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WNT signaling plays a major role in patterning the dermomyotome of the somitic mesoderm. However, knowledge of downstream target genes and their regulation is limited. To identify new genes involved in the development and early patterning of the somite, we performed a comparison of gene expression by microarray between the presomitic mesoderm and the 5 most recently formed somites of the mouse at embryonic day 9.5. We identified 207 genes upregulated and 120 genes downregulated in somite formation. Expression analysis and functional categorization of these genes demonstrate this to be a diverse pool that provides a valuable resource for studying somite development. Thus far, we have found three genes expressed in the dermomyotome of the early somite. Consistent with their expression patterns, these genes are transcriptional targets of WNT signals, but display differential activation by different WNTs. We further demonstrate that 1 of these genes, Troy, is a direct target of canonical WNT signaling, while the other 2 genes, Selp and Arl4, are not. Thus, our microarray study using microdissected tissues not only provides global information on gene expression during somite development, it also provides novel targets to study the inductive signaling pathways that direct somite patterning.

More reliable methods are needed to uncover novel biomarkers associated with atrial fibrillation (AF). Our objective is to identify significant network modules and newly AF-associated genes by integrative genetic analysis approaches. The single nucleotide polymorphisms with nominal relevance significance from the AF-associated genome-wide association study (GWAS) data were converted into the GWAS discovery set using ProxyGeneLD, followed by merging with significant network modules constructed by weighted gene coexpression network analysis (WGCNA) from one expression profile data set, composed of left and right atrial appendages (LAA and RAA). In LAA, two distinct network modules were identified (blue: p = 0.0076; yellow: p = 0.023). Five AF-associated biomarkers were identified (ERBB2 , HERC4 , MYH7 , MYPN , and PBXIP1), combined with the GWAS test set. In RAA, three distinct network modules were identified and only one AF-associated gene LOXL1 was determined. Using human LAA tissues by real-time quantitative polymerase chain reaction, the differentially expressive results of ERBB2 , MYH7 , and MYPN were observed (p < 0.05). This study first demonstrated the feasibility of fusing GWAS with expression profile data by ProxyGeneLD and WGCNA to explore AF-associated genes. In particular, two newly identified genes ERBB2 and MYPN via this approach contribute to further understanding the occurrence and development of AF, thereby offering preliminary data for subsequent studies. [ABSTRACT FROM AUTHOR]

We focus this report on the nucleus of the lateral olfactory tract (NLOT), a superficial amygdalar nucleus receiving olfactory input. Mixed with its Tbr1-expressing layer 2 pyramidal cell population (NLOT2), there are Sim1-expressing cells whose embryonic origin and mode of arrival remain unclear. We examined this population with Sim1-ISH and a Sim1-tauLacZ mouse line. An alar hypothalamic origin is apparent at the paraventricular area, which expresses Sim1 precociously. This progenitor area shows at E10.5 a Sim1-expressing dorsal prolongation that crosses the telencephalic stalk and follows the terminal sulcus, reaching the caudomedial end of the pallial amygdala. We conceive this Sim1-expressing hypothalamo-amygdalar corridor (HyA) as an evaginated part of the hypothalamic paraventricular area, which participates in the production of Sim1-expressing cells. From E13.5 onwards, Sim1-expressing cells migrated via the HyA penetrate the posterior pallial amygdalar radial unit and associate therein to the incipient Tbr1-expressing migration stream which swings medially past the amygdalar anterior basolateral nucleus (E15.5), crosses the pallio-subpallial boundary (E16.5), and forms the NLOT2 within the anterior amygdala by E17.5. We conclude that the Tbr1-expressing NLOT2 cells arise strictly within the posterior pallial amygdalar unit, involving a variety of required gene functions we discuss. Our results are consistent with the experimental data on NLOT2 origin reported by Remedios et al. (Nat Neurosci 10:1141–1150, 2007), but we disagree on their implication in this process of the dorsal pallium, observed to be distant from the amygdala. [ABSTRACT FROM AUTHOR]

To understand the cause of loss of rice blast resistance, we studied the pathogenicity of Magnaporthe oryzae strains isolated from rice hybrid Wuyou 308 and evaluated its resistance genes. A total of 62 M. oryzae strains were isolated and tested in 7 Chinese rice varieties with varying degrees of resistance to rice blast and 30 blast-resistant monogenic lines. Fourteen physiological races of M. oryzae were identified: 8.55% belonging to the ZA group, 86.67% to the ZB group, and 5.00% to the ZC group. ZB15 was the most abundant race (45.00%). Five resistance genes, Pi-3(1), Pi-z5, Pi-k, Pi-kp(C), and Pi-k(C), conferred good resistance to the 62 strains, with resistance frequencies of 95.56, 91.11, 88.89, 82.22, and 82.22%, respectively. In contrast, Pi-a(2) had a resistance frequency of 0%. The hybrid combination Wuyou 308 was found to carry Pi-ta and Pi-b genes. Because Pi-ta and Pi-b both showed low resistance frequencies to M. oryzae isolated from Jiangxi, the hybrid rice variety Wuyou 308 could be infected by most of the 62 M. oryzae strains. The emergence and spread of rice blast disease in Wuyou 308 may thus be difficult to avoid when climatic conditions are favourable. [ABSTRACT FROM AUTHOR]

The basic helix-loop-helix transcription factor MyoD is a central actor that triggers the skeletal myogenic program. Cellautonomous and non-cell-autonomous regulatory pathways must tightly control MyoD expression to ensure correct initiation of the muscle program at different places in the embryo and at different developmental times. In the present study, we have addressed the involvement of Sim2 (single-minded 2) in limb embryonic myogenesis. Sim2 is a bHLH-PAS transcription factor that inhibits transcription by active repression and displays enhanced expression in ventral limb muscle masses during chick and mouse embryonic myogenesis. We have demonstrated that Sim2 is expressed in muscle progenitors that have not entered the myogenic program, in different experimental conditions. MyoD expression is transiently upregulated in limb muscle masses of Sim2-/- mice. Conversely, Sim2 gain-of-function experiments in chick and Xenopus embryos showed that Sim2 represses MyoD expression. In addition, we show that Sim2 represses the activity of the mouse MyoD promoter in primary myoblasts and is recruited to the MyoD core enhancer in embryonic mouse limbs. Sim2 expression is non-autonomously and negatively regulated by the dorsalising factor Lmx1b. We propose that Sim2 represses MyoD transcription in limb muscle masses, through Sim2 recruitment to the MyoD core enhancer, in order to prevent premature entry into the myogenic program. This MyoD repression is predominant in ventral limb regions and is likely to contribute to the differential increase of the global mass of ventral muscles versus dorsal muscles. [ABSTRACT FROM AUTHOR]

Barnacles are one of the most common organisms in intertidal areas. Their life cycle includes seven free-swimming larval stages and sessile juvenile and adult stages. The transition from the swimming to the sessile stages, referred to as larval settlement, is crucial for their survivor success and subsequent population distribution. In this study, we focused on the involvement of calmodulin (CaM) and its binding proteins in the larval settlement of the barnacle, Balanus ( = Amphibalanus) amphitrite. The full length of CaM gene was cloned from stage II nauplii of B. amphitrite (referred to as Ba-CaM), encoding 149 amino acid residues that share a high similarity with published CaMs in other organisms. Quantitative real-time PCR showed that Ba-CaM was highly expressed in cyprids, the stage at which swimming larvae are competent to attach and undergo metamorphosis. In situ hybridization revealed that the expressed Ba-CaM gene was localized in compound eyes, posterior ganglion and cement glands, all of which may have essential functions during larval settlement. Larval settlement assays showed that both the CaM inhibitor compound 48/80 and the CaM-dependent myosin light chain kinase (MLCK) inhibitor ML-7 effectively blocked barnacle larval settlement, whereas Ca2+/CaM-dependent kinase II (CaMKII) inhibitors did not show any clear effects. The subsequent real-time PCR assay showed a higher expression level of Ba-MLCK gene in larval stages than in adults, suggesting an important role of Ba-MLCK gene in larval development and competency. Overall, the results suggest that CaM and CaM-dependent MLCK function during larval settlement of B. amphitrite. [ABSTRACT FROM AUTHOR]

Holprosencephaly (HPE) is the most common disorder of the developing forebrain in humans, and is characterized by varying degrees of abnormal union of the cerebral hemispheres. These defects are typically co-associated with midline craniofacial anomalies. The combination of forebrain and craniofacial defects that comprise HPE can present along a broad and variable phenotypic spectrum. Both the SHH and NODAL signaling pathways play important roles in the pathogenesis of this disorder. Disruption of these pathways by chromosomal rearrangements, mutations in pathway-related genes and/or biochemical alterations are proposed to contribute to HPE in a large number of patients. Additional factors that are not yet fully delineated are also very likely to be involved in the pathogenesis and phenotypic heterogeneity of the disorder. Genetic loss of GAS1, a cell membrane receptor and positive regulator of SHH, has been demonstrated to contribute to the HPE phenotypic spectrum in animal models. We have evaluated the coding and flanking sequence of GAS1 in 394 patients who have clinical findings within the HPE phenotypic spectrum, and now report five novel missense sequence variants among five unrelated HPE probands. Finally, we tested the effect of these variants (as well as previously reported GAS1 variants) on the ability of GAS1 to bind to SHH. Here, we demonstrate that sequence variants in GAS1 can impair its physical interaction with SHH, suggesting a decrease in the SHH downstream signaling cascade as a pathogenic mechanism of disease. [ABSTRACT FROM AUTHOR]

Background: Head-to-head (h2h) genes are prone to have association in expression and in functionality and have been shown conserved in evolution. Currently there are many studies on such h2h gene pairs. We found that the previous studies extremely focused on human genome. Furthermore, they only focused on analyses that require only gene or protein sequences but not conducted a systematic investigation on other promoter features such as the binding evidence of specific transcription factors (TFs). This is mainly because of the incomplete resources of higher organisms, though they are relatively of interest, than model organisms such as Saccharomyces cerevisiae. The authors of this study recently integrated nine promoter features of 6603 genes of S. cerevisiae from six databases and five papers. These resources are suitable to conduct a comprehensive analysis of h2h genes in S. cerevisiae. Results: This study analyzed various promoter features, including transcription boundaries (TSS, 5'UTR and 3'UTR), TATA box, TF binding evidence, TF regulation evidence, DNA bendability and nucleosome occupancy. The expression profiles and gene ontology (GO) annotations were used to measure if two genes are associated. Based on these promoter features, we found that i) the frequency of h2h genes was close to the expectation, namely they were not relatively frequent in genome; ii) the distance between the TSSs of most h2h genes fell into the range of 0-600 bps and was more centralized in 0-200 bps of the highly associated ones; iii) the number of TFs that regulate both h2h genes influenced the co-expression and co-function of the genes, while the number of TFs that bind both h2h genes influenced only the co-expression of the genes; iv) the association of two h2h genes was influenced by the existence of specific TFs such as STP2; v) the association of h2h genes whose bidirectional promoters have no TATA box was slightly higher than those who have TATA boxes; vi) the association of two h2h genes was not influenced by the DNA bendability and nucleosome occupancy. Conclusions: This study analyzed h2h genes with various promoter features that have not been used in analyzing h2h genes. The results can be applied to other genomes to confirm if the observations of this study are limited to S. cerevisiae or universal in most organisms [ABSTRACT FROM AUTHOR]

Jatropha curcas is an economically important plant in terms of its seed oil. However, the molecular mechanisms underlying this plant response to light signals are unknown. One group of DNA-binding with one finger (Dof) transcription factor genes exhibits circadian rhythms and plays a crucial role in the control of flowering time by photoperiod perception in plants. In the present study, a full-length cDNA designated JcDof1, containing a conserved Dof-DNA-binding domain, was isolated from J. curcas seedlings by yeast one hybrid library. Subcellular localization assays and yeast one hybrid systems confirmed that JcDof1 was localized to the onion epidermal cell nucleus, and exhibited DNA-binding and transcriptional activation activities in yeast. The JcDof1 expression was characterized by a circadian-clock oscillation under long day, short day and continuous light conditions, whereas in the etiolated cotyledons under continuous dark conditions, JcDof1 expression remained at relatively basal levels. Red and blue light downregulated the JcDof1 expression, but this effect was not observed under far-red light. Taken together, these results suggested that JcDof1 was a circadian clock-Dof transcription factor gene responding to light signals. [ABSTRACT FROM AUTHOR]

Caffeine is believed to exert its stimulant effects by blocking A2A and A1 adenosine receptors (A2AR and A1R). Although a genetic knockout of A2AR eliminates effects of caffeine, the phenotype of the knockout animal does not resemble that of caffeine treatment. In this study we explored the possibility that a mere reduction of the number of A1Rs and A2ARs, achieved by deleting one of the two copies of the A1R and A2AR genes, would mimic some aspects of long-term caffeine ingestion. The A1R and A2AR double heterozygous (A1R-A2AR dHz) mice indeed had approximately one-half the number of A1R and A2AR, and there were little compensatory changes in A2B or A3 adenosine receptor (A2BR or A3R) expression. The ability of a stable adenosine analog to activate receptors was shifted to the right by caffeine and in A1R-A2AR dHz tissue. Caffeine (0.3 g/l in drinking water for 7-10 days) and A1R-A2AR dHz genotype increased locomotor activity (LA) and decreased heart rate without significantly influencing body temperature. The acute stimulatory effect of a single injection of caffeine was reduced in A1R-A2AR dHz mice and in mice treated long term with oral caffeine. Thus at least some aspects of long-term caffeine use can be mimicked by genetic manipulation of the A1R and A2AR. [ABSTRACT FROM AUTHOR]

Abstract: The hypothalamic paraventricular nucleus (PVN) and supraoptic nucleus (SON) contain neuroendocrine cells that modulate pituitary secretion to maintain homeostasis. These two nuclei have a common developmental origin but they eventually form at locations distant from each other. Little is known about the molecular cues that direct the segregation of PVN and SON. As a means to identify potential factors, we have documented expression patterns of genes with known guidance roles in neural migration. Here, we focus on two groups of ligand/receptor families classified to mediate chemo-repulsion of neurons and their axons: the Slit/Robo and the Semaphorin/Plexin/Neuropilin families. Their dynamic expression patterns within and around the common PVN/SON progenitor as well as the mature PVN and SON may provide a framework for understanding the formation of these two important nuclei. [Copyright &y& Elsevier]

Background: Infection by Helicobacter pylori is often acquired during childhood. Recent studies suggest that inflammatory cytokines may play a role in susceptibility to, and disease phenotype caused by, H. pylori infection, but the association of host genetic variability with risk of H. pylori infection has not been studied in children. Methods: We investigated the relationship between the risk of H. pylori antibody positivity and cytokine gene polymorphisms among 199 two-year-old Jamaicans. H. pylori seropositivity was determined by a validated research enzyme-linked immunosorbent assay. Real-time Taqman® polymerase chain reaction was used to determine variants at 17 loci in 11 cytokine genes ( IL1A, IL1B, IL2, TNF, TLR4, IL4, IL6, IL10, IL10RA, IL12A and IL13). We estimated the odds ratio and the 95% confidence interval for the association of genetic polymorphisms with H. pylori seropositivity, using logistic regression. Results: Forty (20.1%) of 199 children were seropositive. Children's H. pylori seropositivity correlated highly with maternal H. pylori seropositivity (OR = 7.98, 95% CI = 1.05–60.60, p = .02). Children carrying IL1A−889T had a lower risk of H. pylori positivity, compared to those carrying −889C, with each T allele associated with 43% risk reduction (OR = 0.57, 95% CI = 0.33–0.99, p-trend = .05). No other loci we examined were associated with the risk of H. pylori seropositivity. Conclusions: The IL1A−889 T allele, known to express a higher level of cytokine IL-1α, is associated with a lower risk of H. pylori infection among Jamaican children. Our finding supports the hypothesis that an upregulation of pro-inflammatory cytokines may protect against persistent H. pylori colonization. [ABSTRACT FROM AUTHOR]