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Alternative polyadenylation (APA) regulates mRNA translation, stability, and protein localization. However, it is unclear to what extent APA regulates these processes uniquely in specific cell types. Using a new technique, cTag-PAPERCLIP, we discovered significant differences in APA between the principal types of mouse cerebellar neurons, the Purkinje and granule cells, as well as between proliferating and differentiated granule cells. Transcripts that differed in APA in these comparisons were enriched in key neuronal functions and many differed in coding sequence in addition to 3'UTR length. We characterize Memo1, a transcript that shifted from expressing a short 3'UTR isoform to a longer one during granule cell differentiation. We show that Memo1 regulates granule cell precursor proliferation and that its long 3'UTR isoform is targeted by miR-124, contributing to its downregulation during development. Our findings provide insight into roles for APA in specific cell types and establish a platform for further functional studies.

Most humans are exposed to Tropheryma whipplei (Tw). Whipple's disease (WD) strikes only a small minority of individuals infected with Tw (<0.01%), whereas asymptomatic chronic carriage is more common (<25%). We studied a multiplex kindred, containing four WD patients and five healthy Tw chronic carriers. We hypothesized that WD displays autosomal dominant (AD) inheritance, with age-dependent incomplete penetrance. We identified a single very rare non-synonymous mutation in the four patients: the private R98W variant of IRF4, a transcription factor involved in immunity. The five Tw carriers were younger, and also heterozygous for R98W. We found that R98W was loss-of-function, modified the transcriptome of heterozygous leukocytes following Tw stimulation, and was not dominant-negative. We also found that only six of the other 153 known non-synonymous IRF4 variants were loss-of-function. Finally, we found that IRF4 had evolved under purifying selection. AD IRF4 deficiency can underlie WD by haploinsufficiency, with age-dependent incomplete penetrance.

A search for heavy resonances decaying to a pair of Z bosons is performed using data collected with the CMS detector at the LHC. Events are selected by requiring two oppositely charged leptons (electrons or muons), consistent with the decay of a Z boson, and large missing transverse momentum, which is interpreted as arising from the decay of a second Z boson to two neutrinos. The analysis uses data from proton-proton collisions at a center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 35.9 fb(-1). The hypothesis of a spin-2 bulk graviton (X) decaying to a pair of Z bosons is examined for 600 <= m(X) <= 2500 GeV and upper limits at 95% confidence level are set on the product of the production cross section and branching fraction of X -> ZZ ranging from 100 to 4 fb. For bulk graviton models characterized by a curvature scale parameter (k) over tilde = 0.5 in the extra dimension, the region nix < 800 GeV is excluded, providing the most stringent limit reported to date. Variations of the model considering the possibility of a wide resonance produced exclusively via gluon-gluon fusion or q<(q)over bar> annihilation are also examined.

Transcriptional pausing by RNA polymerases (RNAPs) is a key mechanism to regulate gene expression in all kingdoms of life and is a prerequisite for transcription termination. The essential bacterial transcription factor NusA stimulates both pausing and termination of transcription, thus playing a central role. Here, wereport single-particle electron cryo-microscopy reconstructions of NusA bound to paused E. coli RNAP elongation complexes with and without a pause-enhancing hairpin in the RNA exit channel. The structures reveal four interactions between NusA and RNAP that suggest how NusA stimulates RNA folding, pausing, and termination. An asymmetric translocation intermediate of RNA and DNA converts the active site of the enzyme into an inactive state, providing a structural explanation for the inhibition of catalysis. Comparing RNAP at different stages of pausing provides insights on the dynamic nature of the process and the role of NusA as a regulatory factor.

HIV infection has long been known to result in dementia and other forms of neurocognitive deficits. The rate of HIV-associated dementia is decreasing, while mild forms of neurological impairments increase. Treatment of HIV infection has advanced, and patients are living longer, and are thus at a greater risk of cognitive decline. The HIV aging cohort is susceptible to neurocognitive impairment from other medical conditions that have a compounding effect on cognitive decline. The diagnosis of HIV-associated neurocognitive disorders involves identifying neurological dysfunction and then determining that HIV is the most probable cause. Implications for practice include early control of HIV replication and treatment of comorbid diseases.

Social stress can lead to the development of psychological problems ranging from exaggerated anxiety and depression to antisocial and violence-related behaviors. Increasing evidence suggests that the immune system is involved in responses to social stress in adulthood. For example, human studies show that individuals with high aggression traits display heightened inflammatory cytokine levels and dysregulated immune responses such as slower wound healing. Similar findings have been observed in patients with depression, and comorbidity of depression and aggression was correlated with stronger immune dysregulation. Therefore, dysregulation of the immune system may be one of the mediators of social stress that produces aggression and/or depression. Similar to humans, aggressive animals also show increased levels of several proinflammatory cytokines, however, unlike humans these animals are more protected frominfectious organisms and have faster wound healing than animals with low aggression. On the other hand, subordinate animals that receive repeated social defeat stress have been shown to develop escalated and dysregulated immune responses such as glucocorticoid insensitivity in monocytes. In this review we synthesize the current evidence in humans, non-human primates, and rodents to show a role for the immune system in responses to social stress leading to psychiatric problems such as aggression or depression. We argue that while depression and aggression represent two fundamentally different behavioral and physiological responses to social stress, it is possible that some overlapped, as well as distinct, pattern of immune signaling may underlie both of them. We also argue the necessity of studying animal models of maladaptive aggression induced by social stress (i.e., social isolation) for understanding neuro-immune mechanism of aggression, which may be relevant to human aggression.

Events with no charged particles produced between the two leading jets are studied in proton-proton collisions at root s = 7 TeV. The jets were required to have transverse momentum p(T)(jet) > 40 GeV and pseudorapidity 1.5 < vertical bar eta(jet)vertical bar < 4.7, and to have values of eta(jet) with opposite signs. The data used for this study were collected with the CMSdetector during low-luminosity running at the LHC, and correspond to an integrated luminosity of 8 pb(-1). Events with no charged particles with p(T) > 0.2GeV in the interval -1 < eta < 1 between the jets are observed in excess of calculations that assume no color-singlet exchange. The fraction of events with such a rapidity gap, amounting to 0.5-1% of the selected dijet sample, is measured as a function of the pT of the second-leading jet and of the rapidity separation between the jets. The data are compared to previous measurements at the Tevatron, and to perturbative quantum chromodynamics calculations based on the Balitsky-Fadin-Kuraev-Lipatov evolution equations, including different models of the non-perturbative gap survival probability.

Src family kinases (SFKs) coordinate the initiating and propagating activation signals in platelets, but it remains unclear how they are regulated. Here, we show that ablation of C-terminal Src kinase (Csk) and receptor-like protein tyrosine-phosphatase CD148 in mice results in a dramatic increase in platelet SFK activity, demonstrating that these proteins are essential regulators of platelet reactivity. Paradoxically, Csk/CD148-deficient mice exhibit reduced in vivo and ex vivo thrombus formation and increased bleeding following injury rather than a prothrombotic phenotype. This is a consequence of multiple negative feedback mechanisms, including downregulation of the immunoreceptor tyrosine-based activation motif (ITAM)- and hemi-ITAM-containing receptors glycoprotein VI (GPVI)-Fc receptor (FcR) gamma-chain and CLEC-2, respectively and upregulation of the immunoreceptor tyrosine-based inhibition motif (ITIM)-containing receptor G6b-B and its interaction with the tyrosine phosphatases Shp1 and Shp2. Results from an analog-sensitive Csk mouse model demonstrate the unconventional role of SFKs in activating ITIM signaling. This study establishes Csk and CD148 as critical molecular switches controlling the thrombotic and hemostatic capacity of platelets and reveals cell-intrinsic mechanisms that prevent pathological thrombosis from occurring.

The eukaryotic helicase is an 11-subunit machine containing an Mcm2-7 motor ring that encircles DNA, Cdc45 and the GINS tetramer, referred to as CMG (Cdc45, Mcm2-7, GINS). CMG is "built" on DNA at origins in two steps. First, two Mcm2-7 rings are assembled around duplex DNA at origins in G1 phase, forming the Mcm2-7 "double hexamer." In a second step, in S phase Cdc45 and GINS are assembled onto each Mcm2-7 ring, hence producing two CMGs that ultimately form two replication forks that travel in opposite directions. Here, we review recent findings about CMG structure and function. The CMG unwinds the parental duplex and is also the organizing center of the replisome: it binds DNA polymerases and other factors. EM studies reveal a 20-subunit core replisome with the leading Pol epsilon and lagging Pol alpha-primase on opposite faces of CMG, forming a fundamentally asymmetric architecture. Structural studies of CMG at a replication fork reveal unexpected details of how CMG engages the DNA fork. The structures of CMG and the Mcm2-7 double hexamer on DNA suggest a completely unanticipated process for formation of bidirectional replication forks at origins.

Background: Autosomal dominant anhidrotic ectodermal dysplasia with immune deficiency (AD EDA-ID) is caused by heterozygous point mutations at or close to serine 32 and serine 36 or N-terminal truncations in I kappa B alpha that impair its phosphorylation and degradation and thus activation of the canonical nuclear factor kappa light chain enhancer of activated B cells (NF-kappa B) pathway. The outcome of hematopoietic stem cell transplantation is poor in patients with AD EDA-ID despite achievement of chimerism. Mice heterozygous for the serine 32I mutation in I kappa B alpha have impaired noncanonical NF-kappa B activity and defective lymphorganogenesis. Objective: We sought to establish genotype-phenotype correlation in patients with AD EDA-ID. Methods: A disease severity scoring system was devised. Stability of I kappa B alpha mutants was examined in transfected cells. Immunologic, biochemical, and gene expression analyses were performed to evaluate canonical and noncanonical NF-kappa B signaling in skin-derived fibroblasts. Results: Disease severity was greater in patients with IkBa point mutations than in those with truncation mutations. IkBa point mutants were expressed at significantly higher levels in transfectants compared with truncation mutants. Canonical NF-kappa B-dependent IL-6 secretion and upregulation of the NF-kappa B subunit 2/p100 and RELB proto-oncogene, NF-kappa B subunit (RelB) components of the noncanonical NF-kappa B pathway were diminished significantly more in patients with point mutations compared with those with truncations. Noncanonical NF-kappa B-driven generation of the transcriptionally active p100 cleavage product p52 and upregulation of CCL20, intercellular adhesion molecule 1 (ICAM1), and vascular cell adhesion molecule 1 (VCAM1), which are important for lymphorganogenesis, were diminished significantly more in LPS plus alpha-lymphotoxin beta receptor-stimulated fibroblasts from patients with point mutations compared with those with truncations. Conclusions: I kappa B alpha point mutants accumulate at higher levels compared with truncation mutants and are associated with more severe disease and greater impairment of canonical and noncanonical NF-kappa B activity in patients with AD EDA-ID.