Genomic resources for the study of neuropsychiatric disorders.

The National Institute of Mental Health (NIMH) has made sustained investments in the development of genomic resources over the last two decades. These investments have led to the development of the largest biorepository for psychiatric genetics as a centralized national resource. In the realm of genomic resources, NIMH has been supporting large team science (TS) consortia focused on gene discovery, fine mapping of loci, and functional genomics using state-of-the-art technologies. The scientific output from these efforts has not only begun to transform our understanding of the genetic architecture of neuropsychiatric disorders, but it has also led to a broader cultural change among the investigator community towards deeper collaborations and broad pre-publication sharing of data and resources. The NIMH supported efforts have led to a vast increase in the amount of genetic and genomic resources available to the mental health research community. Here we provide an account of the existing resources and estimates of the scale and scope of what will be available in the near future. All biosamples and data described are intended for broad sharing with researchers worldwide, as allowed by the subject consent and applicable laws.

A neurogenetic model for the study of schizophrenia spectrum disorders: the International 22q11.2 Deletion Syndrome Brain Behavior Consortium.

Rare copy number variants contribute significantly to the risk for schizophrenia, with the 22q11.2 locus consistently implicated. Individuals with the 22q11.2 deletion syndrome (22q11DS) have an estimated 25-fold increased risk for schizophrenia spectrum disorders, compared to individuals in the general population. The International 22q11DS Brain Behavior Consortium is examining this highly informative neurogenetic syndrome phenotypically and genomically. Here we detail the procedures of the effort to characterize the neuropsychiatric and neurobehavioral phenotypes associated with 22q11DS, focusing on schizophrenia and subthreshold expression of psychosis. The genomic approach includes a combination of whole-genome sequencing and genome-wide microarray technologies, allowing the investigation of all possible DNA variation and gene pathways influencing the schizophrenia-relevant phenotypic expression. A phenotypically rich data set provides a psychiatrically well-characterized sample of unprecedented size (n=1616) that informs the neurobehavioral developmental course of 22q11DS. This combined set of phenotypic and genomic data will enable hypothesis testing to elucidate the mechanisms underlying the pathogenesis of schizophrenia spectrum disorders.

The genetic architecture of pediatric cognitive abilities in the Philadelphia Neurodevelopmental Cohort.

The objective of this analysis was to examine the genetic architecture of diverse cognitive abilities in children and adolescents, including the magnitude of common genetic effects and patterns of shared and unique genetic influences. Subjects included 3689 members of the Philadelphia Neurodevelopmental Cohort, a general population sample comprising those aged 8-21 years who completed an extensive battery of cognitive tests. We used genome-wide complex trait analysis to estimate the SNP-based heritability of each domain, as well as the genetic correlation between all domains that showed significant genetic influence. Several of the individual domains suggested strong influence of common genetic variants (for example, reading ability, h(2)g=0.43, P=4e-06; emotion identification, h(2)g=0.36, P=1e-05; verbal memory, h(2)g=0.24, P=0.005). The genetic correlations highlighted trait domains that are candidates for joint interrogation in future genetic studies (for example, language reasoning and spatial reasoning, r(g)=0.72, P=0.007). These results can be used to structure future genetic and neuropsychiatric investigations of diverse cognitive abilities.

A possible vulnerability locus for bipolar affective disorder on chromosome 21q22.3.

In a preliminary genome scan of 47 bipolar disorder families, we detected in one family a lod score of 3.41 at the PFKL locus on chromosome 21q22.3. The lod score is robust to marker allele frequencies, phenocopy rates and age-dependent penetrance, and remains strongly positive with changes in affection status. Fourteen other markers in 21q22.3 were tested on this family, with largely positive lod scores. Five of the other 46 families also show positive, but modest lod scores with PFKL. When all 47 families are analysed together, there is little support for linkage to PFKL under homogeneity or heterogeneity using lod score analysis, but the model-free affected-pedigree-member method yields statistically significant results (p < 0.0003). Our results are consistent with the presence of a gene in 21q22.3 predisposing at least one family to bipolar disorder.

Immunogenic and tolerogenic signatures in human immunodeficiency virus (HIV)-infected controllers compared with progressors and a conversion strategy of virus control.

Epidemiological studies have identified a small cohort of controllers of human immunodeficiency virus (HIV)-1 infection, who without treatment have no detectable virus, and others who progress at a variable rate. The objective of this study was to distinguish immune signatures in HIV controllers and progressors, by evaluating tolerogenic and immunogenic factors in untreated HIV-1 infected individuals. The recruited population was divided into putative elite controllers (PEC), long-term non-progressors (LTNP), normal progressors (NP) and fast progressors (FP). The proportion of regulatory T cells [T(regs) , CD4+ CD25+ forkhead box P3 (FoxP3+)], programmed death (PD)-1 and cytotoxic T lymphocyte antigen (CTLA)-inhibitory molecules and CD40L, CD69 and Ki67 activation markers were evaluated in peripheral blood mononuclear cells (PBMC) by flow cytometry. Significant differences were found between HIV controllers and HIV progressors, with up-regulation of T(regs) , PD-1 and CTLA-4 and decrease of CD40L expression in progressors compared with controllers. Expression of CD40L and concentrations of interleukin (IL)-6, CCL-3, and CCL-4 were significantly higher in PEC and LTNP than in NP and FP. In an attempt to convert immune signatures of progressors to those of controllers, seven agents were used to stimulate PBMC from the four cohorts. Treatment with CD40L and IL-4 or PD-1 antibodies in vitro were most effective in converting the immune signatures of progressors to those observed in controllers by down-regulating T(regs) and up-regulating CD40L expression in CD4+ T cells. The conversion concept merits translation to in vivo immune control of HIV infection.

Genetic repositories for the study of major psychiatric conditions: what do we know about ethnic minorities' genetic vulnerability?

In spite of considerable efforts, no genes of major effect have been found across an entire diagnostic category in psychiatry. Possible reasons for this may include difficulties in defining the phenotype, the complex relationship between genotype and gene expression and population stratification. This last problem has often been managed by restricting genetic sampling to only one ethnic group. An unintended consequence of using this strategy is that the major repositories of genetic material for the study of psychiatric conditions in the United States suffer from a paucity of genetic samples from non-Caucasian groups. Thus, these groups are being relatively understudied in terms of the genetic antecedents to psychiatric disease. The authors provide solutions including the need to augment the representation of African-American, Latino and Asian-Americans among research participants; a more nuanced approach to identify ancestry; and the development of analytic and genetic strategies to handle the issue of ethnic heterogeneity in samples.

Allo-immunization elicits CD8+ T cell-derived chemokines, HIV suppressor factors and resistance to HIV infection in women.

We assessed the potential for an allogeneic-based vaccine against HIV infection in women who were allo-immunized with their partners' mononuclear leucocytes to prevent spontaneous recurrent abortion. Within 1 month of allo-immunization, there was significant upregulation in the concentrations of CD8 cell-derived suppressor factor activity, RANTES, and macrophage inflammatory proteins 1alpha and 1beta. Allo-immunization also downregulated the proportion of cells with CCR5 and CXCR4 receptors. We also found a dose-dependent decrease in HIV infectivity of CD4+ cells in vitro after allo-immunization with both primary and T-cell line adapted HIV-1. This study provides a rational basis for an alternative or complementary strategy of allo-immunization against HIV infection.

Characterization of a recombinant plant monoclonal secretory antibody and preventive immunotherapy in humans.

A functional comparison was made between a monoclonal secretory antibody generated in transgenic plants and its parent murine IgG antibody.The affinity constants of both antibodies for a Streptococcus mutans adhesion protein were similar. However the secretory antibody had a higher functional affinity due to its dimeric structure. In the human oral cavity, the secretory antibody survived for up to three days, compared with one day for the IgG antibody. The plant secretory antibody afforded specific protection in humans against oral streptococcal colonization for at least four months. We demonstrate that transgenic plants can be used to produce high affinity, monoclonal secretory antibodies that can prevent specific microbial colonization in humans. These findings could be extended to the immunotherapeutic prevention of other mucosal infections in humans and animals.

Protective mucosal immunity elicited by targeted iliac lymph node immunization with a subunit SIV envelope and core vaccine in macaques.

Prevention of sexually transmitted HIV infection was investigated in macaques by immunization with a recombinant SIV (simian immunodeficiency virus) envelope gp 120 and core p27 vaccine. In two independent series of experiments, we used the novel targeted iliac lymph node (TILN) route of immunization, aiming close to the iliac lymph nodes draining the genitorectal mucosa. Rectal challenge with the SIVmac 32H J5 molecular clone in two series induced total protection in four out of seven macaques immunized by TILN, compared with infection in 13 of 14 unimmunized macaques or immunized by other routes (P = 0.025). The remaining three macaques showed either a decrease in viral load ( > 90%) or transient viremia, indicating that all seven TILN-immunized macaques showed total or partial protection (P = 0.001). Protection was associated with significant increase in the iliac lymph nodes of IgA antibody-secreting cells to p27 (P < 0.02), CD8-suppressor factor (P < 0.01), and the chemokines RANTES and MIP-1 beta (P < 0.01).

Innate immunity and HIV-1 infection.

HIV-1 is predominantly transmitted through mucosal tissues, targeting CD4(+)CCR5(+) T cells, 50% of which are destroyed within 2 weeks of infection. Conventional vaccination strategies have so far failed to prevent HIV-1 infection. Neither antibodies nor cytotoxic lymphocytes are capable of mounting a sufficiently rapid immune response to prevent early destruction of these cells. However, innate immunity is an early-response system, largely independent of prior encounter with a pathogen. Innate immunity can be classified into cellular, extracellular, and intracellular components, each of which is exemplified in this review by γδ T cells, CC chemokines, and APOBEC3G, respectively. First, γδ T cells are found predominantly in mucosal tissues and produce cytokines, CC chemokines, and antiviral factors. Second, the CC chemokines CCL-3, CCL-4, and CCL-5 can be upregulated by immunization of macaques with SIVgp120 and gag p27, and these can bind and downmodulate CCR5, thereby inhibiting HIV-1 entry into the host cells. Third, APOBEC3G is generated and maintained following rectal mucosal immunization in rhesus macaques for over 17 weeks, and the innate anti-SIV factor is generated by CD4(+)CD95(+)CCR7(-) effector memory T cells. Thus, innate anti-HIV-1 or SIV immunity can be linked with immune memory, mediated by CD4(+) T cells generating APOBEC3G. The multiple innate functions may mount an early anti-HIV-1 response and either prevent viral transmission or contain the virus until an effective adaptive immune response develops.

Generation and assembly of secretory antibodies in plants.

Four transgenic Nicotiana tabacum plants were generated that expressed a murine monoclonal antibody kappa chain, a hybrid immunoglobulin A-G heavy chain, a murine joining chain, and a rabbit secretory component, respectively. Successive sexual crosses between these plants and filial recombinants resulted in plants that expressed all four protein chains simultaneously. These chains were assembled into a functional, high molecular weight secretory immunoglobulin that recognized the native streptococcal antigen I/II cell surface adhesion molecule. In plants, single cells are able to assemble secretory antibodies, whereas two different cell types are required in mammals. Transgenic plants may be suitable for large-scale production of recombinant secretory immunoglobulin A for passive mucosal immunotherapy. Plant cells also possess the requisite mechanisms for assembly and expression of other complex recombinant protein molecules.

Induction of mucosal and systemic immunity to a recombinant simian immunodeficiency viral protein.

Heterosexual transmission through the cervico-vaginal mucosa is the principal route of human immunodeficiency virus (HIV) infection in Africa and is increasing in the United States and Europe. Vaginal immunization with simian immunodeficiency virus (SIV) had not yet been studied in nonhuman primates. Immune responses in macaques were investigated by stimulation of the genital and gut-associated lymphoid tissue with a recombinant, particulate SIV antigen. Vaginal, followed by oral, administration of the vaccine elicited three types of immunity: (i) gag protein p27-specific, secretory immunoglobulin A (IgA) and immunoglobulin G (IgG) in the vaginal fluid, (ii) specific CD4+ T cell proliferation and helper function in B cell p27-specific IgA synthesis in the genital lymph nodes, and (iii) specific serum IgA and IgG, with CD4+ T cell proliferative and helper functions in the circulating blood.

Role of defects in determining the magnetic ground state of ytterbium titanate.

Pyrochlore systems are ideally suited to the exploration of geometrical frustration in three dimensions, and their rich phenomenology encompasses topological order and fractional excitations. Classical spin ices provide the first context in which it is possible to control emergent magnetic monopoles, and anisotropic exchange leads to even richer behaviour associated with large quantum fluctuations. Whether the magnetic ground state of Yb2Ti2O7 is a quantum spin liquid or a ferromagnetic phase induced by a Higgs transition appears to be sample dependent. Here we have determined the role of structural defects on the magnetic ground state via the diffuse scattering of neutrons. We find that oxygen vacancies stabilise the spin liquid phase and the stuffing of Ti sites by Yb suppresses it. Samples in which the oxygen vacancies have been eliminated by annealing in oxygen exhibit a transition to a ferromagnetic phase, and this is the true magnetic ground state.

A synthetic peptide adhesion epitope as a novel antimicrobial agent.

The earliest step in microbial infection is adherence by specific microbial adhesins to the mucosa of the oro-intestinal, nasorespiratory, or genitourinary tract. We inhibited binding of a cell surface adhesin of Streptococcus mutans to salivary receptors in vitro, as measured by surface plasmon resonance, using a synthetic peptide (p1025) corresponding to residues 1025-1044 of the adhesin. Two residues within p1025 that contribute to binding (Q1025, E1037) were identified by site-directed mutagenesis. In an in vivo human streptococcal adhesion model, direct application of p1025 to the teeth prevented recolonization of S. mutans but not Actinomyces, as compared with a control peptide or saline. This novel antimicrobial strategy, applying competitive peptide inhibitors of adhesion, may be used against other microorganisms in which adhesins mediate colonization of mucosal surfaces.

Energy partition, scale by scale, in magnetic Archimedes Coriolis weak wave turbulence.

Magnetic Archimedes Coriolis (MAC) waves are omnipresent in several geophysical and astrophysical flows such as the solar tachocline. In the present study, we use linear spectral theory (LST) and investigate the energy partition, scale by scale, in MAC weak wave turbulence for a Boussinesq fluid. At the scale k^{-1}, the maximal frequencies of magnetic (Alfvén) waves, gravity (Archimedes) waves, and inertial (Coriolis) waves are, respectively, V_{A}k,N, and f. By using the induction potential scalar, which is a Lagrangian invariant for a diffusionless Boussinesq fluid [Salhi et al., Phys. Rev. E 85, 026301 (2012)PLEEE81539-375510.1103/PhysRevE.85.026301], we derive a dispersion relation for the three-dimensional MAC waves, generalizing previous ones including that of f-plane MHD "shallow water" waves [Schecter et al., Astrophys. J. 551, L185 (2001)AJLEEY0004-637X10.1086/320027]. A solution for the Fourier amplitude of perturbation fields (velocity, magnetic field, and density) is derived analytically considering a diffusive fluid for which both the magnetic and thermal Prandtl numbers are one. The radial spectrum of kinetic, S_{κ}(k,t), magnetic, S_{m}(k,t), and potential, S_{p}(k,t), energies is determined considering initial isotropic conditions. For magnetic Coriolis (MC) weak wave turbulence, it is shown that, at large scales such that V_{A}k/f≪1, the Alfvén ratio S_{κ}(k,t)/S_{m}(k,t) behaves like k^{-2} if the rotation axis is aligned with the magnetic field, in agreement with previous direct numerical simulations [Favier et al., Geophys. Astrophys. Fluid Dyn. (2012)] and like k^{-1} if the rotation axis is perpendicular to the magnetic field. At small scales, such that V_{A}k/f≫1, there is an equipartition of energy between magnetic and kinetic components. For magnetic Archimedes weak wave turbulence, it is demonstrated that, at large scales, such that (V_{A}k/N≪1), there is an equipartition of energy between magnetic and potential components, while at small scales (V_{A}k/N≫1), the ratio S_{p}(k,t)/S_{κ}(k,t) behaves like k^{-1} and S_{κ}(k,t)/S_{m}(k,t)=1. Also, for MAC weak wave turbulence, it is shown that, at small scales (V_{A}k/sqrt[N^{2}+f^{2}]≫1), the ratio S_{p}(k,t)/S_{κ}(t) behaves like k^{-1} and S_{κ}(k,t)/S_{m}(k,t)=1.

Innate and adaptive mucosal immunity in protection against HIV infection.

The appalling toll on the populations of developing countries as a result of the HIV epidemic shows no signs of abatement. While costly drug therapies are effective in developed nations, the sheer scale of the epidemic elsewhere makes the need for a vaccine an ever more urgent goal. The prevalent DNA prime-viral boost strategy aims to elicit cytotoxic lymphocytes (CTL) against HIV, but this approach is undermined by the rapid mutation of HIV, which thereby escapes CTL control. Alloimmunity has been found to be protective in vertical transmission from infected mothers to their babies, in alloimmunization of women with their partners' mononuclear cells, and in monkeys immunized with SIV grown in human T-cells. Vaginal mucosal immunization, as a result of unprotected sex with a regular partner, induced in vitro protection against HIV infection, and this was confirmed in macaques. The second type of natural protection is found in persons with the homozygous 32 CCR5 mutation, a 32-base-pair deletion of the CCR5 gene, which results in a lack of cell-surface expression of CCR5, which is associated with an increase in CC chemokines and the development of CCR5 antibodies. These two 'experiments of nature' have been used to develop vaccine strategies--first, in vaginal immunization of macaques with CCR5 peptides, in addition to HIV envelope (env) and SIV core (gag) antigens, all of which were linked to the 70-kD heat-shock protein (HSP70); and second, in mucosal allo-immunization of macaques, which also gave rise to in vitro protection from infection. Immunization with this vaccine elicited serum and vaginal IgG and IgA antibodies, IFNgamma- and IL-12-producing cells, and increased concentrations of CCL-3 and CCL-4. Vaginal challenge with a simian immunodeficiency virus engineered to carry a human envelope protein (SHIV 89.6) showed significant clearance of SHIV in the immunized macaques. This platform strategy will now be developed to activate the co-stimulatory pathways with the aim of enhancing the primary allogeneic and CCR5-directed responses which are involved in natural protection against HIV infection.

Instability in stratified accretion flows under primary and secondary perturbations.

We consider horizontal linear shear flow (shear rate denoted by Λ) under vertical uniform rotation (ambient rotation rate denoted by Ω(0)) and vertical stratification (buoyancy frequency denoted by N) in unbounded domain. We show that, under a primary vertical velocity perturbation and a radial density perturbation consisting of a one-dimensional standing wave with frequency N and amplitude proportional to w(0)sin(ɛNx/w(0))≈ɛNx(≪1), where x denotes the radial coordinate and ɛ a small parameter, a parametric instability can develop in the flow, provided N(2)>8Ω(0)(2Ω(0)-Λ). For astrophysical accretion flows and under the shearing sheet approximation, this implies N(2)>8Ω(0)(2)(2-q), where q=Λ/Ω(0) is the local shear gradient. In the case of a stratified constant angular momentum disk, q=2, there is a parametric instability with the maximal growth rate (σ(m)/ɛ)=3√[3]/16 for any positive value of the buoyancy frequency N. In contrast, for a stratified Keplerian disk, q=1.5, the parametric instability appears only for N>2Ω(0) with a maximal growth rate that depends on the ratio Ω(0)/N and approaches (3√[3]/16)ɛ for large values of N.

The expression of Fc receptors for immunoglobulin G in human rectal epithelium.

The rectal mucosa is one of the routes of transmission of the HIV virus, although the mechanism of transmission is unknown. We carried out an immunohistological investigation of human rectal epithelium to detect CD4 glycoprotein and Fc receptors (FcR) for immunoglobulin G which may be involved in HIV infection. CD4 was not detected by monoclonal antibodies (MAb) in normal rectal epithelial cells, although CD4+ mononuclear cells were found in the lamina propria of the rectum. FcR3 and FcR2 were, however, detected in surface or crypt epithelial cells of rectal mucosa, using MAb to CD16 and CD32, respectively. In addition, CD16 messenger RNA (mRNA) was found in surface and crypt epithelial cells by in situ hybridization using an RNA probe. FcR3 and FcR2 were also detected in fetal recto-colonic tissue by immunohistology, suggesting that these are constitutive receptors. FcR3 and FcR2 gene transcripts were then demonstrated in fetal recto-colonic tissue using the polymerase chain reaction to amplify a portion of FcR3 and FcR2 coding sequences in complementary DNA (cDNA) prepared from fetal RNA. These findings suggest the possibility that rectal transmission of HIV-antibody complexes might be facilitated by the expression of FcR3 and FcR2 in rectal epithelial cells.

Generation of diversity in the hierarchy of T-cell epitope responses following different routes of immunization with simian immunodeficiency virus protein.

OBJECTIVES: To examine whether the route of immunization determines the hierarchy of T-cell epitope proliferative responses in macaques. DESIGN: Macaques were immunized with a recombinant simian immunodeficiency virus (SIV) p27 core protein by the intramuscular, male and female genital or rectal route, each of which was augmented by oral immunization, and by the novel targeted lymph-node immunization route. Overlapping peptides were used to identify the proliferative T-cell epitopes and to determine their hierarchy in the circulation, spleen and lymph nodes. METHODS: T-cell epitope mapping of the proliferative responses was studied in short-term cell lines. Dendritic cells and macrophages were enriched by metrizamide gradient and adherence to plastic, respectively. RESULTS: Intramuscular immunization elicited in the circulating T cells a hierarchy of T-cell epitopes within four peptides in the following descending order of frequency: peptides 121-140 (57.9%), 41-60 (28.9%), 61-80 (18.9%) and 101-120 (5.4%). The hierarchy of these four T-cell epitope responses differed significantly with each of the five routes of immunization, when circulating (P < 0.001), splenic (P < 0.02-< 0.001) or iliac lymph-node cells (P < 0.001) were analysed. The effect of antigen-presenting cells was then investigated and enriched dendritic cells were more effective than macrophages in processing and presenting the p27 antigen and the immunodominant (121-140) and 61-80 T-cell epitopes. CONCLUSIONS: The route of immunization may determine the hierarchy of T-cell epitopes in the lymph nodes draining the mucosa in the circulating and splenic lymphocytes. The diversity of T-cell epitopes may affect the control of HIV at different anatomical sites, the administration route of the vaccine, and selection of polypeptides or recombinant antigens for immunization.