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At least 271 records · Page 15Linked to original sources
PubMed2004

Gene cataloging and expression profiling in human gastric cancer cells by expressed sequence tags.

To understand the molecular mechanism associated with gastric carcinogenesis, we identified genes expressed in gastric cancer cell lines and tissues. Of 97,609 high-quality ESTs sequenced from 36 cDNA libraries, 92,545 were coalesced into 10,418 human Unigene clusters (Build 151). The gene expression profile was produced by counting the cluster frequencies in each library. Although the profiles of highly expressed genes varied greatly from library to library, those genes related to cell structure formation, heat shock proteins, the glycolysis pathway, and the signaling pathway were highly represented in human gastric cancer cell lines and in primary tumors. Conversely, the genes encoding immunoglobulins, ribosomal proteins, and digestive proteins were down-regulated in gastric cancer cell lines and tissues compared to normal tissues. The transcription levels of some of these genes were confirmed by RT-PCR. We found that genes related to cell adhesion, apoptosis, and cytoskeleton formation were particularly up-regulated in the gastric cancer cell lines established from malignant ascites compared to those from primary tumors. This comprehensive molecular profiling of human gastric cancer should be useful for elucidating the genetic events associated with human gastric cancer.

Base Sequence↗
PubMed1983

Computer applications in analysis, mapping and cataloging of proteins separated by two dimensional electrophoresis.

Two dimensional electrophoretic separation of complex mixtures of proteins can only be exploited to its fullest potential using sophisticated computerized spot detection, quantification, pattern recognition, pattern normalization, data reduction and data storage. We present a discussion of some of the technical problems and of the options available which will ultimately lead toward full computerization of the data.

Computers↗
PubMed2002

Restriction fragment length polymorphism of rRNA operons for discrimination and intergenic spacer sequences for cataloging of Bacillus subtilis sub-groups.

Restriction fragment length polymorphism of rRNA operons (RFLP) and 16S-23S rRNA intergenic region (ISR) sequences of Bacillus subtilis subsp. subtilis, B. subtilis subsp. spizizenii, and B. atrophaeus were compared. ISR sequences of the B. subtilis subspecies were extremely similar (W23 versus 168 rrn H, J, G,W; 96.8%; rrn D, E; 98.4%; rrnB; 97.9%) and, therefore, not useful for their differentiation. However, RFLP of rRNA operons of the B. subtilis subspecies were distinct in terms of numbers and organization within the genome (e.g. the 168 sub-group generally contained 8.3- and 8.0-kb fragments absent in the W23 sub-group). The more distantly related B. atrophaeus was distinct from both B. subtilis subspecies in terms of ISR sequence and rRNA operon number and organization. RFLP of rRNA operons discriminates the two sub-groups of Bacillus subtilis that are indistinguishable by ISR sequence. However, ISR sequence defines the relatedness of B. subtilis to other species (e.g. B. atrophaeus) within the genus Bacillus.

Bacillus subtilis↗
PubMed1998

Tracing keratin evolution: catalog, expression patterns and primary structure of shark (Scyliorhinus stellaris) keratins.

We have studied individual keratins of an elasmobranch, the shark Scyliorhinus stellaris (the lesser-spotted dogfish). From various shark tissues, notably skin and stomach, cytoskeletal proteins were isolated and then separated by two-dimensional polyacrylamide gel electrophoresis. Using complementary keratin blot-binding assays and immunoblotting, among these proteins we identified a variety of type I and type II keratins. According to their tissue-specific expression, we distinguished Is and IIs keratins from IE and IIE keratins ("S" and "E" from "simple epithelial" and "epidermal", respectively). Guinea pig antibodies which in immunoblots specifically labeled the entire range of identified shark keratins, and a monoclonal antibody specific for IE keratins were used for immunofluorescence microscopy of a broad range of shark tissues. These experiments demonstrated that in this shark, keratin expression is largely restricted to epithelia and - in contrast to the situation in teleost fishes - is lacking in mesenchymally derived cells and tissues. Peptide mass mapping of the major electrophoretically separated shark keratin spots revealed that the identified Is, IIs and IIE polypeptides are modifications of a single genuine keratin, respectively, whereas there are two different IE keratins. It, therefore, appears that in this shark most (if not all) of the keratin cytoskeleton is constituted by only five different gene products (each present in various modifications): a heterologous pair of "S" and three different "E" keratins. We sequenced three of them (Is, IIs and IIE) via cDNA cloning. Sequence alignments showed that the shark Is keratin (termed SstK18) is an ortholog of human K18, whereas the IIs keratin (termed SstK8) corresponds to human K8. In contrast, the shark IIE keratin (termed SstK1; it is the first known primary structure of a fish IIE keratin) apparently has no direct equivalent in human. On the basis of a phylogenetic tree constructed from 37 aligned keratin sequences, these results are discussed with respect to the evolution of keratin diversity in vertebrates.

Amino Acid Sequence↗
PubMed2004

[Development of the "Whittener Activity Catalog of Self-Care in Venous Ulcer"].

Poor rates of healing and high rates of re-ulceration are characteristic of venous leg ulcer. The performing of special health-deviation self-care is important for the successful treatment and prevention of this chronic disease. This study aimed to validate a newly designed instrument for the measurement of specific self-care. The "Wittener Aktivitätenkatalog der Selbstpflege bei venös bedingten offenen Beinen" (WAS-VOB) (a catalogue containing self-care activities for venous leg ulcer) was conceptualized on the basis of Orem's theory and on pathophysiological processes. The items were created by using patient interviews (n = 20) and a literature review. An analysis of the reliability was used to reduce the raw scale. The quality of the WAS-VOB was assessed for face-validity (n = 6), feasibility (n = 8), test-retest-reliability (n = 60) and the internal consistency (n = 234). The involvement of patients was based on an informed consent. The WAS-VOB is a self-describing instrument, includes 59 self-care activities and describes those in eight scales which deal with "general compression", "wearing compression bandages", "wearing compression hosiery", "mobility", "temperature", "overload of the venous system", "prevention of skin damage" and "wound healing". The WAS-VOB is practicable and has good psycho-metric characteristics. The test-retest-coefficient (Kendall's tau b) is 0.58, Cronbach's alpha 0.72. The instrument WAS-VOB is suitable for the assessment of self-care deficits.

Adult↗
PubMed2002

A comprehensive catalog of CpG islands methylated in human lung adenocarcinomas for the identification of tumor suppressor genes.

CpG island methylation is an important mechanism in gene silencing and is a key epigenetic event in cancer development. As yet, the number and identities of the genes that are inactivated in cancer cells has not been determined. In order to address this issue, we have performed a comprehensive isolation of CpG islands that are methylated in human lung adenocarcinomas. We have isolated approximately 200 CpG islands that are methylated in tumor DNA including those of known tumor-associated genes such as the HOXA5 gene. As the library contains the CpG islands of a number of known tumor suppressor genes it is highly likely that additional, previously unidentified tumor suppressor genes, will be present. On average, 1-2% of CpG islands were methylated specifically in tumors although this figure differed greatly between patients. This study provides an important resource in the search for genes inactivated in tumors and for the investigation of epigenetic dysregulation of gene expression by CpG island methylation.

Adenocarcinoma↗
PubMed2000

Identification and cataloging of genes induced by long-lasting long-term potentiation in awake rats.

Maintenance of long-term potentiation (LTP) requires de novo gene expression. Here we report the direct isolation, using PCR-differential display, of genes whose expression level was altered after induction of long-lasting LTP in the hippocampus of freely moving awake rats. Differential display using 480 primer combinations revealed 17 cDNA bands that showed a reproducible change in expression level. These cDNAs represented at least 10 different genes (termed RM1-10), all of which showed up-regulation at 75 min after LTP induction and a return to basal expression levels within 24 h. Three of these genes were known only from expressed sequence tags (RM1-3), two were known genes whose up-regulation by LTP has not been described (GADD153/CHOP and ler5), and five were known genes whose up-regulation by LTP has already been reported (MAPK phosphatase, NGFI-A/zif268, vesl-1S/homer-1a, Ag2, and krox-20). We characterized the expression profiles of genes in the two former categories with respect to NMDA receptor dependency, tissue specificity, and developmental regulation using northern blotting and semiquantitative RT-PCR. The up-regulation of all five of these genes was NMDA receptor-dependent and correlated with the persistence of LTP, suggesting that these genes may play functional roles in prolonged LTP maintenance.

Animals↗
PubMed1999

A partial catalog of proteins secreted by epidermal keratinocytes in culture.

Proteins secreted by epidermal keratinocytes are known to engage in functions other than those directly associated with barrier formation. We have used a previously published culture model to collect proteins secreted by adult human epidermal keratinocytes. Electrophoresis and microsequencing allowed us to identify 20 proteins. The list of proteins includes those known to be produced by keratinocytes (beta-2 microglobulin, betaIG-H3, calgranulin A, cathepsin B and D, E-cadherin, gelatinase B, gelsolin, interstitial collagenase, laminin B2t, plasminogen activator inhibitor-1, protein 14-3-3epsilon, SCC antigen, stratifin, and translationally controlled tumor protein) as well as those not previously known to be secreted by keratinocytes (epididymis secretory protein, maspin, and anti-neoplastic urinary protein). In addition, two proteins were identified that are not known to be secreted (glutathione-S-transferase and heat shock protein 27/28 kDa). The varied nature of the proteins identified suggests that epidermal keratinocytes have physiologic functions that have yet to be identified.

3T3 Cells↗
PubMed2002

[Contribution of psychosomatic medicine to relationship medicine: a catalog of claims in times of crisis].

The medical ideology being based on structure instead of function (specifically on the cgs-logic--centimetre, gram, second) instead of a patient-orientation, the patient's resources are rarely ever even touched. This is the basis for operating difficulties in self- and patient-management. Changes of this uneconomic approach should centre on training, focusing especially on how to increase the professional's sensitivity for the relationship with his patient. Unfortunately, Austria's situation is characterized by deficitary psychosomatic competence in medical professionals. In addition, the absence of universitary or other structures centering on psychosomatic training and co-ordination is to be criticized. An interuniversitary-psychosomatic structure in Austria is proposed as a starting-point to overcome these serious short-comings.

Austria↗
PubMed1982

[Catalog of direct eye muscle injuries].

Eye muscle injuries may occur in isolation or concomitantly with orbital fractures. Depending on their mechanical cause they may be encountered in the form of contusions, overextensions or injuries caused by stabbing or cutting. The authors present case histories from their own patient collective in this order, supplemented by a number of cases described in the literature. Particular attention is paid to the superior oblique, injuries to which are almost without exception trochlear or pretrochlear. The special anatomy of the tendon is a factor that may explain restrictions in motility in upward and downward gaze (dysfunctions). Certain severe cases are described and the principles of reconstructive surgery are discussed.

Adult↗
PubMed2003

Can transcriptome size be estimated from SAGE catalogs?

MOTIVATION: SAGE (Serial Analysis of Gene Expression) can be used to estimate the number of unique transcripts in a transcriptome. A simple estimator that corrects for sequencing and sampling errors was applied to a SAGE library (137 832 tags) obtained from mouse embryonic stem cells, and also to Monte Carlo simulated libraries generated using assumed distributions of 'true' expression levels consistent with the data. RESULTS: When the corrected data themselves were taken as the underlying model of 'ground truth', the estimator converged to the 'true' value (53 535) only after counting 300 000 simulated tags, more than twice the number in the experiment. The SAGE data could also be well fit by a Monte Carlo model based on a truncated inverse-square distribution of expression levels, with 130 000 'true' transcripts and 10(6) samples needed for convergence. We conclude that the size of a transcriptome is ill-determined from SAGE libraries of even moderately large size. In order to obtain a valid estimate, one must sample a number of tags inversely proportional to the lowest abundance level, which is not known a priori. This constrains the design of SAGE experiments intended to determine biological complexity. AVAILABILITY: The 'homemade' software used for this analysis was not designed for general or 'production' use, but the authors will be happy to share Fortran sourcecode with interested parties. CONTACT: sternm@grc.nia.nih.gov

Algorithms↗
PubMed1981

Codon catalog usage is a genome strategy modulated for gene expressivity.

The nucleic acid sequence bank now contains 161 mRNAs, 43 new genes are added. One sequence, that of B. mori fibroin, is dropped due to uncertainty on the starting point for translation. Frequencies of all codons are given for each gene added and for each genome type in the total bank. A new series of correspondence analyses on codon use is presented, substantiating the genome hypothesis. Internal regulation of mRNA expression by different third base choices between quartet and duet codons is proposed for bacterial genes.

Amino Acid Sequence↗