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Autoantibody-mediated glomerulonephritis (AGN) arises from dysregulated renal inflammation, with urgent need for improved treatments. IL-17 is implicated in AGN and drives pathology in a kidney-intrinsic manner via renal tubular epithelial cells (RTECs). Nonetheless, downstream signaling mechanisms provoking kidney pathology are poorly understood. A noncanonical RNA binding protein (RBP), Arid5a, was upregulated in human and mouse AGN. Arid5a−/− mice were refractory to AGN, with attenuated myeloid infiltration and impaired expression of IL-17–dependent cytokines and transcription factors (C/EBPβ, C/EBPδ). Transcriptome-wide RIP-Seq revealed that Arid5a inducibly interacts with conventional IL-17 target mRNAs, including CEBPB and CEBPD. Unexpectedly, many Arid5a RNA targets corresponded to translational regulation and RNA processing pathways, including rRNAs. Indeed, global protein synthesis was repressed in Arid5a-deficient cells, and C/EBPs were controlled at the level of protein rather than RNA accumulation. IL-17 prompted Arid5a nuclear export and association with 18S rRNA, a 40S ribosome constituent. Accordingly, IL-17–dependent renal autoimmunity is driven by Arid5a at the level of ribosome interactions and translation.

Following publication of the original article [1], the authors reported the following errors.

Structural rearrangements of the genome resulting in genic imbalance due to copy number change are often deleterious at the organismal level, but are common in immortalized cell lines and tumors, where they may be an advantage to cells. In order to explore the biological consequences of copy number changes in the Drosophilagenome, we resequenced the genomes of 19 tissue-culture cell lines and generated RNA-Seq profiles. Our work revealed dramatic duplications and deletions in all cell lines. We found three lines of evidence indicating that copy number changes were due to selection during tissue culture. First, we found that copy numbers correlated to maintain stoichiometric balance in protein complexes and biochemical pathways, consistent with the gene balance hypothesis. Second, while most copy number changes were cell line-specific, we identified some copy number changes shared by many of the independent cell lines. These included dramatic recurrence of increased copy number of the PDGF/VEGF receptor, which is also over-expressed in many cancer cells, and of bantam, an anti-apoptosis miRNA. Third, even when copy number changes seemed distinct between lines, there was strong evidence that they supported a common phenotypic outcome. For example, we found that proto-oncogenes were over-represented in one cell line (S2-DRSC), whereas tumor suppressor genes were under-represented in another (Kc167). Our study illustrates how genome structure changes may contribute to selection of cell lines in vitro. This has implications for other cell-level natural selection progressions, including tumorigenesis.

Pedigree information available for Angus (ANG), Devon (DEV), Hereford (HER), and Shorthorn (SHO) cattle in Brazil was analyzed to appraise the genetic diversity and population structure of these breeds. Pedigree records collected from the beginning of the 20th century until 2010 were used in the analyses. Over time, the number of herdbook registrations declined in HER after a peak in the 1970s, remained low in DEV and SHO, and increased steadily in ANG since the 1990s, such that it the latter is now the leading British cattle breed in Brazil. The average number of offspring registered per sire ranged from about 12 (SHO) to 20 (DEV) and the mean generation interval ranged from about 6.0 (HER and SHO) to 6.4 (ANG) years. In the reference population (calves born in 2009 and 2010, plus those born in 2008 for SHO) the mean equivalent number of generations known ranged from about 7 (SHO) to 9 (HER). In the 4 breeds studied, nearly all animals born over the last few years are inbred, even though the mean level of inbreeding in the reference population is below 4% in all breeds. The rate of inbreeding per generation, computed from the individual increase in inbreeding, ranged from about 0.2 (ANG) to 0.5% (DEV), with a corresponding effective population size of 245 and 92, respectively, which is above the recommended minimum critical threshold. The number of founders/ancestors contributing with 50% of the reference population gene pool was 211/26 for ANG, 41/14 for DEV, 164/25 for HER, and 79/10 for SHO, with effective number of founders/ancestors/founder genomes of 470/68/36, 89/33/16, 289/59/30, and 200/28/18 for ANG, DEV, HER, and SHO, respectively. The genetic contribution of different countries to the gene pool of each breed indicated that, throughout the period studied, DEV genes originated predominantly from the United Kingdom, while for the other breeds there was a changing pattern over time. Until the 1970s Argentina was the major supplier of ANG, while HER and SHO genes were mostly from Uruguay, but since then the United States took the leading role as supplier of ANG, HER, and SHO genes to Brazil. Our results reveal a mild increase in inbreeding in all breeds studied, with effective population size estimates indicating that reasonable levels of genetic diversity have been maintained in all 4 breeds. Continuous monitoring of inbreeding trends and of parameters derived from probability of gene origin should be ensured to warrant the long-term maintenance of genetic diversity.

A new method and data analysis pipeline, called Mod-seq, for assaying the structure of RNAs by high-throughput sequencing is described. It can be utilized both in vivo and in vitro, with any small molecule that modifies RNA and consequently impedes reverse transcriptase. As proof-of-principle, we used dimethyl sulfate (DMS) to probe the in vivo structure of total cellular RNAs in Saccharomyces cerevisiae. While this method is applicable to RNAs of any length, its high-throughput nature makes Mod-seq ideal for studying long RNAs and complex RNA mixtures.

Eukaryotic ribosome biogenesis requires a large number (more than 200) assembly factors, one of which is Rlp7. This article shows that Rlp7 binding to pre-rRNA induces conformational changes in ITS2 that may regulate pre-rRNA processing. These findings do not support the hypothesis that Rlp7 serves as a placeholder for ribosomal protein L7.

Genomic imprinting occurs when expression of an allele differs based on the sex of the parent that transmitted the allele. In D. melanogaster,imprinting can occur, but its impact on allelic expression genome-wide is unclear. Here, we search for imprinted genes in D. melanogasterusing RNA-seq to compare allele-specific expression between pools of 7- to 10-day-old adult female progeny from reciprocal crosses. We identified 119 genes with allelic expression consistent with imprinting, and these genes showed significant clustering within the genome. Surprisingly, additional analysis of several of these genes showed that either genomic heterogeneity or high levels of intrinsic noise caused imprinting-like allelic expression. Consequently, our data provide no convincing evidence of imprinting for D. melanogastergenes in their native genomic context. Elucidating sources of false-positive signals for imprinting in allele-specific RNA-seq data, as done here, is critical given the growing popularity of this method for identifying imprinted genes.

Alternative splicing of eukaryotic pre-mRNAs is an important mechanism for generating proteome diversity and regulating gene expression. The Drosophila melanogaster Down Syndrome Cell Adhesion Molecule (Dscam) gene is an extreme example of mutually exclusive splicing. Dscam contains 95 alternatively spliced exons that potentially encode 38,016 distinct mRNA and protein isoforms. We previously identified two sets of conserved sequence elements, the docking site and selector sequences in the Dscam exon 6 cluster, which contains 48 mutually exclusive exons. These elements were proposed to engage in competing RNA secondary structures required for mutually exclusive splicing, though this model has not yet been experimentally tested. Here we describe a new system that allowed us to demonstrate that the docking site and selector sequences are indeed required for exon 6 mutually exclusive splicing and that the strength of these RNA structures determines the frequency of exon 6 inclusion. We also show that the function of the docking site has been conserved for ∼500 million years of evolution. This work demonstrates that conserved intronic sequences play a functional role in mutually exclusive splicing of the Dscam exon 6 cluster.

The highly conserved internal stem-loop (ISL) of U6 spliceosomal RNA is unwound for U4/U6 complex formation during spliceosome assembly and reformed upon U4 release during spliceosome activation. The U6 ISL is structurally similar to Domain 5 of group II self-splicing introns, and contains a dynamic bulge that coordinates a Mg++ ion essential for the first catalytic step of splicing. We have analyzed the causes of growth defects resulting from mutations in the Saccharomyces cerevisiae U6 ISL-bulged nucleotide U80 and the adjacent C67-A79 base pair. Intragenic suppressors and enhancers of the cold-sensitive A79G mutation, which replaces the C-A pair with a C-G pair, suggest that it stabilizes the ISL, inhibits U4/U6 assembly, and may also disrupt spliceosome activation. The lethality of mutations C67A and C67G results from disruption of base-pairing potential between U4 and U6, as these mutations are fully suppressed by compensatory mutations in U4 RNA. Strikingly, suppressor analysis shows that the lethality of the U80G mutation is due not only to formation of a stable base pair with C67, as previously proposed, but also another defect. A U6-U80G strain in which mispairing with position 67 is prevented grows poorly and assembles aberrant spliceosomes that retain U1 snRNP and fail to fully unwind the U4/U6 complex at elevated temperatures. Our data suggest that the U6 ISL bulge is important for coupling U1 snRNP release with U4/U6 unwinding during spliceosome activation.

CC chemokine receptors are important modulators of inflammation. Although CC chemokine receptors have been found predominantly on leukocytes, recent studies have suggested that vascular smooth muscle cells respond to CC chemokines. We now report that human smooth muscle cells express CCR5, a co-receptor for human immunodeficiency virus. CCR5 mRNA was detectable by RNA blot hybridization in human aortic and coronary artery smooth muscle cells. The cDNA generated by reverse transcription-polymerase chain reaction from aortic smooth muscle cells had 100% identity throughout the entire coding region with the CCR5 cloned from THP-1 cells. By immunohistochemistry, CCR5 and the CCR5 ligand, macrophage inflammatory protein-1beta (MIP-1beta), were detected in smooth muscle cells and macrophages of the atherosclerotic plaque. In smooth muscle cell culture, MIP-1beta induced a significant increase in intracellular calcium concentrations, which was blocked by an antibody to CCR5. In addition, MIP-1beta caused a calcium-dependent increase in tissue factor activity. Tissue factor is the initiator of coagulation and is thought to play a key role in arterial thrombosis. These data suggest that human arterial smooth muscle cells express functional CCR5 receptors and MIP-1beta is an agonist for these cells.

SummaryBrazil has various species of domestic animals which developed from breeds brought by the Portuguese settlers soon after the discovery. Over the last five centuries, these breeds have been submitted to natural selection in particular environments and therefore today, they present characteristics adapted to the specific environmental conditions. From the beginning of this century, some exotic breeds, selected in temperate regions, have begun to be imported. Although more productive, these breeds lack adaptation traits, such as resistance to disease and parasites found in breeds considered to be?native? but even so, little by little, they have substituted the native breeds to such an extent that the latter are, today, in danger of extinction. To avoid the loss of this important genetic material, Brazil created an Animal Genetics Resource Conservation Programme, coordinated by the National Research Centre for Genetic Resources and Biotechnology (Cenargen) of the Brazilian Agricultural Research Corporation (EMPRAPA). The conservation has been carried out by various Research Centres of EMPRAPA, Universities, State Research Corporations, as well as by private farmers, with a single coordinator at national level, Cenargen. The conservation is being carried out through Conservation Nuclei, situated in the habitats where the animals have been subjected to natural selection (in situ), and by the storage of semen and embryos (ex situ). The recently created Animal Genetics Laboratory of Cenargen allowed genetic characterisation studies on cattle and horse breeds to begin, and, in the near future, work with asses, buffalo and sheep will be conducted? From the results of this research it will be possible to compare the native breeds and estimate genetic distances between them. The harmonisation of chosen micro-satellites with those which have been used in other Latin America and Iberian Peninsula countries will be extremely useful for comparative studies and will allow future exchange of germplasm between countries.

Measurements are reported of inclusivef2(1270) andf0(975) production in ?p, p±p andK±p collisions at photon beam energies of 65 to 175 GeV and hadron beam energies of 80 and 140 GeV. Thef2 andf0 mesons were found at masses of 1.250 GeV and 0.961 GeV respectively. Inclusivef2 production at lowxF was found to have a similarpT dependence for each beam type, whereas an additional pion-exchange contribution was found for production by pions at highxF. Cross sections are compared with those for ?0 production and give no indication of a non-q component in eitherf-meson state.

Photo- and hadroproduction data in the beam energy range 65–175 GeV have been studied with a view to isolating higher-twist processes in photoproduction from other point-like and hadron-like contributions. With selection of charged tracks havingpT>2 GeV/c and 0.28F<0.84 indications of a higher twist contribution have been found at a level that is consistent with QCD expectations.

The charged particle asymmetry, (n+-n-)/(n++n-), in inclusive photoproduction of charged particles on protons has been studied as a function ofxF andpT in the rangesxF>0 and 0T<2 GeV/c and for photon energies in the range 65?<175 GeV. The asymmetry is found to be positive and decreasing withE?. Asymmetries of p's and K's in the final state have been obtained separately. Data from a carbon target show a significantly lower asymmetry. These results have been compared with a parton, recombination model which provides a qualitative explanation for the asymmetry and itsxF andE? dependences. The model also gives a qualitative understanding of the lower asymmetry seen with the nuclear target.

Abstract: Energy-flow distributions for charged hadrons from interactions of photons, pions and kaons on hydrogen are presented as functions of Σp T2 in the event plane. Data cover the range 0.0<Σp T in2 <10.0(GeV/c)2 and 0.0 F <1.0 for beam momenta from 65 to 170 GeV/c. The comparisons between photon-and hadron-induced data show an excess of events with larger Σp T in2 for the photon-induced data. Using the hadron-induced data to parameterise the hadronic behaviour of the photon, the differences between cross sections are used to measure the contribution of the point-like photon interactions. Quantitative calculations of the point-like photon interactions using the Lund Monte-Carlo program LUCIFER, based on QCD, are in agreement with the data.

Measurements are reported of inclusive production of η-mesons in the beam fragmentation region in γp, πp andKp collisions. Results include a small but significant departure from VMD, and a pronounced rise in theη/π0 ratio with increasingpT.

The inclusive production of ρ0 mesons was measured in γp andh±p collisions at beam energies of 65 GeV≦Eγ≦175 GeV andEh=80, 140 GeV, respectively, whereh is π orK. Cross sections were determined for all beams and energies as functions ofxF (−0.1≦xF≦1.0),pT (0≦pT≦3.5 GeV/c) and the polar decay angle of the ρ0 by fitting the ρ0 signal in π+π- mass distributions. The ρ0 line shape is found to be distorted from a pure Breit-Wigner distribution throughout most of thexF−pT plane for both photon and hadron beams and a simple explanation is suggested. Throughout the paper emphasis is put on the comparison of photon and hadron beam data. The comparison of cross sections of γp andhp data provides a measure of the Vector Meson Dominance factor throughout thexF−pT range of the ρ0. The ρ0 production at lowpT can be described for both photon and hadron beams by a triple regge model at largexF. Similarly central production is well described by the quark-antiquark fusion model. At largepT there is an excess of ρ0 photoproduction which is consistent with the expected onset of pointlike photon interactions.

Inclusive production of ϕ,K*0, and mesons has been measured in γp, π±p andK± p collisions at beam energies of 65 GeVγ<175 GeV andEπ/K =80 and 140 GeV. Cross sections have been determined over the range 0F<1.0 and 0T<1.8 GeV/c. Emphasis is put on the comparison of cross sections for different projectiles as a function ofxF so as to study the effects of common quarks between the beam particle and the detected ϕ,K*0 or . The data are compared with a parton fusion model. Many features of the data are well explained. In detail the strange quark appears to carry a large fraction of the kaon momentum and the contribution of the valence quarks from the proton is small.

An exploratory study of the attitudes of hospital patients to the service provided by hospital chaplains.

Measurements are reported of inclusive production of π0-mesons in the beam fragmentation region in γp, πp andKp collisions. Results include the ratio of π0 production inKp and πp collisions, showing reduced production from fragmentation of theK-meson, and the ratio of π0 production in photon and hadron collisions which shows agreement with modified Vector Meson Dominance at lowPT, and departures at higherPT signalling the onset of direct photon reactions. The pattern of departure from Feynman scaling at highPT points to a contribution of hard parton-parton collisions in both γp and πp collisions.

Single charged-particle inclusive cross sections for photon, pion and kaon beams on hydrogen at the CERN-SPS are presented as functions ofpTandxF. Data cover the range 0.01.6 GeV/c for the photon-induced data. Using the hadron-induced data to estimate the hadronic behaviour of the photon, the difference distributions and ratios of cross sections are a measure of the contribution of the point-like photon interactions. The data are compared with QCD calculations and show broadly similar features.

New breeds can be developed by combining two or more breeds into a composite population, thereby capitalizing on complementarity and retained heterosis. Evaluation of breed formation across generations has not been performed at the molecular level; therefore, we used Brangus cattle (3/8 Brahman x 5/8 Angus) as a model to identify the dynamics of new breed formation across 10 generations. Genotypic data (777,962 SNP) from 68 Brahman, 95 Angus and 59 Brangus prominent AI sires born from 1970 to 2010 were evaluated. Their pedigrees were used to calculate the number of complete Brangus generations using the OptiSel package in R 3.4.2. After standard SNP data filters and linkage disequilibrium pruning, 158,264 SNP genotypes from 220 bulls were chosen. ADMIXTURE analyses were executed using autosomal markers by chromosome, setting K equal to two and three. Brangus animals had 70.4% of Angus composition in all autosomes versus the expected 62.5% (t-test, P< 0.001). When K = 3, the establishment of the Brangus cluster was observed across the genome with a proportional assignment > 0.5. The sex chromosomes deviated from the autosomal pattern. Chromosome X had a high Angus proportion (83%) conserved across generations and Brahman contributed only to 9% of the Y chromosome. Regression analyses of cluster formation among autosomes and across generations showed (P< 0.001) that Angus (β = -0.07) and Brahman (β = -0.03) clusters decreased while Brangus cluster increased (β = 0.10, R2= 0.43). Regressions by each autosome followed a similar pattern. Formation of the Brangus cluster became stable after the 5thgeneration. These results provide a view into the evolution of a new breed.