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At least 667 records · Page 37Linked to original sources
PubMed2006

Proteome analysis of glandular parotid and submandibular-sublingual saliva in comparison to whole human saliva by two-dimensional gel electrophoresis.

The secretions of the salivary parotid and submandibular-sublingual (SMSL) glands constitute the main part of whole human saliva (WS) in which proline-rich proteins (PRPs) and mucins represent dominant groups. Although proteome analysis had been performed on WS, no identification of PRPs or mucins by 2-DE and MS was achieved in WS and no comprehensive analysis of both glandular secretions is available so far. The aim of this study was to compare the protein map of WS to parotid and SMSL secretions for the display of PRPs and mucins. WS and glandular secretions were subjected to 2-DE and spots were analyzed by MALDI-MS. New components identified in WS were cyclophilin-B and prolyl-4-hydroxylase. Also acidic and basic PRPs as well as the proline-rich glycoprotein (PRG) could now be mapped in WS. Acidic PRPs were found equally in parotid and SMSL secretions, whereas basic PRPs and PRG were found primarily in parotid secretion. Salivary mucin MUC7 was identified in SMSL secretion. Thus, the more abundant proteins of WS can be explained mainly by mixed contributions of parotid and SMSL secretions with only few components remaining that may be derived from local sources in the oral cavity.

Amino Acid Sequence↗
PubMed2004

Chemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes.

Quantitative proteome profiling using mass spectrometry and stable isotope dilution is being widely applied for the functional analysis of biological systems and for the detection of clinical, diagnostic or prognostic marker proteins. Because of the enormous complexity of proteomes, their comprehensive analysis is unlikely to be routinely achieved in the near future. However, in recent years, significant progress has been achieved focusing quantitative proteomic analyses on specific protein classes or subproteomes that are rich in biologically or clinically important information. Such projects typically combine the use of chemical probes that are specific for a targeted group of proteins and may contain stable isotope signatures for accurate quantification with automated tandem mass spectrometry and bioinformatics tools for data analysis. In this review, we summarize technical and conceptual advances in quantitative subproteome profiling based on tandem mass spectrometry and chemical probes.

Amino Acids↗
PubMed2000

Laparoscopic splenectomy in chronic idiopathic thrombocytopenic purpura.

Splenectomy remains the definitive treatment for idiopathic thrombocytopenic purpura (ITP). Issues related to timing of splenectomy, perioperative management of platelet count, deep vein thrombosis prophylaxis, and preoperative vaccination are not standardized. Predicting the outcome of splenectomy is desirable but, again, consistent evidence for a particular approach is lacking. Laparoscopic splenectomy, first introduced in 1991, has removed some of the barriers to acceptance of splenectomy and may well change its place in the various treatment algorithms. This article reviews current knowledge with respect to laparoscopic splenectomy and provides an analysis of current evidence regarding issues of safety, efficacy, and cost effectiveness. Surgical technique is briefly reviewed. The information is drawn from a comprehensive analysis of the literature, as well as my own large experience with laparoscopic splenectomy, the majority of which has been focused on laparoscopic splenectomy for ITP.

Chronic Disease↗
PubMed2003

Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry.

Quantitative proteome profiling using stable isotope protein tagging and automated tandem mass spectrometry (MS/MS) is an emerging technology with great potential for the functional analysis of biological systems and for the detection of clinical diagnostic or prognostic marker proteins. Owing to the enormous complexity of proteomes, their comprehensive analysis is an as-yet-unresolved technical challenge. However, biologically or clinically important information can be obtained if specific, information-rich protein classes, or sub-proteomes, are isolated and analyzed. Glycosylation is the most common post-translational modification. Here we describe a method for the selective isolation, identification and quantification of peptides that contain N-linked carbohydrates. It is based on the conjugation of glycoproteins to a solid support using hydrazide chemistry, stable isotope labeling of glycopeptides and the specific release of formerly N-linked glycosylated peptides via peptide- N-glycosidase F (PNGase F). The recovered peptides are then identified and quantified by MS/MS. We applied the approach to the analysis of plasma membrane proteins and proteins contained in human blood serum.

Amino Acid Sequence↗
PubMed2004

Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing.

The NCBI Reference Sequence (RefSeq) project and the NIH Mammalian Gene Collection (MGC) together define a set of approximately 30,000 nonredundant human mRNA sequences with identified coding regions representing 17,000 distinct loci. These high-quality mRNA sequences allow for the identification of transcribed regions in the human genome sequence, and many researchers accept them as the correct representation of each defined gene sequence. Computational comparison of these mRNA sequences and the recently published essentially finished human genome sequence reveals several thousand undocumented nonsynonymous substitution and frame shift discrepancies between the two resources. Additional analysis is undertaken to verify that the euchromatic human genome is sufficiently complete--containing nearly the whole mRNA collection, thus allowing for a comprehensive analysis to be undertaken. Many of the discrepancies will prove to be genuine polymorphisms in the human population, somatic cell genomic variants, or examples of RNA editing. It is observed that the genome sequence variant has significant additional support from other mRNAs and ESTs, almost four times more often than does the mRNA variant, suggesting that the genome sequence is more accurate. In approximately 15% of these cases, there is substantial support for both variants, suggestive of an undocumented polymorphism. An initial screening against a 24-individual genomic DNA diversity panel verified 60% of a small set of potential single nucleotide polymorphisms from which successful results could be obtained. We also find statistical evidence that a few of these discrepancies are due to RNA editing. Overall, these results suggest that the mRNA collections may contain a substantial number of errors. For current and future mRNA collections, it may be prudent to fully reconcile each genome sequence discrepancy, classifying each as a polymorphism, site of RNA editing or somatic cell variation, or genome sequence error.

Computational Biology↗
PubMed1992

Electronystagmographic features in some peripheral and central vestibular disorders: application of multiple discriminant analysis of electronystagmographic parameters.

In routine clinical electronystagmographic (ENG) tests (postrotatory, optokinetic, caloric and tracking tests), eye movement signals were analyzed and a multiple discriminant analysis was carried out with the aid of a microcomputer. Six parameters were selected and, based on these, two functions for discriminating between peripheral and central disorders were established. Discrimination between 35 patients with peripheral lesions and 15 patients with central lesions was made with a correct classification rate of 97.1 and 86.7%, respectively. These rates are significantly higher than that of any single ENG test analysis. Our results indicate that the clinical application of ENG can be improved by searching for more sensitive ENG parameters and adopting the comprehensive analysis approach.

Adult↗
PubMed2002

Novel estrogen and tamoxifen induced genes identified by SAGE (Serial Analysis of Gene Expression).

The breast cancer promoting effects of estrogen and the chemopreventive effects of tamoxifen are thought to be mediated by the estrogen receptor, a ligand-dependent transcription factor. Therefore, comprehensive analysis of gene expression profiles following estrogen or tamoxifen treatment may help us better understand the role estrogen plays in tumorigenesis. We utilized SAGE (Serial Analysis of Gene Expression) technology to identify genes regulated by estrogen and tamoxifen in the ZR75-1 estrogen dependent breast cancer cell line. In this manner we have identified several genes that were regulated by estrogen or tamoxifen. Here we report the identification and initial characterization of EIT-6 (Estrogen Induced Tag-6), a novel nuclear protein and a new member of the evolutionarily conserved SM-20 family of growth regulatory immediate-early genes. EIT-6 appears to be a direct transcriptional target of the estrogen receptor and constitutive expression of EIT-6 promotes colony growth in human breast cancer cells. These data indicate that EIT-6 may play a role in estrogen induced cell growth.

Amino Acid Sequence↗
PubMed1994

Speech rate and rhythm in cerebellar dysarthria: an acoustic analysis of syllabic timing.

Auditory-perceptual studies reported inconsistent data with respect to syllabic timing in cerebellar dysarthria, i.e. both reduced and increased variability of syllable durations. The present study performed a comprehensive analysis of syllabic timing during sentence utterances in 14 subjects with a pure cerebellar syndrome (CA). First, the CA patients presented with reduced speech tempo in terms of syllable and utterance durations. Second, a tendency for intrautterance syllabic isochrony, being an aspect of the percept of 'scanning speech', characterized a subgroup of patients with cerebellar dysarthria. Third, increased interutterance durational variability was found in three out of the five syllables considered. Thus, both reduced intrautterance and increased interutterance variability of syllable durations may pertain to cerebellar dysarthria. The latter dimension, however, seems to be more prominent.

Adult↗
PubMed2006

[Analysis of publication of West China Journal of Stomatology from 2000 to 2005].

OBJECTIVE: To analyze the characteristic of publication of West China Journal of Stomatology (WCJS). METHODS: Making use of literature metrology, a comprehensive analysis of the information publication of West China Journal of Stomatology from 2000 to 2005 was made. RESULTS: The quantity of articles published from 2000 to 2005 in West China Journal of Stomatology was 964, the average fund paper ratio was 0.419, 96.78% of articles had more than one author, and the average paper author cooperating degree was 4.01. The authors scattered in 31 provinces. CONCLUSION: West China Journal of Stomatology is one of the most important information source of stomatology.

Bibliometrics↗
PubMed2026

Human Umbilical Cord Mesenchymal Stem Cells in Metabolic Dysfunction-associated Fatty Liver Disease (MAFLD) Therapy: Mechanisms, Clinical Efficacy, and Future Perspectives.

There is currently no approved drug treatment for metabolic dysfunction-related fatty liver disease (MAFLD). Umbilical cord-derived mesenchymal stem cells (UC-MSCs) show therapeutic potential, but their mechanism of action is remains incompletely understood. Different from previous reviews that focused on a single pathway, this article presents three important contributions: First, it constructs an integrated "multi-target synergy network" model, clarifying how UC-MSCs coordinate and regulate the inflammatory, metabolic and fibrotic processes through the interactions between the AMPK/mTOR, Nrf2/HO-1 and TGF-β/Smad pathways; Second, it systematically assesses recent clinical trials (2022-2025), identifying several unaddressed barriers to transformation, including the lack of histological endpoint indicators, batch-to-batch differences, and the absence of dose exploration studies; Third, we integrate the latest developments from 2024 to 2025, particularly mitochondrial transfer (mediated by tunnel nanotubes and accompanied by quantitative efficacy data) and exosome circular RNA networks [Formula: see text], which have not been covered in previous reviews. Based on the above analysis, we also propose specific suggestions for standardized GMP production, mandatory genomic stability testing, and long-term safety registration. This review provides a comprehensive analysis of elaborates on the treatment of MAFLD with UC-MSCs from a mechanistic and translational perspective, based on the extensive updates of relevant literature.

Humans↗
PubMedDate not supplied

Expanded interaction fingerprint method for analyzing ligand binding modes in docking and structure-based drug design.

An expanded interaction fingerprint method has been developed for analyzing the binding modes of ligands in docking and structure-based design methods. Taking the basic premise of representing a ligand in terms of a binary string that denotes its interactions with a target protein, we have expanded the method to include additional interaction-specific information. By considering the hydrogen-bonding strength and/or accessibility of the hydrogen bonding groups within a binding site as well as their geometric arrangement we aim to provide a better representation of a ligand-protein interaction. These expanded methods have been applied to the postprocessing of binding poses generated in a docking study for 220 different proteins and to the analysis of ligands generated by an automated ligand-generation algorithm for the anthrax oedema factor. In the docking study, the application of the interaction fingerprint method as a postprocessing tool resulted in an increased success rate in identifying the crystallographic binding mode. In the analysis of the ligands generated for the anthrax oedema factor, the incorporation of additional interaction-specific information resulted in a more intuitive and comprehensive analysis of automated ligand-generation output.

Journal Article↗
PubMed2006

Detecting conserved interaction patterns in biological networks.

Molecular interaction data plays an important role in understanding biological processes at a modular level by providing a framework for understanding cellular organization, functional hierarchy, and evolutionary conservation. As the quality and quantity of network and interaction data increases rapidly, the problem of effectively analyzing this data becomes significant. Graph theoretic formalisms, commonly used for these analysis tasks, often lead to computationally hard problems due to their relation to subgraph isomorphism. This paper presents an innovative new algorithm, MULE, for detecting frequently occurring patterns and modules in biological networks. Using an innovative graph simplification technique based on ortholog contraction, which is ideally suited to biological networks, our algorithm renders these problems computationally tractable and scalable to large numbers of networks. We show, experimentally, that our algorithm can extract frequently occurring patterns in metabolic pathways and protein interaction networks from the KEGG, DIP, and BIND databases within seconds. When compared to existing approaches, our graph simplification technique can be viewed either as a pruning heuristic, or a closely related, but computationally simpler task. When used as a pruning heuristic, we show that our technique reduces effective graph sizes significantly, accelerating existing techniques by several orders of magnitude! Indeed, for most of the test cases, existing techniques could not even be applied without our pruning step. When used as a stand-alone analysis technique, MULE is shown to convey significant biological insights at near-interactive rates. The software, sample input graphs, and detailed results for comprehensive analysis of nine eukaryotic PPI networks are available at www.cs.purdue.edu/homes/koyuturk/mule.

Algorithms↗
PubMed2001

The role of introgressive hybridization in the evolution of the Gila robusta complex (Teleostei: Cyprinidae).

The extent and impact of introgressive hybridization was examined in the Gila robusta complex of cyprinid fishes using mitochondrial DNA (mtDNA) sequence variation. Lower Colorado River basin populations of G. robusta, G. elegans, and G. cypha exhibited distinct mtDNAs, with only limited introgression of G. elegans into G. cypha. The impact of hybridization was significant in upper Colorado River basin populations; most upper basin fishes sampled exhibited only G. cypha mtDNA haplotypes, with some individuals exhibiting mtDNA from G. elegans. The complete absence of G. robusta mtDNA, even in populations of morphologically pure G. robusta, indicates extensive introgression that predates human influence. Analysis of the geographic distribution of variation identified two distinctive G. elegans lineages; however, the small number of individuals and localities sampled precluded a comprehensive analysis. Analysis of haplotype and population networks for G. cypha mtDNAs from 15 localities revealed low divergence among haplotypes; however, significant frequency differences among populations within and among drainages were found, largely attributable to samples in the Little Colorado River region. This structure was not associated with G. cypha and G. robusta, as morphotypes from the same location are more similar than conspecific forms in other locations. This indicates that morphological and mtDNA variation are affected by different evolutionary forces in Colorado River Gila and illustrates how both hybridization and local adaptation can play important roles in evolution.

Animals↗
PubMed2002

Analysis of age-dependant alteration in the brain gene expression profile following induction of hydrocephalus in rats.

Hydrocephalus is associated with gradual progressive impairment and destruction of cerebral axons and neurons. To provide a comprehensive analysis of gene expression changes in brain due to experimental hydrocephalus we used a DNA microarray screening technique. Hydrocephalus was induced in 3-week-old and 8- to 10-week-old rats by injection of kaolin into cisterna magna. Following induction of hydrocephalus, samples of frontoparietal cerebrum were studied 3 and 36 weeks later in young rats and 1.5 weeks later in adult rats. At the transcriptional level, young rats with subacute hydrocephalus showed overexpression of genes involved in synaptic transmission in parallel to genes associated with protective and compensatory mechanisms. Those with chronic hydrocephalus exhibited some similar changes among synapse-related genes but suppression of other neuronal genes. Expression of myelin-related genes was increased in both groups of rats with early onset hydrocephalus but suppressed in adult rats with acute hydrocephalus. Changes in genes related to extracellular matrix molecules suggest that there might be remodeling in this compartment. Adult rats showed elevated expression of inflammatory genes, likely related to kaolin-induced inflammation, but they failed to show changes in genes involved in compensatory or protective mechanisms. These results indicate that there is an age- and duration-dependent difference in the gene expression profiles of kaolin-induced hydrocephalus and they present avenues for future research.

Aging↗
PubMed2006

Gene expression analysis in blood cells in response to unmodified and 2'-modified siRNAs reveals TLR-dependent and independent effects.

Ribonucleic nucleic acid recognition by Toll-like receptors (TLRs) induces innate immune responses. However, no comprehensive analysis of gene expression in human blood cells in response to unmodified and 2'-modified immunostimulatory RNAs has been reported. Using oligonucleotide microarrays, we show that around 400 genes were significantly (P<0.001) altered in peripheral blood mononuclear cells (PBMC) in response to either single-stranded (ss) or double-stranded (ds) small interfering RNAs (siRNAs). Most of the upregulated genes encode proteins involved in innate and adaptive immune responses, including proinflammatory cytokines, interferons, chemokines and chemokine receptors. Genes encoding proteins involved in lymphocyte activation (e.g. CD80, CD40, and CD69) and in regulation of the immune responses (e.g. SOCS proteins) were upregulated. Also, genes encoding for antiviral proteins (Mx1, Mx2, TRIM proteins), and interferon regulatory factors (e.g. IRF7) were upregulated. Around 90% of the genes (140 out of 160) affected by R-848, a specific ligand for TLR7 and TLR8, were also affected by ss siRNAs or ds siRNAs, indicating that the signaling pathways activated by R-848 are also activated by immunostimulatory siRNAs. In addition to immunoactivation via TLRs, ss siRNAs and ds siRNAs induced TLR-independent gene alterations. Surprisingly, replacement of only uridine bases with either 2'-fluoro or 2'-O-methyl modified counterparts abrogated all the observed bystander effects. Collectively, these microarray data offer for the first time an insight into human PMBC response to immunostimulatory RNAs such as ss siRNAs and ds siRNAs. The data should help to define strategies to either enhance or avoid the non-specific effects of siRNAs in order to develop safe therapeutics.

Gene Expression Profiling↗
PubMed2005

Cytogenetic alterations in nonmelanoma skin cancer: a review.

Since the advent of cytogenetic analysis, knowledge about fundamental aspects of cancer biology has increased, allowing the processes of cancer development and progression to be more fully understood and appreciated. Classical cytogenetic analysis of solid tumors had been considered difficult, but new advances in culturing techniques and the addition of new cytogenetic technologies have enabled a more comprehensive analysis of chromosomal aberrations associated with solid tumors. Our purpose in this review is to discuss the cytogenetic findings on a number of nonmelanoma skin cancers, including squamous- and basal cell carcinomas, keratoacanthoma, squamous cell carcinoma in situ (Bowen's disease), and solar keratosis. Through classical cytogenetic techniques, as well as fluorescence-based techniques such as fluorescence in situ hybridization and comparative genomic hybridization, numerous chromosomal alterations have been identified. These aberrations may aid in further defining the stages and classifications of nonmelanoma skin cancer and also may implicate chromosomal regions involved in progression and metastatic potential. This information, along with the development of newer technologies (including laser capture microdissection and comparative genomic hybridization arrays) that allow for more refined analysis, will continue to increase our knowledge about the role of chromosomal events at all stages of cancer development and progression and, more specifically, about how they are associated with nonmelanoma skin cancer.

Chromosome Aberrations↗
PubMed2002

Twists, knots, and rings in proteins. Structural definition of the cyclotide framework.

In recent years an increasing number of miniproteins containing an amide-cyclized backbone have been discovered. The cyclotide family is the largest group of such proteins and is characterized by a circular protein backbone and six conserved cysteine residues linked by disulfide bonds in a tight core of the molecule. These form a cystine knot in which an embedded ring formed by two of the disulfide bonds and the connecting backbone segment is threaded by a third disulfide bond. In the current study we have undertaken high resolution structural analysis of two prototypic cyclotides, kalata B1 and cycloviolacin O1, to define the role of the conserved residues in the sequence. We provide the first comprehensive analysis of the topological features in this unique family of proteins, namely rings (a circular backbone), twists (a cis-peptide bond in the Möbius cyclotides) and knots (a knotted arrangement of the disulfide bonds).

Amino Acid Sequence↗
PubMed2006

The impact of ejection fraction on outcomes after percutaneous coronary intervention in patients with congestive heart failure: an analysis of the National Heart, Lung, and Blood Institute Percutaneous Transluminal Coronary Angioplasty Registry and Dynamic Registry.

BACKGROUND: Patients with congestive heart failure (CHF) have higher rates of adverse outcomes after percutaneous coronary intervention (PCI). A comprehensive analysis of outcomes in patients with CHF in the current era has not been done. We studied the outcomes of patients with CHF who underwent PCI in the National Heart, Lung, and Blood Institute-sponsored Percutaneous Transluminal Coronary Angioplasty (PTCA) and Dynamic registries. METHODS: We evaluated demographic and angiographic characteristics and the clinical outcomes of patients with CHF in the Dynamic Registry and the PTCA Registry, excluding patients with acute myocardial infarction. In the Dynamic Registry, patients with CHF (n = 503) were compared with patients without CHF (n = 4194), and patients with CHF with a preserved ejection fraction (EF) (n = 134) were compared with patients with CHF who have a reduced EF (n = 199). The patients with CHF in the 1997 through 2001 Dynamic Registry (n = 236) were then similarly compared with patients with CHF in the earlier PTCA Registry (n = 117). RESULTS: In the Dynamic Registry, compared with patients without CHF, patients with CHF had a higher-risk clinical and angiographic profile, and a higher mortality rate both inhospital (2.6% vs 0.4%, P < or = .001) and at 1 year (13.1% vs 3.0%, P < .001). Patients with reduced EF had higher inhospital mortality rates and a trend toward higher mortality at 1 year. The patients with CHF in the Dynamic Registry compared with those in the PTCA Registry had a higher risk profile yet had significantly higher procedural success rates and improved clinical outcomes. CONCLUSIONS: Although CHF remains a strong predictor of adverse outcomes after PCI, significant improvement seen in the past decade is likely related to improved procedural techniques and improved medical therapy.

Aged↗