Associating quantitative behavioral traits with gene expression in the brain: searching for diamonds in the hay

Gene expression and phenotypic functionality can best be associated when they are measured quantitatively within the same experiment. The analysis of such a complex experiment is presented, searching for associations between measures of exploratory behavior in mice and gene expression in brain regions. The analysis of such experiments raises several methodological problems. First and foremost, the size of the pool of potential discoveries being screened is enormous yet only few biologically relevant findings are expected, making the problem of multiple testing especially severe. We present solutions based on screening by testing related hypotheses, then testing the hypotheses of interest. In one variant the subset is selected directly, in the other one a tree of hypotheses is tested hierarchical; both variants control the False Discovery Rate (FDR). Other problems in such experiments are in the fact that the level of data aggregation may be different for the quantitative traits (one per animal) and gene expression measurements (pooled across animals); in that the association may not be linear; and in the resolution of interest only few replications exist. We offer solutions to these problems as well. The hierarchical FDR testing strategies presented here can serve beyond the structure of our motivating example study to any complex microarray study. Supplementary information: Supplementary data are available at Bioinformatics online.     

Long-term bovine hematopoietic engraftment with clone-derived stem cells

Therapeutic cloning by somatic cell nuclear transfer offers potential for treatment of a wide range of degenerative disease. Nuclear transplantation with neo (r)-marked somatic nuclei from 10-13-year-old cows was used to generate cloned bovine fetuses. Clone fetal liver (FL) hematopoietic stem cells (HSC) were transplanted into two busulfan-treated and one untreated nuclear donor cows. Hematopoiesis was monitored over 13-16 months by in vitro progenitor and HSC assays. Chimerism was demonstrated by PCR in blood, marrow, lymph nodes, and endothelium, peaking at levels of 9-17% in blood granulocytes but at lower levels in lymphocyte subsets (0.1-0.01%). Circulating progenitors showed high levels of chimerism (up to 60% neo (r+)) with persisting fetal features. At sacrifice, the animal that had no pre-transplant myelosupression showed persisting donor cells in blood and lymph nodes, and in marrow 0.25% of progenitor cells and a detectable fraction of stem cells were neo (r+). The fetal HSC showed a 10-fold competition advantage over adult HSC. Cloning generated histocompatible HSC capable of long-term multilineage engraftment in a large animal model.     

Gibberellin regulates post-microsporogenesis processes in petunia anthers

Previous studies have suggested that gibberellins (GAs) are produced in petunia anthers and transported to the corolla to induce growth and pigmentation. In this work, we studied the role of GA in the regulation of anther development. When petunia plants were treated with the GA-biosynthesis inhibitor paclobutrazol, anther development was arrested. Microscopic analysis of these anthers revealed that paclobutrazol inhibits post-meiotic developmental processes. The treated anthers contained pollen grains but the connective tissue and tapetum cells were degenerated. A similar phenotype was obtained when the Arabidopsis GA-signal repressor, SPY, was over-expressed in transgenic petunia plants, i.e. anther development was arrested following microsporogenesis. The expression of the GA-induced gene, GIP , can be used in petunia as a molecular marker to study GA responses. GA₃ treatment of young anthers promoted, and paclobutrazol inhibited, GIP expression, suggesting that the hormone controls the natural activation of the gene in the anthers. Analyses of GIP expression during anther development revealed that the gene is induced only after microsporogenesis. This observation further suggests a role for GA in the regulation of post-meiotic processes during petunia anther development.     

Characterization of Cbl-Nck and Nck-Pak1 Interactions in Myeloid FcγRII Signaling

Fc receptors modulate inflammatory processes, including phagocytosis, serotonin and histamine release, superoxide production, and secretion of cytokines. Aggregation of FcγRIIa, the low-affinity receptor for monomeric IgG, activates nonreceptor protein tyrosine kinases such as Lyn, Hck, and Syk, potentially driving the phosphorylation of the downstream adaptor proteins, including Cbl and/or Nck. Previous work from our laboratory using interferon-γ-differentiated U937 (U937IF) myeloid cells investigated mechanisms which regulate Fcγ receptor-induced assembly of adaptor complexes. Herein we report that FcγRII receptor signaling in U937IF and HEL cells involves Cbl and Nck, suggesting that Cbl–Nck interactions may link FcγRII to downstream activation of Pak kinase. FcγRII crosslinking induced the phosphorylation of Cbl and Nck on tyrosine. The αCbl immunoprecipitations revealed constitutive binding of Nck and Grb2 to Cbl and FcγRII-inducible binding of CrkL to Cbl. The interactions of Cbl with Nck and CrkL were phosphorylation dependent since dephosphorylation of cellular proteins with potato acid phosphatase abrogated binding. GST–Nck fusion protein pulldown experiments show that Cbl and Pak1 bind to the second SH3 domain of Nck. A specific Src inhibitor, PP1, was shown to completely abrogate the FcγR-induced superoxide response, correlating with a decrease in Cbl and Nck tyrosine phosphorylation. Our results provide the first evidence that Src is required for FcγR activation of the respiratory burst in myeloid cells and suggest that Cbl–Nck, Cbl–Pak1, and Nck–Pak1 interactions may regulate this response.     

Listeria monocytogenes Multidrug Resistance Transporters and Cyclic Di-AMP,Which Contribute to Type I Interferon Induction,Play a Role in Cell Wall Stress

The intracellular bacterial pathogen Listeria monocytogenes activates a robust type I interferon response upon infection. This response is partially dependent on the multidrug resistance (MDR) transporter MdrM and relies on cyclic-di-AMP (c-di-AMP) secretion, yet the functions of MdrM and cyclic-di-AMP that lead to this response are unknown. Here we report that it is not MdrM alone but a cohort of MDR transporters that together contribute to type I interferon induction during infection. In a search for a physiological function of these transporters, we revealed that they play a role in cell wall stress responses. A mutant with deletion of four transporter genes (ΔmdrMTAC) was found to be sensitive to sublethal concentrations of vancomycin due to an inability to produce and shed peptidoglycan under this stress. Remarkably, c-di-AMP is involved in this phenotype, as overexpression of the c-di-AMP phosphodiesterase (PdeA) resulted in increased susceptibility of the ΔmdrMTAC mutant to vancomycin, whereas overexpression of the c-di-AMP diadenylate cyclase (DacA) reduced susceptibility to this drug. These observations suggest a physiological association between c-di-AMP and the MDR transporters and support the model that MDR transporters mediate c-di-AMP secretion to regulate peptidoglycan synthesis in response to cell wall stress.     

Anxiolytic effects of a novel herbal treatment in mice models of anxiety

AimsAnxiety and stress disorders are currently among the ten most important public health concerns, and in recent years, have reached epidemic proportions. The current success rate of treatments for anxiety disorders is not high, reaching 50% at most. These treatments are also associated with a wide variety of side effects. The aim of the present study was to investigate the anxiolytic properties of a novel herbal treatment produced in our laboratory compared to a conventional treatment for anxiety disorders, namely SSRIs.Main methodsAnxiety-like behavior was evaluated in adult mice exposed to stress during childhood following 1, 2 and 3 weeks of treatment with the novel herbal treatment or escitalopram, using the novel open field and the elevated plus maze paradigms. The behavioral evaluation in these mice was followed by a biochemical assessment of their brain hippocampal BDNF levels and blood corticosterone levels.Key findingsThe study showed that (1) the novel herbal treatment reduced anxiety-like behaviors in both behavioral tests. Interestingly, this reduction was observed only following a 3-week treatment; (2) following the novel treatment, corticosterone levels in the plasma of treated mice were reduced and this reduction was similar to the one observed following escitalopram treatment; and (3) BDNF levels in the hippocampus of mice treated both with the novel herbal treatment and escitalopram were increased.SignificanceThese behavioral and biological findings indicate that our novel herbal compound has the potential of being highly efficacious in treating anxiety disorders.     

Germline stem cell arrest inhibits the collapse of somatic proteostasis early in Caenorhabditis elegans adulthood

All cells rely on highly conserved protein folding and clearance pathways to detect and resolve protein damage and to maintain protein homeostasis (proteostasis). Because age is associated with an imbalance in proteostasis, there is a need to understand how protein folding is regulated in a multicellular organism that undergoes aging. We have observed that the ability of Caenorhabditis elegans to maintain proteostasis declines sharply following the onset of oocyte biomass production, suggesting that a restricted protein folding capacity may be linked to the onset of reproduction. To test this hypothesis, we monitored the effects of different sterile mutations on the maintenance of proteostasis in the soma of C. elegans. We found that germline stem cell (GSC) arrest rescued protein quality control, resulting in maintenance of robust proteostasis in different somatic tissues of adult animals. We further demonstrated that GSC‐dependent modulation of proteostasis requires several different signaling pathways, including hsf‐1 and daf‐16/kri‐1/tcer‐1, daf‐12, daf‐9, daf‐36, nhr‐80, and pha‐4 that differentially modulate somatic quality control functions, such that each signaling pathway affects different aspects of proteostasis and cannot functionally complement the other pathways. We propose that the effect of GSCs on the collapse of proteostasis at the transition to adulthood is due to a switch mechanism that links GSC status with maintenance of somatic proteostasis via regulation of the expression and function of different quality control machineries and cellular stress responses that progressively lead to a decline in the maintenance of proteostasis in adulthood, thereby linking reproduction to the maintenance of the soma.     

Analysis of the relationships between ATM and the Rad54 paralogs involved in homologous recombination repair

Ataxia-telangiectasia is a pleiotropic genomic instability disorder caused by lack or inactivation of the ATM protein kinase and characterized by progressive ataxia, immunodeficiency, ionizing radiation sensitivity and cancer predisposition. ATM mobilizes the cellular response to DNA double strand breaks by phosphorylating key players in this response. Double strand breaks are repaired by either nonhomologous end-joining or homologous recombination (HR) in which the Rad54 and Rad54B paralogs function. Here, we investigated the functional relationships between Atm and the Rad54 proteins by constructing compound genotypes in mice. Mouse strains were generated that combined inactivation of the Atm, Rad54 and Rad54B genes. All mutant genotypes were viable, but obtained at sub-Mendelian ratios. Double mutants for Atm and each Rad54 paralog exhibited reduced body weight and shorter lifespan, but no distinct neurological phenotype. Concomitant inactivation of ATM and Rad54 did not increase IR sensitivity; however, the triple Atm/Rad54/Rad54B mutant exhibited a significant IR hypersensitivity compared to the other genotypes. Interestingly, Atm?/? animals also exhibited hypersensitivity to the crosslinking agent mitomycin C, which was increased by deficiency of either one of the Rad54 paralogs. Our results reveal a differential interaction of the ATM-mediated DNA damage response and Rad54 paralog-mediated HR depending on the DNA damaging agent that initiates the response.     

Evidence for coupling of membrane targeting and function of the signal recognition particle (SRP) receptor FtsY

Recent studies have indicated that FtsY, the signal recognition particle receptor of Escherichia coli, plays a central role in membrane protein biogenesis. For proper function, FtsY must be targeted to the membrane, but its membrane-targeting pathway is unknown. We investigated the relationship between targeting and function of FtsY in vivo, by separating its catalytic domain (NG) from its putative targeting domain (A) by three means: expression of split ftsY, insertion of various spacers between A and NG, and separation of A and NG by in vivo proteolysis. Proteolytic separation of A and NG does not abolish function, whereas separation by long linkers or expression of split ftsY is detrimental. We propose that proteolytic cleavage of FtsY occurs after completion of co-translational targeting and assembly of NG. In contrast, separation by other means may interrupt proper synchronization of co-translational targeting and membrane assembly of NG. The co-translational interaction of FtsY with the membrane was confirmed by in vitro experiments.