1979 Farm Business Analysis Report Beef Summary

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1979 Farm Business Analysis Report Swine Summary

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1979 Farm Business Analysis Report Dairy Summary by Herd Size

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1979 Farm Business Analysis Report Dairy Summary

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Global Transcriptome Analysis of RNA Abundance Regulation by ADAR in Lung Adenocarcinoma

Despite tremendous advances in targeted therapies against lung adenocarcinoma, the majority of patients do not benefit from personalized treatments. A deeper understanding of potential therapeutic targets is crucial to increase the survival of patients. One promising target, ADAR, is amplified in 13% of lung adenocarcinomas and in-vitro studies have demonstrated the potential of its therapeutic inhibition to inhibit tumor growth. ADAR edits millions of adenosines to inosines within the transcriptome, and while previous studies of ADAR in cancer have solely focused on protein-coding edits, >99% of edits occur in non-protein coding regions. Here, we develop a pipeline to discover the regulatory potential of RNA editing sites across the entire transcriptome and apply it to lung adenocarcinoma tumors from The Cancer Genome Atlas. This method predicts that 1413 genes contain regulatory edits, predominantly in non-coding regions. Genes with the largest numbers of regulatory edits are enriched in both apoptotic and innate immune pathways, providing a link between these known functions of ADAR and its role in cancer. We further show that despite a positive association between ADAR RNA expression and apoptotic and immune pathways, ADAR copy number is negatively associated with apoptosis and several immune cell types' signatures

Vesicle adhesion in the electrostatic strong-coupling regime studied by time-resolved small-angle X-ray scattering

We have used time-resolved small-angle X-ray scattering (SAXS) to study the adhesion of lipid vesicles in the electrostatic strong-coupling regime induced by divalent ions. The bilayer structure and the interbilayer distance d$_w$ between adhered vesicles was studied for different DOPC:DOPS mixtures varying the surface charge density of the membrane, as well as for different divalent ions, such as Ca$^{2+}$, Sr$^{2+}$, and Zn$^{2+}$. The results are in good agreement with the strong coupling theory predicting the adhesion state and the corresponding like-charge attraction based on ion-correlations. Using SAXS combined with the stopped-flow rapid mixing technique, we find that in highly charged bilayers the adhesion state is only of transient nature, and that the adhering vesicles subsequently transform to a phase of multilamellar vesicles, again with an inter-bilayer distance according to the theory of strong binding. Aside from the stopped-flow SAXS instrumentations used primarily for these results, we also evaluate microfluidic sample environments for vesicle SAXS in view of future extension of this work

TSAFinder: exhaustive tumor-specific antigen detection with RNAseq.

MOTIVATION: Tumor-specific antigen (TSA) identification in human cancer predicts response to immunotherapy and provides targets for cancer vaccine and adoptive T-cell therapies with curative potential, and TSAs that are highly expressed at the RNA level are more likely to be presented on major histocompatibility complex (MHC)-I. Direct measurements of the RNA expression of peptides would allow for generalized prediction of TSAs. Human leukocyte antigen (HLA)-I genotypes were predicted with seq2HLA. RNA sequencing (RNAseq) fastq files were translated into all possible peptides of length 8-11, and peptides with high and low expressions in the tumor and control samples, respectively, were tested for their MHC-I binding potential with netMHCpan-4.0. RESULTS: A novel pipeline for TSA prediction from RNAseq was used to predict all possible unique peptides size 8-11 on previously published murine and human lung and lymphoma tumors and validated on matched tumor and control lung adenocarcinoma (LUAD) samples. We show that neoantigens predicted by exomeSeq are typically poorly expressed at the RNA level, and a fraction is expressed in matched normal samples. TSAs presented in the proteomics data have higher RNA abundance and lower MHC-I binding percentile, and these attributes are used to discover high confidence TSAs within the validation cohort. Finally, a subset of these high confidence TSAs is expressed in a majority of LUAD tumors and represents attractive vaccine targets. AVAILABILITY AND IMPLEMENTATION: The datasets were derived from sources in the public domain as follows: TSAFinder is open-source software written in python and R. It is licensed under CC-BY-NC-SA and can be downloaded at https://github.com/RNAseqTSA. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Thermotropic Liquid-crystalline Properties of Extended Viologen Bis(triflimide) Salts

A series of extended, symmetric viologen triflimides were synthesised by the metathesis reaction of lithium triflimide with the respective viologen tosyalates in methanol. Their chemical structures were characterised by Fourier Transform Infrared, 1H and 13C Nuclear Magnetic Resonance spectroscopy and elemental analysis. Their thermotropic liquid-crystalline (LC) properties were examined by a number of experimental techniques including differential scanning calorimetry, thermogravimetric analysis, polarising optical microscopy and variable temperature X-ray diffraction. The viologen salts containing alkyl chain of two carbon and three carbon atoms were relatively low melting salts. Those of alkyl chains of four carbon and five carbon atoms formed ionic liquids at 88 and 42°C, respectively. Those of alkyl chain of 9, 10 and 11 carbon atoms were high melting salts, as high as 166°C. Those of higher alkyl chains of 16, 18 and 20 carbon atoms showed thermotropic LC phases forming SmC, SmA and an unidentified smectic (SmX) phases, and showed SmA to isotropic transitions at high temperatures. As expected, all the viologen triflimides had excellent stabilities in the temperature range of 338–365°C