Frequent emergency department visitors: the end of inappropriateness.
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Emergency Service, Hospital↗
Biomedical subjects
Steven L Bernstein
Publications and source records attributed to Steven L Bernstein.
Analysis of optic nerve stroke by retinal Bex expression.
PURPOSE: Few proteins are known to be selectively expressed in retinal ganglion cells (RGCs), the neurons directly affected by optic nerve stroke and glaucoma. In addition, subsets of RGCs are reported to project to various CNS areas via the retinohypothalamic pathway in rodents and primates. Many of these areas exhibit immunoreactivity for the brain-expressed X-linked (Bex) proteins Bex1 and Bex2. This prompted us to evaluate expression of these proteins in retina. METHODS: We utilized rats and transgenic mice, coupled with a new rodent model of isolated optic nerve stroke (rodent anterior ischemic optic neuropathy, rAION). An anti-Bex1 antibody was reacted to retinal tissue extracts. To evaluate short term effects of rAION on RGC Bex expression, a double transgenic mouse strain was employed expressing cyan fluorescent protein (CFP) under control of the Thy-1 protein promotor, and beta-galactosidase (lacZ) under control of the immediate early stress c-fos gene promotor. Positive identification of rat RGCs was performed by retrograde fluorogold labeling via stereotactic CNS injection. Retinas were analyzed using both diaminobenzidine (DAB)-linked immunochemistry and confocal microscopy. RESULTS: Bex immunoreactivity is present at high levels in the retina. Bex1 and Bex2 are selectively expressed in RGCs and differentially expressed in a subset of large RGC neurons. Bex signal levels are lower in small RGC neurons, which preferentially express high levels of the transcription factor Brn3b. Post-stroke, Bex accumulates in the RGC cytoplasm, consistent with the optic nerve edema produced by clinical AION. CONCLUSIONS: Bex immunoreactivity can be used to evaluate, ex vivo, the distribution of RGC cell bodies and their axons in the retina and rAION effects on RGC axonal loss. Thus, Bex can be utilized to evaluate both long- and short-term effects of optic nerve stroke and may play a significant role in regulating RGC functions in both the axonal and cell body components of RGC neurons.
Animals↗
Gelatin-based biomimetic tissue adhesive. Potential for retinal reattachment.
An adhesive that cures under moist/wet conditions could facilitate surgical procedures for retinal reattachment. We are investigating an adhesive that mimics the factor XIIIa-mediated crosslinking of fibrin that occurs in the late stages of the blood coagulation cascade. Specifically, we use gelatin as the structural protein (in place of fibrin), and crosslink gelatin using a calcium-independent microbial transglutaminase (in place of the calcium-dependent transglutaminase factor XIIIa). Injection of gelatin and microbial transglutaminase (mTG) into the vitreous cavity of Sprague Dawley white rats did not elicit structural or cellular damage to the retina as evidenced from histological evaluation 2 weeks post-injection. Qualitative in vitro studies indicate that the gelatin-mTG adhesive binds to bovine retinal tissue under wet conditions. Quantitative lap-shear tests were performed with more robust bovine tissue from the choroid and sclera. The lap-shear strength of the biomimetic gelatin-mTG adhesive was independent of tissue-type and ranged from 15 to 45 kPa, which is comparable to the values reported for other soft-tissue adhesives. These studies suggest that the mTG-crosslinked gelatin may provide a simple, safe, and effective adhesive for ophthalmic applications.
Adhesiveness↗
Relationship between intensity and relief in patients with acute severe pain.
OBJECTIVE: To test whether a single-category improvement on a Likert pain relief scale equals the minimum clinically significant difference of 1.3 units in pain intensity reduction on a 10-unit numerical rating scale (NRS). METHODS: Prospective cohort of adults with acute severe pain receiving standardized analgesia. Patients rated pain intensity via NRS before receiving morphine and 30 minutes later. Patients described pain relief as "none," "a little," "moderate," "a lot," or "complete." The primary outcome was the difference in NRS scores between each contiguous pair of pain relief categories over 30 minutes. RESULTS: One hundred thirty-one patients, age range 21 to 65 years, median baseline NRS pain score 10 (interquartile range, 9-10). Patients whose relief was "complete," "a lot," "moderate," "mild," and "none" had the following NRS unit reductions in pain, respectively: 9, 5.7, 3.9, 2.1, and -0.1. The difference between each pair of relief categories was 3.3, 1.8, 1.8, and 2.2 units. CONCLUSION: Each single-category improvement on a pain relief scale exceeds the minimum clinically significant difference in pain intensity as measured on an NRS.
Acute Disease↗
Norrie disease gene sequence variants in an ethnically diverse population with retinopathy of prematurity.
PURPOSE: Retinopathy of prematurity (ROP) is a leading cause of visual loss in the pediatric population. Mutations in the Norrie disease gene (NDP) are associated with heritable retinal vascular disorders, and have been found in a small subset of patients with severe retinopathy of prematurity. Varying rates of progression to threshold disease in different races may have a genetic basis, as recent studies suggest that the incidence of NDP mutations may vary in different groups. African Americans, for example, are less likely to develop severe degrees of ROP. We screened a large cohort of ethnically diverse patients for mutations in the entire NDP. METHODS: A total of 143 subjects of different ethnic backgrounds were enrolled in the study. Fifty-four patients had severe ROP (Stage 3 or worse). Of these, 38 were threshold in at least one eye (with a mean gestational age of 26.1 weeks and mean birth weight of 788.4 g). There were 36 patients with mild or no ROP, 31 parents with no history of retinal disease or prematurity, and 22 wild type (normal) controls. There were 70 African American subjects, 55 Caucasians, and 18 of other races. Severe ROP was noted in 29 African American subjects, 17 Caucasians, and 8 of other races. Seven polymerase chain reaction primer pairs spanning the NDP were optimized for denaturing high performance liquid chromatography and direct sequencing. Three primer pairs covered the coding region, and the remaining four spanned the 3' and 5' untranslated regions (UTR). RESULTS: Six of 54 (11%) infants with severe ROP had polymorphisms in the NDP. Five of the infants were African American, and one was Caucasian. Two parents were heterozygous for the same polymorphism as their child. One parent-child pair had a single base pair (bp) insertion in the 3' UTR region. Another parent-child pair had two mutations: a 14 bp deletion in the 5' UTR region of exon 1 and a single nucleotide polymorphism in the 5' UTR region of exon 2. No coding region sequence changes were found. No polymorphisms were observed in infants with mild or no ROP, or in the wild type controls. CONCLUSIONS: Of the six sequence alterations found, five were novel nucleotide changes: One in the 5' UTR region of exon 2, and four in the 3' UTR region of exon 3. The extent of NDP polymorphisms in this large, racially diverse group of infants is moderate. NDP polymorphisms may play a role in the pathogenesis of ROP, but do not appear to be a major causative factor.
3' Untranslated Regions↗
Nicotine dependence, motivation to quit, and diagnosis in emergency department patients who smoke.
OBJECTIVES: To assess the effect of diagnosis on motivation to quit in adult smokers in an emergency department (ED). METHODS: A survey of patients visiting two EDs from September to November, 2003. Patients screening positive for smoking completed a Fagerstrom Test for Nicotine Dependence and Ladder of Contemplation. ICD9 codes and disposition status were recorded. Smoking-related diagnoses were drawn from standard sources. Data were analyzed with parametric and non-parametric statistics. RESULTS: Five hundred and eighty-five were interviewed, median age 40 (interquartile range 29-50); 323 (55%) were female. Ninety percent of all patients were non-White; 69% were uninsured or had Medicaid. Of 152 patients with smoking-related diagnoses, the median Fagerstrom score was 4.7 vs. 4.1 for patients with a non-smoking-related diagnosis (p=0.02, 95% CI for the difference 0.2, 0.9). Patients with smoking-related and non-smoking-related diagnoses had similar levels of motivation to quit (Ladder score, respectively, 5.5 vs. 5.1, p=0.03, 95% CI for difference 0.03, 0.8). CONCLUSIONS: Adult ED smokers exhibit mild-moderate levels of nicotine addiction and interest in quitting. ED-based tobacco control should target all smokers.
Adult↗
Internal marketing of an ED-based public health initiative.
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Advertising↗
Oligodendrocyte dysfunction after induction of experimental anterior optic nerve ischemia.
PURPOSE: The early response and survival of oligodendrocytes after axonal stroke and their potential contribution to neuronal survival in vivo have not been adequately addressed. The purpose of this study was to investigate the changes occurring in the retina and optic nerve (ON) in anterior ischemic optic neuropathy (AION), using a c-fos transgenic mouse model. METHODS: A new mouse model of AION (rodent AION) was developed to evaluate the in vivo stress response of oligodendrocytes and retinal ganglion cells (RGCs) in a transgenic mouse strain, using the immediate early stress-response gene c-fos, RT-QPCR technology, immunohistochemistry, and electron microscopy. Confocal microscopy was used with cell-specific antibodies to characterize the timing of cells responding to rAION. The TUNEL assay detected cells undergoing apoptosis. Ultrastructural changes were analyzed by electron microscopy. RESULTS: In rAION, oligodendrocytes rapidly respond in vivo to ischemic ON damage, with c-fos activation as an early detectable event. Early evidence of progressive oligodendrocyte stress, is followed by demyelination, wallerian degeneration of the ON, and oligodendrocyte and RGC death far from the primary lesion. CONCLUSIONS: After rAION induction oligodendrocytes, as well as RGCs, undergo progressive stress, with dysfunction and apoptosis. The findings lead to a proposal that progressive retrograde oligodendrocyte stress, away from the primary lesion, is an important factor after ischemic optic neuropathy. Postinduction demyelination must be addressed for effective neuroprotection of ischemic and hypoxic white matter.
Animals↗
An electronic chart prompt to decrease proprietary antibiotic prescription to self-pay patients.
OBJECTIVES: Emergency physicians unaware of patients' insurance status may prescribe expensive proprietary antibiotics for patients who cannot afford them. The objective of this study was to develop a clinical decision support system to display patient insurance status before prescription writing for outpatient conditions. METHODS: This was a 26-week "before-and-after" trial at an urban emergency department (ED) with 78,000 visits/year treating a medically underserved population. Sixty-one prescribers, including attending physicians, residents, and physician assistants, participated. All patients older than 18 years of age discharged from the ED receiving antibiotic prescriptions were eligible. The electronic ED chart is linked to prescription-writing software, which includes a menu of 74 antibiotics. The system was programmed so that when an emergency physician accessed the prescription menu, a prompt appeared displaying insurance status. Prescribers also received educational interventions. The main outcome measure was the percentage of prescribers who reduced their prescription writing of proprietary antibiotics to self-pay patients. Data were analyzed with cluster techniques using SPSS 10.0 (SPSS Inc., Chicago, IL). RESULTS: Of 594 prescriptions written for self-pay patients before prompt insertion, 158 (26.6%) were for proprietary antibiotics. After the intervention, self-pay patients received 564 antibiotic prescriptions, of which 117 (20.7%) were for proprietary drugs. Analyzed by prescriber, the reduction in the prescription rate for proprietary antibiotics was statistically significant (p = 0.03, chi(2) test). Patients with respiratory or urinary infections also had a statistically significant reduction in proprietary antibiotic prescription (p = 0.03). CONCLUSIONS: A clinical decision support system, integrated into a prescription-writing program, can decrease the prescription of proprietary antibiotics for self-pay patients in the ED.
Adult↗
Gene expression variation in the adult human retina.
Despite evidence that differences in gene expression levels contribute significantly to phenotypic variation across individuals, there has been only limited effort to study gene expression variation in human tissue. To characterize expression variation in the normal human retina, we utilized a custom retinal microarray to analyze 33 normal retinas from 19 donors, aged 29-90 years. Statistical models were designed to separate and quantify biological and technical sources of variation, including age, gender, eye laterality, gene function and age-by-gender interaction. Although the majority of the 9406 genes analyzed showed relatively stable expression levels across different donors (for an average gene the expression level value of 95 out of a 100 individuals fell within a 1.23-fold range), 2.6% of genes showed significant donor-to-donor variation, with a false discovery rate of 10%. The mean expression ratio standard deviation was 0.15+/-0.8, log2, with a range of 0.09-0.99. Genes selectively expressed in photoreceptors showed higher expression variation than other gene classes. Gender, age and other donor-specific factors contributed significantly to the expression variation of multiple genes, and groups of genes with an age- and gender-associated expression pattern were identified. Our findings show that a significant fraction of gene expression variation in the normal human retina is attributable to identifiable biological factors. The greater expression variability of many genes central to retinal function (including photoreceptor-specific genes) may be partially explained by the dynamics of the vision process, and raises the possibility that photoreceptor gene expression levels may contribute to phenotypic diversity across normal adult retinas. In addition, as such diversity may result in different levels of disease susceptibility, exploring its sources may provide insights into the pathogenesis of retinal disease.
Adult↗
Development and validation of a new index to measure emergency department crowding.
OBJECTIVES: To develop a quantitative measure of emergency department (ED) crowding and busyness. METHODS: A five-week study in spring 2002 in an urban teaching ED compared a new index (the Emergency Department Work Index [EDWIN]) with attending physician and nurse ratings of crowding. EDWIN is defined as summation operator n(i)t(i)/N(a)(B(T)-B(A)), where n(i) = number of patients in the ED in triage category i, t(i) = triage category, N(a) = number of attending physicians on duty, B(T) = number of treatment bays, and B(A) = number of admitted patients in the ED. The triage system used is the Emergency Severity Index (ESI), which was modified by reversing the ranking of triage categories; that is, an ESI score of 1 represented the least acute patient and 5 the sickest. EDWIN was calculated every two hours in a convenience sample of 60 eight-hour shifts. With each measurement, the charge attending physician and nurse estimated how busy/crowded the ED was, using a Likert scale. Nurse and physician assessments were averaged and compared with EDWIN scores. Data were analyzed with SPSS 10.0 (SPSS Inc., Chicago, IL). RESULTS: A total of 2,647 patients aged 18 years and older were assessed at 225 time points over 35 consecutive days. Nurses and physicians showed good interrater agreement of crowding assessment (weighted kappa 0.61, 95% confidence interval = 0.53 to 0.69). Median EDWIN scores and interquartile ranges (IQRs) when the ED was rated as not busy, average, and very busy were 1.07 (IQR = 0.80 to 1.55), 1.55 (IQR = 1.16 to 1.93), and 1.83 (IQR = 1.42 to 2.45) (p < 0.001). The ED was on diversion for 17 time blocks (6.5% of all blocks), with a median EDWIN of 2.77 (IQR = 1.83 to 3.63), compared with an EDWIN of 1.45 (IQR = 1.05 to 2.00) when not on diversion (p < 0.001). EDWIN scores correlated weakly with various process-of-care measures chosen as secondary end points. CONCLUSIONS: EDWIN correlated well with staff assessment of ED crowding and diversion. The index can be programmed into tracking software for use as a "dashboard" to alert staff when the ED is approaching crisis. If validated across other sites, EDWIN may provide a tool to compare crowding levels among different EDs.
Adult↗
Expression of beta-carotene 15,15' monooxygenase in retina and RPE-choroid.
PURPOSE: Beta-carotene 15,15' monooxygenase (beta-CM) catalyzes the central cleavage of beta-carotene to all-trans-retinal, the first step in vitamin A synthesis. This study was conducted to determine the expression of beta-CM in the mammalian retina and RPE, to assess its relevance in carotenoid-retinoid metabolism in the retina and RPE. METHODS: RT-PCR was used to detect expression of beta-CM mRNA in the retina and RPE-choroid of the mouse, cow, human, and monkey and in RPE cells and other cell lines. Immunofluorescence microscopy was used to localize beta-CM in mouse and monkey retina with an anti-peptide antibody specific for beta-CM. RESULTS: By RT-PCR, beta-CM mRNA was detected at a low level in mouse and monkey retina and in the RPE-choroid of the monkey but not of the mouse. Conversely, beta-CM mRNA was expressed at a low level in both human and bovine RPE-choroid, but not in the retina of either. RPE primary cultured cells of the monkey also showed beta-CM mRNA expression, although the three human lines did not. In addition, of nine other cell lines tested, only COS-7 was positive for beta-CM. Immunofluorescence microscopy showed weak immunoreactivity in the inner retina in both the mouse and monkey. beta-CM immunoreactivity was not detectable in RPE of the mouse. Use of a long-wavelength exciting and emitting secondary probe to mitigate lipofuscin autofluorescence, facilitated the detection of a low level of beta-CM immunoreactivity in monkey RPE. CONCLUSIONS: Beta-CM mRNA and protein are expressed at low levels in the mammalian retina and RPE-choroid. Given the low and variable expression of beta-CM in the retina and RPE, it can be concluded that beta-CM is not necessary for a conserved retina or RPE-specific function, but may be necessary for a species-specific function.
Animals↗
Evolutionarily conserved ELOVL4 gene expression in the vertebrate retina.
PURPOSE: The gene elongation of very long chain fatty acids-4 (ELOVL4) has been shown to underlie phenotypically heterogeneous forms of autosomal dominant macular degeneration. In this study, the extent of evolutionary conservation and the existence and localization of retinal expression of this gene was investigated across a wide variety of species. METHODS: Southern blot analysis of genomic DNA and bioinformatic analysis using the human ELOVL4 cDNA and protein sequences, respectively, were performed to identify species in which ELOVL4 orthologues and/or homologues are present. Retinal RNA and protein extracts derived from different species were assessed by Northern hybridization and immunoblot techniques to assess evolutionary conservation of gene expression. Immunohistochemical analysis of tissue sections prepared from various mammalian retinas was performed to determine the distribution of ELOVL4 and homologous proteins within specific retinal cell layers. RESULTS: The existence of ELOVL4 sequence orthologues and homologues was confirmed by both Southern blot analysis and in silico searches of protein sequence databases. Phylogenetic analysis places ELOVL4 among a large family of known and putative fatty acid elongase proteins. Northern blot analysis revealed the presence of multiple transcripts corresponding to ELOVL4 homologues expressed in the retina of several different mammalian species. Conserved proteins were also detected among retinal extracts of different mammals and were found to localize predominantly to the photoreceptor cell layer within retinal tissue preparations. CONCLUSIONS: The ELOVL4 gene is highly conserved throughout evolution and is expressed in the photoreceptor cells of the retina in a variety of different species, which suggests that it plays a critical role in retinal cell biology.
Amino Acid Sequence↗
Functional and cellular responses in a novel rodent model of anterior ischemic optic neuropathy.
PURPOSE: Anterior ischemic optic neuropathy (AION) is caused by sudden loss of vascular supply to retinal ganglion cell (RGC) axons in the anterior portion of the optic nerve and is a major cause of optic nerve dysfunction. There has been no easily obtainable animal model of this disorder. The current study was conducted to design a novel model of rodent AION (rAION), to enable more detailed study of this disease. METHODS: A novel rodent photoembolic stroke model was developed that is directly analogous to human AION. Using histologic, electrophysiological, molecular- and cell biological methods, the early changes associated with isolated RGC axonal ischemia were characterized. RESULTS: Functional (electrophysiological) changes occurred in RGCs within 1 day after rAION, with a loss of visual evoked potential (VEP) amplitude that persisted in the long term. The retinal gene expression pattern rapidly changed after rAION induction, with an early (<1 day) initial induction of c-Fos mRNA, and loss of RGC-specific gene expression. RGC-specific protein expression declined 2 days after detectable mRNA level changes, and immunostaining suggested that multiple retinal layers react to isolated RGC axonal ischemia. CONCLUSIONS: rAION rapidly results in electrophysiological and histologic changes similar to clinical AION, with reactive responses in primary and supporting neuronal cell layers. The rAION model can enable a detailed analysis of the individual retinal and optic nerve changes that occur after optic nerve stroke, which may be useful in determining possible therapeutic interventions for this disorder.
Animals↗
Expressed sequence tag analysis of human RPE/choroid for the NEIBank Project: over 6000 non-redundant transcripts, novel genes and splice variants.
PURPOSE: The retinal pigment epithelium (RPE) and choroid comprise a functional unit of the eye that is essential to normal retinal health and function. Here we describe expressed sequence tag (EST) analysis of human RPE/choroid as part of a project for ocular bioinformatics. METHODS: A cDNA library (cs) was made from human RPE/choroid and sequenced. Data were analyzed and assembled using the program GRIST (GRouping and Identification of Sequence Tags). Complete sequencing, Northern and Western blots, RH mapping, peptide antibody synthesis and immunofluorescence (IF) have been used to examine expression patterns and genome location for selected transcripts and proteins. RESULTS: Ten thousand individual sequence reads yield over 6300 unique gene clusters of which almost half have no matches with named genes. One of the most abundant transcripts is from a gene (named "alpha") that maps to the BBS1 region of chromosome 11. A number of tissue preferred transcripts are common to both RPE/choroid and iris. These include oculoglycan/opticin, for which an alternative splice form is detected in RPE/choroid, and "oculospanin" (Ocsp), a novel tetraspanin that maps to chromosome 17q. Antiserum to Ocsp detects expression in RPE, iris, ciliary body, and retinal ganglion cells by IF. A newly identified gene for a zinc-finger protein (TIRC) maps to 19q13.4. Variant transcripts of several genes were also detected. Most notably, the predominant form of Bestrophin represented in cs contains a longer open reading frame as a result of splice junction skipping. CONCLUSIONS: The unamplified cs library gives a view of the transcriptional repertoire of the adult RPE/choroid. A large number of potentially novel genes and splice forms and candidates for genetic diseases are revealed. Clones from this collection are being included in a large, nonredundant set for cDNA microarray construction.
Aged↗
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↗
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↗
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↗