Testing for association based on excess allele sharing in a sample of related cases and controls

Samples consisting of a mix of unrelated cases and controls, small pedigrees, and much larger pedigrees present a unique challenge for association studies. Few methods are available for efficient analysis of such a broad spectrum of data structures. In this paper we introduce a new matching statistic that is well suited to complex data structures and compare it with frequency-based methods available in the literature. To investigate and compare the power of these methods we simulate datasets based on complex pedigrees. We examine the influence of various levels of linkage disequilibrium (LD) of the disease allele with a marker allele (or equivalently a haplotype). For low frequency marker alleles/haplotypes, frequency-based statistics are more powerful in detecting association. In contrast, for high frequency marker alleles, the matching statistic has greater power. The highest power for frequency-based statistics occurs when the disease allele frequency closely matches the frequency of the linked marker allele. In contrast maximum power of the matching statistic always occurs for intermediate marker allele frequency regardless of the disease allele frequency. Moreover, the matching and frequency-based statistics exhibit little correlation. We conclude that these two approaches can be viewed as complementary in finding possible association between a disease and a marker for many different situations.     

Linkage analysis of a completely ascertained sample of familial schizophrenics and bipolars from Palau, Micronesia

We report on linkage analysis of a completely ascertained population of familial psychosis derived from the oceanic nation of Palau. Palau, an archipelago of islands in the Southern Pacific, currently has a population of approximately 23,000 individuals. The peoples of Palau populated these islands recently in human history, approximately 2,000 years ago. As both historical and genetic evidence suggest, the population is far more homogeneous than most other populations undergoing genetic studies, and should therefore prove quite useful for mapping genetic variants having a meaningful impact on susceptibility to psychotic disorders. Moreover, for our study, essentially all on-island schizophrenics (150) and individuals with other psychotic disorders (25) participated. By analysis of narrow (only schizophrenia) and broad (all psychosis) diagnostic schemes, two-point linkage analyses suggest that two regions of the genome harbor genetic variants affecting liability in most families, 3q28 (LOD=3.03) and 17q32.2 (LOD=2.80). Results from individual pedigrees also support 2q37.2, 2p14, and 17p13 as potentially harboring important genetic variants. Most of these regions have been implicated in other genetic studies of psychosis in populations physically quite distant from this Oceanic population, although some (e.g., 3q28) appear to be novel results for schizophrenia linkage analyses.     

Immunoexpression of Survivin in non-neoplastic lymphoid tissues and malignant lymphomas using a new monoclonal antibody reactive on paraffin sections

Survivin is a member of the inhibitor of apoptosis gene family, which is also implicated in mitosis regulation. Most reports in the literature impute poor prognosis to neoplasms with overexpression of this protein. The purpose of the present study is to validate and compare the immunohistochemical reactivity of malignant lymphomas and reactive lymphoid tissue using a new mouse monoclonal antibody to Survivin produced in our laboratory, 6-78. Survivin was detected by immunohistochemistry on tissue microarrays. It was shown that the antibody anti-Survivin 6-78 reliably stains formalin-fixed, paraffin-embedded reactive and neoplastic lymphoid tissues, mostly in a nuclear pattern. We confirmed using this novel antibody that Survivin immunostaining has a tendency to be lower in reactive lymphoid tissues and low-grade B cell lymphomas than in aggressive lymphomas. This antibody may represent a useful tool for standardizing the study of the immunoexpression of Survivin in neoplasms.     

Structural determinants of human APOBEC3A enzymatic and nucleic acid binding properties

Human APOBEC3A (A3A) is a single-domain cytidine deaminase that converts deoxycytidine residues to deoxyuridine in single-stranded DNA (ssDNA). It inhibits a wide range of viruses and endogenous retroelements such as LINE-1, but it can also edit genomic DNA, which may play a role in carcinogenesis. Here, we extend our recent findings on the NMR structure of A3A and report structural, biochemical and cell-based mutagenesis studies to further characterize A3A’s deaminase and nucleic acid binding activities. We find that A3A binds ssRNA, but the RNA and DNA binding interfaces differ and no deamination of ssRNA is detected. Surprisingly, with only one exception (G105A), alanine substitution mutants with changes in residues affected by specific ssDNA binding retain deaminase activity. Furthermore, A3A binds and deaminates ssDNA in a length-dependent manner. Using catalytically active and inactive A3A mutants, we show that the determinants of A3A deaminase activity and anti-LINE-1 activity are not the same. Finally, we demonstrate A3A’s potential to mutate genomic DNA during transient strand separation and show that this process could be counteracted by ssDNA binding proteins. Taken together, our studies provide new insights into the molecular properties of A3A and its role in multiple cellular and antiviral functions.     

Limited transfer of cytosolic NADH into mitochondria at high cardiac workload

Glycolysis supplements energy synthesis at high cardiac workloads, producing not only ATP but also cytosolic NADH and pyruvate for oxidative ATP synthesis. Despite adequate Po(2), speculation exists that not all cytosolic NADH is oxidized by the mitochondria, leading to lactate production. In this study, we elucidate the mechanism for limited cytosolic NADH oxidation and increased lactate production at high workload despite adequate myocardial blood flow and oxygenation. Reducing equivalents from glycolysis enter mitochondria via exchange of mitochondrial alpha-ketoglutarate (alpha-KG) for cytosolic malate. This exchange was monitored at baseline and at high workloads by comparing (13)C enrichment between the products of alpha-KG oxidation (succinate) and alpha-KG efflux from mitochondria (glutamate). Under general anesthesia, a left thoracotomy was performed on 14 dogs and [2-(13)C]acetate was infused into the left anterior descending artery for 40 min. The rate-pressure product was 9,035 +/- 1,972 and 21,659 +/- 5,266 mmHg.beats.min(-1) (n = 7) at baseline (n = 7) and with dobutamine, respectively. (13)C enrichment of succinate was 57 +/- 10% at baseline and 45 +/- 13% at elevated workload (not significant), confirming oxidation of [2-(13)C]acetate. However, cytosolic glutamate enrichment, a marker of cytosolic NADH transfer to mitochondria, was dramatically reduced at high cardiac workload (11 +/- 1%) vs. baseline (50 +/- 14%, P < 0.05). This reduced exchange of (13)C from alpha-KG to cytosolic glutamate at high work indicates reduced shuttling of cytosolic reducing equivalents into the mitochondria. Myocardial tissue lactate increased 78%, countering this reduced oxidation of cytosolic NADH. The findings elucidate a contributing mechanism to glycolysis outpacing glucose oxidation in the absence of myocardial ischemia.     

Stage-structured interactions between seasonal and permanent residents of an estuarine nekton community

Estuarine assemblages of fishes and natant decapod crustaceans (i.e. nekton) comprise both permanent resident species and juveniles of coastal marine species that use estuaries primarily as nurseries. In an attempt to understand how the young of marine species successfully invade communities of permanent estuarine residents we studied potential interactions between two of the most abundant decapod crustaceans in nekton assemblages of the southeastern United States. Three years of quantitative samples from an intertidal marsh on Sapelo Island, Georgia showed that densities of the resident daggerblade grass shrimp Palaemonetes pugio were reduced during the time that juvenile white shrimp Penaeus setiferus used the estuary as a nursery. Results of a field enclosure experiment showed that white shrimp had no significant lethal or sublethal effects on adult grass shrimp. However, they did reduce survival of both juvenile and larval grass shrimp in laboratory experiments, suggesting the potential importance of a stage-dependent predatorprey interaction between the two shrimp species. The mortality rate of young grass shrimp in the presence of white shrimp was unaffected by grass shrimp density, but larvae (2.6–3.0 mm) suffered higher mortalities than did juveniles (5.0–15.0 mm). We suggest that the vulnerability of grass shrimp to predation by white shrimp is related to their molting cycle. The window of vulnerability opens more often for younger grass shrimp because they molt more frequently. When combined with losses due to other predators and competitors, the impact of early white shrimp cohorts on grass shrimp larvae and juveniles may prevent the resident species from maintaining its population at high densities, thereby freeing resources in the nursery for subsequent cohorts of juvenile white shrimp.     

Day/night differences in the grazing impact of marine copepods

Day/night differences in the removal rate of phytoplankton can occur as a result of increased copepod grazing rates at certain times of the day and diel vertical migration of animals. We conducted shipboard grazing experiments and fine-scale vertical zooplankton sampling to resolve these behaviors. Day/night feeding differences were compared in the center of several warm-core Gulf Stream rings, under conditions of no lateral water mass exchange, in the mesohaline portion of Chesapeake Bay and when following drogues in the Chesapeake Bay plume. Day/night variations in copepod biomass in the surface mixed layer were greater in neritic waters as compared to the open ocean stations. Day/night differences in weight-specific copepod filtration rates varied less than biomass. At the neritic stations copepod grazing was often higher at night, whereas at the oceanic stations day/night grazing rates were similar or daytime grazing rates were highest. The night/day ratio of zooplankton grazing impact on the phytoplankton community (the product of zooplankton biomass and their weight-specific grazing rate) averaged 4.8 in the Chesapeake Bay plume and 1.6 in warm-core Gulf Stream rings. Our results suggest that at lower food levels, there often are less day/night differences in the removal rate of phytoplankton by the copepod community.     

Bottom-up controls on a mixed-species HAB assemblage: A comparison of sympatric Chattonella subsalsa and Heterosigma akashiwo (Raphidophyceae) isolates from the Delaware Inland Bays, USA

Recent novel mixed blooms of several species of toxic raphidophytes have caused fish kills and raised health concerns in the highly eutrophic Inland Bays of Delaware, USA. The factors that control their growth and dominance are not clear, including how these multi-species HAB events can persist without competitive exclusion occurring. We compared and contrasted the relative environmental niches of sympatric Chattonella subsalsa and Heterosigma akashiwo isolates from the bays using classic Monod-type experiments. C. subsalsa grew over a temperature range from 10 to 30 °C and a salinity range of 5–30 psu, with optimal growth occurring from 20 to 30 °C and 15 to 25 psu. H. akashiwo had similar upper temperature and salinity tolerances but also lower limits, with growth occurring from 4 to 30 °C and 5 to 30 psu and optimal growth between 16 and 30 °C and 10 and 30 psu. These culture results were confirmed by field observations of bloom occurrences in the Inland Bays. Maximum nutrient-saturated growth rates (μ_max) for C. subsalsa were 0.6 d⁻¹ and half-saturation concentrations for growth (K_s) were 9 μM for nitrate, 1.5 μM for ammonium, and 0.8 μM for phosphate. μ_max of H. akashiwo (0.7 d⁻¹) was slightly higher than C. subsalsa, but K_s values were nearly an order of magnitude lower at 0.3 μM for nitrate, 0.3 μM for ammonium, and 0.2 μM for phosphate. H. akashiwo is able to grow on urea but C. subsalsa cannot, while both can use glutamic acid. Cell yield experiments at environmentally relevant levels suggested an apparent preference by C. subsalsa for ammonium as a nitrogen source, while H. akashiwo produced more biomass on nitrate. Light intensity affected both species similarly, with the same growth responses for each over a range from 100 to 600 μmol photons m⁻² s⁻¹. Factors not examined here may allow C. subsalsa to persist during multi-species blooms in the bays, despite being competitively inferior to H. akashiwo under most conditions of nutrient availability, temperature, and salinity.     

7-Oxo-4,7-dihydrothieno[3,2-b]pyridine-6-carboxamides: synthesis and biological activity of a new class of highly potent inhibitors of human cytomegalovirus DNA polymerase

We report a new class of non-nucleoside antivirals, the 7-oxo-4,7-dihydrothieno[3,2-b]pyridine-6-carboxamides, some of which possess remarkable potency versus a broad spectrum of herpesvirus DNA polymerases and excellent selectivity compared to human DNA polymerases. A critical factor in the level of activity is hypothesized to be conformational restriction of the key 2-aryl-2-hydroxyethylamine sidechain by an adjacent methyl group.