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At least 775 records · Page 43Linked to original sources
PubMed2003

High-throughput proteomic analysis of human infiltrating ductal carcinoma of the breast.

Large-scale proteomics will play a critical role in the rapid display, identification and validation of new protein targets, and elucidation of the underlying molecular events that are associated with disease development, progression and severity. However, because the proteome of most organisms are significantly more complex than the genome, the comprehensive analysis of protein expression changes will require an analytical effort beyond the capacity of standard laboratory equipment. We describe the first high-throughput proteomic analysis of human breast infiltrating ductal carcinoma (IDCA) using OCT (optimal cutting temperature) embedded biopsies, two-dimensional difference gel electrophoresis (2-D DIGE) technology and a fully automated spot handling workstation. Total proteins from four breast IDCAs (Stage I, IIA, IIB and IIIA) were individually compared to protein from non-neoplastic tissue obtained from a female donor with no personal or family history of breast cancer. We detected differences in protein abundance that ranged from 14.8% in stage I IDCA versus normal, to 30.6% in stage IIB IDCA versus normal. A total of 524 proteins that showed > or = three-fold difference in abundance between IDCA and normal tissue were picked, processed and identified by mass spectrometry. Out of the proteins picked, approximately 80% were unambiguously assigned identities by matrix-assisted laser desorbtion/ionization-time of flight mass spectrometry or liquid chromatography-tandem mass spectrometry in the first pass. Bioinformatics tools were also used to mine databases to determine if the identified proteins are involved in important pathways and/or interact with other proteins. Gelsolin, vinculin, lumican, alpha-1-antitrypsin, heat shock protein-60, cytokeratin-18, transferrin, enolase-1 and beta-actin, showed differential abundance between IDCA and normal tissue, but the trend was not consistent in all samples. Out of the proteins with database hits, only heat shock protein-70 (more abundant) and peroxiredoxin-2 (less abundant) displayed the same trend in all the IDCAs examined. This preliminary study demonstrates quantitative and qualitative differences in protein abundance between breast IDCAs and reveals 2-D DIGE portraits that may be a reflection of the histological and pathological status of breast IDCA.

Adult↗
PubMed2005

Pharmacoproteomics.

Proteomics, the comprehensive analysis of the protein complement of the genome of an organism, is becoming an increasingly important discipline for the identification of disease targets. In addition, the effects of drug treatment and metabolism can now be studied on the protein level in a comprehensive manner.

Clinical Medicine↗
PubMed2006

Extraction and protein component analysis of venom from the dissected venom glands of Latrodectus tredecimguttatus.

Black widow spiders (genus Latrodectus) have attracted increasing attention due to frequently reported human injuries caused by them and the potential applications of biologically active components in their venoms. Although a number of studies have described the biological properties and structures of several venomous proteins such as latrotoxins, a comprehensive analysis of protein component of the venom from the spider is not available. We used combinative proteomic strategies to assess the protein components of the crude venom collected from Latrodectus tredecimguttatus by extracting the dissected venom glands. The experiments demonstrated that the crude venom of L. tredecimguttatus has a high abundance of acidic proteins with molecular masses greater than 15 kDa, and the content of proteins and peptides of below 15 kDa is low. 86 unique proteins were identified, part of which were contaminations of cellular components during the extraction, determined in comparison with venom obtained by electrostimulation. Except for members of latrotoxin family that were commonly considered as the primary toxic components of the venom, several other special enzymes and proteins were detected such as protease, phosphatase, lysozyme, inhibitory protein, and so on. These protein components, particularly the proteases, were speculated to play important roles in the action of L. tredecimguttatus venom.

Animals↗
PubMed2004

A genome-wide screen identifies genes required for centromeric cohesion.

During meiosis, two chromosome segregation phases follow a single round of DNA replication. We identified factors required to establish this specialized cell cycle by examining meiotic chromosome segregation in a collection of yeast strains lacking all nonessential genes. This analysis revealed Sgo1, Chl4, and Iml3 to be important for retaining centromeric cohesin until the onset of anaphase II. Consistent with this role, Sgo1 localizes to centromeric regions but dissociates at the onset of anaphase II. The screen described here provides a comprehensive analysis of the genes required for the meiotic cell cycle and identifies three factors important for the stepwise loss of sister chromatid cohesion.

Cell Cycle↗
PubMed2006

Bacterial type III polyketide synthases: phylogenetic analysis and potential for the production of novel secondary metabolites by heterologous expression in pseudomonads.

Type III polyketide synthases (PKS) were regarded as typical for plant secondary metabolism before they were found in microorganisms recently. Due to microbial genome sequencing efforts, more and more type III PKS are found, most of which of unknown function. In this manuscript, we report a comprehensive analysis of the phylogeny of bacterial type III PKS and report the expression of a type III PKS from the myxobacterium Sorangium cellulosum in pseudomonads. There is no precedent of a secondary metabolite that might be biosynthetically correlated to a type III PKS from any myxobacterium. Additionally, an inactivation mutant of the S. cellulosum gene shows no physiological difference compared to the wild-type strain which is why these type III PKS are assumed to be "silent" under the laboratory conditions administered. One type III PKS (SoceCHS1) was expressed in different Pseudomonas sp. after the heterologous expression in Escherichia coli failed. Cultures of recombinant Pseudomonas sp. harbouring SoceCHS1 turned red upon incubation and the diffusible pigment formed was identified as 2,5,7-trihydroxy-1,4-naphthoquinone, the autooxidation product of 1,3,6,8-tetrahydroxynaphthalene. The successful heterologous production of a secondary metabolite using a gene not expressed under administered laboratory conditions provides evidence for the usefulness of our approach to activate such secondary metabolite genes for the production of novel metabolites.

Acyltransferases↗
PubMed2006

Differential analysis of membrane proteins in mouse fore- and hindbrain using a label-free approach.

The ability to quantitatively compare protein levels across different regions of the brain to identify disease mechanisms remains a fundamental research challenge. It requires both a robust method to efficiently isolate proteins from small amounts of tissue and a differential technique that provides a sensitive and comprehensive analysis of these proteins. Here, we describe a proteomic approach for the quantitative mapping of membrane proteins between mouse fore- and hindbrain regions. The approach focuses primarily on a recently developed method for the fractionation of membranes and on-membrane protein digestion, but incorporates off-line SCX-fractionation of the peptide mixture and nano-LC-MS/MS analysis using an LTQ-FT-ICR instrument as part of the analytical method. Comparison of mass spectral peak intensities between samples, mapping of peaks to peptides and protein sequences, and statistical analysis were performed using in-house differential analysis software (DAS). In total, 1213 proteins were identified and 967 were quantified; 81% of the identified proteins were known membrane proteins and 38% of the protein sequences were predicted to contain transmembrane helices. Although this paper focuses primarily on characterizing the efficiency of this purification method from a typical sample set, for many of the quantified proteins such as glutamate receptors, GABA receptors, calcium channel subunits, and ATPases, the observed ratios of protein abundance were in good agreement with the known mRNA expression levels and/or intensities of immunostaining in rostral and caudal regions of murine brain. This suggests that the approach would be well-suited for incorporation in more rigorous, larger scale quantitative analysis designed to achieve biological significance.

Animals↗
PubMed2002

Biochemical analysis of the damage recognition process in nucleotide excision repair.

XPA, XPC-hHR23B, RPA, and TFIIH all are the damage recognition proteins essential for the early stage of nucleotide excision repair. Nonetheless, it is not clear how these proteins work together at the damaged DNA site. To get insight into the molecular mechanism of damage recognition, we carried out a comprehensive analysis on the interaction between damage recognition proteins and their assembly on damaged DNA. XPC physically interacted with XPA, but failed to stabilize the XPA-damaged DNA complex. Instead, XPC-hHR23B was effectively displaced from the damaged DNA by the combined action of RPA and XPA. A mutant RPA lacking the XPA interaction domain failed to displace XPC-hHR23B from damaged DNA, suggesting that XPA and RPA cooperate with each other to destabilize the XPC-hHR23B-damaged DNA complex. Interestingly, the presence of hHR23B significantly increased RPA/XPA-mediated displacement of XPC from damaged DNA, suggesting that hHR23B may modulate the binding of XPC to damaged DNA. Together, our results suggest that damage recognition occurs in a multistep process such that XPC-hHR23B initiates damage recognition, which was replaced by combined action of XPA and RPA. XPA and RPA, once forming a complex at the damage site, would likely work with TFIIH, XPG, and ERCC1-XPF for dual incision.

Animals↗
PubMed2001

An experimental analysis of aggression.

Iwata, Dorsey, Slifer, Bauman, and Richman developed an assessment method to identify the operant functions of self-injurious behavior. In this study, a similar method was used to assess the operant functions of aggression displayed by children and adolescents with developmental disabilities. Although previous research has shown that aggression is an operant behavior, there has been no comprehensive analysis of aggression using analog functional analysis method. Eight children and adolescents participated. The experimental conditions involved attention, escape, materials, no interaction, and control. Results for 7 of the 8 participants identified clear operant functions (positive or negative reinforcement) for aggression. For 1 child, subsequent analyses suggested that aggression was possibly sensitive to peer attention as reinforcement.

Adolescent↗
PubMed1982

Los Alamos sequence analysis package for nucleic acids and proteins.

An interactive system for computer analysis of nucleic acid and protein sequences has been developed for the Los Alamos DNA Sequence Database. It provides a convenient way to search or verify various sequence features, e.g., restriction enzyme sites, protein coding frames, and properties of coded proteins. Further, the comprehensive analysis package on a large-scale database can be used for comparative studies on sequence and structural homologies in order to find unnoted information stored in nucleic acid sequences.

Amino Acid Sequence↗
PubMed1999

An individualized, sensitive frequency range for early detection of ototoxicity.

OBJECTIVE: The aim of this study was to identify auditory frequencies at which serial threshold testing would provide the greatest sensitivity for early detection of ototoxicity. The overall objective is to develop a more time-efficient ototoxicity monitoring protocol. DESIGN: Threshold data were analyzed from 370 hospitalized patients treated with aminoglycoside antibiotics (AMGs) or cisplatin (CDDP) who received serial auditory monitoring before, during, and after treatment at conventional (0.25 to 8 kHz) and high (9 to 20 kHz) frequencies. RESULTS: For patients showing hearing changes due to ototoxicity, a frequency range was identified for its apparent high sensitivity to initial ototoxicity. This sensitive range is identified according to an individual's hearing threshold configuration, and is, therefore, unique for each patient. The range consists of five frequencies, generally separated by 1/6 octave, e.g., 8, 9, 10, 11.2, and 12.5 kHz. To determine frequencies and combinations of frequencies that were most often involved in ototoxicity detection, threshold data in the sensitive range were analyzed in detail. This analysis suggests that patients receiving treatment with AMG or CDDP can be monitored for hearing thresholds at only five frequencies, resulting in an 84% detection rate for AMG and 94% for CDDP compared with monitoring at all conventional and high frequencies. CONCLUSIONS: This comprehensive analysis supports earlier observations that a sensitive, limited frequency range exists in which serial threshold monitoring will provide early warning of ototoxicity before effects in the speech frequency range. This finding is now being evaluated in a prospective investigation.

Aminoglycosides↗
PubMed2005

A comprehensive classification system for lipids.

Lipids are produced, transported, and recognized by the concerted actions of numerous enzymes, binding proteins, and receptors. A comprehensive analysis of lipid molecules, "lipidomics," in the context of genomics and proteomics is crucial to understanding cellular physiology and pathology; consequently, lipid biology has become a major research target of the postgenomic revolution and systems biology. To facilitate international communication about lipids, a comprehensive classification of lipids with a common platform that is compatible with informatics requirements has been developed to deal with the massive amounts of data that will be generated by our lipid community. As an initial step in this development, we divide lipids into eight categories (fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, prenol lipids, saccharolipids, and polyketides) containing distinct classes and subclasses of molecules, devise a common manner of representing the chemical structures of individual lipids and their derivatives, and provide a 12 digit identifier for each unique lipid molecule. The lipid classification scheme is chemically based and driven by the distinct hydrophobic and hydrophilic elements that compose the lipid. This structured vocabulary will facilitate the systematization of lipid biology and enable the cataloging of lipids and their properties in a way that is compatible with other macromolecular databases.

Database Management Systems↗
PubMed1990

[A clinical evaluation of lymphography in bladder tumor].

A study was conducted in a total of 51 patients with urinary bladder tumor who had received surgical operation associated with removal of regional lymph nodes after lymphography. Abnormal findings were observed in lymphogram of 22 patients. The other 29 patients showed no such abnormality. After the operation pathological metastasis was confirmed in 7 patients. Lymphograms of these patients ith positive lymphatic metastasis revealed filling defects in 85.7% and collaterals in 57.4%. There as correlation between the occurrences of these two findings based on quantification analysis III of multivariate analysis. Lymphography before operation showed 87.5% of sensitivity, 65.1% of specificity and accuracy of 68.6%, not having higher accuracy compared to other studies. These results suggest that lymphography, which may have clinical significance, is not a decisive method in exploration of bladder tumor. Comprehensive analysis of diagnostic imaging should be performed, including CT after lymphography.

Female↗
PubMed2002

The impact of the controlled emptying of in-sewer storage on wastewater treatment plant performance.

The use of in-sewer storage is generally considered to be an effective means of minimising the effects of intermittent discharges into receiving watercourses during combined flows. Despite this, very little information is available about the consequential effects these flows may have on recipient wastewater treatment plant performance. Typical problems may include biomass washout (hydraulic), and reduced biological reactor performance due to dilute loading (biological). A study is described where detailed analysis was carried out to ascertain the consequential effects of prolonged dilute loading on an activated sludge wastewater treatment plant in Perth, Scotland. Consideration was given to likely storage volumes which may have been utilised in the catchment to resolve local problems. A comprehensive analysis of resulting treatment plant performance was carried out for variations in flow and various wet weather loadings. It is concluded that storage may cause little or no benefit with respect to ammonia total emissions due to reduced treatment of dry weather flows subsequent to the prolonged combined loading period. This was exacerbated by the long regeneration times of nitrifying bacteria. However, an overall benefit with respect to BOD total emissions would always be expected, as appropriately sized storage would retain the first foul flush at the CSOs, thereby compensating the increased emissions from the downstream wastewater treatment plant.

Ammonia↗
PubMed2006

Identification of potential regulatory motifs in odorant receptor genes by analysis of promoter sequences.

Mouse odorant receptors (ORs) are encoded by >1000 genes dispersed throughout the genome. Each olfactory neuron expresses one single OR gene, while the rest of the genes remain silent. The mechanisms underlying OR gene expression are poorly understood. Here, we investigated if OR genes share common cis-regulatory sequences in their promoter regions. We carried out a comprehensive analysis in which the upstream regions of a large number of OR genes were compared. First, using RLM-RACE, we generated cDNAs containing the complete 5'-untranslated regions (5'-UTRs) for a total number of 198 mouse OR genes. Then, we aligned these cDNA sequences to the mouse genome so that the 5' structure and transcription start sites (TSSs) of the OR genes could be precisely determined. Sequences upstream of the TSSs were retrieved and browsed for common elements. We found DNA sequence motifs that are overrepresented in the promoter regions of the OR genes. Most motifs resemble O/E-like sites and are preferentially localized within 200 bp upstream of the TSSs. Finally, we show that these motifs specifically interact with proteins extracted from nuclei prepared from the olfactory epithelium, but not from brain or liver. Our results show that the OR genes share common promoter elements. The present strategy should provide information on the role played by cis-regulatory sequences in OR gene regulation.

5' Untranslated Regions↗
PubMed2003

Phylogenetic affinity of a Giardia lamblia cysteine desulfurase conforms to canonical pattern of mitochondrial ancestry.

Among a few potential archezoan groups, only the Metamonada (diplomonads, retortamonads, and oxymonads) still retain the status of amitochondriate protists that diverged before the acquisition or retention of mitochondria. Indeed, finding that diplomonad genomes harbor a gene encoding a mitochondrial type chaperonin 60, the most compelling evidence for their secondarily amitochondriate nature, may be interpreted as an acquisition of this important general chaperone during some transient alpha-proteobacterial endosymbiosis. Recently published data on the cysteine desulfurase IscS demonstrated an alpha-proteobacterial origin of mitochondrial enzymes including a diplomonad Giardia lamblia homolog. An extended phylogenetic analysis of IscS is reported here that revealed a full canonical pattern of mitochondrial ancestry for the giardial enzyme. The above canonical pattern, a sister group relationship of mitochondria and rickettsiae exclusive of free-living alpha-proteobacteria, was robustly confirmed by a comprehensive analysis of Cob and Cox1 subunits of the respiratory chain encoded by resident mitochondrial genes. Given that Fe-S cluster assembly involving IscS represents an essential mitochondrial function, these data strongly suggest that diplomonads once harbored bona fide mitochondria.

Amino Acid Sequence↗
PubMed2026

Phenotypes of Hereditary Diseases Associated With Rauch-Steindl Syndrome.

PURPOSE: Prenatal phenotypic manifestations of genetic disorders associated with NSD2 variants remain poorly characterized. This study presents our institutional experience with the prenatal diagnosis of NSD2-associated genetic disorders, specifically Rauch-Steindl syndrome (RAUST), aiming to improve understanding of both the molecular and clinical features of RAUST. METHODS: We performed a retrospective analysis of six fetuses and one adult diagnosed with RAUST at our institution and thoroughly reviewed the prenatal ultrasound reports of six fetuses. Prenatal and postnatal phenotypes of RAUST cases were summarized alongside findings from previously published literature. Correlations between NSD2 variant locations, variant types, and phenotypes were analyzed. Additionally, protein modeling was used to visualize structural changes in NSD2 protein before and after C-terminal variants. We integrated single-cell transcriptomic and gene expression data from multiple public databases to investigate spatiotemporal expression patterns of NSD2 during human fetal development. RESULTS: Fetal growth restriction (FGR) was the most prevalent prenatal manifestation in RAUST fetuses, followed by microcephaly. Bilateral renal hypoplasia emerged as a novel prenatal ultrasonographic feature. Postnatally, speech and motor developmental delays were the most commonly reported phenotypes, followed by physical developmental delays and intellectual disability. Genotype-phenotype correlation analysis revealed an association between N-terminal truncating variants in NSD2 and impaired fetal growth parameters. Notably, C-terminal truncating variants-predicted not to directly impact NSD2 functional domains-also exerted disease-causing effects. CONCLUSION: This study provides a comprehensive analysis of prenatal phenotypes in RAUST cases, enriching the prenatal phenotypic spectrum of the disease and facilitating early diagnosis and clinical management of RAUST. Furthermore, our genotype-phenotype correlation findings lay a foundational basis for future research into the complex molecular mechanisms underlying NSD2-associated genetic disorders.

Humans↗
PubMed1999

Effectiveness of a writing improvement intervention program on the readability of the research informed consent document.

BACKGROUND: Problems with the comprehensibility of human research informed consent have been documented since the 1970s, and efforts aimed at rewriting consents have not been successful in consistently producing more readable consents. This study employed researched principles of reading comprehension research to create writing intervention program designed to help the research writer produce more comprehensible informed consent documents. The purpose of this study was to determine if this intervention program was effective. METHOD: The key component of the writing improvement intervention packet was a newly formatted consent form that contained annotated instructions for researchers on how to write each section for optimum comprehension. The resulting consent forms were evaluated using a Readability and Processability Form (RPF). The RPF is based on reading research and includes the Fry Scale, which yields an approximate grade reading level. The RPF assigned points to each of the 20 areas of comprehension analysis according to strict scoring criteria, and target scores were established by the authors in consultation with the hospital institutional review board. RESULTS: We evaluated 66 post-intervention informed consents. The mean readability and processability score was 62, resulting in the RPF classification of "good." The established readability and processability target range was good to excellent or 61-100 points; 66% of the forms scored in this range. In our 1995 pre-intervention study, the corresponding score was 12%. The target range for grade reading level was 8th grade: 53% scored in that range as compared with 4% in 1995. A question-by-question analysis of each of the 20 checklist items on the RPF identified important aspects of the consent writing that improved and others that were still weak and needed improvement. CONCLUSIONS: The Hartford Hospital writing improvement intervention program was associated with the production of more comprehensible informed consent documents. Using the intervention materials, investigators from a variety of departments could function independently to produce readable consent forms. This program may help others who wish to assist their research departments in creating consents that are written for optimal reading comprehension.

Cognition↗
PubMed1998

A comparative molecular analysis of four rat smooth muscle cell lines.

Transcriptional regulation of smooth muscle cell (SMC) differentiation is a rapidly growing area of interest that has relevance for understanding intimal disease. Despite the wealth of data accumulating in vitro, however, no study has compared the cell-specific marker profile, transfectability, promoter activity, and growth characteristics among several SMC culture systems. Accordingly, we performed a comprehensive analysis of the marker profile, growth properties, transfectability, and SMC promoter activity in four rat SMC lines (A7r5, adult and pup aortic, and PAC1). Despite alterations in chromosomal number and structure, A7r5, adult aortic, and PAC1 cells express all SMC markers studied including SM alpha-actin, SM calponin, SM22, tropoelastin, and to a lesser extent, SM myosin heavy chain (SMMHC). In contrast, pup aortic cells express very low or undetectable levels of all the above markers except tropoelastin. Adult aortic, pup, and PAC1 cells display similar growth curves and levels of proto-oncogene transcripts, whereas those in the A7r5 line are comparatively less. All cell lines studied except pup cells show expression of SMC differentiation genes during active growth, indicating that growth and differentiation are not mutually exclusive in cultured smooth muscle. Transfection studies reveal dramatic differences in DNA uptake and SMC-restricted promoter activity between cell lines. Collectively, these results provide detailed information relating to SMC molecular biology in culture that should facilitate the selection of a cell line for studying the transcriptional regulatory mechanisms underlying SMC differentiation.

Actins↗