From gene to protein: Investigating the disease etiology of retinitis pigmentosa

Retinitis pigmentosa (RP) is a name given to a group of inherited retinal dystrophies that lead to progressive photoreceptor degeneration, and thus, visual impairment. It is evident at both the clinical and the molecular level that these are heterogeneous disorders, with wide variation in severity, mode of inheritance, and phenotype. The genetics of RP are not simple; the disease can be inherited in dominant, recessive, X-linked, and digenic modes. Autosomal dominant RP (adRP) results from mutations in at least ten mapped loci, but there may be dozens of genetic loci where mutations can cause RP. To date, there are over a hundred genes known to cause retinal degenerative diseases, and less than half of these have been cloned (RetNet). Among the dozens of retinitis pigmentosa loci known to exist, only a few have been identified and the remainders are inferred from linkage studies. Today, the genes for seven of the twelve-adRP loci have been identified, and these are rhodopsin, peripherin/RDS, NRL, ROM1, CRX, RP13 and RP1. My research projects involved a combination of the continued search for genes involved in retinal dystrophies, as well the investigation into the role of peripherin/RDS and RP1 in the disease etiology of autosomal dominant RP. ^ Most of the mutations leading to inherited retinal disorders have been identified in predominately retina expressed genes like rhodopsin, peripherin/RDS, and RP1. Expressed sequence tags (ESTs) that were retina-specific were culled from sequence databases and, together with laboratory analysis, were analyzed as potential candidate genes for retinal dystrophies. Thirteen of the fifty-five identified retina-specific ESTs mapped to within candidate regions for inherited retinopathies. One of these is RP1L1, a homologue of RP1 and a potential cause of adRP. ^ Once a disease-associated gene has been identified, elucidating the role of that gene in the visual process is essential for understanding what happens when the process is defective as it is in adRP. My next projects involved investigating the role of a novel 5′ donor +3 splice site mutation on the mRNA of peripherin/RDS in adRP affected individuals, and comparative sequencing in RP1 to define conserved regions of the protein. Comparative sequencing is a powerful way to delineate critical regions of a sequence because different regions of a gene have different functions, and each region is subject to different levels of functional or structural constraints. Establishing a framework of conserved domains is beneficial not only for structural or functional studies, but can also aid in determining the potential effects of mutations. With the completion of sequencing of human genome, and other organisms such as Saccharomyces cerevisiae, Caenorhabditis elegans , and Drosophila, the facility of comparative sequencing will only increase in the future. Comparative sequencing has already become an established procedure for pinpointing conserved regions of a protein, and is an efficient way to target regions of a protein for experimental and/or evolutionary analysis. ^

Land Inheritance Rules: Theory and Cross-Cultural Analysis

This paper develops a general theory of land inheritance rules. We distinguish between two classes of rules: those that allow a testator discretion in disposing of his land (like a best-qualified rule), and those that constrain his choice (like primogeniture). The primary benefit of the latter is to prevent rent seeking by heirs, but the cost is that testators cannot make use of information about the relative abilities of his heirs to manage the land. We also account for the impact of scale economies in land use. We conclude by offering some empirical tests of the model using a cross-cultural sample of societies.

Women in Eighteenth Century London: Female Coming of Age in Frances Burney’s Evelina, Cecilia, and The Witlings

The late eighteenth-century author Frances Burney is best known for popularizing the “comedy of manners,” a literary style later adopted by Jane Austen. Burney’s novels, journals, and plays offer an intriguing commentary on contemporary social customs and etiquette. In particular, she voices the concerns and desires of women, leading scholars to focus on the feminist overtones of her writing. Although she carefully examined female roles in the household and family structure, Burney also provided an insider’s perspective into London high life. As an acclaimed author and member of the royal court, Burney offers a rare insight into the lives of the urban elite. For these reasons, I have chosen to examine three of her works within the context of their London setting. In Evelina, Cecilia, and The Witlings, Burney examines women’s struggle for independence against the backdrop of the city. These works offer a new interpretation of the female Bildungsroman, or coming of age story. Burney shows how London life influences her heroines’ expectations, ambitions and desires. Evelina’s coming of age centers around the quest for family and social acceptance, while the two Cecilias of Cecilia and The Witlings confront the financial pressures that accompany their inheritance. Ultimately, the three protagonists learn important lessons that are specific to city life. Although Burney concludes each story with the heroine’s marriage, her focus is not on romance, as has been suggested, but on the cultural landscape of the city. Coming of age in her stories is inextricably connected to the diverse challenges and opportunities presented to urban women.

Contribution of activity and skin temperature to the risk of developing pressure ulcers in nursing facility residents

Purpose. The central concepts in pressure ulcer risk are exposure to external pressure caused by inactivity and tissue tolerance to pressure, a factor closely related to blood flow. Inactivity measures are effective in predicting pressure ulcer risk. The purpose of the study is to evaluate whether a physiological measure of skin blood flow improves pressure ulcer risk prediction. Skin temperature regularity and self-similarity, as proxy measures of blood flow, and not previously described, may be undefined pressure ulcer risk factors. The specific aims were to determine whether a sample of nursing facility residents at high risk of pressure ulcers classified using the Braden Scale for Pressure Sore Risk© differ from a sample of low risk residents according to (1) exposure to external pressure as measured by resident activity, (2) tissue tolerance to external pressure as measured by skin temperature, and (3) skin temperature fluctuations and recovery in response to a commonly occurring stressor, bathing and additionally whether (4) scores on the Braden Scale mobility subscale score are related to entropy and the spectral exponent. ^ Methods. A two group observational time series design was used to describe activity and skin temperature regularity and self-similarity, calculating entropy and the spectral exponent using detrended fluctuation analysis respectively. Twenty nursing facility residents wore activity and skin temperature monitors for one week. One bathing episode was observed as a commonly occurring stressor for skin temperature.^ Results. Skin temperature multiscale entropy (MSE), F(1, 17) = 5.55, p = .031, the skin temperature spectral exponent, F(1, 17) = 6.19, p = .023, and the activity mean MSE, F(1, 18) = 4.52, p = .048 differentiated the risk groups. The change in skin temperature entropy during bathing was significant, t(16) = 2.55, p = .021, (95% CI, .04-.40). Multiscale entropy for skin temperature was lowest in those who developed pressure ulcers, F(1, 18) = 35.14, p < .001.^ Conclusions. This study supports the tissue tolerance component of the Braden and Bergstrom conceptual framework and shows differences in skin temperature multiscale entropy between pressure ulcer risk categories, pressure ulcer outcome, and during a commonly occurring stressor. ^

Genetic epidemiology of childhood brain tumors

A rare familial cancer syndrome involving childhood brain tumors (CBT), breast cancer, sarcomas and an array of other tumors has been described (Li and Fraumeni 1969, 1975, 1982, 1987). A survey of CBT identified through the Connnecticut Tumor Registry in 1984 revealed a high frequency of CBT, leukemia and other childhood cancer in siblings of CBT patients (Farwell and Flannery, 1984). Other syndromes such as neurofibromatosis and nevoid basal cell carcinoma syndrome have also been associated with CBT; however, no systematic family studies have been conducted to determine the extent to which cancer aggregates in family members of CBT patients. This family study was designed to determine the frequency of cancer aggregation overall or at specific sites, to determine the frequency of known or potentially hereditary syndromes in families of CBT patients, and to determine a genetic model to characterize familial cancer syndromes and to identify specific kindreds to which such a model(s) might apply. This study includes 244 confirmed CBT patients referred to the University of Texas M. D. Anderson Cancer Center between the years 1944 and 1983, diagnosed under the age of 15 years and resident in the U.S. or Canada. Family histories were obtained on the proband's first (parents, siblings and offspring) and second degree (proband's aunts, uncles and grandparents) relatives following sequential sampling scheme rules. To determine if cancer aggregates in families, we compared the cancer experience in the population to that expected in the general population using Connecticut Tumor Registry calendar year, age, race and sex-specific rates. The standardized incidence ratio (SIR) for cancer overall was 0.91 (41 observed (O) and 44.94 expected (E); 95% Confidence Interval (CI) = 0.65-1.24). We observed a significant excess of colon cancer among the proband's first degree relatives (O/E = 5/1.64; 95% CI = 1.01-7.65), in particular those under age 45 year. Segregation analysis showed evidence for multifactorial inheritance in the small percentage (N = 5) of the families. ^

Genetic variants within the Wnt/ B-catenin signaling pathway as indicators of bladder cancer clinical outcomes

The genetic factors that influence bladder cancer clinical outcomes are largely unknown. In this clinical outcomes study, I assessed genetic variations in the Wnt/β-catenin stem-cell pathway genes for association with recurrence and progression. A total of 230 SNPS in 40 genes from the Wnt/β-catenin pathway were genotyped in 419 histologically confirmed non-muscle invasive bladder cancer cases. Several significant associations were observed in the clinical outcomes analysis. Under the dominant model WNT8B: rs4919464 (HR: 1.55, 95% CI: 1.17-2.06, P=2.2x10-3) and WNT8B: rs3793771 (HR: 1.54, 95% CI: 1.09-1.62, P=4.6x10-3 ) were statistically significantly associated with an increase risk of recurrence while two other variants, APC2: rs11668593 (HR: 2.50, 95% CI: 1.43-4.35, P=1.2x10-3) and LRP5 : rs312778 (HR: 1.81, 95% CI: 1.23-2.65, P=2.7x10-3), were significantly associated with recurrence risk under the recessive model of inheritance. Four SNPs in the recessive model were associated with an increased risk of progression (AXIN2: rs1544427, LRP5: rs312778, AXIN1: rs370681, AXIN1: rs2301522). LRP5: rs312778 had the most significant increased risk of progression with a 2.68 (95% CI: 1.52-4.72, P=6.4x10-4)-fold increased risk. Stratification analysis based on treatment regimen (transurethral resection (TUR) and Bacillus Calmette-Guérin (BCG)) was also performed. Individuals with at least one variant in AXIN2: rs2007085 were found to have a 2.09 (95% CI: 1.24-3.52, P=5.4x10-3) -fold increased risk of recurrence in those that received TUR only, and no statistically significant effect was seen in those that received BCG. Individuals who received TUR with at least one variant in LEF1: rs10516550 were found to have a 2.26 (95% CI: 1.22-4.18, P=9.7x10-3)-fold increase risk of recurrence and no statistically significant effect was found in individuals who received BCG. Also, the recessive model of LRP6: rs2302684 in TUR only treatment was shown to have a 1.95 (95%CI: 1.18-3.21, P=8.8x10 -3)-fold increased risk of recurrence, and a suggested protective effect associated with a (HR: 0.83, 95% CI: 0.51-1.37, P=0.468) decreased risk of recurrence. Together, these findings implicate the Wnt/β-catenin stem-cell pathway as playing a role in bladder cancer clinical outcomes and have important implications for personalization of future treatment regimens. ^

AN ASSESSMENT OF KNOWLEDGE AND ATTITUDES OF GENETIC COUNSELING SERVICES IN U.S. HTCs

Hemophilia is a hereditary bleeding disorder which requires lifelong specialized care. A network of Hemophilia Treatment Centers (HTCs) exists to meet the medical needs of patients affected by hemophilia. Genetic counseling services are an integral part of the HTC model of care; however, many HTCs do not have genetic counselors on staff. As a result, the duty to provide these services must fall to other healthcare providers within the HTC. To assess the knowledge and attitudes of these providers we developed a 49 question survey that was distributed electronically to hematologists and nurses at U.S. HTCs. The survey consisted of a three sections: demographic information, knowledge of hemophilia genetics, and attitudes towards genetic services. A total of 111 complete responses were received and analyzed. The average knowledge score among all participants was 74.8% with a total of 81 participants receiving a passing score of 70% or above. Thirty participants scored below 70% in the knowledge section. In general, attitude scores were high indicating that the majority of hematologists and nurses in HTCs feel confident in their ability to provide genetic counseling services. Over 90% of participants reported that they have some form of access to genetic counseling services at their center. Hematologists and nurses practicing in U.S. HTCs demonstrate sufficient knowledge of the genetics of hemophilia, and they generally feel confident in their ability to provide genetic counseling services to their patients. While their knowledge is sufficient, the average knowledge score was lower than 75%. Certain questions covering new genetic technologies and testing practices were more commonly missed than questions asking about more basic aspects of hemophilia genetics, such as inheritance and carrier testing. Finally, many clinics report having access to a counselor, but it is oftentimes a hematologist or nurse who is providing genetic counseling services to patients. Given the inconsistency in knowledge among providers coupled with the high confidence in one’s ability to counsel patients, it leaves room to question whether information about the genetics of hemophilia is being communicated to patients in the most appropriate and accurate manner.

Zircons, isotope ratios and element analyses from tonalite and oxide gabbro of the mid-ocean ridge from ODP Hole 176-735B

A limiting factor in the accuracy and precision of U/Pb zircon dates is accurate correction for initial disequilibrium in the 238U and 235U decay chains. The longest-lived-and therefore most abundant-intermediate daughter product in the 235U isotopic decay chain is 231Pa (T1/2 = 32.71 ka), and the partitioning behavior of Pa in zircon is not well constrained. Here we report high-precision thermal ionization mass spectrometry (TIMS) U-Pb zircon data from two samples from Ocean Drilling Program (ODP) Hole 735B, which show evidence for incorporation of excess 231Pa during zircon crystallization. The most precise analyses from the two samples have consistent Th-corrected 206Pb/238U dates with weighted means of 11.9325 ± 0.0039 Ma (n = 9) and 11.920 ± 0.011 Ma (n = 4), but distinctly older 207Pb/235U dates that vary from 12.330 ± 0.048 Ma to 12.140 ± 0.044 Ma and 12.03 ± 0.24 to 12.40 ± 0.27 Ma, respectively. If the excess 207Pb is due to variable initial excess 231Pa, calculated initial (231Pa)/(235U) activity ratios for the two samples range from 5.6 ± 1.0 to 9.6 ± 1.1 and 3.5 ± 5.2 to 11.4 ± 5.8. The data from the more precisely dated sample yields estimated DPazircon/DUzircon from 2.2-3.8 and 5.6-9.6, assuming (231Pa)/(235U) of the melt equal to the global average of recently erupted mid-ocean ridge basaltic glasses or secular equilibrium, respectively. High precision ID-TIMS analyses from nine additional samples from Hole 735B and nearby Hole 1105A suggest similar partitioning. The lower range of DPazircon/DUzircon is consistent with ion microprobe measurements of 231Pa in zircons from Holocene and Pleistocene rhyolitic eruptions (Schmitt (2007; doi:10.2138/am.2007.2449) and Schmitt (2011; doi:10.1146/annurev-earth-040610-133330)). The data suggest that 231Pa is preferentially incorporated during zircon crystallization over a range of magmatic compositions, and excess initial 231Pa may be more common in zircons than acknowledged. The degree of initial disequilibrium in the 235U decay chain suggested by the data from this study, and other recent high precision datasets, leads to resolvable discordance in high precision dates of Cenozoic to Mesozoic zircons. Minor discordance in zircons of this age may therefore reflect initial excess 231Pa and does not require either inheritance or Pb loss.

Major element concentrations in spinel, olivine and pyroxene from peridotites of ODP Hole 210-1277 of the Newfoundland margin

Serpentinized spinel peridotites of the Newfoundland margin drilled during ODP Leg 210 at Site 1277 have preserved, relic mineral compositions similar to the most depleted abyssal peridotites worldwide and different from those of the conjugate Iberian margin. The samples are derived from mass flows containing clasts of peridotite and gabbro and from in-situ basement, and are mostly mylonitic cpx-poor spinel harzburgites with Cr-rich spinels (Cr#0.35-0.66). Melting of the Newfoundland mantle occurred in the spinel peridotite field and probably exceeded the cpx-out phase boundary for some samples. Using proposed spinel peridotite melting models and experimentally derived phase diagrams, the Newfoundland harzburgites can be modeled as a residue after extraction of 14 to 20-25% melting. Basalts that are interleaved with mass flow deposits on top of the peridotite basement resemble normal to transitional mid-ocean ridge basalt. This, together with the unusually high Cr# of some spinel harzburgites suggest that the formation of basalts and partial melting of the underlying peridotite are not cogenetic. Among mantle samples some of the Newfoundland harzburgites approach mineral compositions of the Bay of island ophiolite and ophiolites from Japan that represent peridotites formed in an arc-setting. Thus, the peridotites drilled at Site 1277 may represent inherited (Caledonian or older) subarc mantle that was exhumed close to the ocean floor during the rifting evolution of the Atlantic. Compared to the spinel harzburgites from Newfoundland, the peridotites from the conjugate Iberian margin are, on average, less depleted and provide evidence for local equilibration in the plagioclase stability field. This can either be explained by an inherited, primary, Ca-richer composition of the Iberia peridotite, or, alternatively, by local melt impregnation and stagnation during continental rifting, and thus refertilizing previously depleted (arc-related) peridotite.

Chemical and isotopic compositions of authigenic carbonates from bottom sediments of Northwest Pacific marginal seas

The paper presents data on authigenic carbonate distribution in Holocene - Upper Pleistocene deposits of the Okhotsk, Japan, East China, Philippine and South China Seas. Description of carbonate samples, their chemical and isotope compositions are given. Chemical analysis of the samples indicates that almost all authigenic carbonates are composed of calcite or magnesian calcite; and only in one case, of siderite. Oxygen isotopic composition (d18O) ranges from +37.7 to +26.1 per mil (SMOW); it is, probably, connected with different temperatures of carbonate formation. A distinct geographic regularity is traced. Decrease in d18O values is observed from the cold Okhotsk Sea to the warm South China Sea. A very wide range of carbon isotopic composition (d13C from -42 to +3.8 per mil) indicates different sources of carbonic acid required for formation of these carbonates. As a basis for carbon isotopic composition we can distinguish three sources of carbonic acid in the studied sediments: microbiological methane oxidation, organic matter destruction during sediment diagenesis, and dissolved organogenic limestone. Thus, formation of authigenic carbonates in sediments from the marginal seas of the Northwest Pacific results from: 1) sediment diagenesis, 2) methane oxidation in zones of gas anomalies, 3) their precipitation from the supersaturated by carbonates sea shoal waters of tropical sea lagoons.

Chemistry and mineralogy of ODP Leg 124 sediment samples

From X-ray mineralogical studies and chemical analyses of the whole rocks and the fine fractions (<2 µm) of ten to fifteen samples at each site of ODP Leg 124, two major sources were identified in the sedimentary components of the Celebes and Sulu basins: (1) a terrestrial and continental contribution; (2) a volcanic influx that gives way to well-defined volcanic units or to a dilute contamination, consisting of coarse-grained minerals (Plagioclase, pyroxene, olivine, spinel) or a smectitic-rich fraction produced by the alteration of volcanic glasses and ashes. The continental signature increases the amount of quartz in the rocks and the phyllitic association is complex: micas, kaolinite, disordered interstratified clay-minerals. The chemical compositions of the bulk rocks and the fractions <2 µm are more potassic and aluminum-rich. The volcanic imprint depends on the grain-size and chemical properties of the components. Ca/Na contents highly variable compared to the K content of the bulk composition are due to the presence of coarse-grained volcanic Plagioclase. The fractions <2 µm are more magnesian than in the continental regime. The diagenesis is revealed by the crystallization of zeolites, the fixation of magnesium into the smectites that depletes the pore fluids in this element. Smectitization of the disordered interstratified clay minerals enriches the alkalinity of the pore fluids. Some deep formations of the Sulu Basin are affected by a thermal event, but no thermal event was recognized in the Celebes Basin.

Upper Cretaceous sediments of ODP Hole 122-762C

Well-developed Campanian to Maestrichtian pelagic cyclic sediments were recovered from Hole 762C on the Exmouth Plateau, off northwest Australia, during Ocean Drilling Program Leg 122. The cycles consist of nannofossil chalk (light beds) and clayey nannofossil chalk (dark beds). Both light and dark beds are strongly to moderately bioturbated, alternate on a decimeter scale, and exhibit gradual boundaries. Bioturbation introduces materials from a bed of one color into an underlying bed of another color, indicating that diagenesis is not responsible for the cyclicity. Differences in composition between the light and dark beds, revealed by calcium carbonate measurement and X-ray diffraction analysis, together with trace fossil evidence, indicate that the cycles in the sediments are a depositional feature. Diagenetic processes may have intensified the appearance of the cycles. Spectral analysis was applied to the upper Campanian to lower Maestrichtian cyclic sediments to examine the regularity of the cycles. Power spectra were calculated from time series using Walsh spectral analysis. The most predominant wavelengths of the color cycles are 34-41 cm and 71-84 cm. With an average sedimentation rate of 1.82 cm/k.y. in this interval, we found the time durations of the cycles to be around 41 k.y. and 21 k.y., respectively, comparable to the obliquity and precession periods of the Earth's rotation, which strongly suggests an orbital origin for the cycles. On the basis of sedimentological evidence and plate tectonic reconstruction, we propose the following mechanism for the formation of the cyclic sediments from Hole 762C. During the Late Cretaceous, when there was no large-scale continental glaciation, the cyclic variations in insolation, in response to cyclic orbital changes, controlled the alternation of two prevailing climates in the area. During the wetter, equable, and warmer climatic phases under high insolation, more clay minerals and other terrestrial materials were produced on land and supplied by higher runoff to a low bioproductivity ocean, and the dark clayey beds were deposited. During the drier and colder climatic phases under low insolation, fewer clay minerals were produced and put into the ocean, where bioproductivity was increased and the light beds were deposited.