Importance of replication in analyzing time-series gene expression data: Corticosteroid dynamics and circadian patterns in rat liver

Background  

Comprehensively understanding corticosteroid pharmacogenomic effects is an essential step towards an insight into the underlying molecular mechanisms for both beneficial and detrimental clinical effects. Nevertheless, even in a single tissue different methods of corticosteroid administration can induce different patterns of expression and regulatory control structures. Therefore, rich in vivo datasets of pharmacological time-series with two dosing regimens sampled from rat liver are examined for temporal patterns of changes in gene expression and their regulatory commonalities.     

Porcine lactoferrin as feedstuff additive elevates avian immunity and potentiates vaccination

In this study, recombinant porcine lactoferrin (PLF) was used as feedstuff additive to investigate the effects of peripheral lymphocyte proliferation and serum antibody titers in chickens vaccinated against the infectious bursal disease (IBD) virus. Treatment groups were fed three doses of PLF powder in their diet (0.5, 1.0, and 2.0% w/w), and the IBD vaccine was administrated at 1 and 3 weeks of age. At 8, 12, and 16 weeks after vaccination, serum IBD antibody titers were measured via the micro-method and T cell proliferation rates were evaluated. The results revealed that a high dose of PLF led to significant increases in serum IgA, IgG and IBD-specific antibody titers (P < 0.05). PLF administration, at either low or high doses, enhanced the expression of IFN-γ and IL-12 in chicken T lymphocytes. These results suggest that PLF enhances cell-mediated immunity and augment the ability of IBD vaccination to strengthen subsequent anti-viral responses.     

Neuronal activation in the hypothalamus and brainstem during feeding in rats

We trained rats to a regime of scheduled feeding, in which food was available for only 2 hr each day. After 10 days, rats were euthanized at defined times relative to food availability, and their brains were analyzed to map Fos expression in neuronal populations to test the hypothesis that some populations are activated by hunger whereas others are activated by satiety signals. Fos expression accompanied feeding in several hypothalamic and brainstem nuclei. Food ingestion was critical for Fos expression in noradrenergic and non-noradrenergic cells in the nucleus tractus solitarii and area postrema and in the supraoptic nucleus, as well as in melanocortin-containing cells of the arcuate nucleus. However, anticipation of food alone activated other neurons in the arcuate nucleus and in the lateral and ventromedial hypothalamus, including orexin neurons. Thus orexigenic populations are strongly and rapidly activated at the onset of food presentation, followed rapidly by activity in anorexigenic populations when food is ingested.     

Variants in Deleted in AZoospermia-Like (DAZL) are correlated with reproductive parameters in men and women

Qualitative and quantitative defects in human germ cell production that result in infertility are common and determined at least in part by genetic factors [Matzuk and Lamb, Nat Cell Biol 4(Suppl):s41–s49, 2002]. Yet, very few genes that are associated with germ cell defects in humans have been identified. In this study, we examined whether variants of the Deleted in AZoospermia-Like (DAZL) gene are associated with measures of germ cell production in three distinct populations of men and women. We identified 95 sequence variants in DAZL and further analyzed twelve single nucleotide polymorphisms (SNPs) that were present across ethnicities. We found that seven of the twelve SNPs were associated with at least one of the parameters studied (age at premature ovarian failure or menopause, total sperm count, or total motile sperm count). Surprisingly, many alleles exhibited opposing effects in men and women, which may be a result of different genetic requirements in male and female germ cells. Single SNP and haplotype analysis suggested that SNPs in the DAZL gene may act jointly to affect common reproductive characteristics in the human population. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users. Joyce Y. Tung and Mitchell P. Rosen have contributed equally     

Synthesis and evaluation of N-[(1S,2S)-3-(4-chlorophenyl)-2-(3-cyanophenyl)-1-methylpropyl]-2-methyl-2-aminopropanamide as human cannabinoid-1 receptor (CB1R) inverse agonists

Obesity is a chronic medical condition that is affecting large population throughout the world. CB1 as a target for treatment of obesity has been under intensive studies. Taranabant was discovered and then developed by Merck as the 1st generation CB1R inverse agonist. Reported here is part of our effort on the 2nd generation of CB1R inverse agonist from the acyclic amide scaffold. We replaced the oxygen linker in taranabant with nitrogen and prepared a series of amino heterocyclic analogs through a divergent synthesis. Although in general, the amine linker gave reduced binding affinity, potent and selective CB1R inverse agonist was identified from the amino heterocycle series. Molecular modeling was applied to study the binding of the amino heterocycle series at CB1 binding site. The in vitro metabolism of representative members was studied and only trace glucuronidation was found. Thus, it suggests that the right hand side of the molecule may not be the appropriate site for glucuronidation.     

An acidic extracellular pH disrupts adherens junctions in HepG2 cells by Src kinases‐dependent modification of E‐cadherin

We have previously shown that culturing HepG2 cells in pH 6.6 culture medium increases the c‐Src‐dependent tyrosine phosphorylation of β‐catenin and induces disassembly of adherens junctions (AJs). Here, we investigated the upstream mechanism leading to this pH 6.6‐induced modification of E‐cadherin. In control cells cultured at pH 7.4, E‐cadherin staining was linear and continuous at cell–cell contact sites. Culturing cells at pH 6.6 was not cytotoxic, and resulted in weak and discontinuous junctional E‐cadherin staining, consistent with the decreased levels of E‐cadherin in membrane fractions. pH 6.6 treatment activated c‐Src and Fyn kinase and induced tyrosine phosphorylation of p120 catenin (p120ctn) and E‐cadherin. Inhibition of Src family kinases by PP2 attenuated the pH 6.6‐induced tyrosine phosphorylation of E‐cadherin and p120ctn, and prevented the loss of these proteins from AJs. In addition, E‐cadherin was bound to Hakai and ubiquitinated. Furthermore, pH 6.6‐induced detachment of E‐cadherin from AJs was blocked by pretreatment with MG132 or NH₄Cl, indicating the involvement of ubiquitin‐proteasomal/lysosomal degradation of E‐cadherin. An early loss of p120ctn prior to E‐cadherin detachment from AJs was noted, concomitant with a decreased association between p120ctn and E‐cadherin at pH 6.6. PP2 pretreatment prevented the dissociation of these two proteins. In conclusion, pH 6.6 activated Src kinases, resulting in tyrosine phosphorylation of E‐cadherin and p120ctn and a weakening of the association of E‐cadherin with p120ctn and contributing to the instability of E‐cadherin at AJs. J. Cell. Biochem. 108: 851–859, 2009. © 2009 Wiley‐Liss, Inc.     

Seeing red: behavioral evidence of trichromatic color vision in strepsirrhine primates

Among primates, catarrhines (Old World monkeys and apes) andcertain platyrrhines (New World monkeys) possess trichromaticcolor vision, which might confer important evolutionary advantages,particularly during foraging. Recently, a polymorphism has beenshown to shift the spectral sensitivity of the X-linked opsinprotein in certain strepsirrhines (e.g., Malagasy lemurs); however,its behavioral significance remains unknown. We assign genotypesat the X-linked variant to 45 lemurs, representing 4 species,and test if the genetic capacity for trichromacy impacts foragingperformance, particularly under green camouflage conditionsin which red detection can be advantageous. We confirm polymorphismat the critical site in sifakas and ruffed lemurs and fail tofind this polymorphism in collared lemurs and ring-tailed lemurs.We show that this polymorphism may be linked to "behavioraltrichromacy" in heterozygous ruffed lemurs but find no comparableevidence in a single heterozygous sifaka. Despite their putativedichromatic vision, female collared lemurs were surprisinglyefficient at retrieving both red and green food items undercamouflage conditions. Thus, species-specific feeding ecologiesmay be as important as trichromacy in influencing foraging behavior.Although the lemur opsin polymorphism produced measurable behavioraleffects in at least one species, the ruffed lemur, these effectswere modest, consistent with the modest shift in spectral sensitivity.Additionally, the magnitude of these effects varied across individualsof the same genotype, emphasizing the need for combined geneticand behavioral studies of trichromatic vision. We conclude thattrichromacy may be only one of several routes toward increasedforaging efficiency in visually complex environments.     

Nomifensine attenuates d-amphetamine-induced dopamine terminal neurotoxicity in the striatum of rats

Long-term or high dose administration of d-amphetamine (AMPH) in the rat has been shown to result in dopamine terminal neurotoxicity in the striatum of rats. This phenomenon includes depletion of dopamine content, decreased activity of tyrosine hydroxylase and diminish in the number of dopamine reuptake transporter. Recent studies implicate a role of oxidative stress induced by dopamine in the AMPH-induced neurotoxicity. However, the primary source of dopamine responsible for radical formation during AMPH challenge has remained elusive. To elucidate this issue, the study was designed to examine the effects of nomifensine, a dopamine transporter blocker, and deprenyl, a monoamine oxidase B (MAO-B) inhibitor, on the prevention of striatal dopamine neurotoxicity in AMPH-treated rats. The results showed that nomifensine but not deprenyl protected against AMPH-induced long-term dopamine depletion. Correspondingly, the hydroxyl radical formation caused by AMPH in the striatum was attenuated by nomifensine, whereas its formation was not abolished by deprenyl. In conclusion, this study suggests that intracellular oxidative stress is more likely involved in the AMPH-induced dopamine terminal toxicity in the rat striatum, while this phenomenon is not mediated by MAO-B pathway.