients.

Methods

We included 95 CFS/ME patients and 50 healthy controls. All participants were assessed on natural killer (NK) and CD8+T cell cytotoxic activities, Th1 and Th2 cytokine profile of CD4+T cells, expression of vasoactive intestinal peptide receptor 2 (VPACR2), levels of NK phenotypes (CD56brightand CD56dim) and regulatory T cells expressing FoxP3 transcription factor.

Results

Compared to healthy individuals, CFS/ME patients displayed significant increases in IL-10, IFN-γ, TNF-α, CD4+CD25+T cells, FoxP3 and VPACR2 expression. Cytotoxic activity of NK and CD8+T cells and NK phenotypes, in particular the CD56brightNK cells were significantly decreased in CFS/ME patients. Additionally granzyme A and granzyme K expression were reduced while expression levels of perforin were significantly increased in the CFS/ME population relative to the control population. These data suggest significant dysregulation of the immune system in CFS/ME patients.

Conclusions

Our study found immunological abnormalities which may serve as biomarkers in CFS/ME patients with potential for an application as a diagnostic tool.