bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined partial exon skipping and cryptic splice site activation as a new molecular mechanism for recessive type 1 von Willebrand disease
Authors: Gallinaro Lisa , Sartorello Francesca , Pontara Elena , Cattini Maria , Bertomoro Antonella , Bartoloni Lucia , Pagnan Antonio , Casonato Alessandra 
Published: December 2006

SummaryWe describe the complex picture associated with a mutated splice junction in intron 13 of von Willebrand factor (VWF) gene. The proband, characterized by a marked decrease in plasma and platelet VWF and near normal multimer organization, was classified as recessive type 1 von Willebrand disease (VWD). Genetic analysis demonstrated that he was homozygous for the 1534–3C>A mutation in the consensus sequence of the acceptor splicing site of intron 13 of the VWF gene. Platelet mRNA analysis documented three VWF transcripts: a wild type generated by the correct recognition of the mutated splice site, a smaller transcript not containing exon 14, and a longer one that, in addition to exons 13 and 14, included a 62bp fragment corresponding to the end of intron 13. The small transcript derives from the skipping of exon 14, the long one from the activation of a cryptic splice site in intron 13; both show a premature stop codon inVWF propeptide, so the probandVWF derives entirely from the correct splice site recognition. Combined incomplete exon skipping and cryptic splice site activation are first recognized in VWD. Since the 1534–3C>A mutation does not abolish the normal processing of mRNA, it is unlikely to be found in type 3VWD. This mutation therefore appears to be peculiar to type 1 VWD.
A non-anticoagulant synthetic pentasaccharide reduces inflammation in a murine model of kidney ischemia-reperfusion injury
Authors: Frank Rolf , Holscher Todd , Schabbauer Gernot , Tencati Michael , Pawlinski Rafal , Weitz Jeffrey , Mackman Nigel 
Published: December 2006

SummaryFondaparinux is a synthetic pentasaccharide that selectively inhibits factor Xa (FXa) in an antithrombin-dependent fashion.This newly developed anticoagulant is used in the prevention and treatment of venous thromboembolism. Recently, we showed that fondaparinux reduces inflammation and protects the kidney from ischemia-reperfusion (I/R) injury. However, the relative contributions of the anticoagulant and anti-inflammatory activities of fondaparinux to the observed protection is unknown.To address this, we chemically modified fondaparinux to abolish its affinity for antithrombin and analyzed the effect of this non-anti- coagulant (NAC)-pentasaccharide on binding of U937 cells to P-selectin in vitro and on inflammation in a murine model of kidney I/R injury. NAC-pentasaccharide was as effective as fondaparinux at inhibiting the binding of U937 cells to P-selectin.In addition, NAC-pentasaccharide significantly reduced IL-6 and MIP-2 expression and injury in the kidney I/R model.These findings indicate that the anti-inflammatory activity of fondaparinux can be dissociated from its anticoagulant activity and that NACpentasaccharide is protective in kidney I/R injury.
Focal arterial inflammation is augmented in mice with a deficiency of the protein C gene
Authors: Ganopolsky Jorge , Noria Francisco , Sandoval-Cooper Mayra , Ploplis Victoria , Castellino Francis 
Published: December 2006

SummaryIncreased risk of thrombosis, with propitious conditions for fibrin deposition, along with upregulation of inflammation, are important factors that enhance plaque formation in atherosclerosis. Evidence supporting the role of anticoagulant protein C (PC) as an inflammatory agent has emerged, supplementing its wellknown function as an anticoagulant. Thus, we sought to examine whethera PC deficiency would lead to an enhanced response to an acute arterial hyperplasic challenge. The presentation of early arterial inflammation was studied using a copper/silicone arterial cuff model of accelerated focal neointimal remodeling in mice with a heterozygous total deficiency of PC (PC+/−). Increased inflammation, cell proliferation, cell migration, fibrin elevation, and tissue necrosis were observed in the treated arteries of PC+/−mice, as compared to arteries of equally challenged age- and gender-matched WT mice. These results indicate that PC+/−mice subjected to this challenge displayed enhanced focal arterial inflammation and thrombosis, leading to larger neointimas and subsequent localized occlusion, as compared to their WT counterparts.
Effect of antiplatelet agents clopidogrel, aspirin, and cilostazol on circulating tissue factor procoagulant activity in patients with peripheral arterial disease
Authors: Vaidyula Vijender , Bagga Shagun , Jalagadugula Gauthami , Gaughan John , Wilhite Douglas , Comerota Anthony , Rao A. 
Published: December 2006

SummaryTissue factor (TF) is the physiological initiating mechanism for blood coagulation. Platelets play an important role in monocyte TF expression, thrombosis and inflammation. Aspirin, clopidogrel and cilostazol, which inhibit platelet responses by different mechanisms, are widely used in patients with arterial diseases. We tested the hypothesis that platelet-inhibiting agents inhibit the levels of circulatingTF procoagulant activity (TF-PCA) in patients with peripheral arterial disease (PAD).Twenty-six patients with lower extremity PAD, average age 65.9 ± 8.4 years (mean± SEM), were studied at baseline and following sequential twoweek treatment regimens with aspirin (325 mg daily), clopidogrel (75 mg daily) or a phosphodiesterase inhibitor cilostazol (100 mg twice daily) singly, and with each possible combination of these agents. Circulating TF-PCA in whole blood, and plasma factor VIIa, prothrombin fragment F1.2, thrombin-antithrombin complexes (TAT), and P-selectin were measured. Baseline TFPCA levels in the patients were elevated (131 ± 19 U/ml) compared to control subjects (23 ± 2, p<0.0001).TF-PCA levels declined following treatment with clopidogrel alone, and with combinations of clopidogrel with aspirin or cilostazol, with the lowest levels being with the triple-drug combination. Plasma P-selectin declined in all treatment groups. No changes were noted in plasma factorVIIa, F1.2 or TAT.In conclusion, treatment of PAD patients with antiplatelet agents decreases circulatingTF, a molecule with prothrombotic and proinflammatory effects. These findings suggest an unrecognized mechanism, beyond inhibiting aggregation responses, for the efficacy of antiplatelet drugs in patients with arterial diseases.
Palmitoylation at Cys595 is essential for PECAM-1 localisation into membrane microdomains and for efficient PECAM-1-mediated cytoprotection
Authors: Sardjono Caroline , Harbour Stacey , Yip Jana , Paddock Cathy , Tridandapani Susheela , Newman Peter , Jackson Denise 
Published: December 2006

SummaryThe Ig-ITIM superfamily member, PECAM-1 acts as a negative regulator of ITAM-signalling pathways in platelets involving GPVI/FcR gamma chain and FcγRIIa. This negative feedback loop involves regulation of collagen and GPVI-dependent aggregation events, platelet-thrombus-growth on immobilised collagen under flow and FcγRIIa-mediated platelet responses. In this study, we show that PECAM-1 is selectively palmitoylated involving a thioester linkage with an unpaired cysteine residue at amino acid position 595 in its cytoplasmic domain. As palmitoylation is known to target proteins to membrane microdomains, we investigated the microdomain localisation for PECAM-1 in platelets and nucleated cells. In unstimulated platelets, ∼20% of PECAM-1 is localised toTriton-insoluble microdomain fractions and it does not increase with platelet activation by collagen, collagen-related peptide, thrombin-or human-aggregated IgG. PECAM-1 is in close physical proximity with GPVI in platelet microdomains. Removal of platelet cytoskeleton prior to sucrose-density-gradient separation showed that PECAM-1 was associated with both theTriton-soluble and membrane skeleton in microdomain-associated fractions. Disruption of microdomains by membrane-cholesterol depletion resulted in loss of PECAM-1 localisation to membrane microdomains. Mutational analysis of juxtamembrane cysteine residue to alanine (C595A) of human PECAM-1 resulted in loss of palmitoylation and a sixfold decrease in association with membrane microdomains. Functionally, the palmitoylated cysteine 595 residue is required, in part, for efficient PECAM-1-mediated cytoprotection. These results show that cysteine 595 is required for constitutive association of PECAM-1 with membrane microdomains and PECAM-1-mediated cytoprotection, where it may act as a crucial regulator of signaling and apoptosis events.
Comparison of VASP-phosphorylation assay to light-transmission aggregometry in assessing inhibition of the platelet ADP P2Y12 receptor
Authors: Pampuch Agnieszka , de Gaetano Giovanni , Cerletti Chiara 
Published: December 2006

SummaryThere is need to improve platelet function testing to monitor the response to antiplatelet drugs. We compared flow-cytometric analysis of intraplatelet vasodilator-stimulated phosphoprotein phosphorylation (VASP-P) to light-transmission aggregometry for the detection of drug-induced in-vitro inhibition of the platelet P2Y12 ADP receptor on 22 healthy subjects (10 males, 12 females, 28.5 ± 6.6 years). The platelet reactivity index (PRI) of VASP was calculated both from mean fluorescence intensity (MFI) and percent of fluorescence-positive platelets in the presence of PGE1 with or without ADP (10 µM). Platelet aggregation was induced by ADP (1.25, 2.5 and 5 µM). Cangrelor, a competitive inhibitor of the P2Y12 receptor, preincubated 5 minutes, induced a concentration-dependent inhibition of platelet ADP-receptor function in both tests. Indeed PRI (%) based on either MFI or percent platelets gated were highly correlated with each other (r = 0.97, p<0.0001) and with aggregation in- duced by ADP. The IC50 of cangrelor against each of the three ADP concentrations used in aggregometry increased from 5.8 ± 3.4 nM to 23.1 ± 4.0 nM and to 98 ± 25 nM, respectively. The IC50 of cangrelor based on VASP-P was within the same range (25.5 ± 7.7 nM). No correlation was observed between IC50 values of cangrelor and ADP concentrations giving 50% effect (EC50) in the absence of the drug. However, at 10 nM cangrelor seven subjects could be identified by the VASP-P assay as “low responders” to the drug (PRI> 50%), and six of them also had an aggregation response to 5 µM ADP > 50%. These six subjects showed the lowest ADP EC50 values in the absence of the drug, possibly reflecting high sensitivity of their platelet P2Y12 receptors to ADP. In conclusion, both the VASP-P assay and light-transmission aggregometry detect in a comparable way in-vitro pharmacological inhibition of the platelet P2Y12 ADP receptor and its individual variability.
Identification of new members of hydrophobin family using primary structure analysis
Authors: Yang Kuan , Deng Youping , Zhang Chaoyang , Elasri Mohamed 
Published: December 2006

Abstract

Background
Hydrophobins are fungal proteins that can turn into amphipathic membranes at hydrophilic/hydrophobic interfaces by self-assembly. The assemblages by Class I hydrophobins are extremely stable and possess the remarkable ability to change the polarity of the surface. One of its most important industrial applications is its usage as paint. Without detailed knowledge of the 3D structure and self-assembly principles of hydrophobins, it is difficult to make significant progress in furthering its research.

Results
In order to provide useful information to hydrophobin researchers, we analyzed primary structure of hydrophobins to gain more insight about these proteins. In this paper, we presented an in-depth primary sequence analysis using batch BLAST search of the database, sequence filtering by programming and motif finding by MEME. We used batch BLAST to find similar sequences in the NCBI nr database. Then we used MEME to find out motifs. Based on the newly found motifs and the well-known C-CC-C-C-CC-C pattern we used MAST to search the entire nr database. At the end, domain search and phylogenetic analysis were conducted to confirm the result. After searching the nr database with the new PSSM-format motifs identified by MEME, many sequences from various species were found by MAST. Filtering process by pattern, domain and length left 9 qualified candidates.

Conclusion
All of 9 newly identified potential hydrophobins possess the common pattern and hydrophobin domain. From the multiple sequence alignment result, we can see that some of them are grouped very close to other known hydrophobins, which means their phylogenetic relationship is very close and it is highly plausible that they are indeed hydrophobin proteins.
In silico modelling of hormone response elements
Authors: Stepanova Maria , Lin Feng , Lin Valerie C-L 
Published: December 2006

Abstract

Background
An important step in understanding the conditions that specify gene expression is the recognition of gene regulatory elements. Due to high diversity of different types of transcription factors and their DNA binding preferences, it is a challenging problem to establish an accurate model for recognition of functional regulatory elements in promoters of eukaryotic genes.

Results
We present a method for precise prediction of a large group of transcription factor binding sites – steroid hormone response elements. We use a large training set of experimentally confirmed steroid hormone response elements, and adapt a sequence-based statistic method of position weight matrix, for identification of the binding sites in the query sequences. To estimate the accuracy level, a table of correspondence of sensitivity vs. specificity values is constructed from a number of independent tests. Furthermore, feed-forward neural network is used for cross-verification of the predicted response elements on genomic sequences.

Conclusion
The proposed method demonstrates high accuracy level, and therefore can be used for prediction of hormone response elements de novo. Experimental results support our analysis by showing significant improvement of the proposed method over previous HRE recognition methods.
Estimate haplotype frequencies in pedigrees
Authors: Zhang Qiangfeng , Zhao Yuzhong , Chen Guoliang , Xu Yun 
Published: December 2006

Abstract

Background
Haplotype analysis has gained increasing attention in the context of association studies of disease genes and drug responsivities over the last years. The potential use of haplotypes has led to the initiation of the HapMap project which is to investigate haplotype patterns in the human genome in different populations. Haplotype inference and frequency estimation are essential components of this endeavour.

Results
We present a two-stage method to estimate haplotype frequencies in pedigrees, which includes haplotyping stage and estimation stage. In the haplotyping stage, we propose a linear time algorithm to determine all zero-recombinant haplotype configurations for each pedigree. In the estimation stage, we use the expectation-maximization (EM) algorithm to estimate haplotype frequencies based on these haplotype configurations. The experiments demonstrate that our method runs much faster and gives more credible estimates than other popular haplotype analysis software that discards the pedigree information.

Conclusion
Our method suggests that pedigree information is of great importance in haplotype analysis. It can be used to speedup estimation process, and to improve estimation accuracy as well. The result also demonstrates that the whole haplotype configuration space can be substituted by the space of zero-recombinant haplotype configurations in haplotype frequency estimation, especially when the considered haplotype block is relatively short.
FM-test: a fuzzy-set-theory-based approach to differential gene expression data analysis
Authors: Liang Lily R , Lu Shiyong , Wang Xuena , Lu Yi , Mandal Vinay , Patacsil Dorrelyn , Kumar Deepak 
Published: December 2006

Abstract

Background
Microarray techniques have revolutionized genomic research by making it possible to monitor the expression of thousands of genes in parallel. As the amount of microarray data being produced is increasing at an exponential rate, there is a great demand for efficient and effective expression data analysis tools. Comparison of gene expression profiles of patients against those of normal counterpart people will enhance our understanding of a disease and identify leads for therapeutic intervention.

Results
In this paper, we propose an innovative approach, fuzzy membership test (FM-test), based on fuzzy set theory to identify disease associated genes from microarray gene expression profiles. A new concept of FM d-value is defined to quantify the divergence of two sets of values. We further analyze the asymptotic property of FM-test, and then establish the relationship between FM d-value and p-value. We applied FM-test to a diabetes expression dataset and a lung cancer expression dataset, respectively. Within the 10 significant genes identified in diabetes dataset, six of them have been confirmed to be associated with diabetes in the literature and one has been suggested by other researchers. Within the 10 significantly overexpressed genes identified in lung cancer data, most (eight) of them have been confirmed by the literatures which are related to the lung cancer.

Conclusion
Our experiments on synthetic datasets show that FM-test is effective and robust. The results in diabetes and lung cancer datasets validated the effectiveness of FM-test. FM-test is implemented as a Web-based application and is available for free at http://database.cs.wayne.edu/bioinformatics.
The impact of sample imbalance on identifying differentially expressed genes
Authors: Yang Kun , Li Jianzhong , Gao Hong 
Published: December 2006

Abstract

Background
Recently several statistical methods have been proposed to identify genes with differential expression between two conditions. However, very few studies consider the problem of sample imbalance and there is no study to investigate the impact of sample imbalance on identifying differential expression genes. In addition, it is not clear which method is more suitable for the unbalanced data.

Results
Based on random sampling, two evaluation models are proposed to investigate the impact of sample imbalance on identifying differential expression genes. Using the proposed evaluation models, the performances of six famous methods are compared on the unbalanced data. The experimental results indicate that the sample imbalance has a great influence on selecting differential expression genes. Furthermore, different methods have very different performances on the unbalanced data. Among the six methods, the welch t-test appears to perform best when the size of samples in the large variance group is larger than that in the small one, while the Regularized t-test and SAM outperform others on the unbalanced data in other cases.

Conclusion
Two proposed evaluation models are effective and sample imbalance should be taken into account in microarray experiment design and gene expression data analysis. The results and two proposed evaluation models can provide some help in selecting suitable method to process the unbalanced data.
Degenerated primer design to amplify the heavy chain variable region from immunoglobulin cDNA
Authors: Wang Ying , Chen Wei , Li Xu , Cheng Bing 
Published: December 2006

Abstract

Background
The amplification of variable regions of immunoglobulins has become a major challenge in the cloning of antibody genes, whether from hybridoma cell lines or splenic B cells. Using conventional protocols, the heavy-chain variable region genes often are not amplified successfully from the hybridoma cell lines.

Results
A novel method was developed to design the degenerated primer of immunoglobulin cDNA and to amplify cDNA ends rapidly. Polymerase chain reaction protocols were performed to recognize the VH gene from the hybridoma cell line. The most highly conserved region in the middle of the VH regions of the Ig cDNA was identified, and a degenerated 5'primer was designed, using our algorithms. The VH gene was amplified by both the 3'RACE and 5'RACE. The VH sequence of CSA cells was 399 bp.

Conclusion
The new protocol rescued the amplifications of the VH gene that had failed under conventional protocols. In addition, there was a notable increase in amplification specificity. Moreover, the algorithm improved the primer design efficiency and was shown to be useful both for building VH and VL gene libraries and for the cloning of unknown genes in gene families.
Implantation Serine Proteinases heterodimerize and are critical in hatching and implantation
Authors: Sharma Navneet , Liu Shiying , Tang Lin , Irwin Jackie , Meng Guoliang , Rancourt Derrick E 
Published: December 2006

Abstract

Background
We have recently reported the expression of murine Implantation Serine Proteinase genes in pre-implantation embryos (ISP1) and uterus (ISP1 and ISP2). These proteinases belong to the S1 proteinase family and are similar to mast cell tryptases, which function as multimers.

Results
Here, we report the purification and initial characterization of ISP1 and 2 with respect to their physico-chemical properties and physiological function. In addition to being co-expressed in uterus, we show that ISP1 and ISP2 are also co-expressed in the pre-implantation embryo. Together, they form a heterodimer with an approximate molecular weight of 63 kD. This complex is the active form of the enzyme, which we have further characterized as being trypsin-like, based on substrate and inhibitor specificities. In addition to having a role in embryo hatching and outgrowth, we demonstrate that ISP enzyme is localized to the site of embryo invasion during implantation and that its activity is important for successful implantation in vivo.

Conclusion
On the basis of similarities in structural, chemical, and functional properties, we suggest that this ISP enzyme complex represents the classical hatching enzyme, strypsin. Our results demonstrate a critical role for ISP in embryo hatching and implantation.
Fast sequence evolution of Hox and Hox-derived genes in the genus Drosophila
Authors: Casillas Sònia , Negre Bárbara , Barbadilla Antonio , Ruiz Alfredo 
Published: December 2006

Abstract

Background
It is expected that genes that are expressed early in development and have a complex expression pattern are under strong purifying selection and thus evolve slowly. Hox genes fulfill these criteria and thus, should have a low evolutionary rate. However, some observations point to a completely different scenario. Hox genes are usually highly conserved inside the homeobox, but very variable outside it.

Results
We have measured the rates of nucleotide divergence and indel fixation of three Hox genes, labial (lab), proboscipedia (pb) and abdominal-A (abd-A), and compared them with those of three genes derived by duplication from Hox3, bicoid (bcd), zerknüllt (zen) and zerknüllt-related (zen2), and 15 non-Hox genes in sets of orthologous sequences of three species of the genus Drosophila. These rates were compared to test the hypothesis that Hox genes evolve slowly. Our results show that the evolutionary rate of Hox genes is higher than that of non-Hox genes when both amino acid differences and indels are taken into account: 43.39% of the amino acid sequence is altered in Hox genes, versus 30.97% in non-Hox genes and 64.73% in Hox-derived genes. Microsatellites scattered along the coding sequence of Hox genes explain partially, but not fully, their fast sequence evolution.

Conclusion
These results show that Hox genes have a higher evolutionary dynamics than other developmental genes, and emphasize the need to take into account indels in addition to nucleotide substitutions in order to accurately estimate evolutionary rates.