Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver

BackgroundRNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript. Mammalian C-to-U RNA editing represents a distinct subtype of base modification, whose prototype is intestinal apolipoprotein B mRNA, mediated by the catalytic deaminase Apobec-1. However, the genome-wide identification, tissue-specificity and functional implications of Apobec-1-mediated C-to-U RNA editing remain incompletely explored.ResultsDeep sequencing, data filtering and Sanger-sequence validation of intestinal and hepatic RNA from wild-type and Apobec-1-deficient mice revealed 56 novel editing sites in 54 intestinal mRNAs and 22 novel sites in 17 liver mRNAs, all within 3' untranslated regions. Eleven of 17 liver RNAs shared editing sites with intestinal RNAs, while 6 sites are unique to liver. Changes in RNA editing lead to corresponding changes in intestinal mRNA and protein levels for 11 genes. Analysis of RNA editing in vivo following tissue-specific Apobec-1 adenoviral or transgenic Apobec-1 overexpression reveals that a subset of targets identified in wild-type mice are restored in Apobec-1-deficient mouse intestine and liver following Apobec-1 rescue. We find distinctive polysome profiles for several RNA editing targets and demonstrate novel exonic editing sites in nuclear preparations from intestine but not hepatic apolipoprotein B RNA. RNA editing is validated using cell-free extracts from wild-type but not Apobec-1-deficient mice, demonstrating that Apobec-1 is required.ConclusionsThese studies define selective, tissue-specific targets of Apobec-1-dependent RNA editing and show the functional consequences of editing are both transcript- and tissue-specific

Prevalence and determinants of use of traditional methods of infertility treatment among women attending infertility clinic in Southeast Nigeria

Infertility, an obstacle to healthy living, makes its victims patronize traditional methods of infertility treatment (TMIT) in spite of associated complications. They turn to hospitals when this method fails. This is actually a serious issue because the presence of contaminated herbal products and the relationship between the use of TMIT and noncompliance with biomedical treatment regimens constitutes a major concern in medical practice. And the use of traditional methods of infertility treatment has been correlated with severe and fatal consequences. Therefore, the study assessed prevalence/determinants of TMIT use among patients visiting the gynaecology clinic at Alex Ekwueme Federal University Teaching Hospital Abakaliki (AE-FUTHA). Descriptive cross-sectional design was adopted for the research. Only 263 women took part in the study. The research instrument was questionnaire. Data were analyzed using descriptive statistics. Findings revealed that 95.4% of these women have used traditional methods for infertility treatment and factors influencing infertile women’s use of TMIT are demographic characteristics, infertility duration, husbands’ relatives’ pressure and cheap cost of traditional medical treatment. Again, inability of infertile women to disclose TMIT use to healthcare providers makes effective treatment difficult. Therefore, these impediments expose infertile women to use TMIT. The result is a guide to healthcare providers who are expected to know the extent of their parents’ use of TMIT

Two and four-loop β\beta-functions of rank 4 renormalizable tensor field theories

A recent rank 4 tensor field model generating 4D simplicial manifolds has been proved to be renormalizable at all orders of perturbation theory [arXiv:1111.4997 [hep-th]]. The model is built out of $\phi^6$ ($\phi^6_{(1/2)}$), $\phi^4$ ($\phi^4_{(1)}$) interactions and an anomalous term ($\phi^4_{(2)}$). The $\beta$-functions of this model are evaluated at two and four loops. We find that the model is asymptotically free in the UV for both the main $\phi^6_{(1/2)}$ interactions whereas it is safe in the $\phi^4_{(1)}$ sector. The remaining anomalous term turns out to possess a Landau ghost.Comment: 31 pages, 31 figures; improved versio

Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions

Babesia microti, a tick-transmitted, intraerythrocytic protozoan parasite circulating mainly among small mammals, is the primary cause of human babesiosis. While most cases are transmitted by Ixodes ticks, the disease may also be transmitted through blood transfusion and perinatally. A comprehensive analysis of genome composition, genetic diversity, and gene expression profiling of seven B. microti isolates revealed that genetic variation in isolates from the Northeast United States is almost exclusively associated with genes encoding the surface proteome and secretome of the parasite. Furthermore, we found that polymorphism is restricted to a small number of genes, which are highly expressed during infection. In order to identify pathogen-encoded factors involved in host-parasite interactions, we screened a proteome array comprised of 174 B. microti proteins, including several predicted members of the parasite secretome. Using this immuno-proteomic approach we identified several novel antigens that trigger strong host immune responses during the onset of infection. The genomic and immunological data presented herein provide the first insights into the determinants of B. microti interaction with its mammalian hosts and their relevance for understanding the selective pressures acting on parasite evolution

Theoretical Analysis of Quantum Ghost Imaging Through Turbulence

Atmospheric turbulence generally affects the resolution and visibility of an image in long-distance imaging. In a recent quantum ghost imaging experiment [P. B. Dixon et al., Phys. Rev. A 83, 051803 (2011)], it was found that the effect of the turbulence can nevertheless be mitigated under certain conditions. This paper gives a detailed theoretical analysis to the setup and results reported in the experiment. Entangled photons with a finite correlation area and a turbulence model beyond the phase screen approximation are considered

SB04-22/23: Resolution Authorizing Approval of Staff Senate Signature of Bear Necessities Statement to University Administration

Passed during May 10, 2023 Staff Senate meeting. Documents from the May 10, 2023 meeting of the University of Montana S by University of Montana--Missoula. Staff Senate (umt.edu) Resolution authorizing approval of Staff Senate to sign support to the ASUM Bear Necessities statement to the University of Montana Administration. Resolution Authored by Kat Cowley. Additional Authors, including Cowley, listed for letter. Letter discusses concerns regarding the status of marginalized and vulnerable student populations and offers suggestions on some ways the University of Montana can support students at a basic human level. These include continued advocacy for increase support from the State of Montana, increased housing availability, meal plan affordability, open education resources, campus accessibility, and addressing staffing issues

Assessment of Serum Proteomics to Detect Large Colon Adenomas

A non-invasive blood test that could reliably detect early CRC or large adenomas would provide an important advance in colon cancer screening. The purpose of this study was to determine whether a serum proteomics assay could discriminate among persons with and without a large (≥1cm) colon adenoma. To avoid problems of ‘bias’ that have affected many studies about molecular markers for diagnosis, specimens were obtained from a previously-conducted study of CRC etiology in which bloods had been collected before the presence or absence of neoplasm had been determined by colonoscopy, helping to assure that biases related to differences in sample collection and handling would be avoided. Mass spectra of 65 unblinded serum samples were acquired using a nano-electrospray ionization source on a QSTAR-XL mass spectrometer. Classification patterns were developed using the ProteomeQuest® algorithm, performing measurements twice on each specimen, and then applied to a blinded validation set of 70 specimens. After removing 33 specimens that had discordant results, the “test group” comprised 37 specimens that had never been used in training. Although in the primary analysis no discrimination was found, a single post-hoc analysis, done after hemolyzed specimens had been removed, showed sensitivity of 78%, specificity of 53%, and an accuracy of 63% (95% CI: 53% to 72%). The results of this study, although preliminary, suggest that further study of serum proteomics, in a larger number of appropriate specimens, could be useful. They also highlight the importance of understanding sources of ‘noise’ and ‘bias’ in studies of proteomics assays

Renormalization Group Approach to Field Theory at Finite Temperature

Scalar field theory at finite temperature is investigated via an improved renormalization group prescription which provides an effective resummation over all possible non-overlapping higher loop graphs. Explicit analyses for the lambda phi^4 theory are performed in d=4 Euclidean space for both low and high temperature limits. We generate a set of coupled equations for the mass parameter and the coupling constant from the renormalization group flow equation. Dimensional reduction and symmetry restoration are also explored with our improved approach.Comment: 29 pages, can include figures in the body of the text using epsf.st