Comparison of genetic behaviour of the transposable element Tam3 at two unlinked pigment loci in Antirrhinum majus

Summary In Antirrhinum majus the transposable element Tam3 has been described at two unlinked loci pallida and nivea, both of which are required for the production of anthocyanin pigment in flowers. In each case the element is inserted in the promoter region and gives a variegated phenotype. We show that the rate of Tam3 excision at both loci is greatly affected by temperature, being approximately 1000-fold higher at 15°C compared with 25°C. Tam3 is also controlled by an unlinked gene Stabiliser, which considerably reduces excision rate. We show that the high degree of sensitivity to temperature and Stabiliser is an intrinsic property of Tam3 which is not shared by an unrelated element, Tam1. The Tam3 insertion at nivea gives rise to a series of alleles which confer reduced pigmentation, novel spatial patterns and changed instability. These are probably a result of imprecise excision and rearrangements of the Tam3 element.     

Estimating treatment effects with partially observed covariates using outcome regression with missing indicators

Missing data is a common issue in research using observational studies to investigate the effect of treatments on health outcomes. When missingness occurs only in the covariates, a simple approach is to use missing indicators to handle the partially observed covariates. The missing indicator approach has been criticized for giving biased results in outcome regression. However, recent papers have suggested that the missing indicator approach can provide unbiased results in propensity score analysis under certain assumptions. We consider assumptions under which the missing indicator approach can provide valid inferences, namely, (1) no unmeasured confounding within missingness patterns; either (2a) covariate values of patients with missing data were conditionally independent of treatment or (2b) these values were conditionally independent of outcome; and (3) the outcome model is correctly specified: specifically, the true outcome model does not include interactions between missing indicators and fully observed covariates. We prove that, under the assumptions above, the missing indicator approach with outcome regression can provide unbiased estimates of the average treatment effect. We use a simulation study to investigate the extent of bias in estimates of the treatment effect when the assumptions are violated and we illustrate our findings using data from electronic health records. In conclusion, the missing indicator approach can provide valid inferences for outcome regression, but the plausibility of its assumptions must first be considered carefully.     

Childhood adversity and epigenetic modulation of the leukocyte glucocorticoid receptor: preliminary findings in healthy adults

Background

A history of early adverse experiences is an important risk factor for adult psychopathology. Changes in stress sensitivity and functioning of the hypothalamic-pituitary-adrenal (HPA) axis may underlie the association between stress and risk for psychiatric disorders. Preclinical work in rodents has linked low levels of maternal care to increased methylation of the promoter region of the glucocorticoid receptor (GR) gene, as well as to exaggerated hormonal and behavioral responses to stress. Recent studies have begun to examine whether early-life stress leads to epigenetic modifications of the GR gene in humans.

Methods

We examined the degree of methylation of a region of the promoter of the human GR gene (NR3C1) in leukocyte DNA from 99 healthy adults. Participants reported on their childhood experiences of parental behavior, parental death or desertion, and childhood maltreatment. On a separate day, participants completed the dexamethasone/corticotropin-releasing hormone (Dex/CRH) test, a standardized neuroendocrine challenge test.

Results

Disruption or lack of adequate nurturing, as measured by parental loss, childhood maltreatment, and parental care, was associated with increased NR3C1 promoter methylation (p<.05). In addition, NR3C1 promoter methylation was linked to attenuated cortisol responses to the Dex/CRH test (p<.05).

Conclusions

These findings suggest that childhood maltreatment or adversity may lead to epigenetic modifications of the human GR gene. Alterations in methylation of this gene could underlie the associations between childhood adversity, alterations in stress reactivity, and risk for psychopathology.     

A Modeling Framework to Describe the Transmission of Bluetongue Virus within and between Farms in Great Britain

Background

Recently much attention has been given to developing national-scale micro-simulation models for livestock diseases that can be used to predict spread and assess the impact of control measures. The focus of these models has been on directly transmitted infections with little attention given to vector-borne diseases such as bluetongue, a viral disease of ruminants transmitted by Culicoides biting midges. Yet BT has emerged over the past decade as one of the most important diseases of livestock.

Methodology/Principal Findings

We developed a stochastic, spatially-explicit, farm-level model to describe the spread of bluetongue virus (BTV) within and between farms. Transmission between farms was modeled by a generic kernel, which includes both animal and vector movements. Once a farm acquired infection, the within-farm dynamics were simulated based on the number of cattle and sheep kept on the farm and on local temperatures. Parameter estimates were derived from the published literature and using data from the outbreak of bluetongue in northern Europe in 2006. The model was validated using data on the spread of BTV in Great Britain during 2007. The sensitivity of model predictions to the shape of the transmission kernel was assessed.

Conclusions/Significance

The model is able to replicate the dynamics of BTV in Great Britain. Although uncertainty remains over the precise shape of the transmission kernel and certain aspects of the vector, the modeling approach we develop constitutes an ideal framework in which to incorporate these aspects as more and better data become available. Moreover, the model provides a tool with which to examine scenarios for the spread and control of BTV in Great Britain.     

Normal human pluripotent stem cell lines exhibit pervasive mosaic aneuploidy

Human pluripotent stem cell (hPSC) lines have been considered to be homogeneously euploid. Here we report that normal hPSC--including induced pluripotent--lines are karyotypic mosaics of euploid cells intermixed with many cells showing non-clonal aneuploidies as identified by chromosome counting, spectral karyotyping (SKY) and fluorescent in situ hybridization (FISH) of interphase/non-mitotic cells. This mosaic aneuploidy resembles that observed in progenitor cells of the developing brain and preimplantation embryos, suggesting that it is a normal, rather than pathological, feature of stem cell lines. The karyotypic heterogeneity generated by mosaic aneuploidy may contribute to the reported functional and phenotypic heterogeneity of hPSCs lines, as well as their therapeutic efficacy and safety following transplantation.     

GROWTH CHARACTERISTICS OF PHYTOPLANKTON DETERMINED BY CELL CYCLE PROTEINS: PCNA IMMUNOSTAINING OF DUNALIELLA TERTIOLECTA (CHLOROPHYCEAE)1

By immunohistochemistry and immunofluorescence methods, we observed that the analog of proliferating cell nuclear antigen (PCNA) in Dunaliella tertiolecta Butcher (Chlorophyceae) was exclusively located in the nucleus. Among positively stained cells, PCNA abundance varied, being highest in S-phase cells, lower in others, and undetectable in early G1- or late M-phase cells. In exponentially growing and partially synchronized cultures, the percentage of PCNA-stained cells (% PCNA-stained cells) oscillated in the photocycle (12:12 h LD). It increased during the light period and reached a peak (75%) before the onset of the dark period when the culture was mainly (71%) in the S phase of the cell cycle. The DNA synthesis inhibitor, hydroxyurea, depressed PCNA abundance, whereas no effect was detected for the mitosis inhibitor colchicine. We conclude that PCNA in D. tertiolecta is associated with the S phase of the cell cycle where it is accumulated and functioning. PCNA was used to characterize the growth pattern of cultures grown in different media, temperatures, and growth stages. The time lag between the PCNA-stained phase and the M phase was very short in a continuous culture grown in reduced f/2 medium at 22°C and was considerably longer in the cultures grown in f/2 at 15°C. When an exponentially growing culture grew older, % PCNA-stained cells decreased. In a late stationary culture where there was no net growth, a small number of cells were still cycling through the PCNA-stained phase and cell division. In the continuous culture grown at 22°C, the duration of the PCNA-stained phase (T_s) was 13 h. Calculations with this T_s and % PCNA-stained cells yielded a growth rate of 0.77 d^?1, which was close to that obtained by cell counts (0.69 d^?1). Taken together, the results suggest that PCNA is a useful indicator of growth status and a promising cell cycle marker for estimation of species-specific growth rate.     

Response of phytoplankton and bacteria to nutrients and zooplankton: a mesocosm experiment

Although both nutrient inputs and zooplankton grazing are importantto phytoplankton and bacteria in lakes, controversy surroundsthe relative importance of grazing pressure for these two groupsof organisms. For phytoplankton, the controversy revolves aroundwhether zooplankton grazers, especially large cladocerans likeDaphnia, can effectively reduce phytoplankton populations regardlessof nutrient conditions. For bacteria, little is known aboutthe balance between possible direct and indirect effects ofboth nutrients and zooplankton grazing. However, there is evidencethat bacteria may affect phytoplankton responses to nutrientsor zooplankton grazing through direct or apparent competition.We performed a mesocosm experiment to evaluate the relativeimportance of the effects of nutrients and zooplankton grazingfor phytoplankton and bacteria, and to determine whether bacteriamediate phytoplankton responses to these factors. The factorialdesign crossed two zooplankton treatments (unsieved and sieved)with four nutrient treatments (0, 0.5, 1.0 and 2.0 µgphosphorus (P) l^–1 day^–1 together with nitrogen(N) at a N:P ratio of 20:1 by weight). Weekly sieving with 300µm mesh reduced the average size of crustacean zooplanktonin the mesocosms, decreased the numbers and biomass of Daphnia,and increased the biomass of adult copepods. Nutrient enrichmentcaused significant increases in phytoplankton chlorophyll a(4–5x), bacterial abundance and production (1.3x and 1.6x,respectively), Daphnia (3x) and total zooplankton biomass (2x).Although both total phytoplankton chlorophyll a and chlorophylla in the <35 µm size fraction were significantly lowerin unsieved mesocosms than in sieved mesocosms, sieving hadno significant effect on bacterial abundance or production.There was no statistical interaction between nutrient and zooplanktontreatments for total phytoplankton biomass or bacterial abundance,although there were marginally significant interactions forphytoplankton biomass <35 µm and bacterial production.Our results do not support the hypothesis that large cladoceransbecome less effective grazers with enrichment; rather, the differencebetween phytoplankton biomass in sieved versus unsieved zooplanktontreatments increased across the gradient of nutrient additions.Furthermore, there was no evidence that bacteria buffered phytoplanktonresponses to enrichment by either sequestering P or affectingthe growth of zooplankton.     

Characterization of the interaction of reticuloendotheliosis virus with the avian lymphoid system.

Splenic lymphocytes from chickens infected with reticuloendotheliosis virus (REV) are cytostatically impaired in their ability to undergo mitogen-induced blastogenesis ([³H]TdR uptake and proliferation), but are fully capable of eliciting cytotoxic reactions against allogeneic, ⁵¹Chromium-labeled chicken erythrocytes. Spleen cells from birds with reticuloendotheliosis (RE_s) are able to suppress DNA synthesis of normal splenic lymphocytes (N_s), but are unable to inhibit ¹[³H]TdR uptake by chick embryo fibroblasts. The suppression of the N_s mitogenic response is not restricted by major histocompatibility (B-locus) differences between populations of RE_s suppressor and N_s target cells. Moreover, infection of birds with an attenuated form of REV, which replicates in the host but does not cause tumorigenesis, also leads to suppression of phytohemagglutinin-induced, [³H]TdR uptake by host lymphocytes. These results are discussed in terms of the interaction between viral-infected/transformed cells and host defense mechanisms.     

Crystal structure of the C1 domain of cardiac myosin binding protein-C: implications for hypertrophic cardiomyopathy

C-protein is a major component of skeletal and cardiac muscle thick filaments. Mutations in the gene encoding cardiac C-protein [cardiac myosin binding protein-C (cMyBP-C)] are one of the principal causes of hypertrophic cardiomyopathy. cMyBP-C is a string of globular domains including eight immunoglobulin-like and three fibronectin-like domains termed C0-C10. It binds to myosin and titin, and probably to actin, and may have both a structural and a regulatory role in muscle function. To help to understand the pathology of the known mutations, we have solved the structure of the immunoglobulin-like C1 domain of MyBP-C by X-ray crystallography to a resolution of 1.55 Å. Mutations associated with hypertrophic cardiomyopathy are clustered at one end towards the C-terminus, close to the important C1C2 linker, where they alter the structural integrity of this region and its interactions.