The rockefeller university

Interleukin (IL)-12 is composed of p35 and p40 subunits; in this case, IL-12p40 deficiency is a rare genetic etiology of Mendelian susceptibility to mycobacterial disease. Salmonellosis has been reported in almost half of these patients and mostly present in recurrent extraintestinal form. In this report, we described an 18-month-old boy with absence of IL-12p40 production suffering from chronic disseminated nontyphoidal salmonellosis. To the best of our knowledge, this is the first-reported case.

The similar to 9.5 kilobase HIV-1 genome contains RNA sequences and structures that control many aspects of viral replication, including transcription, splicing, nuclear export, translation, packaging and reverse transcription. Nonetheless, chemical probing and other approaches suggest that the HIV-1 genome may contain many more RNA secondary structures of unknown importance and function. To determine whether there are additional, undiscovered cis-acting RNA elements in the HIV-1 genome that are important for viral replication, we undertook a global silent mutagenesis experiment. Sixteen mutant proviruses containing clusters of similar to 50 to similar to 200 synonymous mutations covering nearly the entire HIV-1 protein coding sequence were designed and synthesized. Analyses of these mutant viruses resulted in their division into three phenotypic groups. Group 1 mutants exhibited near wild-type replication, Group 2 mutants exhibited replication defects accompanied by perturbed RNA splicing, and Group 3 mutants had replication defects in the absence of obvious splicing perturbation. The three phenotypes were caused by mutations that exhibited a clear regional bias in their distribution along the viral genome, and those that caused replication defects all caused reductions in the level of unspliced RNA. We characterized in detail the underlying defects for Group 2 mutants. Second-site revertants that enabled viral replication could be derived for Group 2 mutants, and generally contained point mutations that reduced the utilization of proximal splice sites. Mapping of the changes responsible for splicing perturbations in Group 2 viruses revealed the presence of several RNA sequences that apparently suppressed the use of cryptic or canonical splice sites. Some sequences that affected splicing were diffusely distributed, while others could be mapped to discrete elements, proximal or distal to the affected splice site(s). Overall, our data indicate complex negative regulation of HIV-1 splicing by RNA elements in various regions of the HIV-1 genome that enable balanced splicing and viral replication.

Nuclear RNA metabolism is influenced by protein complexes connecting to both RNA-productive and -destructive pathways. The ZC3H18 protein binds the cap-binding complex (CBC), universally present on capped RNAs, while also associating with the nuclear exosome targeting (NEXT) complex, linking toRNAdecay. To dissect ZC3H18 function, we conducted interaction screening and mutagenesis of the protein, which revealed a phosphorylationdependent isoform. Surprisingly, the modified region of ZC3H18 associates with core histone proteins. Further examination of ZC3H18 function, by genome-wide analyses, demonstrated its impact on transcription of a subset of protein-coding genes. This activity requires the CBC-interacting domain of the protein, with some genes being also dependent on the NEXT-and/or histone-interacting domains. Our data shed light on the domain requirements of a protein positioned centrally in nuclear RNA metabolism, and they suggest that post-translational modification may modulate its function.

Isolated photons with high transverse energy have been studied in deep in-elastic ep scattering with the ZEUS detector at HERA, using an integrated luminosity of 326 pb(-1) in the range of exchanged-photon virtuality 10-350 GeV2. Outgoing isolated photons with transverse energy 4 < E-T(gamma) < 15 GeV and pseudorapidity -0.7 < eta(gamma) < 0.9 were measured with accompanying jets having transverse energy and pseudorapidity 2 : 5 < E-T(jet) < 35 GeV and -1.5 < eta(jet) < 1.8, respectively. Differential cross sections are presented for the following variables: the fraction of the incoming photon energy and momentum that is transferred to the outgoing photon and the leading jet; the fraction of the incoming proton energy transferred to the photon and leading jet; the differences in azimuthal angle and pseudorapidity between the outgoing photon and the leading jet and between the outgoing photon and the scattered electron. Comparisons are made with theoretical predictions: a leading-logarithm Monte Carlo simulation, a next-to-leading-order QCD prediction, and a prediction using the k(T)-factorisation approach.

Spontaneous otoacoustic emissions (SOAEs) are a universal feature of all classes of tetrapods. Although the generation mechanism of SOAEs are incompletely understood, these emissions are undoubtedly associated with the active process of the inner ear. In most lizards, unlike mammals and amphibians, robust SOAEs can ordinarily be detected from both ears. In this work, we investigated the interactions between emissions recorded simultaneously from the two ears of tokay geckos. We found that the frequency spectra of SOAEs from both ears of an individual animal are partially correlated: the peaks of several emissions occur at identical frequencies. To investigate the underlying mechanisms of these identical-frequency SOAEs, we perturbed the emissions from one or both ears by manipulating the pressure in the ear canals or by decreasing the local temperature in the vicinity of one inner ear. Suppression of SOAEs due to large positive pressures revealed that some identical-frequency emissions were generated unilaterally, whereas others were contributed by both ears at identical or slightly different frequencies. These bilaterally generated SOAEs became desynchronized as their frequency detuning grew sufficiently large, a phenomenon consistent with the synchronization of two active oscillators. Finally, we found that manipulations of the volume of the oral cavity or altering the impedance of the tympanum strongly affected the synchronization of SOAEs. These findings agreed with previous studies suggesting that the tokay gecko, like other lizards, exhibits strong acoustic coupling between its tympani through the oral cavity.

The recent development of DNA sequencing technology has given rise to many statistical methods for Rare Variant Association Studies (RVASs), such as burden and sequence kernel association tests. However, these methods, which usually require large samples, can lose power in association studies with small samples. In this study, we propose two statistical approaches applicable for RVASs when the sample size is not large. Our approaches are based on the Hamming distance, which compares the dissimilarity of Single Nucleotide Polymorphisms (SNPs) components between cases and controls. Existing Hamming distance-based methods mainly analyse common variants. For rare variant data with a small sample size, we extended two existing methods by using the weight based on minor allele frequency. Through simulation studies, we show that our proposed approaches control type 1 error rates and are more powerful even when given very small sample sizes. They also work well regardless of the direction of causal SNP effects. Applying these methods to real data, we confirmed that they identified true causal genes well. Based on the results of this study, we firmly believe that our proposed methods are powerful for small sample data.

While the cell-intrinsic pathways governing beige adipocyte development and phenotype have been increasingly delineated, comparatively little is known about how beige adipocytes interact with other cell types in fat. Here, we introduce a whole-tissue clearing method for adipose that permits immunolabeling and three-dimensional profiling of structures including thermogenic adipocytes and sympathetic innervation. We found that tissue architecture and sympathetic innervation differ significantly between subcutaneous and visceral depots. Subcutaneous fat demonstrates prominent regional variation in beige fat biogenesis with localization of UCP1(+) beige adipocytes to areas with dense sympathetic neurites. We present evidence that the density of sympathetic projections is dependent on PRDM16 in adipocytes, providing another potential mechanism underlying the metabolic benefits mediated by PRDM16. This powerful imaging tool highlights the interaction of tissue components during beige fat biogenesis and reveals a previously undescribed mode of regulation of the sympathetic nervous system by adipocytes.

The CDF and D0 experiments at the Fermilab Tevatron have measured the asymmetry between yields of forward- and backward-produced top and antitop quarks based on their rapidity difference and the asymmetry between their decay leptons. These measurements use the full data sets collected in proton-antiproton collisions at a center-of-mass energy of root s = 1.96 TeV. We report the results of combinations of the inclusive asymmetries and their differential dependencies on relevant kinematic quantities. The combined inclusive asymmetry is A(FB)(t (t) over bar) = 0.128 +/- 0.025. The combined inclusive and differential asymmetries are consistent with recent standard model predictions.

Background: Cannabis use disorders (CUDs) cause substantial neuropsychiatric morbidity and comorbidity. There is evidence for gender-based differences in CUDs, for instance, a greater prevalence in males than in females. The main active component of cannabis is delta 9-tetrahydrocannabinol (delta 9-THC), a partial agonist of the cannabinoid type 1 receptor. Preclinical studies show that genetic or pharmacological manipulation of the kappa opioid receptor/dynorphin system modulates the effects of delta 9-THC. Methods: In this case-control study of adult African Americans (n=476; 206 females, 270 males), we examined the association of the functional prodynorphin 68 bp (PDYN 68 bp) promoter repeats with categorical diagnoses of cannabis dependence (Diagnostic and Statistical Manual of Mental Disorders-IV criteria), as well as with a rapid dimensional measure of maximum lifetime cannabis exposure (the Kreek-McHugh-Schluger-Kellogg cannabis scale). Results: The PDYN 68 bp genotype (examined as short-short [SS], short-long [SL], or long-long [LL], based on the number of repeats) was not significantly associated with categorical cannabis-dependence diagnoses, either in males or in females. However, in males, the PDYN 68 bp SS+SL genotype was associated with both greater odds of any use of cannabis (p<0.05) and earlier age of first cannabis use, compared to the LL genotype (ie, 15 versus 16.5 years of age; p<0.045). Males in the SS+SL group also had greater odds of high lifetime exposure to cannabis, compared to the LL group (p<0.045). Of interest, none of the aforementioned genetic associations were significant in females. Conclusion: This study provides the first data on how the PDYN 68 bp genotype is associated with gender-specific patterns of exposure to cannabis. Overall, this study shows that PDYN 68 bp polymorphisms affect behaviors involved in early stages of nonmedical cannabis use and potentially lead to increasing self-exposure. These data may eventually lead to improvements in personalized medicine for the prevention and treatment of highly prevalent CUDs and neuropsychiatric comorbidities.

Purpose: We conducted a phase I vaccine trial to determine safety, toxicity, and immunogenicity of autologous Langerhans-type dendritic cells (LCs), electroporated with murine tyrosinase-related peptide-2 (mTRP2) mRNA in patients with resected AJCC stage IIB, IIC, III, or IV (MIa) melanoma. Experimental Design: Nine patients received a priming immunization plus four boosters at three week intervals. Vaccines comprised 10 x 10(6) mRNA-electroporated LCs, based on absolute number of CD83(+)CD86(bright)HLA-DR(bright)CD14(neg) LCs by flow cytometry. Initial vaccines used freshly generated LCs, whereas booster vaccines used viably thawed cells from the cryopreserved initial product. Post-vaccination assessments included evaluation of delayed-type hypersensitivity (DTH) reactions after booster vaccines and immune response assays at one and three months after the final vaccine. Results: All patients developed mild DTH reactions at injection sites after booster vaccines, but there were no toxicities exceeding grade 1 (CTCAE, v4.0). At one and three months post-vaccination, antigen-specific CD4 and CD8 T cells increased secretion of proinflammatory cytokines (IFN-, IL-2, and TNF-), above pre-vaccine levels, and also upregulated the cytotoxicity marker CD107a. Next-generation deep sequencing of the TCR-V- CDR3 documented fold-increases in clonality of 2.11 (range 0.85-3.22) for CD4 and 2.94 (range 0.98-9.57) for CD8 T cells at one month post-vaccines. Subset analyses showed overall lower fold-increases in clonality in three patients who relapsed (CD4: 1.83, CD8: 1.54) versus non-relapsed patients (CD4: 2.31, CD8: 3.99). Conclusions: TRP2 mRNA-electroporated LC vaccines are safe and immunogenic. Responses are antigen-specific in terms of cytokine secretion, cytolytic degranulation, and increased TCR clonality, which correlates with clinical outcomes.