Sequence Analysis of the Mouse RAG Locus lntergenic Region

The recombination activating genes RAG-1 and RAG-2 are highly conserved throughout evolution and are necessary and essential for the DNA rearrangement of antigen-receptor gene segments. These convergently transcribed genes are expressed primarily by developing B and T lineage cells. In addition, recent data suggest that the RAG locus can be reactivated in mouse germinal center B cells. Despite these well-defined patterns of expression, little is known about mechanism(s) regulating transcription of the RAG locus. Experiments with a mouse fibroblast line stably transfected with a genomic fragment of the RAG locus suggest that the intergenic region between RAG-1 and RAG-2 may contain information modulating RAG transcription. In order to begin testing this hypothesis, we have sequenced the 7.0-kb RAG intergenic region of the mouse. The sequence did not contain open reading frames larger than 60 amino acids. Analysis with GCG software identified several potential transcription-factor binding sequences within this region. Many of these are associated with transcriptional regulation of the Ig locus

Sequence of the RAG1 and RAG2 Intergenic Region in Zebrafish (Danio rerio)

The recombination activating genes, rag1 and rag2 are essential for the rearrangement of antigen receptor V, D, and J gene segments (Oettinger et al., 1990, Mombaerts et al., 1992; Sehatz and Oettinger, 1992; Shinkai et al., 1992). Both genes are found in all species that are known to rearrange their antigenspecific receptors. The coding regions as well as the genomic organization of the rag locus are highly conserved throughout evolution. Rag1 and rag2, which are convergently transcribed, are separated by an intergenic region of DNA that varies in size among species, being, for example, about 11 kb in the human (Homo sapiens), 8 kb in the mouse (Mus musculus), 5.2 kb in the frog (Xenopus laevis), 2.8 kb in the rainbow trout (Oncorhynchus mykiss) (Oettinger et al., 1990; Ichicara et al., 1992; Greenhalgh et al., 1993; Greenhalgh and Steiner., 1995; Hansen and Kaattari, 1996), and 2.6 kb in the zebrafish (Danio rerio).National Institutes of Health (U.S.) (Grant 2R01 AI08054)National Institutes of Health (U.S.) (Grant 5T32 AI07436)National Institutes of Health (U.S.) (Grant 1F32 AI09072

Causal inference in paired two-arm experimental studies under non-compliance with application to prognosis of myocardial infarction

Motivated by a study about prompt coronary angiography in myocardial infarction, we propose a method to estimate the causal effect of a treatment in two-arm experimental studies with possible non-compliance in both treatment and control arms. The method is based on a causal model for repeated binary outcomes (before and after the treatment), which includes individual covariates and latent variables for the unobserved heterogeneity between subjects. Moreover, given the type of non-compliance, the model assumes the existence of three subpopulations of subjects: compliers, never-takers, and always-takers. The model is estimated by a two-step estimator: at the first step the probability that a subject belongs to one of the three subpopulations is estimated on the basis of the available covariates; at the second step the causal effects are estimated through a conditional logistic method, the implementation of which depends on the results from the first step. Standard errors for this estimator are computed on the basis of a sandwich formula. The application shows that prompt coronary angiography in patients with myocardial infarction may significantly decrease the risk of other events within the next two years, with a log-odds of about -2. Given that non-compliance is significant for patients being given the treatment because of high risk conditions, classical estimators fail to detect, or at least underestimate, this effect

Towards a better understanding of the generation of fructan structure diversity in plants: molecular and functional characterization of a sucrose:fructan 6-fructosyltransferase (6-SFT) cDNA from perennial ryegrass (Lolium perenne)

The main storage compounds in Lolium perenne are fructans with prevailing β(2–6) linkages. A cDNA library of L. perenne was screened using Poa secunda sucrose:fructan 6-fructosyltransferase (6-SFT) as a probe. A full-length Lp6-SFT clone was isolated as shown by heterologous expression in Pichia pastoris. High levels of Lp6-SFT transcription were found in the growth zone of elongating leaves and in mature leaf sheaths where fructans are synthesized. Upon fructan synthesis induction, Lp6-SFT transcription was high in mature leaf blades but with no concomitant accumulation of fructans. In vitro studies with the recombinant Lp6-SFT protein showed that both 1-kestotriose and 6G-kestotriose acted as fructosyl acceptors, producing 1- and 6-kestotetraose (bifurcose) and 6G,6-kestotetraose, respectively. Interestingly, bifurcose formation ceased and 6G,6-kestotetraose was formed instead, when recombinant fructan:fructan 6G-fructosyltransferase (6G-FFT) of L. perenne was introduced in the enzyme assay with sucrose and 1-kestotriose as substrates. The remarkable absence of bifurcose in L. perenne tissues might be explained by a higher affinity of 6G-FFT, as compared with 6-SFT, for 1-kestotriose, which is the first fructan formed. Surprisingly, recombinant 6-SFT from Hordeum vulgare, a plant devoid of fructans with internal glucosyl residues, also produced 6G,6-kestotetraose from sucrose and 6G-kestotriose. In the presence of recombinant L. perenne 6G-FFT, it produced 6G,6-kestotetraose from 1-kestotriose and sucrose, like L. perenne 6-SFT. Thus, we demonstrate that the two 6-SFTs have close catalytic properties and that the distinct fructans formed in L. perenne and H. vulgare can be explained by the presence of 6G-FFT activity in L. perenne and its absence in H. vulgare

Contamination Control and Assay Results for the Majorana Demonstrator Ultra Clean Components

The MAJORANA DEMONSTRATOR is a neutrinoless double beta decay experiment utilizing enriched Ge-76 detectors in 2 separate modules inside of a common solid shield at the Sanford Underground Research Facility. The DEMONSTRATOR has utilized world leading assay sensitivities to develop clean materials and processes for producing ultra-pure copper and plastic components. This experiment is now operating, and initial data provide new insights into the success of cleaning and processing. Post production copper assays after the completion of Module 1 showed an increase in U and Th contamination in finished parts compared to starting bulk material. A revised cleaning method and additional round of surface contamination studies prior to Module 2 construction have provided evidence that more rigorous process control can reduce surface contamination. This article describes the assay results and discuss further studies to take advantage of assay capabilities for the purpose of maintaining ultra clean fabrication and process design.Comment: Proceedings of Low Radioactivity Techniques (LRT May 2017, Seoul