Appropriately differentiated ARPE-19 cells regain phenotype and gene expression profiles similar to those of native RPE cells.

PurposeThe RPE cell line ARPE-19 provides a dependable and widely used alternative to native RPE. However, replication of the native RPE phenotype becomes more difficult because these cells lose their specialized phenotype after multiple passages. Compounding this problem is the widespread use of ARPE-19 cells in an undifferentiated state to attempt to model RPE functions. We wished to determine whether suitable culture conditions and differentiation could restore the RPE-appropriate expression of genes and proteins to ARPE-19, along with a functional and morphological phenotype resembling native RPE. We compared the transcriptome of ARPE-19 cells kept in long-term culture with those of primary and other human RPE cells to assess the former's inherent plasticity relative to the latter.MethodsARPE-19 cells at passages 9 to 12 grown in DMEM containing high glucose and pyruvate with 1% fetal bovine serum were differentiated for up to 4 months. Immunocytochemistry was performed on ARPE-19 cells grown on filters. Total RNA extracted from ARPE-19 cells cultured for either 4 days or 4 months was used for RNA sequencing (RNA-Seq) analysis using a 2 × 50 bp paired end protocol. The RNA-Seq data were analyzed to identify the affected pathways and recognize shared ontological classification among differentially expressed genes. RPE-specific mRNAs and miRNAs were assessed with quantitative real-time (RT)-PCR, and proteins with western blotting.ResultsARPE-19 cells grown for 4 months developed the classic native RPE phenotype with heavy pigmentation. RPE-expressed genes, including RPE65, RDH5, and RDH10, as well as miR-204/211, were greatly increased in the ARPE-19 cells maintained at confluence for 4 months. The RNA-Seq analysis provided a comprehensive view of the relative abundance and differential expression of the genes in the differentiated ARPE-19 cells. Of the 16,757 genes with detectable signals, nearly 1,681 genes were upregulated, and 1,629 genes were downregulated with a fold change of 2.5 or more differences between 4 months and 4 days of culture. Gene Ontology analysis showed that the upregulated genes were associated with visual cycle, phagocytosis, pigment synthesis, cell differentiation, and RPE-related transcription factors. The majority of the downregulated genes play a role in cell cycle and proliferation.ConclusionsThe ARPE-19 cells cultured for 4 months developed a phenotype characteristic of native RPE and expressed proteins, mRNAs, and miRNAs characteristic of the RPE. Comparison of the ARPE-19 RNA-Seq data set with that of primary human fetal RPE, embryonic stem cell-derived RPE, and native RPE revealed an important overall similar expression ratio among all the models and native tissue. However, none of the cultured models reached the absolute values in the native tissue. The results of this study demonstrate that low-passage ARPE-19 cells can express genes specific to native human RPE cells when appropriately cultured and differentiated

Weather and Climate Change Drive Annual Variation of Reproduction by an Aerial Insectivore

For many bird species, but especially aerial insectivores, reproduction depends on weather. Climate change is likely to intensify effects, but with uncertain consequences. We report 22 years of data on Eastern Kingbird (Tyrannus tyrannus) reproduction for two populations located in different hygric environments undergoing climate change; mesic central New York, USA, (NY; 12 years) and xeric southeastern Oregon, USA, (OR: 10 years). Laying date became earlier with increasing temperature in the 30-day period preceding laying in identical fashion at both sites, and in years of early laying, clutch size was larger, length of laying season increased, and failed initial nesting attempts were more often replaced. High temperature in the 10-days preceding mean laying date was associated with shorter laying seasons, while a site by 10-day temperature interaction reflected an increase and decrease of clutch size with increasing 10-day temperature in NY and OR, respectively. Seasonal rate of clutch size decline was higher when the laying season was short but also slowed in xeric OR when rain was abundant in the 10-days prior to mean laying date. Nest predation drove annual variation in young fledged/nest, but the latter also increased and decreased with increasing maximum temperature during the nestling phase in mesic NY and xeric OR, respectively. Potential effects of climate change on kingbird populations are thus high given the dependence of reproduction on weather, and climate change likely contributed to declines of kingbirds in OR. Declines of kingbirds in NY appear unrelated to warming climates because higher temperatures advanced laying dates and yielded greater nest productivity. However, length of laying season declined across years at both sites, and thus early season gains may be negated by poor conditions late in the season that may be causing shorter laying seasons. Further work is needed to identify causes for the latter changes

The Ursinus Weekly, May 11, 1972

Travelin\u27 5 talent ready • Campus Chest presents: You can\u27t take it with you • U.C. students offered esoteric subject matter • Warren Robinson named St. Andrews scholar • U.C. receives grant • U.C. graduate presents piano concert • Executives discuss gift solicitation on campus • Editorial: Reflections; Need for a counselor • Focus: Barbara Dando • Fidler on the wax: Humble Pie • Faculty portrait: Dr. Louis DeCatur • Strike • College scholars • Letters to the editor: U.S. government defended; Collegeville\u27s smut store; Apathy habit • Final examination schedule • Spring Parents\u27 Day • Ursinus pounds Penn • U.C. baseball loses to Haverford in top of 9th • The Ersinus Weaklyhttps://digitalcommons.ursinus.edu/weekly/1124/thumbnail.jp

Trend Identification in Twentieth-Century U.S. Snowfall: The Challenges

There is an increasing interest in examining long-term trends in measures of snow climatology. An examination of the U.S. daily snowfall records for 1900–2004 revealed numerous apparent inconsistencies. For example, long-term snowfall trends among neighboring lake-effect stations differ greatly from insignificant to +100% century -1. Internal inconsistencies in the snow records, such as a lack of upward trends in maximum seasonal snow depth at stations with large upward trends in snowfall, point to inhomogeneities. Nationwide, the frequency of daily observations with a 10:1 snowfall-to-liquid-equivalent ratio declined from 30% in the 1930s to a current value of around 10%, a change that is clearly due to observational practice. There then must be biases in cold-season liquid-equivalent precipitation, or snowfall, or both. An empirical adjustment of snow-event, liquid-equivalent precipitation indicates that the potential biases can be statistically significant. Examples from this study show that there are nonclimatic issues that complicate the identification of and significantly change the trends in snow variables. Thus, great care should be taken in interpretation of time series of snow-related variables from the Cooperative Observer Program (COOP) network. Furthermore, full documentation of optional practices should be required of network observers so that future users of these data can properly account for such practices

Expression of ABCA4 in the retinal pigment epithelium and its implications for Stargardt macular degeneration.

Recessive Stargardt disease (STGD1) is an inherited blinding disorder caused by mutations in the Abca4 gene. ABCA4 is a flippase in photoreceptor outer segments (OS) that translocates retinaldehyde conjugated to phosphatidylethanolamine across OS disc membranes. Loss of ABCA4 in Abca4 -/- mice and STGD1 patients causes buildup of lipofuscin in the retinal pigment epithelium (RPE) and degeneration of photoreceptors, leading to blindness. No effective treatment currently exists for STGD1. Here we show by several approaches that ABCA4 is additionally expressed in RPE cells. (i) By in situ hybridization analysis and by RNA-sequencing analysis, we show the Abca4 mRNA is expressed in human and mouse RPE cells. (ii) By quantitative immunoblotting, we show that the level of ABCA4 protein in homogenates of wild-type mouse RPE is about 1% of the level in neural retina homogenates. (iii) ABCA4 immunofluorescence is present in RPE cells of wild-type and Mertk -/- but not Abca4 -/- mouse retina sections, where it colocalizes with endolysosomal proteins. To elucidate the role of ABCA4 in RPE cells, we generated a line of genetically modified mice that express ABCA4 in RPE cells but not in photoreceptors. Mice from this line on the Abca4 -/- background showed partial rescue of photoreceptor degeneration and decreased lipofuscin accumulation compared with nontransgenic Abca4 -/- mice. We propose that ABCA4 functions to recycle retinaldehyde released during proteolysis of rhodopsin in RPE endolysosomes following daily phagocytosis of distal photoreceptor OS. ABCA4 deficiency in the RPE may play a role in the pathogenesis of STGD1

A comprehensive clinical and biochemical functional study of a novel RPE65 hypomorphic mutation

PURPOSE. Later onset and progression of retinal dystrophy occur with some RPE65 missense mutations. The functional consequences of the novel P25L RPE65 mutation was correlated with its early-childhood phenotype and compared with other pathogenic missense mutations. METHODS. In addition to typical clinical tests, fundus autofluorescence (FAF), optical coherence tomography (OCT), and two-color threshold perimetry (2CTP) were measured. RPE65 mutations were screened by SSCP and direct sequencing. Isomerase activity of mutant RPE65 was assayed in 293F cells and quantified by HPLC analysis of retinoids. RESULTS. A very mild phenotype was detected in a now 7-yearold boy homozygous for the P25L mutation in RPE65. Although abnormal dark adaptation was noticed early, best corrected visual acuity was 20/20 at age 5 years and 20/30 at age 7 years. Nystagmus was absent. Cone electroretinogram (ERG) was measurable, rod ERG severely reduced, and FAF very low. 2CTP detected mainly cone-mediated responses in scotopic conditions, and light-adapted cone responses were approximately 1.5 log units below normal. High-resolution spectral domain OCT revealed morphologic changes. Isomerase activity in 293F cells transfected with RPE65/P25L was reduced to 7.7% of wild-type RPE65-transfected cells, whereas RPE65/ L22P-transfected cells had 13.5%. CONCLUSIONS. The mild clinical phenotype observed is consistent with the residual activity of a severely hypomorphic mutant RPE65. Reduction to Ͻ10% of wild-type RPE65 activity by homozygous P25L correlates with almost complete rod function loss and cone amplitude reduction. Functional survival of cones is possible in patients with residual RPE65 isomerase activity. This patient should profit most from gene therapy. (Invest Ophthalmol Vis Sci. 2008;49:5235-5242) DOI: 10.1167/iovs.07-1671 H uman mutations in the gene for the highly preferentially expressed RPE protein RPE65 are associated with a spectrum of retinal dystrophies ranging from more severe earlyonset conditions, variously described as Leber congenital amaurosis type 2/autosomal recessive childhood-onset severe retinal dystrophy or early-onset severe retinal dystrophy (LCA2/arCSR, EOSRD) to later onset conditions described as autosomal recessive retinitis pigmentosa (arRP). 1-7 Recently, RPE65 has been established as the isomerase central to the retinoid visual cycle. 8 -10 This cycle 11 is crucial for supply of the chromophore 11-cis retinal for visual pigment regeneration. Animal models have contributed greatly to our understanding of the role of RPE65 in the visual cycle, regeneration, and retinal dystrophy. Rpe65 knockout mice display a biochemical phenotype consisting of extreme chromophore starvation (no rhodopsin) in the photoreceptors concurrent with overaccumulation of all-trans retinyl esters in the RPE 10 and are extremely insensitive to light. This insensitivity to light protects Rpe65 Ϫ/Ϫ mice from light damage, establishing rhodopsin as the mediator of light-induced retinal damage. 12 There is also a natural mutation in mouse Rpe65 called rd12. 14,15 The utility of gene therapy was established by preclinical trials in these dogs. 21 This level appears to be more than enough to maintain near-normal function. In contrast, human RPE65 EOSRD displays a wide spectrum of severity, age of onset, and progression not seen in animal models. In this article, we present the mild phenotypic consequences of a homozygous P25L missense mutation in a young patient and correlate these with the biochemical effect of this mutation on RPE65 activity. We show that even though the isomerase activity of the mutant RPE65 was quite impaired, the patient had near-normal visual acuity. However, rod function was extremely impaired. In addition, short-wavelength cones appeared more impaired than long-wavelength cones, consistent with findings in other patients with RPE65 mutations that blue color vision is much more and earlier impaired than is red vision, opposite to the usual case in cone dystrophies. These From th

Recent Studies in Andean Prehistory and Protohistory: Papers from the Second Annual Northeast Conference on Andean Archaeology and Ethnohistory

The contributions in this volume represent nine of the twenty-three papers presented at the Second Annual Northeast Conference on Andean Archaeology and Ethnohistory (NCAAE) held at the American Museum of Natural History on November 19-20, 1983. Papers include The Preceramic and Formative Period Occupations in the Cordillera Negra: Preliminary Report by Michael A. Malpass, The Early Horizon--Early Intermediate Period Transition: A View from the Nepena and Viru Valleys by Richard E. Daggett, Paracas in Chincha and Pisco: A Reappraisal of the Ocucaje Sequence by Dwight T. Wallace, Impressions in Metal: Reconstructing Burial Context at Loma Negra, Peru by Anne-Louise Schaeffer, The Moche Moon by Elizabeth P. Benson, Archaeological Investigation in the Andean Piedmont and High Llanos of Western Venezuela: A Preliminary Report by Charles S. Spencer and Elsa M. Redmond, Pachacamac--An Andean Oracle Under Inca Rule by Thomas C. Patterson, The Spanish League and Inca Sites: A Reassessment of the Itinerary of Juan de Matienzo through N.W. Argentina by Gordon C. Pollard, and Written Sources on Andean Cosmogony by George Kubler.https://digitalcommons.library.umaine.edu/andean_past_special/1001/thumbnail.jp

Biochemical evidence for the tyrosine involvement in cationic intermediate stabilization in mouse β-carotene 15, 15'-monooxygenase

<p>Abstract</p> <p>Background</p> <p>β-carotene 15,15'-monooxygenase (BCMO1) catalyzes the crucial first step in vitamin A biosynthesis in animals. We wished to explore the possibility that a carbocation intermediate is formed during the cleavage reaction of BCMO1, as is seen for many isoprenoid biosynthesis enzymes, and to determine which residues in the substrate binding cleft are necessary for catalytic and substrate binding activity. To test this hypothesis, we replaced substrate cleft aromatic and acidic residues by site-directed mutagenesis. Enzymatic activity was measured <it>in vitro </it>using His-tag purified proteins and <it>in vivo </it>in a β-carotene-accumulating <it>E. coli </it>system.</p> <p>Results</p> <p>Our assays show that mutation of either Y235 or Y326 to leucine (no cation-π stabilization) significantly impairs the catalytic activity of the enzyme. Moreover, mutation of Y326 to glutamine (predicted to destabilize a putative carbocation) almost eliminates activity (9.3% of wt activity). However, replacement of these same tyrosines with phenylalanine or tryptophan does not significantly impair activity, indicating that aromaticity at these residues is crucial. Mutations of two other aromatic residues in the binding cleft of BCMO1, F51 and W454, to either another aromatic residue or to leucine do not influence the catalytic activity of the enzyme. Our <it>ab initio </it>model of BCMO1 with β-carotene mounted supports a mechanism involving cation-π stabilization by Y235 and Y326.</p> <p>Conclusions</p> <p>Our data are consistent with the formation of a substrate carbocation intermediate and cation-π stabilization of this intermediate by two aromatic residues in the substrate-binding cleft of BCMO1.</p

Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes