Biomedical subjects

Steven L Bernstein

Publications and source records attributed to Steven L Bernstein.

24 records · Page 2Linked to original sources

PubMed2002

Expressed sequence tag analysis of human retina for the NEIBank Project: retbindin, an abundant, novel retinal cDNA and alternative splicing of other retina-preferred gene transcripts.

PURPOSE: Expressed sequence tag (EST) analysis was performed on un-normalized, unamplified cDNA libraries constructed from adult human retina to examine the expression profile of the tissue and to contribute resources for functional genomics studies. METHODS: Two size fractionated cDNA libraries (designated hd and he) were constructed from human retina RNA. Clones were randomly selected for sequencing and analyzed using the bioinformatics program GRIST (GRouping and Identification of Sequence Tags). PCR, Northern blotting and other techniques have been used to examine selected novel transcripts. RESULTS: After informatics analysis, 2200 retina cDNAs yield 1254 unique clusters, potentially representing individual genes. Opsin is the most abundant transcript and other retina transcripts are prominently represented. One abundant cluster of cDNAs encodes retbindin, a novel, retina preferred transcript which has sequence similarity to riboflavin binding proteins and whose gene is on chromosome 19. Variant transcripts of known retina genes are also observed, including an alternative exon in the coding sequence of the transcription factor NRL and a skipped coding sequence exon in the phosphodiesterase gammasubunit (PDE6G). CONCLUSIONS: The new retina cDNA libraries compare favorably in quality with those already represented in public databases. They are rich in retina specific sequences and include abundant cDNAs for a novel protein, retbindin. The function of retbindin remains to be determined, but it is a candidate for flavinoid or carotenoid binding. Analysis of multiple clones for highly expressed retina genes reveals several alternative splice variants in both coding and noncoding sequences which may have functional significance. The validated set of retina cDNAs will contribute to a nonredundant set for microarray construction.

Aged↗

PubMed2002

Expressed sequence tag analysis of adult human iris for the NEIBank Project: steroid-response factors and similarities with retinal pigment epithelium.

PURPOSE: The iris is a specialized tissue with important roles in the development and function of the eye. It is involved in diseases, including glaucoma and ocular melanoma, and its pigmented cells share an origin with the retinal pigment epithelium (RPE). Expressed sequence tag (EST) analysis of human iris has been performed to explore the repertoire of genes expressed in this tissue. METHODS: An unamplified, un-normalized cDNA library (designated bx) was constructed from pooled (4-80 years old) human iris tissue. Over 2000 clones were picked and sequenced. Sequences were analyzed and clustered using GRIST (GRouping and Identification of Sequence Tags). The library was then normalized (and designated fg) and a further 2200 clones were sequenced for deeper examination of rarer sequence. Some sequences of interest were investigated further by standard methods. RESULTS: From bx and fg libraries respectively, 1263 and 1604 clusters of expressed genes have been identified, giving a combined total of almost 2700 potentially unique genes. The most abundant novel transcript in bx is oculoglycan/opticin. Others include glucocorticoid induced leucine zipper protein (GILZ), Ris, a novel member of the Ras family, Iris Ring Finger (IRF), a member of the midline family, melastatin 2 (MLSN2), a member of the transient receptor potential calcium channel family, and iris expressed growth factor (IEGF), a member of the VEGF/PDGF family. Several factors involved in steroid responses are also represented. CONCLUSIONS: The iris libraries are a rich source of novel as well as known genes, including molecular markers for pigmented cells that are also shared with RPE. A number of transcripts code for proteins involved in steroid response, with interesting implications for control of intraocular pressure. These sequence verified clones provide a nonredundant set for micro-array construction.

Adolescent↗

PubMed2002

Expressed sequence tag analysis of adult human lens for the NEIBank Project: over 2000 non-redundant transcripts, novel genes and splice variants.

PURPOSE: To explore the expression profile of the human lens and to provide a resource for microarray studies, expressed sequence tag (EST) analysis has been performed on cDNA libraries from adult lenses. METHODS: A cDNA library was constructed from two adult (40 year old) human lenses. Over two thousand clones were sequenced from the unamplified, un-normalized library. The library was then normalized and a further 2200 sequences were obtained. All the data were analyzed using GRIST (GRouping and Identification of Sequence Tags), a procedure for gene identification and clustering. RESULTS: The lens library (by) contains a low percentage of non-mRNA contaminants and a high fraction (over 75%) of apparently full length cDNA clones. Approximately 2000 reads from the unamplified library yields 810 clusters, potentially representing individual genes expressed in the lens. After normalization, the content of crystallins and other abundant cDNAs is markedly reduced and a similar number of reads from this library (fs) yields 1455 unique groups of which only two thirds correspond to named genes in GenBank. Among the most abundant cDNAs is one for a novel gene related to glutamine synthetase, which was designated "lengsin" (LGS). Analyses of ESTs also reveal examples of alternative transcripts, including a major alternative splice form for the lens specific membrane protein MP19. Variant forms for other transcripts, including those encoding the apoptosis inhibitor Livin and the armadillo repeat protein ARVCF, are also described. CONCLUSIONS: The lens cDNA libraries are a resource for gene discovery, full length cDNAs for functional studies and microarrays. The discovery of an abundant, novel transcript, lengsin, and a major novel splice form of MP19 reflect the utility of unamplified libraries constructed from dissected tissue. Many novel transcripts and splice forms are represented, some of which may be candidates for genetic diseases.

Adult↗

PubMed2002

Grouping and identification of sequence tags (GRIST): bioinformatics tools for the NEIBank database.

NEIBank is a project to develop and organize genomics and bioinformatics resources for the eye. As part of this effort, tools have been developed for bioinformatics analysis and web based display of data from expressed sequence tag (EST) analyses. EST sequences are identified and formed into groups or clusters representing related transcripts from the same gene. This is carried out by a rules-based procedure called GRIST (GRouping and Identification of Sequence Tags) that uses sequence match parameters derived from BLAST programs. Linked procedures are used to eliminate non-mRNA contaminants. All data are assembled in a relational database and assembled for display as web pages with annotations and links to other informatics resources. Genome projects generate huge amounts of data that need to be classified and organized to become easily accessible to the research community. GRIST provides a useful tool for assembling and displaying the results of EST analyses. The NEIBank web site contains a growing set of pages cataloging the known transcriptional repertoire of eye tissues, derived from new NEIBank cDNA libraries and from eye-related data deposited in the dbEST section of GenBank.

Animals↗

PubMed2002

The impact of smoking-related illness in the ED: an attributable risk model.

The objective of this study was to estimate the clinical and economic impact of smoking among adult emergency department (ED) patients. An attributable risk analysis of patients seen in 2 urban EDs in 1998 was performed. Data were obtained from hospital databases, national sources describing the prevalence of smoking in the state, and risk ratios for smoking-related illnesses. Of 78,617 patient visits, 12,573 (16.0%) had any smoking-related International Classification of Diseases, 9th Revision code. The smoking-attributable risk fraction (SARF) for all patients was 4.9% (95% confidence interval [CI] 4.7%-5.0%). Of 13,245 admissions, 6.8% (95% CI 6.4%-7.2%) were smoking attributable. Of $296,962,685 in hospital charges, 10.0% (95% CI 9.9%-10.1%) were smoking attributable. The SARFs for ED visits, admissions, and charges for men were higher than for women (all P <.0001). Smoking-attributable illness accounts for 4.9% of ED adult visits, 6.8% of ED adult admissions, and 10.0% of hospital charges. The use of ED-based smoking intervention remains to be determined.

Adult↗

PubMed2002

Preventive care in the emergency department: diagnosis and management of smoking and smoking-related illness in the emergency department: a systematic review.

UNLABELLED: Smoking remains the leading preventable cause of morbidity and mortality in the United States. The efficacy of emergency department (ED)-based patient screening and counseling for smoking cessation is not currently known. OBJECTIVES: To perform a structured, systematic review of the medical literature to assess the efficacy of limited screening and counseling for tobacco use cessation among adults in the primary care and ED settings, and develop recommendations for emergency physicians based on these data. METHODS: A two-person template-driven review of all English-language articles from Medline, the Cochrane Database, and two recent smoking cessation guidelines, with evidence graded according to the scheme of the U.S. Preventive Services Task Force (USPSTF), was performed. Recommendations were developed, and strength graded, based on this evidence. RESULTS: Of 2,078 citations reviewed, 16 were selected for inclusion, based on their methodologic strength and relevance to emergency medicine. Routine physician screening and counseling may increase quit rates at 6-12 months from 3% (usual care) to 8-11%. Interventions include brief counseling (<3 minutes), possibly supplemented with self-help literature, nicotine replacement therapy (NRT), and follow-up telephone calls. CONCLUSIONS: Strong evidence exists, in the primary care setting, that smoking cessation screening and counseling are effective. Limited data exist for ED-based practice, but, based on the burden of disease, relative ease of intervention, and likely efficacy, routine screening of all patients for tobacco use and referral of smokers to primary care and cessation programs are recommended.

Adult↗