Gorges partition diversity within New Zealand flathead Galaxias populations

Understanding the landscape factors governing population connectivity in riverine ecosystems represents an ongoing challenge for freshwater biologists. We used DNA sequence analysis to test the hypothesis that major geomorphological features underpin freshwater-limited fish diversity in a tectonically dynamic region of New Zealand. Phylogeographic analysis of 101 Galaxias depressiceps cytochrome b sequences, incorporating 55 localities from southern New Zealand, revealed 26 haplotypes, with only one shared among rivers. We detect strong hierarchical genetic differentiation both among and within river systems. Genetic structuring is particularly pronounced across the Taieri River system (63 individuals from 35 sites, 18 haplotypes), with 92% of variation partitioned among locations. Distinctive within-river genetic clusters are invariably associated with major subcatchment units, typically isolated by substantial gorges. The anomalous distribution of a single lineage across a major drainage divide is consistent with local, tectonically driven headwater capture. We conclude that major landscape features such as gorges can strongly partition riverine fish diversity and constrain freshwater biodiversity.

ebony underpins Batesian mimicry in melanic stoneflies

The evolution of Batesian mimicry - whereby harmless species avoid predation through their resemblance to harmful species - has long intrigued biologists. In rare cases, Batesian mimicry is linked to intraspecific colour variation, in which only some individuals within a population resemble a noxious 'model'. Here, we assess intraspecific colour variation within a widespread New Zealand stonefly, wherein highly melanized individuals of Zelandoperla closely resemble a chemically defended aposematic stonefly, Austroperla cyrene. We assess convergence in the colour pattern of these two species, compare their relative palatability to predators, and use genome-wide association mapping to assess the genetic basis of this resemblance. Our analysis reveals that melanized Zelandoperla overlap significantly with Austroperla in colour space but are significantly more palatable to predators, implying that they are indeed Batesian mimics. Analysis of 194,773 genome-wide SNPs reveals an outlier locus (ebony) strongly differentiating melanic versus non-melanic Zelandoperla. Genotyping of 338 specimens from a single Zelandoperla population indicates that ebony explains nearly 70% of the observed variance in melanism. As ebony has a well-documented role in insect melanin biosynthesis, our findings indicate this locus has a conserved function across deeply divergent hexapod lineages. Distributional records suggest a link between the occurrence of melanic Zelandoperla and the forested ecosystems where the model Austroperla is abundant, suggesting the potential for adaptive shifts in this system underpinned by environmental change.

Catalogue of New Zealand land, freshwater and estuarine molluscan taxa named by Frederick Wollaston Hutton between 1879 and 1904

Details are provided on 16 land snail genera, eight freshwater molluscan species, one estuarine species, 47 land snail species and varieties from New Zealand, and a further three land snail species putatively from New Zealand, which were described by Frederick Wollaston Hutton between 1879 and 1904. Original primary type material of 54 species was located during the present study. Lectotypes are designated for: Amphidoxa cornea Hutton, 1882, Amphidoxa jacquenetta Hutton, 1883, Amphidoxa perdita Hutton, 1883, Charopa cassandra Hutton, 1883, Cyclotus charmian Hutton, 1883, Fruticicola adriana Hutton, 1883, Gerontia cordelia Hutton, 1883, Gerontia pantherina Hutton, 1882, Microphysa pumila Hutton, 1882, Patula jessica Hutton, 1883, Patula lucetta Hutton, 1884, Patula sylvia Hutton, 1883, Patula tapirina Hutton, 1882, Pfeifferia cressida Hutton, 1883, Phrixgnathus celia Hutton, 1883, Phrixgnathus haasti Hutton, 1883, Phrixgnathus marginatus Hutton, 1882, Phrixgnathus phrynia Hutton, 1883, Rhytida australis Hutton, 1882, Strobila leiodon Hutton, 1882, Thalassia propinqua Hutton, 1882, Therasia thaisa Hutton, 1883, Therasia valeria Hutton, 1883 and Zonites helmsii Hutton, 1882. A neotype is designated for Rhytida citrina Hutton, 1882. Primary type material of the following taxa is figured herein for the first time: Amphidoxa lavinia Hutton, 1883, Cyclotus charmian Hutton, 1883, Fruticicola adriana Hutton, 1883, Leptopoma pannosa Hutton, 1882, Patula lucetta Hutton, 1884, Patula sylvia Hutton, 1883, Patula tapirina Hutton, 1882, Phacussa helmsi var. maculata Hutton, 1884, Phrixgnathus ariel Hutton, 1883, Phrixgnathus celia Hutton, 1883, Rhytida australis Hutton, 1882, Rissoa vana Hutton, 1873, Testacella vagans Hutton, 1882, Trochomorpha hermia Hutton, 1883 and Zonites helmsii Hutton, 1882. New taxonomic combinations introduced herein include Phacussa lucetta (Hutton, 1884) and Therasia propinqua (Hutton, 1882). Amphidoxa lavinia Hutton, 1883, Charopa cassandra Hutton, 1883, Patula timandra Hutton, 1883 and Trochomorpha hermia Hutton, 1883 are treated as junior synonyms of Tasmaphena sinclairii (Pfeiffer, 1846), Phacussa fulminata (Hutton, 1882), Fectola infecta (Reeve, 1852) and Advena campbellii (Gray, 1834), respectively.

Effect of corn residue harvest method with ruminally undegradable protein supplementation on performance of growing calves and fiber digestibility

Two experiments evaluated the effects of corn residue harvest method on animal performance and diet digestibility. Experiment 1 was designed as a 2 × 2 + 1 factorial arrangement of treatments using 60 individually fed crossbred steers (280 kg [SD 32] initial BW; = 12). Factors were the corn residue harvest method (high-stem and conventional) and supplemental RUP at 2 concentrations (0 and 3.3% diet DM). A third harvest method (low-stem) was also evaluated, but only in diets containing supplemental RUP at 3.3% diet DM because of limitations in the amount of available low-stem residue. Therefore, the 3 harvest methods were compared only in diets containing supplemental RUP. In Exp. 2, 9 crossbred wethers were blocked by BW (42.4 kg [SD 7] initial BW) and randomly assigned to diets containing corn residue harvested 1 of 3 ways (low-stem, high-stem, and conventional). In Exp. 1, steers fed the low-stem residue diet had greater ADG compared with the steers fed conventionally harvested corn residue ( = 0.03; 0.78 vs. 0.63 kg), whereas steers fed high-stem residue were intermediate ( > 0.17; 0.69 kg), not differing from either conventional or low-stem residues. Results from in vitro OM digestibility suggest that low-stem residue had the greatest ( < 0.01) amount of digestible OM compared with the other 2 residue harvest methods, which did not differ ( = 0.32; 55.0, 47.8, and 47.1% for low-stem, high-stem, and conventional residues, respectively). There were no differences in RUP content (40% of CP) and RUP digestibility (60%) among the 3 residues ( ≥ 0.35). No interactions were observed between harvest method and the addition of RUP ( ≥ 0.12). The addition of RUP tended to result in improved ADG (0.66 ± 0.07 vs. 0.58 ± 0.07 for supplemental RUP and no RUP, respectively; = 0.08) and G:F (0.116 ± 0.006 vs. 0.095 ± 0.020 for supplemental RUP and no RUP, respectively; = 0.02) compared with similar diets without the additional RUP. In Exp. 2, low-stem residue had greater DM and OM digestibility and DE ( < 0.01) than high-stem and conventional residues, which did not differ ( ≥ 0.63). Low-stem residue also had the greatest NDF digestibility (NDFD; < 0.01), whereas high-stem residue had greater NDFD than conventional residue ( < 0.01). Digestible energy was greatest for low-stem residue ( < 0.05) and did not differ between high-stem and conventional residues ( = 0.50). Reducing the proportion of stem in the bale through changes in the harvest method increased the nutritive quality of corn residue.

Crossing the front: contrasting storm-forced dispersal dynamics revealed by biological, geological and genetic analysis of beach-cast kelp

The subtropical front (STF) generally represents a substantial oceanographic barrier to dispersal between cold-sub-Antarctic and warm-temperate water masses. Recent studies have suggested that storm events can drastically influence marine dispersal and patterns. Here we analyse biological and geological dispersal driven by two major, contrasting storm events in southern New Zealand, 2017. We integrate biological and physical data to show that a severe southerly system in July 2017 disrupted this barrier by promoting movement of substantial numbers of southern sub-Antarctic Durvillaea kelp rafts across the STF, to make landfall in mainland NZ. By contrast, a less intense easterly storm (Cyclone Cook, April 2017) resulted in more moderate dispersal distances, with minimal dispersal between the sub-Antarctic and mainland New Zealand. These quantitative analyses of approximately 200 freshly beach-cast kelp specimens indicate that storm intensity and wind direction can strongly influence marine dispersal and landfall outcomes.

Rafting dispersal in a brooding southern sea star (Asteroidea : Anasterias)

Marine biogeographers have long speculated that macroalgal rafting presents a dispersal mechanism for brooding marine invertebrates of the Southern Ocean, but few direct observations of rafting by echinoderm taxa have been documented. Here we report rafting of the brooding benthic sea star Anasterias suteri, along with two mollusc taxa (Onithochiton neglectus – also a brooder – and Cantharidus roseus), on detached bull-kelp Durvillaea antarctica in Foveaux Strait, southern New Zealand. The rafting journey, intercepted at sea, likely lasted for 2–3 weeks and may have covered several hundred kilometres. We use DNA sequences, together with meteorological and prevailing oceanographic data, to infer the likely Fiordland (mainland) origins of the raft and its epifauna. This rafting dispersal mechanism provides an explanation for the broad (circum-subantarctic) but disjunct distribution of brooding Anasterias populations, and for the genetic connectivity observed between their populations.

Anal phyllodes tumor in a male patient: a unique case presentation and literature review

Abstract

Lesions of anogenital mammary-like glands are rare, and only 44 female cases have been reported. Herein, we describe a particularly rare case of phyllodes tumor of anogenital mammary-like glands in a 41-year-old male presenting anal bleeding. Papillectomy was performed. The excised tumor was circumscribed in shape, and after it was sliced into sections, it was noted that there were leaf-like slits on the surface of cut side. Under the microscope, the tumor was found to be biphasic, with a bland glandular epithelium and low-to-intermediate cellular stroma, which together created the leaf-like slits. Gynecomastoid hyperplasia was evident at the periphery. The epithelium showed immuno-activity for ER, PR(focal), AR, and GCDFP-15. The stromal cells showed positive staining for CD34 and vimentin. The morphology and immunophenotype were similar to benign phyllodes tumors of breast. To the best of our knowledge, this case report represents the first case of phyllodes tumor of anogenital mammary-like glands with gynecomastoid hyperplasia at the periphery in a male patient. To make a diagnosis, we had to differentiate this lesion from hidradenoma papilliferum of skin appendage, phyllodes tumor of ectopic prostatic tissue, and other tumors of anogenital mammary-like glands analogous to the breast tumor (e.g., fibroadenoma phyllodes, periductal stromal sarcoma, and spindle cell carcinoma). While gynecomastia of male breast is usually a result of hormone imbalance, our patient’s tumor did not seem to be related to peripheral hormone status in the anogenital mammary-like glands. Nevertheless, because hormone imbalance has been strongly related to male breast cancer, hormone levels may need to be followed in male patients who have this rare malady.

Virtual slides

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1509145815899177

Variation at innate immunity Toll-like receptor genes in a bottlenecked population of a New Zealand robin

Toll-like receptors (TLRs) are an ancient family of genes encoding transmembrane proteins that bind pathogen-specific molecules and initiate both innate and adaptive aspects of the immune response. Our goal was to determine whether these genes show sufficient genetic diversity in a bottlenecked population to be a useful addition or alternative to the more commonly employed major histocompatibility complex (MHC) genotyping in a conservation genetics context. We amplified all known avian TLR genes in a severely bottlenecked population of New Zealand's Stewart Island robin (Petroica australis rakiura), for which reduced microsatellite diversity was previously observed. We genotyped 17-24 birds from a reintroduced island population (including the 12 founders) for nine genes, seven of which were polymorphic. We observed a total of 24 single-nucleotide polymorphisms overall, 15 of which were non-synonymous, representing up to five amino-acid variants at a locus. One locus (TLR1LB) showed evidence of past directional selection. Results also confirmed a passerine duplication of TLR7. The levels of TLR diversity that we observe are sufficient to justify their further use in addressing conservation genetic questions, even in bottlenecked populations.

Presacral teratocarcinoma presenting as anal fistula and rectal adenocarcinoma: a unique case presentation and literature review

Somatic malignancy arising from presacral or retroperitoneal primary teratoma is extremely rare. We report the case of a 37-year-old male patient with adenocarcinoma of respiratory type arising from primary presacral teratoma, but which first presented as anal fistula and rectal adenocarcinoma. The two tumors show the same morphology and immunophenotype (CK7–CK20+CDx2+). Malignant adenocarcinoma transformations from the normal respiratory epithelium are also found. To the best of our knowledge, this is the second case of respiratory type adenocarcinoma arising from primary presacral mature cystic teratoma.

Does fish ecology predict dispersal across a river drainage divide?

Obligate freshwater taxa are frequently distributed among catchments isolated by marine and terrestrial barriers. Such distributions can arise through vicariant changes in drainage geometry, or dispersal via intermittent freshwater connections. We employed two adjacent rivers in southern New Zealand to test for interdrainage dispersal while controlling for historical drainage geometry, and analyzed four ecologically distinct freshwater-limited fish taxa to assess any relationship with habitat preference. Individuals from the Mararoa and Oreti catchments (n >100 per species) were sequenced for a minimum of 1297 bp of mitochondrial DNA (cytochrome b and control region). Phylogeographic relationships were consistent with ecological expectations of interdrainage dispersal capability, with the two obligate riverine taxa each exhibiting reciprocal monophyly between catchments, whereas the two facultative swamp dwellers revealed paraphyletic relationships, one of which shared a haplotype between catchments. Statistical phylogeography, accommodating taxon-specific mutation rates and the known age of the last major riverine connection between these catchments, rejected complete isolation of populations for one of the swamp dwellers. Therefore, dispersal across a young (145-240 kyr) drainage divide is inferred for one species, and can be predicted to some extent by species ecology. Moreover, our study highlights the importance of historical drainage geometry when assessing the causes of contemporary genetic structuring in freshwater taxa.

The effect of lopinavir/ritonavir on the renal clearance of tenofovir in HIV-infected patients

We determined the effects of lopinavir/ritonavir on tenofovir renal clearance. Human immunodeficiency virus-infected subjects taking tenofovir disoproxil fumarate (TDF) were matched on age, race, and gender and were enrolled into one of the following two groups: group 1: subjects taking TDF plus lopinavir/ritonavir plus other nucleoside reverse transcriptase inhibitors (NRTIs); group 2: subjects taking TDF plus NRTIs and/or non-NRTIs but no protease inhibitors. Twenty-four-hour blood and urine collections were carried out in subjects for tenofovir quantification. Drug transporter genotype associations with tenofovir pharmacokinetics were examined. In 30 subjects, median (range) tenofovir apparent oral clearance, renal clearance, and fraction excreted in urine were 34.6 l/h (20.6-89.5), 11.3 l/h (6.2-22.6), and 0.33 (0.23-0.5), respectively. After adjusting for renal function, tenofovir renal clearance was 17.5% slower (P=0.04) in subjects taking lopinavir/ritonavir versus those not taking a protease inhibitor, consistent with a renal interaction between these drugs. Future studies should clarify the exact mechanism and whether there is an increased risk of nephrotoxicity.

Geological Dates and Molecular Rates: Rapid Divergence of Rivers and Their Biotas

We highlight a novel molecular clock calibration system based on geologically dated river reversal and river capture events. Changes in drainage pattern may effect vicariant isolation of freshwater taxa, and thus provide a predictive framework for associated phylogeographic study. As a case in point, New Zealand's Pelorus and Kaituna rivers became geologically isolated from the larger Wairau River system 70 to 130 kyr BP. We conducted mitochondrial DNA phylogeographic analyses of two unrelated freshwater-limited fish taxa native to these river systems (Gobiomorphus breviceps, n = 63; Galaxias divergens, n = 95). Phylogenetic analysis of combined control region and cytochrome b sequences yielded reciprocally monophyletic clades of Pelorus-Kaituna and Wairau haplotypes for each species. Calibrated rates of molecular change based on this freshwater vicariant event are substantially faster than traditionally accepted rates for fishes but consistent with other recent inferences based on geologically young calibration points. A survey of freshwater phylogeographic literature reveals numerous examples in which the ages of recent evolutionary events may have been substantially overestimated through the use of "accepted" calibrations. We recommend that--wherever possible--biologists should start to reassess the conclusions of such studies by using more appropriate molecular calibrations derived from recent geological events.

Promotor genotype of the platelet-derived growth factor receptor-alpha gene shows population stratification but not association with spina bifida meningomyelocele

Neural tube defects (NTDs) constitute a major group of congenital malformations with an overall incidence of approximately 1-2 in 1,000 live births in the United States. Hispanic Americans have a 2.5 times higher risk than the Caucasian population. Spina bifida meningomyelocele (SBMM) is a major clinical presentation of NTDs resulting from lack of closure of the spinal cord caudal to the head. In a previous study of spina bifida (SB) patients of European Caucasian descent, it was suggested that specific haplotypes of the platelet-derived growth factor receptor-alpha (PDGFRA) gene P1 promoter strongly affected the rate of NTD genesis. In our study, we evaluated the association of PDGFRA P1 in a group of 407 parent-child triads (167 Caucasian, 240 Hispanics) and 164 unrelated controls (89 Caucasian, 75 Hispanic). To fully evaluate the association of PDGFRA P1, we performed both transmission-disequilibrium test (TDT) and association analyses to test the hypotheses that PDGFRA P1 was (1) transmitted preferentially in SBMM affected children and (2) associated with the condition of SBMM comparing affected children to unaffected controls. We did find that there was a different allelic and genotypic distribution of PDGFRA P1 when comparing Hispanics and Caucasians. However, neither ethnic group showed strong association between SBMM and the PDGFRA P1 region. These findings suggest that PDGFRA P1 does not have a major role in the development of SBMM.

Patterns of male sterility in a grasshopper hybrid zone imply accumulation of hybrid incompatibilities without selection

It is now widely accepted that post-zygotic reproductive isolation is the result of negative epistatic interactions between derived alleles fixed independently at different loci in diverging populations (the Dobzhansky-Muller model). What is less clear is the nature of the loci involved and whether the derived alleles increase in frequency through genetic drift, or as a result of natural or sexual selection. If incompatible alleles are fixed by selection, transient polymorphisms will be rare and clines for these alleles will be steep where divergent populations meet. If they evolve by drift, populations are expected to harbour substantial genetic variation in compatibility and alleles will introgress across hybrid zones once they recombine onto a genetic background with which they are compatible. Here we show that variation in male sterility in a naturally occurring Chorthippus parallelus grasshopper hybrid zone conforms to the neutral expectations. Asymmetrical clines for male sterility have long tails of introgression and populations distant from the zone centre show significant genetic variation for compatibility. Our data contrast with recent observations on 'speciation genes' that have diverged as a result of strong natural selection.

Phylogeographical disjunction in abundant high-dispersal littoral gastropods

Abstract Phylogeographical disjunctions in high-dispersal marine taxa are variously ascribed to palaeogeographical conditions or contemporary ecological factors. Associated biogeographical studies, however, seldom incorporate the sampling design required to confidently discriminate among such competing hypotheses. In the current study, over 7800 gastropod specimens were examined for operculum colour, and 129 specimens genetically, to test ecological and historical biogeographical hypotheses relating to biogeographical disjunction in the Southern Hemisphere, and to southern Australia in particular. Mitochondrial DNA sequence analysis of the high-dispersal intertidal gastropod Nerita atramentosa in southern Australia (88 specimens; 18 localities) revealed an east-west phylogeographical split involving two highly divergent clades (26.0 +/- 1.9%) exhibiting minimal geographical overlap in the southeast. The eastern clade of Nerita atramentosa is also widespread in northern New Zealand (43 specimens, 10 localities), but no significant genetic differentiation is explained by the Tasman Sea, a 2000-km-wide oceanic barrier. Spatial genetic structure was not detected within either clade, consistent with the species' dispersive planktotrophic phase lasting for 5-6 months. Digital analysis of operculum colouration revealed substantial differences between eastern (tan) and western (black) specimens. Genetic analysis and visual inspection of 88 Australian specimens revealed a completely nonrandom association between mtDNA data and operculum colouration. Independent examination of a further 7822 specimens from 14 sites in southern Australia revealed both colour morphs at all localities, but reinforced the phylogeographical data by indicating a marked turnover in colour morph abundance associated with a palaeogeographical barrier: Wilsons Promontory. This sharp biogeographical disjunction is in marked contrast to the species' high dispersal abilities. The genetic similarity of Nerita morio (Easter Island) and the eastern Australian + New Zealand lineage (1.1 +/- 0.3%) provides further evidence of long-distance dispersal in southern Nerita. Phylogenetic relationships of nine species (four genera) of Neritidae, an almost exclusively tropical gastropod family, are consistent with the hypothesis that southern temperate black nerites comprise a monophyletic radiation.

Heritability of life span in the Old Order Amish

Although a familial contribution to human longevity is recognized, the nature of this contribution is largely unknown. We have examined the familial contribution to life span in the Old Order Amish (OOA) population of Lancaster County, Pennsylvania. Analyses were conducted on 1,655 individuals, representing all those born prior to 1890 and appearing in the most widely available genealogy, surviving until at least age 30 years, and with known date of death. Mean age at death (+/-SD) in this population was 70.7 +/- 15.6 years, and this did not change appreciably over time. Parental and offspring ages at death were significantly correlated, as were ages of death among siblings. Offspring longevity was correlated with longevity of both parents, and in more or less additive fashion. For example, mean offspring age at death was 69.4 +/- 15.3 years in individuals for whom both parents died before the age of 75 years (n = 280) and increased to 73.5 +/- 16.0 years in individuals for whom neither parent died before the age of 75 years (n = 311). These differences were highly significant (P = 0.006). We estimated heritability of life span to be 25% +/- 5%, suggesting that the additive effects of genes account for one quarter of the total variability in life span in the OOA. We conclude that longevity is moderately heritable in the OOA, that the genetic effects are additive, and that genetic influences on longevity are likely to be expressed across a broad range of ages. Published 2001 Wiley-Liss, Inc.

International Genetic Epidemiology Society: commentary on Darkness in El Dorado by Patrick Tierney

The International Genetic Epidemiology Society (IGES) has examined the charges against James V. Neel and his colleagues contained in the recently published book by Patrick Tierney entitled Darkness in El Dorado: How Scientists and Journalists Devastated the Amazon (W.W. Norton, 2000). The book implicates Neel in causing or promoting an epidemic of measles among the Yanomamö Indians of Venezuela in 1968 leading to "hundreds if not thousands" of deaths by using a "dinosaur" vaccine (Edmonston B) as a deliberate "experiment" to test his "eugenic" theories. Tierney also attempts to link this research, funded by the Atomic Energy Commission (AEC), with a broader tapestry of human radiation experiments. To investigate these serious charges, the IGES undertook a thorough examination of most source documents referenced in Tierney's book, Neel's field logs, notes, first-hand reports, contemporary writings, film sound tracks, etc., and conducted interviews with many relevant persons. The IGES finds that these allegations are false. Neel was not a eugenicist and was in fact highly critical of both the scientific basis of eugenics and its coercive social policies. In this regard, Tierney has grossly misrepresented Neel's views on a wide range of social implications of modern civilization for the long-term health of the gene pool. Far from causing an epidemic of measles, Neel did his utmost to protect the Yanomamö from the ravages of the impending epidemic by a vaccination program using a vaccine that was widely used at the time and administered in an appropriate manner. There was nothing experimental about the vaccination program, which in fact severely hindered the primary scientific objectives of the expedition. Although the research was funded in large part by the AEC, there was no element of radiation research and the work had no connection with the ethical abuses that have been reported from AEC-sponsored radiation research, such as studies of heavy isotopes. Neel's seminal contributions to a broad range of topics in human genetics have been extensively chronicled elsewhere. His research on the Yanomamö in particular has provided unique insights into the evolutionary biology of our species, the role of sociocultural practices, such as kinship relationships and selective pressures in shaping the genetic diversity of primitive population isolates, as well as the general picture of health in such populations. The IGES decries the damage done to the reputation of one of its founders and its first President and the misperception this book may have caused about the conduct of research in genetic epidemiology. Ethical issues about scientific research in primitive populations deserve serious and wide discussion, but the IGES condemns the gross misrepresentation of the facts and demonization of the principal characters in this book.

Linked markers and age at diagnosis

This paper examines the relationship between age at diagnosis and markers linked to a disease trait using 100 replicates from Problem 2A in Genetic Analysis Workshop 10. After establishing the relationship between age and the quantitative trait used to define affection status, Q1, we evaluated the relationship between age at diagnosis and a marker which was linked with Q1. We found that the presence of an F allele at marker 15 on chromosome 5 was significantly associated with delayed age of diagnosis. When we evaluated 100 replicates, we found that the regression coefficients in the survival analyses were separated into two approximately normal distributions. The location of these distributions was solely reflective of the presence of affected individuals with the F allele in a particular replicate. In the replicates in one of the distributions, we found tremendous changes in the variance after employing survival models for dependent data. While we suggest that survival analysis of dependent data may be an important tool in investigating genotype specific alterations in age at event, the findings of this study indicate that the method used may be very sensitive to certain types of missing data.

Familial analysis of event related potentials

This report summarizes our analysis of the auditory and visual event related evoked potentials. These data were collected as a component of the Collaborative Study on the Genetics of Alcoholism and distributed as a part of the data available for the Genetic Analysis Workshop 11. For this analysis, we collapsed the data collected from eight leads using principal components methods. Using four collapsed variables derived from the principal components, we used regression analysis to adjust for environmental and demographic variables. We then fit the best fitting regression model and calculated the residuals. Using the residuals, we performed segregation analysis using S.A.G.E. Finally, we applied Markov chain Monte Carlo reverse jump methods to identify areas with potential quantitative trait loci. Our findings indicate that there may be an underlying genetic component to the potentials.

A genome-wide search for susceptibility genes linked to alcohol dependence

We performed two-point linkage analysis during a genome-wide search for susceptibility genes that predispose to alcohol dependence with the Collaborative Study on the Genetics on Alcoholism (COGA) data made available for the Genetic Analysis Workshop 11 (GAW11). For chromosomes 1 and 4 our findings supported results reported by Reich et al. [1998] based on the same data. We found similarity between our findings in regions on chromosomes 8 and 10 and reported results for schizophrenia linkage studies. Differences between our results with COGA data and those obtained by Reich et al. [1998] are due to our use of a lod score method versus their use of the affected relative pair (sib pair) method.

Assessing linkage of monoamine oxidase B in a genome-wide scan using a univariate variance components approach

We report results when one alcoholism related quantitative trait, monoamine oxidase B (MAOB), is analyzed by the variance components approach for linkage [Amos, 1994; Amos et al., 1996] using the Collaborative Study on the Genetics of Alcoholism data set provided for the Genetic Analysis Workshop 11. We used two different covariate models, one with age at interview, sex, ethnicity, and smoking status and the other with age at interview, sex, and ethnicity. The univariate analysis showed 24 markers on four different chromosomes (1, 4, 9, and 12) to have evidence for linkage with the quantitative trait (single-point and multipoint linkage). However, when outliers for MAOB were removed, the significant evidence for linkage disappeared.

Assessment of estimation procedures for risk and onset hazard with dependent data

Analysis of the role of candidate genes as risk factors for age-dependent hereditary conditions often ignores the importance of dependence among sibships or other family clusters for age of onset. We examined the performance of several methods of survival analysis with dependent data using Collaborative Study on the Genetics of Alcoholism families as submitted for GAW11. Additionally, an arbitrary truncation of cluster size was performed to explore the potential impact of heterogeneity of family size on the resulting inferences concerning the role of candidate genes. Our results showed substantial differences in attribution of risk to candidate genes according to whether the method utilized allowed for dependence in onset age and according to whether the sample was truncated or arbitrarily stratified. Further work needs to be done to clarify the importance of properly accounting for dependent data in age-dependent phenotypes and in integrating these methods into widely used genetic analysis computer programs.

Genome scans for genetic predisposition to alcoholism by use of transmission disequilibrium test analyses

We report the results of the analysis of three measures of alcoholism and six associated symptoms using transmission disequilibrium (TDT) analysis on data from the Collaborative Study on the Genetics of Alcoholism data set. Implementation of identity-by-state (IBS) routines for error checking revealed 10 reported full siblings that were rejected as a full sibling to all of their purported full siblings with p < 0.05. TDT analysis revealed two loci with significant transmission disequilibrium (p < 0.001) on chromosomes 1 and 7. Analysis by parental origin found alleles at three loci displaying significant disequilibrium in the transmission of the paternal alleles for at least three of the nine tested traits. These loci are on chromosomes 6, 9, and 13. Analyses of Caucasian families alone and the use of a single affected individual from each family also yielded significant results for the loci on chromosomes 6, 9, and 13.

The effect of inbreeding on early childhood mortality: twelve generations of an Amish settlement

An unresolved issue in research on child survival is the extent to which familial mortality risk in infancy is due to biological influences net of sociodemographic and economic factors. We examine the effect of consanguinity on early childhood mortality in an Old Order Amish settlement by using the inbreeding coefficient, an explicit measure of the degree of relatedness in one's ancestry. Inbreeding has a net positive effect on neonatal and postneonatal deaths. We find social, demographic, and population-based sociocultural explanations for this effect among the Amish population which is known to experience certain genetically transmitted defects associated with mortality.

Acceleration-deceleration injuries to the brain in blunt force trauma

Blunt force trauma to the stationary head is generally associated with cortical-subcortical injuries located at the site of impact (i.e., coup contusions). We present 2 cases of cerebral contusion injury secondary to falling tree limbs hitting the head, illustrating an exception to this observation. In each case, the most prominent lesions were white matter hemorrhagic contusions similar to those associated with acceleration-deceleration types of injuries characterizing falls or motor vehicle accidents (i.e., contrecoup contusions). The proposed pathogenesis for these observed lesions is a forceful impact resulting in the acceleration of the head and brain of a magnitude comparable with that in a motor vehicle accident or a fall.

Linkage analysis of chromosome 1q markers in 136 prostate cancer families. The Cancer Research Campaign/British Prostate Group U.K. Familial Prostate Cancer Study Collaborators

Prostate cancer shows evidence of familial aggregation, particularly at young ages at diagnosis, but the inherited basis of familial prostate cancer is poorly understood. Smith et al. recently found evidence of linkage to markers on 1q, at a locus designated "HPC1," in 91 families with multiple cases of early-onset prostate cancer. Using both parametric and nonparametric methods, we attempted to confirm this finding, in 60 affected related pairs and in 76 families with three or more cases of prostate cancer, but we found no significant evidence of linkage. The estimated proportion of linked families, under a standard autosomal dominant model, was 4%, with an upper 95% confidence limit of 31%. We conclude that the HPC1 locus is responsible for only a minority of familial prostate cancer cases and that it is likely to be most important in families with at least four cases of the disease.

A clinical trial to evaluate the effect of vitamin C supplementation on in vitro mutagen sensitivity. The University of Texas M. D. Anderson Clinical Community Oncology Program Network

Mutagen sensitivity, as measured by an in vitro assay, has been described as a risk factor for the development of several tobacco-related epithelial cancers. In vitro studies have indicated that sensitivity to the clastogenic effects of bleomycin on chromosomes was reduced with the introduction of ascorbic acid in a dose-dependent relationship. We report the results of a randomized clinical trial to determine whether increasing levels of oral ascorbic acid could reduce the levels of mutagen sensitivity. For this study, we recruited 228 healthy smokers from 21 centers around the country through the Clinical Community Oncology Program. Each individual was randomly assigned to one of four daily regimens: placebo, 1 g of ascorbic acid, 2 g of ascorbic acid, or 4 g of ascorbic acid. Treatments were administered for 16 weeks. Assessment of mutagen sensitivity was made at baseline and at weeks 4, 16, and 20 (4 weeks after cessation of treatment). Serum ascorbic acid levels were measured at baseline and at weeks 4 and 16. Demographic and risk factor data were collected at baseline and at each-measurement point. Analyses measured the differences of mutagen sensitivity levels across the four treatment arms, as well as investigating the correlation between serum ascorbic acid level and mutagen sensitivity levels in individuals. We did not find a dose-response relationship between ascorbic acid intake and mutagen sensitivity. Additionally, we did not find an association between serum ascorbic acid levels and mutagen sensitivity.

Morphological and electrophysiological properties of neurons in an area of the chick brain involved in learning

The intermediate, medial part of the hyperstriatum ventrale (IMHV) is an area of the avian forebrain which is essential for two forms of early learning in the domestic chick. We have developed an in vitro slice preparation which contains part of the IMHV and have found that the electrophysiological properties of the area show a considerable degree of plasticity. In particular, age and prior learning appear to modify the properties of single neurons recorded intracellularly. We have used the in vitro slice preparation to make intracellular recordings from 38 single neurons in the IMHV and have then dye-injected each cell to find out whether there is any relationship between electrophysiological and morphological characteristics. The basic membrane properties of each neuron were measured. Responses to standard electrical stimuli, delivered extracellularly, were also recorded, and each neuron was classified on this basis. Finally, the presence or absence of spontaneously occurring bursts of EPSPs was noted. At the end of recording biocytin was injected into the cell. After the tissue had been processed, each cell was drawn. The area of the cell body was measured, the number of dendrites was counted, and dendritic extent and branching were estimated. Each cell was also classified as 'spiny' or 'non-spiny'. We found that neurons displaying one particular type of response to external stimulation possessed a well defined set of morphological and electrical properties. In addition, three parameters--electrical resistance, somatic area, and the presence or absence of dendritic spines--were related to specific subsets of anatomical and physiological characteristics. The possible relevance of these findings to the plasticity of the IMHV is discussed.

Inheritance of susceptibility to bleomycin-induced pulmonary fibrosis in the mouse

Based on the range of patient responses to treatment, and on animal studies, it is hypothesized that individual variation in sensitivity to bleomycin-induced pulmonary fibrosis is controlled genetically. A genetic model has been developed by (a) establishing a distinct difference in bleomycin-induced lung damage in two inbred strains of mice [parental generation: C57BL/6J (fibrosis-prone phenotype) and C3Hf/Kam (fibrosis-resistant phenotype)] and (b) characterizing inheritance of the fibrosing phenotype in the F1 (first filial) and F2 (F1 intercross; second filial) generations derived from the parental strains. Male mice received 100 mg/kg and female mice 125 mg/kg of bleomycin via s.c. osmotic minipump. The animals were sacrificed 8 weeks after treatment or when their breathing rate indicated respiratory distress. The percentage of lung with fibrosis for each mouse was quantified with image analysis of a histological section of the left lung. The mean percentage of fibrosis for the C57BL/6J males was 8.4 +/- 0.8% (SE) and 4.4 +/- 0.8% for females, and the C3Hf/Kam mice of either sex did not present the fibrosing lesion (mean score, 0%). Significant difference (P = 6 x 10(-6)) was measured in percentage of fibrosis between the two strains of F1 males, but not F1 females (P = 0.38), suggesting the presence of an X-linked factor associated with the fibrosing phenotype. From an ANOVA the X-linked factor is estimated to contribute 19% of the fibrosis phenotype. A genetic model of two or three loci controlling the fibrosing phenotype is proposed from the data of the parental, F1, and F2 generations. The mouse model demonstrates that susceptibility to bleomycin-induced pulmonary fibrosis is a heritable trait controlled by a few genetic loci.

Effect of systemic steroids on ileal pouch-anal anastomosis in patients with ulcerative colitis

BACKGROUND

Long-term steroid therapy predisposes to postsurgical complications, especially in patients with inflammatory bowel disease.

PURPOSE

This study was undertaken to determine incidence of early septic complications after ileal pouch-anal anastomosis (IPAA) in patients who are undergoing prolonged steroid therapy.

METHODS

We reviewed charts of 692 patients undergoing restorative proctocolectomy and IPAA to treat ulcerative colitis. Incidence of early (within 30 days) septic complications and sepsis-related reoperations, in patients who were having high-dose (>20 mg of prednisone per day) and low-dose steroid therapy (<20 mg of prednisone per day) for more than one month before surgery, was compared with patients who were not receiving steroid therapy. Follow-up included an annual questionnaire and physical examination.

RESULTS

Patients without steroid dose data recorded were excluded (n = 21). Of the 671 remaining patients, 310 received no steroids, 169 received low-dose steroids, and 192 received high-dose steroids. These three groups were similar in gender composition, age at surgery, types of anastomosis (stapled or handsewn), and incidence of diabetes mellitus, peripheral vascular disease, and obesity. Early septic complications were found in 18 (6 percent), 14 (8 percent), and 12 (6 percent) patients without steroid therapy, those having low-dose steroid therapy, and those having high-dose steroid therapy (P = 0.57), respectively. Sepsis- related reoperation rate (P = 0.73) and number of sepsis-related pouch excisions (P = 0.79) did not differ between groups. In patients undergoing IPAA without ileostomy, early septic complications were found in one (3.8 percent), two (20 percent), and five (50 percent) patients without steroid treatment, low-dose steroid therapy, and high-dose steroid therapy (P = 0.004), respectively.

CONCLUSION

In patients who are undergoing IPAA with diversion for ulcerative colitis, prolonged systemic steroid therapy before surgery is not associated with increased septic complications.

Stapled ileal pouch anal anastomoses are safer than handsewn anastomoses in patients with ulcerative colitis

BACKGROUND

One of the theoretic advantages of using a stapled versus handsewn ileal pouch anal anastomosis (IPAA) in restorative proctocolectomy is a reduction in septic complications. We performed this study to compare the incidence of early septic complications in patients undergoing restorative proctocolectomy with stapled or handsewn IPAA.

PATIENTS AND METHODS

A chart review of 692 patients undergoing restorative proctocolectomy for treatment of ulcerative colitis was performed. The incidence of early septic complications in patients having stapled IPAA was compared to that in patients having handsewn IPAA. Follow-up studies included an annual questionnaire and physical examination.

RESULTS

Of the 692 patients, 238 had handsewn IPAA and 454 had stapled IPAA; these two groups were similar in sex, duration of disease, age at surgery, and type of surgical procedure performed. In the handsewn IPAA group, 25 patients (10.5%) had 32 septic complications, and 24 required 89 reparations. In 7 patients, the pouch was excised. In the stapled IPAA group, 21 patients (4.6%) had 23 septic complications, and 14 required 40 reparations. One patient needed pouch excision. There were more patients (P=0.0001) with early septic complications, and more (P<0.0001) pouch excisions because of these complications, in patients with handsewn IPAA than in patients with stapled IPAA. The sepsis-related reoperation rates did not differ significantly.

CONCLUSIONS

The stapled technique for IPAA has fewer septic complications and results in fewer sepsis-related pouch excisions, in our hands, than the handsewn technique technique, for treating patients with ulcerative colitis.

Electrophysiological correlates of prior training: an in vitro study of an area of the avian brain which is essential for early learning

Day-old domestic chicks will peck at any small, distinct object, such as a metal bead. One-trial passive avoidance learning can be established by coating the metal bead with methyl anthranilate (MeA) and allowing the birds to peck it once, after which they conspicuously avoid it. We have used birds successfully trained not to peck metal beads, and a control set of chicks where the training beads were innocuously dipped in water. Brain slices were prepared from both groups, containing the left, intermediate, medial part of the hyperstriatum ventrale (IMHV)--a region essential for this form of early learning. The electrophysiological properties of neurones in the IMHV were examined in vitro. Neurones recorded intracellularly in slices taken from MeA-trained birds had higher membrane resistances than did cells from water-trained controls. MeA training was also associated with an increased incidence of spontaneous, large EPSPs. Field responses to local electrical stimulation appeared to be somewhat greater in MeA-trained birds than in water-trained controls. In contrast, field potentials proved harder to potentiate with a burst of relatively high frequency stimulation in MeA-trained birds: the change in amplitude was less in MeA-trained birds, and there was less variability than in slices from water-trained controls.

Comparison of methods for survival analysis of dependent data

Analysis of dependent survival data by conventional partial likelihood methods produces unbiased estimates of the regression coefficients but incorrectly estimates their variance. Here we compared the conventional partial likelihood methods with two alternative methods for analyzing dependent survival data. The first alternative method estimated the regression coefficient by the partial likelihood approach but adjusted the variance to account for clustering. The second alternative method used marginal likelihoods to estimate both the regression coefficient and its variance. We evaluated the performance of the three methods using simulated and actual data. Simulated data were used to examine bias, efficiency, type I errors, and power. An Old Order Amish genealogy was analyzed under these models to illustrate their performance on real data. The simulation study showed that all three methods provided unbiased estimates of the regression coefficient, but the efficiency of the estimated regression coefficient varied according to the simulation conditions. The standard partial likelihood method showed increasing type I error as the dependence increased within clusters. Both alternative methods had acceptable levels of type I errors at all dependence levels. In the analysis of genealogic data, the regression coefficient was similar in the three methods showing stable estimates of the regression coefficients. The variance estimates from the alternative methods were slightly different from the conventional method, suggesting a flow level of dependence. This study displays the effect of violating the independence assumption and provides guidelines for using alternative statistical methods.

Age and the effects of 2-D,L-amino-5-phosphonovalerate in an area of the chick forebrain which is essential for early learning

The intermediate, medial part of the hyperstriatum ventrale (IMHV) is a region of the avian forebrain which is known to be essential for early learning in the domestic chick. The IMHV in an in vitro slice preparation displays two forms of synaptic plasticity. The incidence of both varies with age and is maximal between 3 and 5 days post-hatch. Since NMDA receptors are critical for at least one of these plasticities, we have investigated the relationship between age and the contribution of NMDA receptors to the field response evoked by local, low-frequency stimulation and have found that the magnitude of the NMDA-dependent component of the response varies with age peaking between 3 and 5 days post-hatch. Spontaneous neural activity, recorded intracellularly, can be completely and reversibly silenced by NMDA receptor blockade and the incidence of spontaneous activity also varies with age, peaking between 3 and 5 days. These results suggest that the IMHV contains NMDA receptors which can be activated near resting membrane potential. Either the efficiency or the numbers of these receptors is maximal at a specific point in development and their peak activity coincides with a peak in synaptic plasticity. These characteristics are similar to those reported for young mammals.

Genetic susceptibility to lung cancer as determined by lymphocytic chromosome analysis

Chromosomal anomalies were analyzed in the lymphocyte cultures among 96 untreated lung cancer patients and 74 clinically normal comparison subjects. The analysis revealed that >15% of the lung cancer patients showed structural or numerical rearrangements in chromosomes 1,3,5,7,9,12,14, and 21. A case control comparison showed that these aberrations were significantly higher in chromosome 7 [odds ratio (OR) = 2.32; 95% confidence interval (CI), 1.14 and 4.82], chromosome 9 (OR = 2.61; 95% CI, 1.27 and 5.48), chromosome 12 (OR = 4.10; 95% CI, 1.40 and 14.54), and chromosome 21 (OR = 7.75; 95% CI, 1.73 and 70.80) of the patients than in the controls. However, only chromosome 9 (OR = 3.57; 95% CI, 1.33 and 9.46) and chromosome 21 (OR = 6.94; 95% CI, 3.15 and 9.98) retained significance after stratifying on smoking status. Among the lung cancer patients, the breakpoints cluster in specific regions of some of these chromosomes. These regions are 1p13-q21, 3q21-q13, 7p12-q12, 7q12-q12,7q22, 7q32, 9p13-q13, 12p13, 14q11, and 14q32. The distribution of lung cancer patients, according to histological types, showed that aberrations in chromosomes 1,7, and 9 dominated the scenario of chromosomal changes in non-small cell lung carcinomas. Thus, the data on lymphocytic chromosomal rearrangements in lung cancer patients not only indicate the importance of specific genetic changes in the etiology of lung cancer but also emphasizes the putative role of such analysis in determining primary genetic abnormalities in the large heterogeneous group of lung cancers.