Comparative functional genomics and the bovine macrophage response to strains of the Mycobacterium genus

Mycobacterial infections are major causes of morbidity and mortality in cattle and are also potential zoonotic agents with implications for human health. Despite the implementation of comprehensive animal surveillance programs, many mycobacterial diseases have remained recalcitrant to eradication in several industrialized countries. Two major mycobacterial pathogens of cattle are Mycobacterium bovis and Mycobacterium avium subspecies paratuberculosis (MAP), the causative agents of bovine tuberculosis (BTB) and Johne's disease (JD), respectively. BTB is a chronic, granulomatous disease of the respiratory tract that is spread via aerosol transmission, while JD is a chronic granulomatous disease of the intestines that is transmitted via the fecal-oral route. Although these diseases exhibit differential tissue tropism and distinct complex etiologies, both M. bovis and MAP infect, reside, and replicate in host macrophages - the key host innate immune cell that encounters mycobacterial pathogens after initial exposure and mediates the subsequent immune response. The persistence of M. bovis and MAP in macrophages relies on a diverse series of immunomodulatory mechanisms, including the inhibition of phagosome maturation and apoptosis, generation of cytokine-induced necrosis enabling dissemination of infection through the host, local pathology, and ultimately shedding of the pathogen. Here, we review the bovine macrophage response to infection with M. bovis and MAP. In particular, we describe how recent advances in functional genomics are shedding light on the host macrophage-pathogen interactions that underlie different mycobacterial diseases. To illustrate this, we present new analyses of previously published bovine macrophage transcriptomics data following in vitro infection with virulent M. bovis, the attenuated vaccine strain M. bovis BCG, and MAP, and discuss our findings with respect to the differing etiologies of BTB and JD

Advances in neuroimaging in frontotemporal dementia

Frontotemporal dementia (FTD) is a clinically and neuroanatomically heterogeneous neurodegenerative disorder with multiple underlying genetic and pathological causes. Whilst initial neuroimaging studies highlighted the presence of frontal and temporal lobe atrophy or hypometabolism as the unifying feature in patients with FTD, more detailed studies have revealed diverse patterns across individuals, with variable frontal or temporal predominance, differing degrees of asymmetry, and the involvement of other cortical areas including the insula and cingulate, as well as subcortical structures such as the basal ganglia and thalamus. Recent advances in novel imaging modalities including diffusion tensor imaging, resting-state functional magnetic resonance imaging and molecular positron emission tomography imaging allow the possibility of investigating alterations in structural and functional connectivity and the visualisation of pathological protein deposition. This review will cover the major imaging modalities currently used in research and clinical practice, focusing on the key insights they have provided into FTD, including the onset and evolution of pathological changes and also importantly their utility as biomarkers for disease detection and staging, differential diagnosis and measurement of disease progression. Validating neuroimaging biomarkers that are able to accomplish these tasks will be crucial for the ultimate goal of powering upcoming clinical trials by correctly stratifying patient enrolment and providing sensitive markers for evaluating the effects and efficacy of disease-modifying therapies

GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data

Background: Identification of gene expression profiles that differentiate experimental groups is critical for discovery and analysis of key molecular pathways and also for selection of robust diagnostic or prognostic biomarkers. While integration of differential expression statistics has been used to refine gene set enrichment analyses, such approaches are typically limited to single gene lists resulting from simple two-group comparisons or time-series analyses. In contrast, functional class scoring and machine learning approaches provide powerful alternative methods to leverage molecular measurements for pathway analyses, and to compare continuous and multi-level categorical factors. Results: We introduce GOexpress, a software package for scoring and summarising the capacity of gene ontology features to simultaneously classify samples from multiple experimental groups. GOexpress integrates normalised gene expression data (e.g., from microarray and RNA-seq experiments) and phenotypic information of individual samples with gene ontology annotations to derive a ranking of genes and gene ontology terms using a supervised learning approach. The default random forest algorithm allows interactions between all experimental factors, and competitive scoring of expressed genes to evaluate their relative importance in classifying predefined groups of samples. Conclusions: GOexpress enables rapid identification and visualisation of ontology-related gene panels that robustly classify groups of samples and supports both categorical (e.g., infection status, treatment) and continuous (e.g., time-series, drug concentrations) experimental factors. The use of standard Bioconductor extension packages and publicly available gene ontology annotations facilitates straightforward integration of GOexpress within existing computational biology pipelines.Department of Agriculture, Food and the MarineEuropean Commission - Seventh Framework Programme (FP7)Science Foundation IrelandUniversity College Dubli

Mechanobiology Of Mice Cervix: Expression Profile Of Mechano-Related Molecules During Pregnancy

There is a known reciprocation between the chronic exertion of force on tissue and both increased tissue density (e.g. bone) and hypertrophy (e.g. heart). This can also be seen in cervical tissue where the excessive gravitational forces associated with multiple fetal pregnancies promote preterm births. While there is a well-known regulation of cervical remodeling (CR) by sex steroid hormones and growth factors, the role of mechanical force is less appreciated. Using proteome-wide technology, we previously provided evidence for the presence of and alteration in mechano-related signaling molecules in the mouse cervix during pregnancy. Here we profile the expression of select cytoskeletal factors (Filamin A, gelsolin, vimentin, actinin-1, caveolin-1, transgelin, keratin-8, profilin-1) and their associated signaling molecules [Focal adhesion kinase (FAK) and the Rho-GTPases Cdc42, RhoA, and RhoB] in cervices of pregnant mice by real time PCR and confocal immunofluorescent microscopy. Messenger RNA and protein levels increased for each of these 12 factors, except for 3 (keratin-8, profilin-1, RhoA) that decreased during the course of pregnancy, and this corresponded with an increase in gravitational force exerted by the fetus on the cervix. We therefore conclude that size or weight of the growing fetus likely plays a key role in CR through mechano-transduction processes

State-wide support for teacher leadership : implementing standards to evaluate teacher leader practices and inform professional growth activities

This project used the improvement-science structure of a 90-Day-Cycle to support theimplementation of the NC Teacher Leadership Specialist (TLS) Standards in two CountySchool Districts in North Carolina by providing professional development with facilitatedreflection activities and by collecting data regarding the depth and appropriateness of thestandards for guiding and evaluating district-specific teacher leadership roles andactivities. The outcomes from this project offered NCDPI deeper state-level awareness ofdistrict-specific teacher leadership roles by identifying models of teacher leadershippractice and existing support structures and assessing the level of alignment between theTLS standards and those practices. The outcomes of this project yieldedrecommendations to guide the development of statewide resources for supporting teacherleadership, in order to better align them with actual district-level teacher leader roles, aswell as identify focus areas for the development of future professional developmentresources. The narrative concludes with recommendations moving forward in light ofnew legislative influences on teacher leadership in North Carolina

Increased Rates of Soil Respiration and Microbial Enzyme Activity Under Two Complementary Experimental Warming Methods: Implications for Carbon-Climate Feedbacks

Soils contain large amounts of carbon which is susceptible to increased decomposition with increasing global surface temperatures under climate change. It is uncertain how soil carbon will react to long-term climate change because of the differences in the decomposability of carbon sources in the soils. The interaction with the above-ground plant community, which has the potential to increase carbon sequestration in biomass, is also uncertain. By observing large soil mesocosms (29000 cm3) with tulip poplar seedlings that we reciprocally transplanted along a 700 m elevation, temperature, and moisture gradient in the Appalachian Mountains, we aimed to better understand the interactions under natural field conditions. Cylindrical soil microcosms (10 x 15 cm) were also collected from elevational and latitudinal gradients and warmed in the laboratory at ambient field temperature, ambient +3 °C, and ambient +6 °C. Soil respiration increased with increasing temperature for both experiments. Microbial enzyme activity was also increased for microcosms that originated from a low native temperature site. High elevation mesocosms transplanted to low elevations also increased their microbial enzyme activity rates such that they exceeded all other treatments. This indicates that soils from high elevations and low native temperatures may be more sensitive to warming

Chromophoric dissolved organic matter in coastal rainwater

Chromophoric dissolved organic matter (DOM) was measured in 37 rain events in Wilmington, NC, between September 15, 2005 to September 6, 2006. Each rain event was analyzed via 3D fluorescence, UV-Vis absorption spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, and dissolved organic carbon measurements were acquired. All rain events had measurable CDOM, although there was much variability between events. Chromophoric DOM was found in both the C18 extract (hydrophobic) and the C18 filtrate (hydrophilic) fraction, but surprisingly a large fraction of the chromophoric DOM is relatively hydrophilic (~50%). Using NMR, it was determined that in all rain events the majority of the protons were alkyl. A strong positive correlation was found between the fluorescence and the overall integration of the NMR spectra. A correlation was also found between fluorescence and the various integral regions of the NMR with the greatest contribution to fluorescence coming from the aromatic region. The abundance and characteristics of rainwater DOM was affected by season and storm origin. Marine storms contained a larger percentage of aromatic protons relative to the terrestrial storms. This coupled with lower spectral slopes and a higher percentage fluorescence in the C18 extract samples from marine storms suggests that while the dissolved organic carbon (DOC) concentrations in these storms are low, the DOM in marine storms likely contains recalcitrant DOM which is globally distributed. The composition of DOM in rainwater is also influenced by season. Samples collected during the warm season had lower spectral slopes and lower percent DOC in the reconstituted fraction which suggests that warm season storms contain smaller molecular weight DOM. This is a result of photodegredation during the warm season

Equipment preferences of men and women employed in early childhood education

During the last four decades early childhood educators have stressed the importance of male workers entering the occupation. Claims have been made that both children and programs benefit from the presence of male caregivers. However, the actual percentage of men working with young children is very small and has not increased. While professionals have accepted, as a matter of faith, that the presence of male workers is beneficial, no empirical data support this claim. Research efforts have failed to document unique male contributions to the early childhood environment. The current study suggests that previous studies may have been measuring the wrong variables. The current study measured the different equipment and supply preferences of men and women working in the field of early childhood education. Participants were each given a booklet with 50 pictures of daycare equipment and supplies and requested to choose 15 items that they would like to use to supplement an already equipped classroom. A panel had previously rated these items on a 5 point scale from very feminine to very masculine. Participants were also requested to complete an education and experience survey as well as a Sex Role Preference scale

RNA-seq transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis

Bovine tuberculosis, caused by infection with Mycobacterium bovis, is a major endemic disease affecting cattle populations worldwide, despite the implementation of stringent surveillance and control programs in many countries. The development of high-throughput functional genomics technologies, including gene expression microarrays and RNA-sequencing (RNA-seq), has enabled detailed analysis of the host transcriptome to M. bovis infection, particularly at the macrophage and peripheral blood level. In the present study, we have analyzed the peripheral blood leukocyte (PBL) transcriptome of eight natural M. bovis-infected and eight age- and sex-matched non-infected control Holstein-Friesian animals using RNA-seq. In addition, we compared gene expression profiles generated using RNA-seq with those previously generated using the high-density Affymetrix(®) GeneChip(®) Bovine Genome Array platform from the same PBL-extracted RNA. A total of 3,250 differentially expressed (DE) annotated genes were detected in the M. bovis-infected samples relative to the controls (adjusted P-value ≤0.05), with the number of genes displaying decreased relative expression (1,671) exceeding those with increased relative expression (1,579). Ingenuity(®) Systems Pathway Analysis (IPA) of all DE genes revealed enrichment for genes with immune function. Notably, transcriptional suppression was observed among several of the top-ranking canonical pathways including Leukocyte Extravasation Signaling. Comparative platform analysis demonstrated that RNA-seq detected a larger number of annotated DE genes (3,250) relative to the microarray (1,398), of which 917 genes were common to both technologies and displayed the same direction of expression. Finally, we show that RNA-seq had an increased dynamic range compared to the microarray for estimating differential gene expression