Specificity and sensitivity evaluation of novel and existing Bacteroidales and Bifidobacteria-specific PCR assays on feces and sewage samples and their application for microbial source tracking in Ireland

Three novel ruminant-specific PCR assays, an existing ruminant-specific PCR assay and five existing human-specific PCR assays, which target 16S rDNA from Bacteroidales or Bifidobacteria, were evaluated. The assays were tested on DNA extracted from ruminant (n = 74), human (n = 59) and non-ruminant animal (n = 44) sewage/fecal samples collected in Ireland. The three novel PCR assays compared favourably to the existing ruminant-specific assay, exhibiting sensitivities of 91 - 100% and specificities of 95 - 100% as compared to a sensitivity of 95% and specificity of 94%, for the existing ruminant-specific assay. Of the five human-specific PCR assays, the assay targeting the Bifidobacterium catenulatum group was the most promising, exhibiting a sensitivity of 100% (with human sewage samples) and a specificity of 87%. When tested on rural water samples that were naturally contaminated by ruminant feces, the three novel PCR assays tested positive with a much greater percentage (52 - 87%) of samples than the existing ruminant-specific assay (17%). These novel ruminant-specific assays show promise for microbial source tracking and merit further field testing and specificity evaluation.ERTD

Microbial Cell Factories / Monitoring the Dynamics of Transcription and Translation Within the Time Course of Recombinant E. coli Cultivations

Oral presentation from The 4th Recombinant Protein Production Meeting: a comparative view on host physiology, Barcelona, Spain. 21\u201323 September 200

Title IX and Consent Education

This presentation details the lesson design and implementation of a COR 101 lesson around consent and title IX. The goal of the presentation was to create a comfortable atmosphere and have a student led discussion surrounding topics regarding sex, consent, and resources around the campus and community. The presentation demonstrates the mixed success of lesson implementation and takeaways.https://digitalcommons.cortland.edu/corslides/1027/thumbnail.jp

Enhanced expression of the stemness-related factors OCT4, SOX15 and TWIST1 in ectopic endometrium of endometriosis patients

Abstract Background Current evidence suggests that endometrial-derived stem cells, spilled in the peritoneal cavity via retrograde menstruation, are key players in the establishment of endometriotic lesions. The aim of this study was to determine the presence and distribution of the stemness-related factors OCT4, SOX15, TWIST1 and DCAMLK1 in women with and without endometriosis. Methods Immunohistochemical analysis was used to determine stromal and epithelial expression of OCT4, SOX15, TWIST1 and DCAMLK1 in endometriosis patient (EP) endometrium (n = 69) and endometriotic tissue (n = 90) and in control endometrium (n = 50). Quantitative Real-Time PCR of OCT4, SOX15 TWIST1 and DCAMLK1 was performed in paired samples of EP endometrium and endometriotic tissue. Co-immunofluorescence staining was performed for OCT4 and SOX15. For statistical analyses we used unpaired t-test, Fisher combination test and Spearman test. For paired analyses, paired t-test and McNemar test were used. Results We detected a significant correlation between the expression of the established stem cell marker OCT4 and the stemness-related markers SOX15 (p < 0.001) and TWIST1 (p = 0.002) but not DCAMLK1. We showed a colocalization of SOX15 and OCT4 in epithelial and stromal cells of endometriotic tissue by coimmunofluorescence. A concordant expression of OCT4 and SOX15 in the same sample was observed in epithelial cells of the endometriotic tissue (71.7%). The expression of stemness-related factors was not associated with proliferative or secretory phase of the menstrual cycle in endometriosis patients but was found to be differentially expressed during the menstrual cycle in the control group. Increased expression of epithelial OCT4, SOX15 and TWIST1 was detected in endometriotic tissue compared to EP endometrium in paired (p = 0.021, p < 0.001 and p < 0.001) and unpaired analysis (p = 0.040, p < 0.001 and p = 0.001). Conclusion Our findings support the hypothesis that upregulation of stem cell-related factors contribute to the establishment of endometriotic lesions. Trial registration The study was approved by the institutional review board (545/2010 on 6th of May 2014) of the Medical University of Vienna ( http://ethikkommission.meduniwien.ac.at/fileadmin/ethik/media/dokumente/register/alle_2010.pdf )

An Analysis of Trade Credit and Macroeconomic Fluctuations

Trade credit in the form of delayed input payments is an important source of financing for all types of firms. Empirical evidence on business cycle patterns and the usage of trade credit in the US economy suggests that trade credit comoves strongly with GDP and was severely affected at the onset of the 2008-2009 Financial Crisis. Motivated by these observations, this thesis studies the role of trade credit for the propagation of financial shocks in a production network and its implications for aggregate and sectoral outcomes. To this end, I introduce a static quantitative multisector model featuring trade in intermediate inputs and endogenous trade credit linkages and costs between representative firms in each sector. Firms face working capital constraints and are required to finance their production costs using both bank and supplier credit. In response to a tightening of credit conditions, the endogenous adjustment in the volume and cost of trade credit captures two counteracting mechanisms: (1) Firms smooth interest rate shocks by substituting bank and supplier finance. (2) Any increase in the interest rate that a firm charges on trade credit tightens the financing terms of its customers thereby amplifying financial shocks. In equilibrium, the working capital constraint distorts the demand for production inputs and aggregate output as common to models with distortions. The interdependency of credit distortions further affects the propagation of financial shocks and it is shown that sectors extending a lot of trade credit to their customers relative to their own financing needs play a crucial role in the transmission of shocks to the cost of external funds. In a quantitative application of the model to the US economy during the crisis, simulations featuring financial shocks only show that the model captures approximately a third of the drop in output, half of which can be attributed to the existence of trade credit linkages alone. I also show that the ability of firms to adjust their borrowing portfolio overall decreases aggregate volatility by less than two percent. This suggests that the smoothing mechanism of trade credit was operative, though small. In a final application, I quantify the predictions of the model and show that firms acting as important financial intermediaries for their customers are systemically important and generate large spillovers

Analytic philosophy for biomedical research: the imperative of applying yesterday's timeless messages to today's impasses

The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal in this chapter is that philosophy is essential in this process. By reviewing select examples from the history of science and philosophy, disciplines which were indistinguishable until the mid-nineteenth century, I argue that progress toward the many impasses in biomedicine can be achieved by emphasizing theoretical work (in the true sense of the word 'theory') as a vital foundation for experimental biology. Furthermore, a philosophical biology program that could provide a framework for theoretical investigations is outlined

Performance Characteristics of qPCR Assays Targeting Human- and Ruminant-Associated Bacteroidetes for Microbial Source Tracking across Sixteen Countries on Six Continents

Numerous quantitative PCR assays for microbial fecal source tracking (MST) have been developed and evaluated in recent years. Widespread application has been hindered by a lack of knowledge regarding the geographical stability and hence applicability of such methods beyond the regional level. This study assessed the performance of five previously reported quantitative PCR assays targeting human-, cattle-, or ruminant-associated Bacteroidetes populations on 280 human and animal fecal samples from 16 countries across six continents. The tested cattle-associated markers were shown to be ruminant-associated. The quantitative distributions of marker concentrations in target and nontarget samples proved to be essential for the assessment of assay performance and were used to establish a new metric for quantitative source-specificity. In general, this study demonstrates that stable target populations required for marker-based MST occur around the globe. Ruminant-associated marker concentrations were strongly correlated with total intestinal Bacteroidetes populations and with each other, indicating that the detected ruminant-associated populations seem to be part of the intestinal core microbiome of ruminants worldwide. Consequently tested ruminant-targeted assays appear to be suitable quantitative MST tools beyond the regional level while the targeted human-associated populations seem to be less prevalent and stable, suggesting potential for improvements in human-targeted methods

Capabilities of an optical direct push probe for 2D-subsurface imaging

Characterization of hydrological conditions at polluted sites is critical for understanding of contaminant distribution and transport. Standard techniques for site characterization, such as soil coring together with well installation for piezometric measurements and water sampling, allow only some insights into subsurface properties and processes. To obtain additional data, direct-push techniques are often used in soils and unconsolidated formations. The various available techniques provide high resolution information on cm to mm scale. Recently, the Optical Imaging Profiler (OIP) was developed for detection of fluorescent contaminants. Here, we have investigated the applicability of the OIP for groundwater tracing using fluorophores. Our laboratory experiments show that it is possible to qualitatively trace various fluorophores meaning that light emitted by the fluorophores can be detected by a standard digital camera sensor. The measured fluorescence depends on the number of fluorophore molecules present in the pore space adjacent to the OIP and decreases with smaller pore size as well as fluorophore concentration. In a field trial, an injected eosin Y solution could be very clearly detected after the injection within a radius of 0.5 m around the injection point. When the OIP is equipped with a second light source emitting visible light, images of the soil texture and color can be captured. Sediment color can act as a proxy for various soil properties. Tests at a second field site, indicate that detected variation in soil color depend on water saturation and redox processes. Hence, the OIP is a flexible, cost effective and multifunctional tool for characterization of contaminated sites