bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative Analyses of the Secretome from Dedifferentiated and Redifferentiated Adult Articular Chondrocytes
Authors: Polacek Martin , Bruun Jack-Ansgar , Johansen Oddmund , Martinez Inigo
Published: October 2010

Objective:

The main goal of this study was to compare the secretion products derived from human articular chondrocytes established in either long-term monolayer cultures or in scaffold-free 3-dimensional (3-D) cultures.

Methods:

Stable isotope labeling of amino acids in cell culture (SILAC) was applied to investigate quantitatively the differences between proteins secreted from dedifferentiated and redifferentiated chondrocytes. Proteins in cell supernatants were resolved by 1-D gel electrophoresis and analyzed by mass spectrometry. The results from the proteomic analyses were validated by immunoblotting. Additionally, antibody arrays were used to screen culture supernatants for 79 different morphogens.

Results:

Quantitative SILAC showed that some relevant growth factors such as CTGF or GAS6 were elevated in monolayers, along with proteins characteristic of a dedifferentiated phenotype such as collagen type I and tenascin. In spheroids, data showed overexpression of some cartilage-specific proteins such as aggrecan, together with important matrix regulators such as chitinase-3–like protein and stromelysin-1. Antibody arrays revealed that chondrocytes in monolayer secrete higher levels of leukocyte-activating agents such as MCP-1 and GRO, whereas the spheroid configuration favors the production of cell morphogens such as MCSF and VEGF.

Conclusion:

Our results show that some classic dedifferentiation and redifferentiation markers are differentially expressed in 2-D or 3-D culture configurations. Other cell/matrix regulatory molecules are also found to be differentially expressed by chondrocytes in 2-D and 3-D conditions by SILAC and antibody arrays. Our data bring new information for understanding the biology of chondrocytes in general and the process of cartilage tissue reconstruction in particular.
Characterization of a rare IL-10–competent B-cell subset in humans that parallels mouse regulatory B10 cells
Authors: Iwata Yohei , Matsushita Takashi , Horikawa Mayuka , DiLillo David J. , Yanaba Koichi , Venturi Guglielmo M. , Szabolcs Paul M. , Bernstein Steven H. , Magro Cynthia M. , Williams Armistead D. , Hall Russell P. , St Clair E. William , Tedder Thomas F.
Published: October 2010

Regulatory B cells control inflammation and autoimmunity in mice, including the recently identified IL-10–competent B10 cell subset that represents 1% to 3% of spleen B cells. In this study, a comparable IL-10–competent B10 cell subset was characterized in human blood. B10 cells were functionally identified by their ability to express cytoplasmic IL-10 after 5 hours of ex vivo stimulation, whereas progenitor B10 (B10pro) cells required 48 hours of in vitro stimulation before they acquired the ability to express IL-10. B10 and B10pro cells represented 0.6% and approximately 5% of blood B cells, respectively. Ex vivo B10 and B10pro cells were predominantly found within the CD24hiCD27+ B-cell subpopulation that was able to negatively regulate monocyte cytokine production through IL-10–dependent pathways during in vitro functional assays. Blood B10 cells were present in 91 patients with rheumatoid arthritis, systemic lupus erythematosus, primary Sjögren syndrome, autoimmune vesiculobullous skin disease, or multiple sclerosis, and were expanded in some cases as occurs in mice with autoimmune disease. Mean B10 + B10pro-cell frequencies were also significantly higher in patients with autoimmune disease compared with healthy controls. The characterization of human B10 cells will facilitate their identification and the study of their regulatory activities during human disease.
Translocation t(14;16) and multiple myeloma: is it really an independent prognostic factor?
Authors: Avet-Loiseau Hervé , Malard Florent , Campion Loic , Magrangeas Florence , Sebban Catherine , Lioure Bruno , Decaux Olivier , Lamy Thierry , Legros Laurence , Fuzibet Jean-Gabriel , Michallet Mauricette , Corront Bernadette , Lenain Pascal , Hulin Cyrille , Mathiot Claire , Attal Michel , Facon Thierry , Harousseau Jean-Luc , Minvielle Stephane , Moreau Philippe ,   for the Intergroupe Francophone du Myélome
Published: October 2010

Many trials in myeloma are stratified on cytogenetic abnormalities. Among them, the most commonly chosen are the t(4;14), the del(17p), and the t(14;16). If data are well established for t(4;14) and del(17p), very few data support the use of t(14;16). To address this issue, we retrospectively analyzed 1003 patients with newly diagnosed myeloma for this abnormality. We identified 32 patients with the t(14;16). Compared with patients lacking the t(14;16), we did not observe any difference in overall survival (P = .28). Moreover, in multivariate analyses, the t(14;16) was not prognostic (P = .39). In conclusion, our data do not support the use of t(14;16)-specific probes in the diagnostic panels of multiple myeloma.
Analysis of X-ray Structures of Matrix Metalloproteinases via Chaotic Map Clustering
Authors: Giangreco Ilenia , Nicolotti Orazio , Carotti Angelo , De Carlo Francesco , Gargano Gianfranco , Bellotti Roberto
Published: October 2010

Background

Matrix metalloproteinases (MMPs) are well-known biological targets implicated in tumour progression, homeostatic regulation, innate immunity, impaired delivery of pro-apoptotic ligands, and the release and cleavage of cell-surface receptors. With this in mind, the perception of the intimate relationships among diverse MMPs could be a solid basis for accelerated learning in designing new selective MMP inhibitors. In this regard, decrypting the latent molecular reasons in order to elucidate similarity among MMPs is a key challenge.

Results

We describe a pairwise variant of the non-parametric chaotic map clustering (CMC) algorithm and its application to 104 X-ray MMP structures. In this analysis electrostatic potentials are computed and used as input for the CMC algorithm. It was shown that differences between proteins reflect genuine variation of their electrostatic potentials. In addition, the analysis has been also extended to analyze the protein primary structures and the molecular shapes of the MMP co-crystallised ligands.

Conclusions

The CMC algorithm was shown to be a valuable tool in knowledge acquisition and transfer from MMP structures. Based on the variation of electrostatic potentials, CMC was successful in analysing the MMP target family landscape and different subsites. The first investigation resulted in rational figure interpretation of both domain organization as well as of substrate specificity classifications. The second made it possible to distinguish the MMP classes, demonstrating the high specificity of the S1' pocket, to detect both the occurrence of punctual mutations of ionisable residues and different side-chain conformations that likely account for induced-fit phenomena. In addition, CMC demonstrated a potential comparable to the most popular UPGMA (Unweighted Pair Group Method with Arithmetic mean) method that, at present, represents a standard clustering bioinformatics approach. Interestingly, CMC and UPGMA resulted in closely comparable outcomes, but often CMC produced more informative and more easy interpretable dendrograms. Finally, CMC was successful for standard pairwise analysis (i.e., Smith-Waterman algorithm) of protein sequences and was used to convincingly explain the complementarity existing between the molecular shapes of the co-crystallised ligand molecules and the accessible MMP void volumes.
A statistical approach to finding overlooked genetic associations
Authors: Rider Andrew K , Siwo Geoffrey , Chawla Nitesh V , Ferdig Michael , Emrich Scott J
Published: October 2010

Background

Complexity and noise in expression quantitative trait loci (eQTL) studies make it difficult to distinguish potential regulatory relationships among the many interactions. The predominant method of identifying eQTLs finds associations that are significant at a genome-wide level. The vast number of statistical tests carried out on these data make false negatives very likely. Corrections for multiple testing error render genome-wide eQTL techniques unable to detect modest regulatory effects.

We propose an alternative method to identify eQTLs that builds on traditional approaches. In contrast to genome-wide techniques, our method determines the significance of an association between an expression trait and a locus with respect to the set of all associations to the expression trait. The use of this specific information facilitates identification of expression traits that have an expression profile that is characterized by a single exceptional association to a locus.

Our approach identifies expression traits that have exceptional associations regardless of the genome-wide significance of those associations. This property facilitates the identification of possible false negatives for genome-wide significance. Further, our approach has the property of prioritizing expression traits that are affected by few strong associations. Expression traits identified by this method may warrant additional study because their expression level may be affected by targeting genes near a single locus.

Results

We demonstrate our method by identifying eQTL hotspots in Plasmodium falciparum (malaria) and Saccharomyces cerevisiae (yeast). We demonstrate the prioritization of traits with few strong genetic effects through Gene Ontology (GO) analysis of Yeast. Our results are strongly consistent with results gathered using genome-wide methods and identify additional hotspots and eQTLs.

Conclusions

New eQTLs and hotspots found with this method may represent regions of the genome or biological processes that are controlled through few relatively strong genetic interactions. These points of interest warrant experimental investigation.
CCRaVAT and QuTie - enabling analysis of rare variants in large-scale case control and quantitative trait association studies
Authors: Lawrence Robert , Day-Williams Aaron G , Elliott Katherine S , Morris Andrew P , Zeggini Eleftheria
Published: October 2010

Background

Genome-wide association studies have been successful in finding common variants influencing common traits. However, these associations only account for a fraction of trait heritability. There has been a shift in the field towards studying low frequency and rare variants, which are now widely recognised as putative complex trait determinants. Despite this increasing focus on examining the role of low frequency and rare variants in complex disease susceptibility, there is a lack of user-friendly analytical packages implementing powerful association tests for the analysis of rare variants.

Results

We have developed two software tools, CCRaVAT (Case-Control Rare Variant Analysis Tool) and QuTie (Quantitative Trait), which enable efficient large-scale analysis of low frequency and rare variants. Both programs implement a collapsing method examining the accumulation of low frequency and rare variants across a locus of interest that has more power than single variant analysis. CCRaVAT carries out case-control analyses whereas QuTie has been developed for continuous trait analysis.

Conclusions

CCRaVAT and QuTie are easy to use software tools that allow users to perform genome-wide association analysis on low frequency and rare variants for both binary and quantitative traits. The software is freely available and provides the genetics community with a resource to perform association analysis on rarer genetic variants.
Evolutionary history of tall fescue morphotypes inferred from molecular phylogenetics of the Lolium-Festucaspecies complex
Authors: Hand Melanie L , Cogan Noel OI , Stewart Alan V , Forster John W
Published: October 2010

Background

The agriculturally important pasture grass tall fescue (Festuca arundinaceaSchreb. syn.Lolium arundinaceum(Schreb.) Darbysh.) is an outbreeding allohexaploid, that may be more accurately described as a species complex consisting of three major (Continental, Mediterranean and rhizomatous) morphotypes. Observation of hybrid infertility in some crossing combinations between morphotypes suggests the possibility of independent origins from different diploid progenitors. This study aims to clarify the evolutionary relationships between each tall fescue morphotype through phylogenetic analysis using two low-copy nuclear genes (encoding plastid acetyl-CoA carboxylase [Acc1] andcentroradialis[CEN]), the nuclear ribosomal DNA internal transcribed spacer (rDNA ITS) and the chloroplast DNA (cpDNA) genome-locatedmatKgene. Other taxa within the closely relatedLolium-Festucaspecies complex were also included in the study, to increase understanding of evolutionary processes in a taxonomic group characterised by multiple inter-specific hybridisation events.

Results

Putative homoeologous sequences from both nuclear genes were obtained from each polyploid species and compared to counterparts from 15 diploid taxa. Phylogenetic reconstruction confirmedF. pratensisandF. arundinaceavar.glaucescensas probable progenitors to Continental tall fescue, and these species are also likely to be ancestral to the rhizomatous morphotype. However, these two morphotypes are sufficiently distinct to be located in separate clades based on the ITS-derived data set. All four of the generated data sets suggest independent evolution of the Mediterranean and Continental morphotypes, with minimal affinity between cognate sequence haplotypes. No obvious candidate progenitor species for Mediterranean tall fescues were identified, and only two putative sub-genome-specific haplotypes were identified for this morphotype.

Conclusions

This study describes the first phylogenetic analysis of theFestucagenus to include representatives of each tall fescue morphotype, and to use low copy nuclear gene-derived sequences to identify putative progenitors of the polyploid species. The demonstration of distinct tall fescue lineages has implications for both taxonomy and molecular breeding strategies, and may facilitate the generation of morphotype and/or sub-genome-specific molecular markers.
A widespread peroxiredoxin-like domain present in tumor suppression- and progression-implicated proteins
Authors: Pawłowski Krzysztof , Muszewska Anna , Lenart Anna , Szczepińska Teresa , Godzik Adam , Grynberg Marcin
Published: October 2010

Background

Peroxide turnover and signalling are involved in many biological phenomena relevant to human diseases. Yet, all the players and mechanisms involved in peroxide perception are not known. Elucidating very remote evolutionary relationships between proteins is an approach that allows the discovery of novel protein functions. Here, we start with three human proteins, SRPX, SRPX2 and CCDC80, involved in tumor suppression and progression, which possess a conserved region of similarity. Structure and function prediction allowed the definition of P-DUDES, a phylogenetically widespread, possibly ancient protein structural domain, common to vertebrates and many bacterial species.

Results

We show, using bioinformatics approaches, that the P-DUDES domain, surprisingly, adopts the thioredoxin-like (Thx-like) fold. A tentative, more detailed prediction of function is made, namely, that of a 2-Cys peroxiredoxin. Incidentally, consistent overexpression of all three human P-DUDES genes in two public glioblastoma microarray gene expression datasets was discovered. This finding is discussed in the context of the tumor suppressor role that has been ascribed to P-DUDES proteins in several studies. Majority of non-redundant P-DUDES proteins are found in marine metagenome, and among the bacterial species possessing this domain a trend for a higher proportion of aquatic species is observed.

Conclusions

The new protein structural domain, now with a broad enzymatic function predicted, may become a drug target once its detailed molecular mechanism of action is understood in detail.
Incidence, risk factors and clinical epidemiology of melioidosis: a complex socio-ecological emerging infectious disease in the Alor Setar region of Kedah, Malaysia
Authors: Hassan Muhammad RA , Pani Subhada P , Peng Ng P , Voralu Kirtanaa , Vijayalakshmi Natesan , Mehanderkar Ranjith , Aziz Norasmidar A , Michael Edwin
Published: October 2010

Background

Melioidosis, a severe and fatal infectious disease caused by Burkholderia pseudomallei, is believed to an emerging global threat. However, data on the natural history, risk factors, and geographic epidemiology of the disease are still limited.

Methods

We undertook a retrospective analysis of 145 confirmed cases extracted from a hospital-based Melioidosis Registry set up from 2005 in Hospital Sultanah Bahiyah, Alor Setar, Kedah state, Malaysia, in order to provide a first description of the contemporary incidence, risk factors, and clinical epidemiology of the disease in this putatively high risk region of the country.

Results

The incidence of melioidosis in Alor Setar is remarkably high at 16.35 per 100,000 population per year. The mean age of patients was 50.40 years, with infection varying nonlinearly with age. Males (75.2%; P < 0.0001) predominated and the majority of cases were Malays (88.9%). The overall, crude mortality rate among the study patients was 33.8%. The proportions of cases and deaths were significantly greater among patients involved in farming, forestry and fishing and the unemployed (χ2 = 30.57, P < 0.0001). A majority of cases (62.75%) were culture positive, with mortality in these patients being 45.05%. A large proportion (83.0%) of culture positives was also bacteremic. Pneumonia accounted for 42.06% of primary diagnoses followed in importance by soft tissue abscess. In patients with pneumonia and who were culture positive, the mortality rate was as high as 65.00%. Diabetes mellitus constituted the major underlying risk factor for developing and dying from melioidosis, occurring in 57% of all diagnosed cases. The age distribution of diabetes paralleled that of melioidosis cases. There were linear associations between cases and deaths with monthly rainfall.

Conclusions

Melioidosis represents a complex socio-ecological public health problem in Kedah, being strongly related with age, occupation, rainfall and predisposing chronic diseases, such as diabetes mellitus. Among cases, bacteremic patients were associated with significantly high mortality despite provision of the recommended antibacterial therapy. The burden of this disease is likely to grow in this region unless better informed interventions targeted at high-risk groups and associated diseases are urgently implemented.
Genome profiling of ERBB2-amplified breast cancers
Authors: Sircoulomb Fabrice , Bekhouche Ismahane , Finetti Pascal , Adélaïde José , Hamida Azza Ben , Bonansea Julien , Raynaud Stéphane , Innocenti Charlène , Charafe-Jauffret Emmanuelle , Tarpin Carole , Ayed Farhat Ben , Viens Patrice , Jacquemier Jocelyne , Bertucci François , Birnbaum Daniel , Chaffanet Max
Published: October 2010

Background

Around 20% of breast cancers (BC) show ERBB2 gene amplification and overexpression of the ERBB2 tyrosine kinase receptor. They are associated with a poor prognosis but can benefit from targeted therapy. A better knowledge of these BCs, genomically and biologically heterogeneous, may help understand their behavior and design new therapeutic strategies.

Methods

We defined the high resolution genome and gene expression profiles of 54 ERBB2-amplified BCs using 244K oligonucleotide array-comparative genomic hybridization and whole-genome DNA microarrays. Expression of ERBB2, phosphorylated ERBB2, EGFR, IGF1R and FOXA1 proteins was assessed by immunohistochemistry to evaluate the functional ERBB2 status and identify co-expressions.

Results

First, we identified the ERBB2-C17orf37-GRB7 genomic segment as the minimal common 17q12-q21 amplicon, and CRKRS and IKZF3 as the most frequent centromeric and telomeric amplicon borders, respectively. Second, GISTIC analysis identified 17 other genome regions affected by copy number aberration (CNA) (amplifications, gains, losses). The expression of 37 genes of these regions was deregulated. Third, two types of heterogeneity were observed in ERBB2-amplified BCs. The genomic profiles of estrogen receptor-postive (ER+) and negative (ER-) ERBB2-amplified BCs were different. The WNT/β-catenin signaling pathway was involved in ER- ERBB2-amplified BCs, and PVT1 and TRPS1 were candidate oncogenes associated with ER+ ERBB2-amplified BCs. The size of the ERBB2 amplicon was different in inflammatory (IBC) and non-inflammatory BCs. ERBB2-amplified IBCs were characterized by the downregulated and upregulated mRNA expression of ten and two genes in proportion to CNA, respectively. IHC results showed (i) a linear relationship between ERBB2 gene amplification and its gene and protein expressions with a good correlation between ERBB2 expression and phosphorylation status; (ii) a potential signaling cross-talk between EGFR or IGF1R and ERBB2, which could influence response of ERBB2-positive BCs to inhibitors. FOXA1 was frequently coexpressed with ERBB2 but its expression did not impact on the outcome of patients with ERBB2-amplified tumors.

Conclusion

We have shown that ER+ and ER- ERBB2-amplified BCs are different, distinguished ERBB2 amplicons in IBC and non-IBC, and identified genomic features that may be useful in the design of alternative therapeutical strategies.
Standards of lithium monitoring in mental health trusts in the UK
Authors: Collins Noel , Barnes Thomas RE , Shingleton-Smith Amber , Gerrett David , Paton Carol
Published: October 2010

Background

Lithium is a commonly prescribed drug with a narrow therapeutic index, and recognised adverse effects on the kidneys and thyroid. Clinical guidelines for the management of bipolar affective disorder published by The National Institute for Health and Clinical Excellence (NICE) recommend checks of renal and thyroid function before lithium is prescribed. They further recommend that all patients who are prescribed lithium should have their renal and thyroid function checked every six months, and their serum lithium checked every three months. Adherence to these recommendations has not been subject to national UK audit.

Methods

The Prescribing Observatory for Mental Health (POMH-UK) invited all National Health Service Mental Health Trusts in the UK to participate in a benchmarking audit of lithium monitoring against recommended standards. Data were collected retrospectively from clinical records and submitted electronically.

Results

436 clinical teams from 38 Trusts submitted data for 3,373 patients. In patients recently starting lithium, there was a documented baseline measure of renal or thyroid function in 84% and 82% respectively. For patients prescribed lithium for a year or more, the NICE standards for monitoring lithium serum levels, and renal and thyroid function were met in 30%, 55% and 50% of cases respectively.

Conclusions

The quality of lithium monitoring in patients who are in contact with mental health services falls short of recognised standards and targets. Findings from this audit, along with reports of harm received by the National Patient Safety Agency, prompted a Patient Safety Alert mandating primary care, mental health and acute Trusts, and laboratory staff to work together to ensure systems are in place to support recommended lithium monitoring by December 2010.
Risk-reducing strategies for women carrying brca1/2 mutations with a focus on prophylactic surgery
Authors: Salhab Mohamed , Bismohun Selina , Mokbel Kefah
Published: October 2010

Background

Women who have inherited mutations in the BRCA1 or BRCA2 genes have substantially elevated risks of breast and ovarian cancer. Mutation carriers have various options, including extensive and regular surveillance, chemoprevention and risk-reducing surgery. The aim of this review is to provide an up-to-date analysis and to subsequently summarise the available literature in relation to risk-reducing strategies, with a keen focus on prophylactic surgery.

Methods

The literature review is facilitated by Medline and PubMed databases. The cross-referencing of the obtained articles was used to identify other relevant studies.

Results

Prophylactic surgery (bilateral mastectomy, bilateral salpingo-oophorectomy or a combination of both procedures) has proved to be the most effective risk-reducing strategy. There are no randomised controlled trials able to demonstrate the potential benefits or harms of prophylactic surgery; therefore, the evidence has been derived from retrospective and short follow-up prospective studies, in addition to hypothetical mathematical models.

Based on the current knowledge, it is reasonable to recommend prophylactic oophorectomy for BRCA1 or BRCA2 mutation carriers when childbearing is completed in order to reduce the risk of developing breast and ovarian cancer. In addition, women should be offered the options of rigorous breast surveillance, chemoprevention with anti-oestrogens--especially for carriers of BRCA2--or bilateral prophylactic mastectomy.

Conclusion

The selection of the most appropriate risk-reducing strategy is not a straightforward task. The impact of risk-reducing strategies on cancer risk, survival, and overall quality of life are the key criteria considered for decision-making. Notably, various other factors should be taken into consideration when evaluating individual mutation carriers' individual circumstances, namely woman's age, morbidity, type of mutation, and individual preferences and expectations.

Although prospective randomised controlled trials concerned with examining the various interventions in relation to the woman's age and type of mutation are needed, randomisation is extremely difficult and rather deemed unethical given the current available evidence from retrospective studies.
Caloric beverage consumption patterns in Mexican children
Authors: Barquera Simon , Campirano Fabricio , Bonvecchio Anabelle , Hernández-Barrera Lucia , Rivera Juan A , Popkin Barry M
Published: October 2010

Background

Mexico has seen a very steep increase in child obesity level. Little is known about caloric beverage intake in this country as well as all other countries outside a few high income countries. This study examines overall patterns and trends in all caloric beverages from two nationally representative surveys from Mexico.

Methods

The two nationally representative dietary intake surveys (1999 and 2006) from Mexico are used to study caloric beverage intake in 17, 215 children. The volume (ml) and caloric energy (kcal) contributed by all beverages consumed by the sample subjects were measured. Results are weighted to be nationally representative.

Results

The trends from the dietary intake surveys showed very large increases in caloric beverages among pre-school and school children. The contribution of whole milk and sugar-sweetened juices was an important finding. Mexican pre-school children consumed 27.8% of their energy from caloric beverages in 2006 and school children consumed 20.7% of their energy from caloric beverages during the same time. The three major categories of beverage intake are whole milk, fruit juice with various sugar and water combinations and carbonated and noncarbonated sugared-beverages.

Conclusion

The Mexican government, greatly concerned about obesity, has identified the large increase in caloric beverages from whole milk, juices and soft drinks as a key target and is initiating major changes to address this problem. They have already used the data to shift 20 million persons in their welfare and feeding programs from whole to 1.5% fat milk and in a year will shift to nonfat milk. They are using these data to revise school beverage policies and national regulations and taxation policies related to an array of less healthful caloric beverages.
TRIzol treatment of secretory phase endometrium allows combined proteomic and mRNA microarray analysis of the same sample in women with and without endometriosis
Authors: Fassbender Amelie , Simsa Peter , Kyama Cleophas M , Waelkens Etienne , Mihalyi Attila , Meuleman Christel , Gevaert Olivier , Van de Plas Raf , de Moor Bart , D'Hooghe Thomas M
Published: October 2010

Background

According to mRNA microarray, proteomics and other studies, biological abnormalities of eutopic endometrium (EM) are involved in the pathogenesis of endometriosis, but the relationship between mRNA and protein expression in EM is not clear. We tested for the first time the hypothesis that EM TRIzol extraction allows proteomic Surface Enhanced Laser Desorption/Ionisation Time-of-Flight Mass Spectrometry (SELDI-TOF MS) analysis and that these proteomic data can be related to mRNA (microarray) data obtained from the same EM sample from women with and without endometriosis.

Methods

Proteomic analysis was performed using SELDI-TOF-MS of TRIzol-extracted EM obtained during secretory phase from patients without endometriosis (n = 6), patients with minimal-mild (n = 5) and with moderate-severe endometriosis (n = 5), classified according to the system of the American Society of Reproductive Medicine. Proteomic data were compared to mRNA microarray data obtained from the same EM samples.

Results

In our SELDI-TOF MS study 32 peaks were differentially expressed in endometrium of all women with endometriosis (stages I-IV) compared with all controls during the secretory phase. Comparison of proteomic results with those from microarray revealed no corresponding genes/proteins.

Conclusion

TRIzol treatment of secretory phase EM allows combined proteomic and mRNA microarray analysis of the same sample, but comparison between proteomic and microarray data was not evident, probably due to post-translational modifications.
The VHL-dependent regulation of microRNAs in renal cancer
Authors: Neal Calida S , Michael Michael Z , Rawlings Lesley H , Van der Hoek Mark B , Gleadle Jonathan M
Published: October 2010

Background

The commonest histological type of renal cancer, clear cell renal cell carcinoma (cc RCC), is associated with genetic and epigenetic changes in the von Hippel-Lindau (VHL) tumour suppressor. VHL inactivation leads to induction of hypoxia-inducible factors (HIFs) and a hypoxic pattern of gene expression. Differential levels of specific microRNAs (miRNAs) are observed in several tumours when compared to normal tissue. Given the central role of VHL in renal cancer formation, we examined the VHL-dependent regulation of miRNAs in renal cancer.

Methods

VHL-dependent miRNA expression in cc RCC was determined by microarray analysis of renal cell line RCC4 with mutated VHL (RCC4-VHL) and reintroduced wild-type VHL (RCC4 + VHL). Five miRNAs highly upregulated in RCC4 + VHL and five miRNAs highly downregulated in RCC4 + VHL were studied further, in addition to miR-210, which is regulated by the HIF-VHL system. miRNA expression was also measured in 31 cc RCC tumours compared to adjacent normal tissue.

Results

A significant increase in miR-210, miR-155 and miR-21 expression was observed in the tumour tissue. miR-210 levels also showed a correlation with a HIF-regulated mRNA, carbonic anhydrase IX (CAIX), and with VHL mutation or promoter methylation. An inverse correlation was observed between miR-210 expression and patient survival, and a putative target of miR-210, iron-sulfur cluster assembly protein (ISCU1/2), shows reciprocal levels of mRNA expression in the tumours.

Conclusions

We have identified VHL-regulated miRNAs and found that for some the regulation is HIF-dependent and for others it is HIF-independent. This pattern of regulation was also seen in renal cancer tissue for several of these miRNAs (miR-210, miR-155, let-7i and members of the miR-17-92 cluster) when compared with normal tissue. miR-210 showed marked increases in expression in renal cancer and levels correlated with patient survival. The inverse correlation between miR-210 levels and ISCU1/2 provides support for the hypothesis that ISCU1/2 is a target of miR-210 and that it may contribute to the anaerobic respiration seen in renal (and other) tumours.

See Commentary:http://www.biomedcentral.com/1741-7015/8/65
Genetic background modifies neurodegeneration and neuroinflammation driven by misfolded human tau protein in rat model of tauopathy: implication for immunomodulatory approach to Alzheimer's disease
Authors: Stozicka Zuzana , Zilka Norbert , Novak Petr , Kovacech Branislav , Bugos Ondrej , Novak Michal
Published: October 2010

Background

Numerous epidemiological studies demonstrate that genetic background modifies the onset and the progression of Alzheimer's disease and related neurodegenerative disorders. The efficacious influence of genetic background on the disease pathway of amyloid beta has been meticulously described in rodent models. Since the impact of genetic modifiers on the neurodegenerative and neuroinflammatory cascade induced by misfolded tau protein is yet to be elucidated, we have addressed the issue by using transgenic lines expressing the same human truncated tau protein in either spontaneously hypertensive rat (SHR) or Wistar-Kyoto (WKY) genetic background.

Methods

Brains of WKY and SHR transgenic rats in the terminal stage of phenotype and their age-matched non-transgenic littermates were examined by means of immunohistochemistry and unbiased stereology. Basic measures of tau-induced neurodegeneration (load of neurofibrillary tangles) and neuroinflammation (number of Iba1-positive microglia, their activated morphology, and numbers of microglia immunoreactive for MHCII and astrocytes immunoreactive for GFAP) were quantified with an optical fractionator in brain areas affected by neurofibrillary pathology (pons, medulla oblongata). The stereological data were evaluated using two-way ANOVA and Student's t-test.

Results

Tau neurodegeneration (neurofibrillary tangles (NFTs), axonopathy) and neuroinflammation (microgliosis, astrocytosis) appeared in both WKY and SHR transgenic rats. Although identical levels of transgene expression in both lines were present, terminally-staged WKY transgenic rats displayed significantly lower final NFT loads than their SHR transgenic counterparts. Interestingly, microglial responses showed a striking difference between transgenic lines. Only 1.6% of microglia in SHR transgenic rats expressed MHCII in spite of having a robust phagocytic phenotype, whereas in WKY transgenic rats, 23.2% of microglia expressed MHCII despite displaying a considerably lower extent of transformation into phagocytic phenotype.

Conclusions

These results show that the immune response represents a pivotal and genetically variable modifying factor that is able to influence vulnerability to neurodegeneration. Therefore, targeted immunomodulation could represent a prospective therapeutic approach to Alzheimer's disease.
An RNA replication-center assay for high content image-based quantifications of human rhinovirus and coxsackievirus infections
Authors: Jurgeit Andreas , Moese Stefan , Roulin Pascal , Dorsch Alexander , Lötzerich Mark , Lee Wai-Ming , Greber Urs F
Published: October 2010

Background

Picornaviruses are common human and animal pathogens, including polio and rhinoviruses of the enterovirus family, and hepatits A or food-and-mouth disease viruses. There are no effective countermeasures against the vast majority of picornaviruses, with the exception of polio and hepatitis A vaccines. Human rhinoviruses (HRV) are the most prevalent picornaviruses comprising more than one hundred serotypes. The existing and also emerging HRVs pose severe health risks for patients with asthma or chronic obstructive pulmonary disease. Here, we developed a serotype-independent infection assay using a commercially available mouse monoclonal antibody (mabJ2) detecting double-strand RNA.

Results

Immunocytochemical staining for RNA replication centers using mabJ2 identified cells that were infected with either HRV1A, 2, 14, 16, 37 or coxsackievirus (CV) B3, B4 or A21. MabJ2 labeled-cells were immunocytochemically positive for newly synthesized viral capsid proteins from HRV1A, 14, 16, 37 or CVB3, 4. We optimized the procedure for detection of virus replication in settings for high content screening with automated fluorescence microscopy and single cell analysis. Our data show that the infection signal was dependent on multiplicity, time and temperature of infection, and the mabJ2-positive cell numbers correlated with viral titres determined in single step growth curves. The mabJ2 infection assay was adapted to determine the efficacy of anti-viral compounds and small interfering RNAs (siRNAs) blocking enterovirus infections.

Conclusions

We report a broadly applicable, rapid protocol to measure infection of cultured cells with enteroviruses at single cell resolution. This assay can be applied to a wide range of plus-sense RNA viruses, and hence allows comparative studies of viral infection biology without dedicated reagents or procedures. This protocol also allows to directly compare results from small compound or siRNA infection screens for different serotypes without the risk of assay specific artifacts.
Death-related gastric necrosis after Laparoscopic Adjustable Gastric Banding in the early post-operative period
Authors: Fragkouli Kleio , Mitselou Antigoni , Vougiouklakis Theodore
Published: October 2010

We report a case of a rare complication of Laparoscopic Adjustable Gastric Banding (LAGB) as a cause of death in the immediate post-operative period. The number of relevant reports and postmortem images presented in the literature is extremely restricted. Gastric necrosis may constitute a cause of death after LAGB in the early post-operative period. Postmortem examination reveals the extension of gastric ischemia and necrosis, responsible for the lethal outcome. To date, only one case of gastric necrosis after LAGB in the immediate post-operative period leading to death has been reported, according to authors' knowledge. The diagnosis of this complication may be delayed on the grounds of its rarity. In our opinion, surgeons should be aware of the clinical state implying gastric ischemia early after LAGB, so as to recognize and, in turn, to treat it promptly.
Challenges to conservation: land use change and local participation in the Al Reem Biosphere Reserve, West Qatar
Authors: Sillitoe Paul , Alshawi Ali A , Al-Amir Hassan Abdul K
Published: October 2010

One response to humanity's unsustainable use of natural resources and consequent degradation, even destruction of the environment, is to establish conservation areas to protect Nature and preserve biodiversity at least in selected regions. In Qatar, the government has shown strong support for this approach, confronted by the environmental consequences of oil and gas extraction and rapid urban development, by designating about one-tenth of the country a conservation area. Located in the west of the peninsula, it comprises the Al Reem Reserve, subsequently declared a UNESCO Biosphere Reserve. Several approaches have figured in conservation, currently popular is co-management featuring participation of the local population, which recognises that people's activities often contribute to today's environment, with the promotion of bio-cultural diversity. However, these assumptions may not hold where rapid social and cultural change occurs, as in Qatar. We explore the implications of such change, notably in land use. We detail changes resulting with the move from nomadic to sedentary lifestyles: in land access, which now features tribal-state control, and herding strategies, which now feature migrant labour and depend on imported fodder and water, underwritten by the country's large gas and oil revenues. Current stocking arrangements - animals herded in much smaller areas than previously - are thought responsible for the degradation of natural resources. The place of animals, notably camels, in Qatari life, has also changed greatly, possibly further promoting overstocking. Many local people disagree. What are the implications of such changes for the participatory co-management of conservation areas? Do they imply turning the clock back to centrally managed approaches that seek to control access and local activities?
Mapping the cellular and molecular heterogeneity of normal and malignant breast tissues and cultured cell lines
Authors: Keller Patricia J , Lin Amy F , Arendt Lisa M , Klebba Ina , Jones Ainsley D , Rudnick Jenny A , DiMeo Theresa A , Gilmore Hannah , Jefferson Douglas M , Graham Roger A , Naber Stephen P , Schnitt Stuart , Kuperwasser Charlotte
Published: October 2010

Introduction

Normal and neoplastic breast tissues are comprised of heterogeneous populations of epithelial cells exhibiting various degrees of maturation and differentiation. While cultured cell lines have been derived from both normal and malignant tissues, it remains unclear to what extent they retain similar levels of differentiation and heterogeneity as that found within breast tissues.

Methods

We used 12 reduction mammoplasty tissues, 15 primary breast cancer tissues, and 20 human breast epithelial cell lines (16 cancer lines, 4 normal lines) to perform flow cytometry for CD44, CD24, epithelial cell adhesion molecule (EpCAM), and CD49f expression, as well as immunohistochemistry, and in vivo tumor xenograft formation studies to extensively analyze the molecular and cellular characteristics of breast epithelial cell lineages.

Results

Human breast tissues contain four distinguishable epithelial differentiation states (two luminal phenotypes and two basal phenotypes) that differ on the basis of CD24, EpCAM and CD49f expression. Primary human breast cancer tissues also contain these four cellular states, but in altered proportions compared to normal tissues. In contrast, cultured cancer cell lines are enriched for rare basal and mesenchymal epithelial phenotypes, which are normally present in small numbers within human tissues. Similarly, cultured normal human mammary epithelial cell lines are enriched for rare basal and mesenchymal phenotypes that represent a minor fraction of cells within reduction mammoplasty tissues. Furthermore, although normal human mammary epithelial cell lines exhibit features of bi-potent progenitor cells they are unable to differentiate into mature luminal breast epithelial cells under standard culture conditions.

Conclusions

As a group breast cancer cell lines represent the heterogeneity of human breast tumors, but individually they exhibit increased lineage-restricted profiles that fall short of truly representing the intratumoral heterogeneity of individual breast tumors. Additionally, normal human mammary epithelial cell lines fail to retain much of the cellular diversity found in human breast tissues and are enriched for differentiation states that are a minority in breast tissues, although they do exhibit features of bi-potent basal progenitor cells. These findings suggest that collections of cell lines representing multiple cell types can be used to model the cellular heterogeneity of tissues.
Methylation Allelic Polymorphism (MAP) in Chorionic Gonadotropin β5 (CGB5) and Its Association with Pregnancy Success
Authors: Uusküla Liis , Rull Kristiina , Nagirnaja Liina , Laan Maris
Published: October 2010

Context: Increased epigenetic variability in the placenta may have evolved in response to its role in mediating the conflicting demands of the mother and fetus. One essential guardian of early pregnancy maintenance is the placental hormone human chorionic gonadotropin (HCG).

Objective: Among the four primate-specific duplicate HCGβ-coding genes, chorionic gonadotropin-β8 (CGB8) and chorionic gonadotropin-β5 (CGB5) jointly contribute 62–82% of the total HCGβ transcript pool. Because these genes share common features with known imprinted placenta-expressed loci, we addressed the role of epigenetic mechanisms affecting their action.

Design and Subjects: Parental origin of CGB5 and CGB8 transcripts and promoter methylation patterns were addressed in trophoblastic tissues from 23 mother-offspring duos and nine mother-father-offspring trios including the following: 1) third-trimester normal delivery at term (n = 14), 2) first-trimester elective termination of uncomplicated pregnancy (n = 10), and 3) first-trimester recurrent (≥3) miscarriage (n = 8).

Results: A normal uncomplicated pregnancy was characterized by balanced, biallelic expression of CGB5 and CGB8. However, in three (two recurrent miscarriage and one early elective termination of uncomplicated pregnancy) of nine genetically informative cases of CGB5, monoallelic expression of maternal alleles and hemimethylated gene promoters were identified.

Conclusion: Our finding may represent a novel methylation allelic polymorphism or gain of imprinting in CGB5 promoter leading to expressional silencing of paternal alleles and increasing susceptibility to pregnancy loss. Aberrant methylation patterns in placenta may result from random reprogramming defects affecting normal implantation process. Alternatively, methylation allelic polymorphism in the placenta favoring the failure of pregnancy may arise as a response to cellular stress caused by, in general, aneuploidy or conditions in placental-maternal interface.
Prediction of Aqueous Solubility of Drug-Like Compounds by Using an Artificial Neural Network and Least-Squares Support Vector Machine
Authors: Fatemi Mohammad Hossein , Heidari Afsane , Ghorbanzade Mehdi
Published: October 2010

In this work the aqueous solubilities of 145 drug-like compounds were predicted from their theoretical derived molecular descriptors. Descriptors which were selected by stepwise multiple subset selection methods are; 1st-order solvation connectivity index, average span R, overall hydrogen bond basicity, and percent of hydrophilic surface area. These descriptors can encode features of molecules which are effected on dispersion, hydrophobic and steric interactions between solute and solvent molecules. To develop quantitative structure–activity relationship (QSAR) models, the methods of multiple linear regressions, least-squares support vector machine, and artificial neural network (ANN) were used by applying the selected descriptors as their inputs. The obtained statistical parameters of these models revealed that ANN model was superior to other methods. The standard error (SE), average error (AE), and average absolute error (AAE) for ANN model are: SE = 0.714, AE = −0.178, and AAE = 0.546, while these values for internal test set are: SE = 0.830, AE = −0.056, and AAE = 0.630 and for external test set are: SE = 0.762, AE = −0.431, and AAE = 0.626, respectively. Moreover the leave-many-out cross validation test was used to further investigate the prediction power and robustness of model, which lead to RL10O2 = 0.816 and SPRESS = 0.32 for ANN model, which revealed the reliability of this model.
Ethyl 2-Cyano-2-(hydroxyimino)acetate (Oxyma): An Efficient and Convenient Additive Used with Tetramethylfluoroformamidinium Hexafluorophosphate (TFFH) to Replace 1-Hydroxybenzotriazole (HOBt) and 1-Hydroxy-7-azabenzotriazole (HOAt) during Peptide Synthesis
Authors: Khattab Sherine N
Published: October 2010

The appropriateness of ethyl 2-cyano-2-(hydroxyimino)acetate (Oxyma) as a substitute for benzotriazole-based additives, for use in the TFFH approach for peptide synthesis, is discussed in terms of its capacity to control racemization, its coupling efficiency in difficult couplings either for stepwise or segment coupling in solution- and solid-phase coupling. In addition, Boc-based solution-phase peptide synthesis and its stability in the presence of growing peptide chains were studied. Oxyma displayed remarkable results in terms of racemization depression together with impressive coupling efficiency in both solution- and solid-phase synthesis. Furthermore, Oxyma suggests a lower risk of explosion than HOBt and HOAt.