Daniel Gillis

MicroRNA-34 family expression in bovine gametes and preimplantation embryos

BackgroundOocyte fertilization and successful embryo implantation are key events marking the onset of pregnancy. In sexually reproducing organisms, embryogenesis begins with the fusion of two haploid gametes, each of which has undergone progressive stages of maturation. In the final stages of oocyte maturation, minimal transcriptional activity is present and regulation of gene expression occurs primarily at the post-transcriptional level. MicroRNAs (miRNA) are potent effectors of post-transcriptional gene silencing and recent evidence demonstrates that the miR-34 family of miRNA are involved in both spermatogenesis and early events of embryogenesis.MethodsThe profile of miR-34 miRNAs has not been characterized in gametes or embryos of Bos taurus. We therefore used quantitative reverse transcription PCR (qRT-PCR) to examine this family of miRNAs: miR-34a, -34b and -34c as well as their precursors in bovine gametes and in vitro produced embryos. Oocytes were aspirated from antral follicles of bovine ovaries, and sperm cells were isolated from semen samples of 10 bulls with unknown fertility status. Immature and in vitro matured oocytes, as well as cleaved embryos, were collected in pools. Gametes, embryos and ovarian and testis tissues were purified for RNA.ResultsAll members of the miR-34 family are present in bovine spermatozoa, while only miR-34a and -34c are present in oocytes and cleaved (2-cell) embryos. Mir-34c demonstrates variation among different bulls and is consistently expressed throughout oocyte maturation and in the embryo. The primary transcript of the miR-34b/c bicistron is abundant in the testes and present in ovarian tissue but undetectable in oocytes and in mature spermatozoa.ConclusionsThe combination of these findings suggest that miR-34 miRNAs may be required in developing bovine gametes of both sexes, as well as in embryos, and that primary miR-34b/c processing takes place before the completion of gametogenesis. Individual variation in sperm miR-34 family abundance may offer potential as a biomarker of male bovine fertility.

Effect of information availability on assessment and designation of species at risk.

Information required to evaluate the extent to which species are at risk of extinction is usually limited and characterized as highly uncertain. In this context, we define information availability as the presence or absence of information used to determine the value of an ecological variable. We examined which of three hypothetical approaches best matched how levels of risk are assigned to species: (1) precautionary approach in which analysts designate levels of risk regardless of the amount of information available, (2) worst-case approach in which analysts assign the maximum level of risk possible from the criteria, and (3) insurance approach in which analysts assign poorly known species to a high-risk category when little information is available. We used the quantitative assessment criteria of the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) as a case study. We created a binary (0/1) matrix of all 2.4192 × 10(7) logical combinations of available information for the 14 ecological variables included in the quantitative criteria. We processed each combination of information availability represented in the matrix with a computer algorithm designed to emulate COSEWIC decision-making rules. Low information availability was associated with a relatively high frequency of not being able to assign a candidate taxon to a risk category, which does not follow the precautionary principle. Information availability and the level of risk assigned to species were directly related, which is associated with the worst-case approach, and counter to the insurance approach. Our results suggest that information availability can have a major effect on the level of risk assigned to a species. We recommend a conscious determination of whether such effects are desired, and we recommend the development of methods to explicitly characterize and incorporate information availability and other sources of uncertainty in decision-making processes.

Multiple decrement modeling in the presence of interval censoring and masking

A self-consistent algorithm will be proposed to non-parametrically estimate the cause-specific cumulative incidence functions (CIFs) in an interval censored, multiple decrement context. More specifically, the censoring mechanism will be assumed to be a mixture of case 2 interval-censored data with the additional possibility of exact observations. The proposed algorithm is a generalization of the classical univariate algorithms of Efron and Turnbull. However, unlike any previous non-parametric models proposed in the literature to date, the algorithm will explicitly allow for the possibility of any combination of masked modes of failure, where failure is known only to occur due to a subset from the set of all possible causes. A simulation study is also conducted to demonstrate the consistency of the estimators of the CIFs produced by the proposed algorithm, as well as to explore the effect of masking. The paper concludes by applying the method to masked mortality data obtained for Pueblo County, CO, for three risks: death by cancer; cardiovascular failure; or other.

Systemic and local anti-Mullerian hormone reflects differences in the reproduction potential of Zebu and European type cattle

This study was conducted to evaluate plasma anti-Mullerian hormone (Pl AMH), follicular fluid AMH (FF AMH) and granulosa cell AMH transcript (GC AMH) levels and their relationships with reproductive parameters in two cattle subspecies, Bos taurus indicus (Zebu), and Bos taurus taurus (European type cattle). Two-dimensional ultrasound examination and serum collection were performed on Zebu, European type and crossbreed cows to determine antral follicle count (AFC), ovary diameter (OD) and Pl AMH concentration. Slaughterhouse ovaries for Zebu and European type cattle were collected to determine FF AMH concentrations, GC AMH RNA levels, AFC, oocyte number, cleavage and blastocyst rate. Additionally GC AMH receptor 2 (AMHR2) RNA level was measured for European type cattle. Relationship between AMH and reproductive parameters was found to be significantly greater in Zebu compared to European cattle. Average Pl AMH mean ± SE for Zebu and European cattle was 0.77 ± 0.09 and 0.33 ± 0.24 ng/ml respectively (p = 0.01), whereas average antral FF AMH mean ± SE for Zebu and European cattle was 4934.3 ± 568.5 and 2977.9 ± 214.1 ng/ml respectively (p < 0.05). This is the first published report of FF and GC AMH in Zebu cattle. Levels of GC AMHR2 RNA in European cattle were correlated to oocyte number (p = 0.01). Crossbred animals were found more similar to their maternal Zebu counterparts with respect to their Pl AMH to AFC and OD relationships. These results demonstrate that AMH reflects differences between reproduction potential of the two cattle subspecies therefore can potentially be used as a reproductive marker. Furthermore these results reinforce the importance of separately considering the genetic backgrounds of animals when collecting or interpreting bovine AMH data for reproductive performance.

Fetal sex alters maternal anti-Mullerian hormone during pregnancy in cattle

Anti-Mullerian hormone (AMH) is expressed by both male and female fetuses during mammalian development, with males expressing AMH earlier and at significantly higher concentration. The aim of the current study was to explore the potential impact of pregnancy and fetal sex on maternal AMH and to determine if plasma (Pl) AMH or placenta intercotyledonary membrane and cotyledonary AMH receptor 2 (AMHR2) mRNA expression differ in pregnant cows carrying male vs. female fetuses. AMH levels in blood were measured using a bovine optimized ELISA kit. Cows pregnant with a male fetus were observed to have a significantly greater difference in Pl AMH between day 35 and 135 of gestation. Average fetal AMH level between 54 and 220days of gestation was also observed to be significantly higher in male vs. female fetuses. Intercotyledonary membranes and cotyledons were found to express AMHR2 between days 38 and 80 of gestation at similar levels in both fetal sexes. These findings support the hypothesis that fetal sex alters maternal Pl AMH during pregnancy in cattle.

Biological Response of Positron Emission Tomography Scan Exposure and Adaptive Response in Humans

The biological effects of exposure to radioactive fluorodeoxyglucose (18F-FDG) were investigated in the lymphocytes of patients undergoing positron emission tomography (PET) procedures. Low-dose, radiation-induced cellular responses were measured using 3 different end points: (1) apoptosis; (2) chromosome aberrations; and (3) γH2AX foci formation. The results showed no significant change in lymphocyte apoptosis, or chromosome aberrations, as a result of in vivo 18F-FDG exposure, and there was no evidence the PET scan modified the apoptotic response of lymphocytes to a subsequent 2 Gy in vitro challenge irradiation. However, lymphocytes sampled from patients following a PET scan showed an average of 22.86% fewer chromosome breaks and 39.16% fewer dicentrics after a subsequent 2 Gy in vitro challenge irradiation. The effect of 18F-FDG exposure on phosphorylation of histone H2AX (γH2AX) in lymphocytes of patients showed a varied response between individuals. The relationship between γH2AX foci formation and increasing activity of 18F-FDG was not directly proportional to dose. This variation is most likely attributed to differences in the factors that combine to constitute an individual’s radiation response. In summary, the results of this study indicate18F-FDG PET scans may not be detrimental but can elicit variable responses between individuals and can modify cellular response to subsequent radiation exposures.

Touching the Data: Exploring Data Sonification on Mobile Touchscreen Devices

Abstract This paper suggests using mobile touchscreen devices to assist students with vision loss in working with data. It presents an integrated approach that combines current sonification methods with interactive multi-touch gesture-based exploration of data, designed to aid students in mental visualization and comprehension of data and function plots. This approach aims to help students with vision loss study independently of support centres, collaborate with their peers, and participate in group studies. Initial user study evaluating this approach and demonstrating its feasibility is presented; further research pathways are also discussed.

Exploring anthropogenic activities and management decisions using a novel environmental agent based model

Lake whitefish (Coregonus clupeaformis) are an ecologically, economically, and culturally important species to the native and non-native fishers of Lake Huron, Canada. Studying the effects of anthropogenic activity on lake whitefish is of utmost importance to ensure this species remains viable in its environment for sustainable harvest. One analysis tool that is frequently used for ecological population risk assessments are agent-based models (ABMs), in which the population is represented as a network of heterogeneous individual agents that interact with one another and their environment. However, in an ABM that incorporates a high level of biological detail to model a large population moving within a spatial environment over time, significant computation is required to manage, manipulate, and store the relevant data for each agent over successive time iterations. We introduce a new approach to ABMs known as environmental ABMs (enviro-ABMs) to reduce this computational expense and simulation runtime. Specifically, we divide the environment into a collection of spatially indexed cells and treat each of these as a single agent, allowing fish to move from one contiguous cell to another. This reduces the computational requirements to a limited number of active cells. In addition to more predictable computational requirements, this method keeps all fish sorted by age and location for efficient mortality, spawning, and harvest operations, and reduces the amount of computational overhead needed. Applying the enviro-ABM to our case study in Lake Huron, we demonstrate how it can be used to model anthropogenic activities and stressors that may affect lake whitefish, and how the model can be used to facilitate fisheries management decision making. While the model is applied specifically to the case of whitefish in Lake Huron, it can be generalized to conduct risk assessment for other species in a variety of habitats.