Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation.

Background: Differentiation of metazoan cells requires execution of different gene expression programs but recent single-cell transcriptome profiling has revealed considerable variation within cells of seeming identical phenotype. This brings into question the relationship between transcriptome states and cell phenotypes. Additionally, single-cell transcriptomics presents unique analysis challenges that need to be addressed to answer this question.

Rear seat safety: Variation in protection by occupant, crash and vehicle characteristics.

Objectives: Current information on the safety of rear row occupants of all ages is needed to inform further advances in rear seat restraint system design and testing. The objectives of this study were to describe characteristics of occupants in the front and rear rows of model year 2000 and newer vehicles involved in crashes and determine the risk of serious injury for restrained crash-involved rear row occupants and the relative risk of fatal injury for restrained rear row vs. front passenger seat occupants by age group, impact direction, and vehicle model year.

Expression and roles of CCN2 in dental epithelial cells.

Connective tissue growth factor (CCN2) regulates diverse cellular functions, including tooth development. In order to delineate the precise role of CCN2 in the epithelium during odontogenesis, we investigated how it is expressed and what roles it may have in primary cultures of epithelial cells derived from developing tooth germ of the bovine fetus. Ccn2 mRNA and protein were strongly expressed in the inner dental epithelium, which is consistent with the expression of transforming growth factor-β2 mRNA and proliferating cell nuclear antigen.

Functional diversification and specialization of cytosolic 70-kDa heat shock proteins.

A fundamental question in molecular evolution is how protein functional differentiation alters the ability of cells and organisms to cope with stress and survive. To answer this question we used two paralogous Hsp70s from mouse and explored whether these highly similar cytosolic molecular chaperones, which apart their temporal expression have been considered functionally interchangeable, are differentiated with respect to their lipid-binding function. We demonstrate that the two proteins bind to diverse lipids with different affinities and therefore are functionally specialized.

DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions.

FOXP3 is a lineage-specific transcription factor that is required for regulatory T cell development and function. In this study, we determined the crystal structure of the FOXP3 forkhead domain bound to DNA. The structure reveals that FOXP3 can form a stable domain-swapped dimer to bridge DNA in the absence of cofactors, suggesting that FOXP3 may play a role in long-range gene interactions.

Crk and CrkL are required for cell transformation by v-fos and v-ras.

Crk and CrkL are SH2- and SH3-containing cytosolic adaptor proteins that can induce anchorage-independent growth of fibroblasts. Crk and CrkL play key roles in maintaining cytoskeletal integrity, cell motility and migration. We investigated the role of these two proteins in oncogenic transformation induced by v-fos and v-ras oncogenes using cell lines and fibroblasts carrying conditional alleles of Crk or CrkL.

Sirt1-deficient mice have hypogonadotropic hypogonadism due to defective GnRH neuronal migration.

Hypogonadatropic hypogonadism (HH) can be acquired through energy restriction or may be inherited as congenital hypogonadotropic hypogonadism and its anosmia-associated form, Kallmann's syndrome. Congenital hypogonadotropic hypogonadism is associated with mutations in a group of genes that impact fibroblast growth factor 8 (FGF8) function. The Sirt1 gene encodes a nicotinamide adenine dinucleotide-dependent histone deacetylase that links intracellular metabolic stress to gene expression.

Adjuvant therapies for HIV-associated neurocognitive disorders.

Objective: HIV-associated neurocognitive disorder (HAND) is a frequent and heterogeneous complication of HIV, affecting nearly 50% of infected individuals in the combined antiretroviral therapy (cART) era. This is a particularly devastating statistic because the diagnosis of HAND confers an increased risk of HIV-associated morbidity and mortality in affected patients. While cART is helpful in the treatment of the more severe forms of HAND, there is a therapeutic gap in the milder forms of HAND, where cART is less effective.

mtDNA Variation and Analysis Using Mitomap and Mitomaster.

The Mitomap database of human mitochondrial DNA (mtDNA) information has been an important compilation of mtDNA variation for researchers, clinicians and genetic counselors for the past twenty-five years. The Mitomap protocol shows how users may look up human mitochondrial gene loci, search for public mitochondrial sequences, and browse or search for reported general population nucleotide variants as well as those reported in clinical disease. Within Mitomap is the powerful sequence analysis tool for human mitochondrial DNA, Mitomaster.

Immune markers predictive of neuropsychiatric symptoms in HIV-infected youth.

The purpose of this study was to evaluate possible associations between systemic immune dysregulation (activated CD8(+) T lymphocytes and natural killer [NK] cell count/function) and symptoms of depression and anxiety in youth with horizontally (behaviorally) acquired HIV infection. This secondary analysis of a previously collected prospective cohort included 323 youth with horizontally acquired HIV infection enrolled in the Reaching for Excellence in Adolescent Care and Health (REACH) cohort of the NICHD/NIH. A multivariable linear regression model with generalized estimating equations for intraindividual repeated measures was used to examine the relationship between flow cytometry measurements of activated T lymphocytes (CD8(+) CD38(+)), NK cells (CD3(-) CD16(+) CD56(+)), and NK cell functional activity (lytic units per NK cell and per peripheral blood mononuclear cell) and their association with subsequent symptoms of depression (Center for Epidemiologic Studies depression scale) and anxiety (Revised Children's Manifest Anxiety Scale).

Mitochondrial dysfunction in peripheral blood mononuclear cells in pediatric septic shock.

Objectives: Mitochondrial dysfunction in peripheral blood mononuclear cells has been linked to immune dysregulation and organ failure in adult sepsis, but pediatric data are limited. We hypothesized that pediatric septic shock patients exhibit mitochondrial dysfunction within peripheral blood mononuclear cells which in turn correlates with global organ injury.

Design: Prospective observational study.

Modeling and simulation approach to support dosing and study design requirements for treating HIV-related neuropsychiatric disease with the NK1-R antagonist aprepitant.

Psychiatric illness is common in HIV-infected patients and underlines the importance for screening not only for cognitive impairment but also for co-morbid mental disease. The rationale for combining immunomodulatory neurokinin- 1 receptor (NK1-R) antagonists with combined antiretroviral therapy (cART) is based on multimodal pharmacologic mechanisms. The NK1-R antagonist aprepitant's potential utility as a drug for depression is complicated by >99.

Extending the value of police crash reports for traffic safety research: collecting supplemental data via surveys of drivers.

Background: Police crash reports have been used to advance motor vehicle safety research, though their value is limited by their focus on the crash event rather than outcomes of the crash.

Objective: To develop and evaluate the effect of enhanced recruitment methods, including a monetary incentive, on response rates of drivers identified on police reports in a national MVC surveillance system.

Methods: The National Automotive Sampling System-General Estimates System (NASS-GES) was used to identify passenger vehicle crashes between 1 July and 30 October 2012 involving drivers ≥16 years old with at least one child occupant ≤17 years old.

Genetic susceptibility to type 2 diabetes and obesity: follow-up of findings from genome-wide association studies.

Elucidating the underlying genetic variations influencing various complex diseases is one of the major challenges currently facing clinical genetic research. Although these variations are often difficult to uncover, approaches such as genome-wide association studies (GWASs) have been successful at finding statistically significant associations between specific genomic loci and disease susceptibility. GWAS has been especially successful in elucidating genetic variants that influence type 2 diabetes (T2D) and obesity/body mass index (BMI).

Regulation of T cell differentiation and alloimmunity by the cyclin-dependent kinase inhibitor p18ink4c.

Cellular proliferation in response to mitogenic stimuli is negatively regulated by the Cip/Kip and the Ink4 families of cyclin-dependent kinase (CDK) inhibitors. Several of these proteins are elevated in anergic T cells, suggesting a potential role in the induction or maintenance of tolerance. Our previous studies showed that p27kip1 is required for the induction of T cell anergy and transplantation tolerance by costimulatory blockade, but a role for Ink4 proteins in these processes has not been established.

Rectal microRNAs are perturbed in pediatric inflammatory bowel disease of the colon.

Background And Aims: Changes in intestinal microRNAs have been reported in adult patients with ulcerative colitis or Crohn's disease. The goal of this study was to identify changes in microRNA expression associated with colitis in children with inflammatory bowel disease.

Methods: Rectal mucosal biopsies (n = 50) and blood samples (n = 47) were collected from patients with known or suspected inflammatory bowel disease undergoing endoscopy.

New roles for cyclin-dependent kinases in T cell biology: linking cell division and differentiation.

The proliferation of a few antigen-reactive lymphocytes into a large population of effector cells is a fundamental property of adaptive immunity. The cell division that fuels this process is driven by signals from antigen, co-stimulatory molecules and growth factor receptors, and is controlled by the cyclin-dependent kinase (CDK) cascade. In this Opinion article, we discuss how the CDK cascade provides one potential link between cell division and differentiation through the phosphorylation of immunologically relevant transcription factors, and how components of this pathway might ultimately participate in the decision between tolerance and immunity.

HIV infection of macrophages is enhanced in the presence of increased expression of CD163 induced by substance P.

Activation of NK1R by SP contributes to increased HIV-1 infection in macrophages. The scavenger receptor CD163 is expressed on cells of monocyte-macrophage origin. Our main goal was to determine if there is interplay among SP, CD163 expression, and HIV infection in macrophages.

Mitochondrial DNA variant in COX1 subunit significantly alters energy metabolism of geographically divergent wild isolates in Caenorhabditis elegans.

Mitochondrial DNA (mtDNA) sequence variation can influence the penetrance of complex diseases and climatic adaptation. While studies in geographically defined human populations suggest that mtDNA mutations become fixed when they have conferred metabolic capabilities optimally suited for a specific environment, it has been challenging to definitively assign adaptive functions to specific mtDNA sequence variants in mammals. We investigated whether mtDNA genome variation functionally influences Caenorhabditis elegans wild isolates of distinct mtDNA lineages and geographic origins.

Proof of principle for epitope-focused vaccine design.

Vaccines prevent infectious disease largely by inducing protective neutralizing antibodies against vulnerable epitopes. Several major pathogens have resisted traditional vaccine development, although vulnerable epitopes targeted by neutralizing antibodies have been identified for several such cases. Hence, new vaccine design methods to induce epitope-specific neutralizing antibodies are needed.

Crk1/2 and CrkL form a hetero-oligomer and functionally complement each other during podocyte morphogenesis.

Activation of the slit diaphragm protein nephrin induces actin cytoskeletal remodeling, resulting in lamellipodia formation in podocytes in vitro in a phosphatidylinositol-3 kinase-, focal adhesion kinase-, Cas-, and Crk1/2-dependent fashion. In mice, podocyte-specific deletion of Crk1/2 prevents or attenuates foot process effacement in two models of podocyte injury. This suggests that cellular mechanisms governing lamellipodial protrusion in vitro are similar to those in vivo during foot process effacement.

Evidence of native α-synuclein conformers in the human brain.

α-Synuclein aggregation is central to the pathogenesis of several brain disorders. However, the native conformations and functions of this protein in the human brain are not precisely known. The native state of α-synuclein was probed by gel filtration coupled with native gradient gel separation, an array of antibodies with non-overlapping epitopes, and mass spectrometry.

A liquid chromatography-mass spectrometry assay for quantification of Exendin[9-39] in human plasma.

Exendin[9-39] is a glucagon-like peptide-1 receptor (GLP-R) antagonist and a potential therapeutic drug for treatment of congenital hyperinsulism by lowering insulin concentration in plasma. A specific and sensitive LC-MS/MS method was validated for quantification of Exendin[9-39] in human plasma. Exendin[9-39] and the stable isopically labeled internal standard eluted at 9.

Essential roles of Crk and CrkL in fibroblast structure and motility.

Cytosolic proteins containing SH2 and SH3 domains, such as Crk and Crk-like (CrkL), are broadly expressed adapters that interact with a variety of proteins to fulfill key roles in signal transduction pathways triggered by activation of receptor and non-receptor tyrosine kinases. Crk and CrkL are similar to each other in structure and biochemical function, although they provide both distinct, as well as overlapping, biological roles during development. We developed a systematic approach to investigate Crk family functions at the cellular level by generating a conditional knock-out system for ablation of Crk and CrkL in cultured fibroblasts.