Analysis Of Individual Genes Research Articles

Topological conflicts in phylogenetic analysis of different regions of the sable (Martes zibellina L.) mitochondrial genome

Phylogenetic analysis of different regions of the mitochondrial genome of the sable showed the presence of several topologies of phylogenetic trees, but the most statistically significant topology is A-BC, which was obtained as a result of the analysis of the mitochondrial genome as a whole, as well as of the individual CO1, ND4, and ND5 genes. Analysis of the intergroup divergence of the mtDNA haplotypes (Dxy) indicated that the maximum Dxy values between A and BC groups were accompanied by minimum differences between B and C groups only for six genes showing the A-BC topology (12S rRNA; CO1, CO2, ND4, ND5, and CYTB). It is assumed that the topological conflicts observed in the analysis of individual sable mtDNA genes are associated with the uneven distribution of mutations along the mitochondrial genome and the mitochondrial tree. This may be due to random causes, as well as the nonuniform effect of selection.

Time-Course Gene Set Analysis for Longitudinal Gene Expression Data.

Gene set analysis methods, which consider predefined groups of genes in the analysis of genomic data, have been successfully applied for analyzing gene expression data in cross-sectional studies. The time-course gene set analysis (TcGSA) introduced here is an extension of gene set analysis to longitudinal data. The proposed method relies on random effects modeling with maximum likelihood estimates. It allows to use all available repeated measurements while dealing with unbalanced data due to missing at random (MAR) measurements. TcGSA is a hypothesis driven method that identifies a priori defined gene sets with significant expression variations over time, taking into account the potential heterogeneity of expression within gene sets. When biological conditions are compared, the method indicates if the time patterns of gene sets significantly differ according to these conditions. The interest of the method is illustrated by its application to two real life datasets: an HIV therapeutic vaccine trial (DALIA-1 trial), and data from a recent study on influenza and pneumococcal vaccines. In the DALIA-1 trial TcGSA revealed a significant change in gene expression over time within 69 gene sets during vaccination, while a standard univariate individual gene analysis corrected for multiple testing as well as a standard a Gene Set Enrichment Analysis (GSEA) for time series both failed to detect any significant pattern change over time. When applied to the second illustrative data set, TcGSA allowed the identification of 4 gene sets finally found to be linked with the influenza vaccine too although they were found to be associated to the pneumococcal vaccine only in previous analyses. In our simulation study TcGSA exhibits good statistical properties, and an increased power compared to other approaches for analyzing time-course expression patterns of gene sets. The method is made available for the community through an R package.

The role of KIR and HLA polymorphism in HIV acquisition: association and in vitro functional studies (VIR1P.1159)

Abstract Polymorphism in the genes that encode the HLA antigens and the KIR receptors on NK cells influence both adaptive and innate immunity. We analyzed the role of HLA and KIR polymorphisms in HIV acquisition by comparing 405 HIV+ and 523 HIV- men in the Chicago MACS cohort. We found no significant association with any HLA allele, in contrast to the well established strongly protective effect of HLA-B*57:01 for HIV disease progression. The inhibitory KIR ligands are HLA class I epitopes and fall into the groups: HLA-C1,C2, HLA-Bw4, and HLA-A3/A11. Association analyses of individual KIR genes in the presence/absence of their cognate HLA ligand revealed that one KIR/HLA ligand genotype combination was protective for HIV acquisition. The HLA ligand genotype C1/C1 was protective compared to C1/C2 and C2/C2 but only with genotype KIR2DL3+/KIR2DL2- (OR = 1.76, p = 0.007). This KIR genotype marks homozygosity for the centromeric KIR A haplotype, which is more inhibitory, has fewer genes, and less diverse than KIR B haplotypes. Since C2 is the ligand for the KIR2DL1 receptor, and C1 is the ligand for the KIR2DL3 receptor, the protective association observed with C1/C1 homozygotes suggests that a lack of signaling via the strongly inhibitory KIR2DL1 receptor in addition to signaling via the KIR2DL3 receptor is protective. In vitro assays of NK cells from KIR2DL3 homozygous individuals demonstrate that C1/C1 vs C1/C2 and C2/C2 (C2+) genotypes are more active in terms of cytokine release.

Abstract P3-06-21: Next generation sequencing to find predictors for chemotherapy response in triple negative breast cancer

Abstract Background: Neoadjuvant chemotherapy is the standard of care for locally advanced triple negative breast cancer (TNBC). A complete remission after chemotherapy is associated with a good prognosis. However, patients with a poor response often relapse and die of metastatic disease. Biomarkers are urgently needed to predict which patients will respond to standard chemotherapy. In the current study we deep-sequenced responding and non-responding tumors to find response prediction markers. In addition, the encountered mutations might provide clues for targeted treatment options. Methods: Next generation sequencing (NGS) was performed for 2,000 genes involved in oncogenesis with an average coverage of 150 reads. DNA from 56 pre-treatment TNBC-biopsies was sequenced, as was non-tumor DNA from each patient for comparison. Biopsies were obtained from patients scheduled to receive neoadjuvant chemotherapy with doxorubicin/cyclophosphamide. The median follow up was 2.5 years. The presence of a BRCA1 germline mutation or BRCA1 promoter methylation was also known. We assessed three variables. First, we compared samples with a pathological complete remission (pCR) with those that did not achieve a pCR, to find mutations predicting chemotherapy response. Second, we performed the same comparison with relapse free survival as outcome measure. Third, we compared tumors with BRCA mutations or BRCA1 promoter methylation with tumors with a functional copy of the BRCA genes. The goal of this analysis was to detect mutations associated with BRCAness. Results: The mutations observed were diverse and few recurrent mutations were detected. Most mutations were in TP53, TTN, and PIK3CA (57%, 22%, 9%). The mutation rates were similar between responders and non-responders (average mutation rate of 13 versus 16 mutations per tumor, p=0.27). The analysis of individual genes did not reveal significant differences between responders and non-responders. NOTCH4 mutations showed an association with relapse free survival, with three out of nine relapsing patients bearing a mutation and no mutations occurring in the relapse-free patients (p=0.008). Interestingly, PIK3CA mutations were only observed in patients with a functional BRCA gene (5/26 (19%) versus 0/30, p=0.017). Tumors with BRCA impairment may develop via different routes than tumors with functioning BRCA genes, and the PI3K pathway may play a role in the latter. This finding has also been observed in an independent dataset (Severson et al, 2014, submitted). Conclusions: Although few recurrent mutations were found, two interesting leads for follow up studies were identified. First, three out of nine tumors with a relapse had a NOTCH4 mutation while NOTCH4 mutations were not occurring in the relapse free group. Second, PIK3CA mutations were associated with BRCA proficient tumors. After validation in larger series, triple negative tumors with PI3K or NOTCH4 mutations can be candidates for agents targeting these oncogenic pathways. In this manner, a more individualized treatment of triple negative breast cancer might become possible in the near future. Citation Format: Esther H Lips, Magali Michaut, Marlous L Hoogstraat, Lennart Mulder, Nicolle Besselink, Marco J Koudijs, Emile E Voest, Rene Bernards, Petra M Nederlof, Jelle Wesseling, Sjoerd Rodenhuis, Lodewyk FA Wessels. Next generation sequencing to find predictors for chemotherapy response in triple negative breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P3-06-21.

Sex-specific and developmental expression of Dmrt genes in the starlet sea anemone, Nematostella vectensis.

BackgroundThe molecular mechanisms underlying sex determination and differentiation in animals are incredibly diverse. The Dmrt (doublesex and mab-3 related transcription factor) gene family is an evolutionary ancient group of transcription factors dating to the ancestor of metazoans that are, in part, involved in sex determination and differentiation in numerous bilaterian animals and thus represents a potentially conserved mechanism for differentiating males and females dating to the protostome-deuterostome ancestor. Recently, the diversity of this gene family throughout animals has been described, but the expression and potential function for Dmrt genes is not well understood outside the bilaterians.ResultsHere, we report sex- and developmental-specific expression of all 11 Dmrts in the starlet sea anemone Nematostella vectensis. Nine out of the eleven Dmrts showed significant differences in developmental expression, with the highest expression typically in the adult stage and, in some cases, with little or no expression measured during embryogenesis. When expression was compared in females and males, seven of the eleven Dmrt genes had significant differences in expression with higher expression in males than in females for six of the genes. Lastly, expressions of two Dmrt genes with differential expression in each sex are located in the mesenteries and into the pharynx in polyps.ConclusionsOur results show that the phylogenetic diversity of Dmrt genes in N. vectensis is matched by an equally diverse pattern of expression during development and in each sex. This dynamic expression suggests multiple functions for Dmrt genes likely present in early diverging metazoans. Detailed functional analyses of individual genes will inform hypotheses regarding the antiquity of function for these transcription factors.Electronic supplementary materialThe online version of this article (doi:10.1186/s13227-015-0013-7) contains supplementary material, which is available to authorized users.

Emerging technologies in paediatric leukaemia.

Genetic changes, in particular chromosomal aberrations, are a hallmark of acute lymphoblastic lymphoma (ALL) and accurate detection of them is important in ensuring assignment to the appropriate drug protocol. Our ability to detect these genetic changes has been somewhat limited in the past due to the necessity to analyse mitotically active cells by conventional G-banded metaphase analysis and by mutational analysis of individual genes. Advances in technology include high resolution, microarray-based techniques that permit examination of the whole genome. Here we will review the current available methodology and discuss how the technology is being integrated into the diagnostic setting.

80-OR

Objectives The traditional approach to understand health and disease has relied on the analyses of individual genes or proteins. Yet, biological functions are the expression of integrated and interdependent networks. We examined the behavior of protein networks in peripheral blood of normal pregnant women and those with preeclampsia (PE). Methods A cross-sectional study was conducted to include: (1) normal pregnancy ( n = 50); (2) early PE (delivered n = 44); and (3) late PE ( n = 43). Multiplex assay systems were used to measure proteins. Log transformed and normalized protein concentrations in normal pregnancies were modeled using locally weighted linear quantile regression. Protein abundance was represented as MOM. Differentially expressed proteins were retained to conduct a network analysis. Results (1) Eighty-six and 24 proteins were differentially expressed in early and late PE, respectively (fold >1.5 and adjusted p 4); (2) network analysis demonstrated a more coordinated protein activity in early PE with four distinct modules (Figure). These modules represented proteins involved in cell adhesion molecules, cytokine-cytokine receptor interaction; and coagulation cascade; and (3) the cyan module which was enriched in proteins involved in cell adhesion molecules pathway was present in early, but not in normal or late PE. Conclusions We report for the first time increased connectivity in protein–protein correlation networks in PE. We propose that characterizing the protein network structure and behavior provides insight into complex diseases. Figure Legend Protein correlation network in early preeclampsia. Four protein modules were identified (green, blue, gold, magenta). (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.) Disclosures P. Chaemsaithong: None. R. Romero: None. A.L. Tarca: None. Z. Xu: None. M. Shaman: None. K. Lannaman: None. A.I. Ahmed: None. S.S. Hassan: None. L. Yeo: None. T. Chaiworapongsa: None.

A multigene phylogenetic analysis results in a redefinition of the genus Notonomus Chaudoir (Coleoptera, Carabidae) and descriptions of new species of the subgenus Leiradira Castelnau

Bayesian analysis of four partial gene sequences (28S rDNA, wg, CAD and COI mtDNA) from exemplars of all genera and 12 of 17 informal groups of the Notonomus-series of pterostichine carabids strongly supports a clade requiring redefinition of Notonomus Chaudoir, 1862. Notonomus is redefined to include all species currently placed in Notonomus by Lorenz (2005a) plus two Sarticus Motschulsky, 1865 species (S. blackburni (Sloane, 1895) and S. impar (Sloane, 1893)), all species of Leiradira Castelnau, 1867, Conchitella Moore, 1962 Loxodactylus Chaudoir, 1865 and Acanthoferonia Moore, 1965. Analysis of combined data places Sarticus sister to Notonomus with low support. Individual gene analyses indicated wg is in conflict with other loci and analyses exclusive of wg place Parhypates Motschulsky, 1866 sister to Notonomus with very high support. Leiradira species form a clade within Notonomus including Notonomus dimorphicus Darlington, 1961 and N. flos Darlington, 1961. Six new species of the subgenus Leiradira from Queensland are described; Notonomus (Leiradira) thynnefiliarum, N. (L.) vadosus, N. (L.) viridis, N. (L.) spectabilis, N. (L.) iridescens and N. (L.) barrae. Two additional species of Notonomus s.l. are described; Notonomus hephaestus from the Lamb Range, Queensland, which is part of a mimicry complex with Notonomus (Leiradira) aurifer (Darlington, 1961); and Notonomus nocturnocappellus, from New South Wales, which represents a unique combination of characteristics for the genus. Descriptions of all species of Notonomus (Leiradira) with a wide gula, a grouping equivalent to Darlington’s concept of Leiradira, are given. An identification key to species of Notonomus (Leiradira), the two newly described Notonomus s.l. species and all recognised subgenera of Notonomus is provided.

Genetics and insect pest management in agriculture.

Abstract Genetics has long played a role in the history of insect pest management, and changes in the genetic methods used reflect changes that have occurred in the field itself over time. Beginning from simple collections of mutations and the development of chromosome linkage maps, many of the early applications of genetic technology were focused on the development of new strains for the sterile insect technique as a form of biological control. Since that time, and as the field of genetics underwent a true merger with molecular biology, the focus shifted almost entirely to methods using molecular technology. These methods had the advantage of being more broadly applicable to control of a wide range of pest species, and this did much to move the field away from the frustrations often associated with attempts to transfer genetic tools developed in Drosophila directly to these species. The latest applications of molecular genetic technologies in the area of genetically based control methods now also include cutting-edge systems for genome editing and the use of RNA inhibition for selectively knocking out the expression of individual genes. Finally, as the field of genetics has shifted its focus from the analysis of individual genes to that of entire genomes, new and exciting prospects are opening up for improvements in use of genetic technology for the management of insect pests.

Abstract 16260: Aspirin-Responsive Platelet Genes Are Associated With Platelet Function and Cardiovascular Events

Background: Aspirin prevents myocardial infarction (MI); the pathways with which aspirin interacts are not fully described. We hypothesized that genes that changed in response to aspirin exposure would be associated with platelet function and death/MI. Methods: Discovery (healthy volunteers; n=53) and Validation (diabetic patients; n=45) cohorts were exposed to aspirin 325mg/day. Before and after aspirin exposure, we measured platelet function by aggregometry and gene/platelet protein expression by whole blood RNA microarray analysis and unbiased proteomics of purified platelet protein, respectively. Gene Set Enrichment Analysis (GSEA) identified gene sets that changed in response to aspirin. Paired t-tests and regression were used to test individual genes and proteins for changes in expression with aspirin or association with platelet function, respectively. Cox regression models tested gene sets in aggregate using the 1st principal component of gene expression for association with death/MI in patients (n =638) using RNA collected at cardiac catheterization. Results: In the discovery cohort we identified 25 gene sets that changed in response to aspirin (family wise error rate [FWER] < 0.05). Of these, we chose to follow up on one set of 43 genes because it represented abundant platelet genes. This gene set was down regulated in the discovery and validation cohorts (FWER p = 0.01 and 0.04, respectively). We identified 4 of 43 genes in the platelet protein dataset; the expression of 3 changed (p < 0.03) in response to aspirin and was associated (p < 0.01) with platelet function after accounting for aspirin. The aggregate expression of this platelet gene set was associated with death/MI (p = 0.03) with the majority of genes associated with increased risk. Analysis of individual genes in this gene set identified several (HLA-E, H3F3A, GNAS, FTH1, TUBA4A, OAZ1, FLNA) that were significantly (p < 0.05) down-regulated by aspirin and also associated with an increased risk of death/MI. Conclusion: By using aspirin as a probe to uncover novel biology we identified a set of aspirin-responsive platelet genes associated with an increased risk of cardiovascular events. These findings may help to explain the effects of aspirin on preventing MI.

Heritability and molecular-genetic basis of the P3 event-related brain potential: a genome-wide association study.

P3 amplitude is a candidate endophenotype for disinhibitory psychopathology, psychosis, and other disorders. The present study is a comprehensive analysis of the behavioral- and molecular-genetic basis of P3 amplitude and a P3 genetic factor score in a large community sample (N = 4,211) of adolescent twins and their parents, genotyped for 527,829 single nucleotide polymorphisms (SNPs). Biometric models indicated that as much as 65% of the variance in each measure was due to additive genes. All SNPs in aggregate accounted for approximately 40% to 50% of the heritable variance. However, analyses of individual SNPs did not yield any significant associations. Analyses of individual genes did not confirm previous associations between P3 amplitude and candidate genes but did yield a novel association with myelin expression factor 2 (MYEF2). Main effects of individual variants may be too small to be detected by GWAS without larger samples.

Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells.

The roles of Argonaute proteins in cytoplasmic microRNA and RNAi pathways are well established. However, their implication in small RNA-mediated transcriptional gene silencing in the mammalian cell nucleus is less understood. We have recently shown that intronic siRNAs cause chromatin modifications that inhibit RNA polymerase II elongation and modulate alternative splicing in an Argonaute-1 (AGO1)-dependent manner. Here we used chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) to investigate the genome-wide distribution of AGO1 nuclear targets. Unexpectedly, we found that about 80% of AGO1 clusters are associated with cell-type-specific transcriptional enhancers, most of them (73%) overlapping active enhancers. This association seems to be mediated by long, rather than short, enhancer RNAs and to be more prominent in intragenic, rather than intergenic, enhancers. Paradoxically, crossing ChIP-seq with RNA-seq data upon AGO1 depletion revealed that enhancer-bound AGO1 is not linked to the global regulation of gene transcription but to the control of constitutive and alternative splicing, which was confirmed by an individual gene analysis explaining how AGO1 controls inclusion levels of the cassette exon 107 in the SYNE2 gene.

Abstract 5060: Dietary sodium, potassium and fluid intake and clear cell renal cell cancer: heterogeneous effects by DNA methylation of genes involved in renal salt homeostasis

Abstract Introduction: Sodium, potassium and fluid play a key role in renal salt homeostasis. We showed that sodium intake is associated with higher renal cell cancer (RCC) risk. Promoter CpG island methylation, leading to silencing of tumor suppressor genes, may also affect RCC carcinogenesis. We investigated whether associations between sodium, potassium and fluid intake and RCC risk differed for RCC subtypes defined by promoter methylation of genes involved in renal salt homeostasis. Methods: The Netherlands Cohort Study (NLCS) with case-cohort design included 120,852 subjects aged 55-69 years. Diet was measured with a food frequency questionnaire. After 20.3 years of follow-up, paraffin-embedded tumor blocks from 454 incident RCC cases were collected, of which 80% had clear cell (cc) histology. Methylation-specific PCR was used to analyze promoter CpG island methylation in tumor DNA. Genes involved in renal salt homeostasis were of interest if exhibiting 1) promoter CpG island methylation in ccRCC cell lines and not in normal kidney tissue in a genome-wide methylation screen (MBD-affinity massive parallel sequencing) and 2) ccRCC-specific down-regulation in public expression data. We identified ARHGDIG, ATP1A1, SCNN1B and SLC8A3 as candidate genes, which were then combined into a methylation sum score and categorized representing no (0 genes methylated), low (1 gene methylated) and high (≥2 genes methylated) methylation. Cox regression analyses were stratified accordingly and included 4,439 subcohort members and 348 ccRCC cases. Results: ARHGDIG, ATP1A1, SCNN1B and SLC8A3 were methylated in 22.7%, 16.4%, 42.2% and 5.5% of ccRCC tumors. High sodium intake increased overall ccRCC risk [HR(95%CI): 1.42(1.06-1.89)] regardless of methylation status (P-heterogeneity = 0.69). High potassium intake was differently associated with ccRCC risk (P-heterogeneity = 0.02); ccRCC risk was lower for tumors without methylation [HR(95%CI): 0.59(0.36-0.98)], but higher for tumors with high methylation [HR(95%CI): 1.50(0.89-2.52)]. For fluid intake, HRs similarly differed across the methylation subtypes, but heterogeneity was not significant (P-heterogeneity = 0.45). Individual gene analyses showed that SCNN1B was most indicative of the heterogeneous effects. Discussion: Our findings indicate for the first time a joint influence of diet and epigenetics to determine ccRCC risk. By investigating specific dietary intakes and DNA methylation in selected genes we provide a biological rational for the role of renal salt homeostasis in the development of ccRCC. In particular, we show that, besides sodium intake, also potassium and fluid intake may be implicated in ccRCC etiology, when the epigenetic environment is considered. Further exploration of the temporal relationship and exact pathological pathway is however warranted. Citation Format: Ivette A. G. Deckers, Piet A. van den Brandt, Manon van Engeland, Patricia M. M. B. Soetekouw, Marcella M. L. L. Baldewijns, András P. Keszei, Leo J. Schouten. Dietary sodium, potassium and fluid intake and clear cell renal cell cancer: heterogeneous effects by DNA methylation of genes involved in renal salt homeostasis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5060. doi:10.1158/1538-7445.AM2014-5060

Abstract 1461: A miR-221 multigene pharmacodynamic signature for assessing miR-221 inhibition

Abstract miR-221 targets key cancer pathways, inhibits translation of important tumor suppressors, and is overexpressed in hepatocellular carcinoma (HCC). Aberrant miR-221 expression has been linked to HCC progression, while inhibition of miR-221 has been shown to reduce tumor growth. In preclinical models, miR-221 inhibition can be assessed by measuring de-repression of known miR-221 target genes such as p27. However, changes in individual microRNA target genes are often small and model-dependent; and comprehensive assessment of pharmacodynamic (PD) effects following microRNA inhibition is often challenging. Herein, we present a miR-221 multigene PD signature that can assess miR-221 target engagement with a large dynamic window and work across different human HCC models following miR-221 inhibition. In the first stage, we transfected five different human HCC lines with two chemically-modified oligonucleotides that inhibit miR-221 functions (miR-221 anti-miRs) and a microRNA-duplex that mimics miR-221/222 functions (mimic). The resulting global mRNA expression changes were compared to mock treated cells using GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix). Ninety unique human genes with transcripts containing conserved and/or 8-mer target seeds (TargetScan), that significantly went up and down after anti-miR-221s and mimic treatment respectively, were further profiled with qPCR in the second stage. Out of the 90 tested transcripts, 62 of them were significantly up-regulated by anti-miR-221s but not by control oligonucleotides (either mismatch or targeting unrelated microRNAs). From the 62 genes, an optimal multigene signature consisted of 13 unique human genes normalized by 6 reference housekeeping genes was identified. We also devised a “miR-221 signature score” and demonstrated that our multigene signature can separate miR-221 anti-miRs treatment from control oligonucleotides with a high degree of sensitivity and specificity. We further validated this multigene signature by demonstrating that it correctly distinguished miR-221 anti-miRs treatment from controls in three additional HCC cell lines in vitro and one HCC model in vivo. In summary, our miR-221 multigene PD signature analysis provided a comprehensive assessment of miR-221 inhibition, with significantly larger dynamic window compare to individual gene analysis, that may be used to discover, rank order and guide the development of novel miR-221 anti-miRs for the treatment of human cancers. Citation Format: Adam Pavlicek, Thomas Vincent, Oivin Guicherit, Nelson Chau, Sonya Zabludoff, Neil Gibson, Edmund C. Lee. A miR-221 multigene pharmacodynamic signature for assessing miR-221 inhibition. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1461. doi:10.1158/1538-7445.AM2014-1461

Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus

Phylogenetic relationships among 108 oak species (genus Quercus L.) were inferred using DNA sequences of six nuclear genes selected from the existing genomic resources of the genus. Previous phylogenetic reconstructions based on traditional molecular markers are inconclusive at the deeper nodes. Overall, weak phylogenetic signals were obtained for each individual gene analysis, but stronger signals were obtained when gene sequences were concatenated. Our data support the recognition of six major intrageneric groups Cyclobalanopsis, Cerris, Ilex, Quercus, Lobatae and Protobalanus. Our analyses provide resolution at deeper nodes but with moderate support and a more robust infrageneric classification within the two major clades, the ‘Old World Oaks’ (Cyclobalanopsis, Cerris, Ilex) and ‘New World Oaks’ (Quercus, Lobatae, Protobalanus). However, depending on outgroup choice, our analysis yielded two alternative placements of the Cyclobalanopsis clade within the genus Quercus. When Castanea Mill. was chosen as outgroup, our data suggested that the genus Quercus comprised two clades corresponding to two subgenera as traditionally recognized by Camus: subgenus Euquercus Hickel and Camus and subgenus Cyclobalanopsis Øersted (Schneider). However, when Notholithocarpus Manos, Cannon and S. Oh was chosen as an outgroup subgenus Cyclobalanopsis clustered with Cerris and Ilex groups to form the Old World clade. To assess the placement of the root, we complemented our dataset with published data of ITS and CRC sequences. Based on the concatenated eight gene sequences, the most likely root position is at the split between the ‘Old World Oaks’ and the ‘New World Oaks’, which is one of the alternative positions suggested by our six gene analysis. Using a dating approach, we inferred an Eocene age for the primary divergences in Quercus and a root age of about 50–55 Ma, which agrees with palaeobotanical evidence. Finally, irrespective of the outgroup choice, our data boost the topology within the New World clade, where (Protobalanus + Quercus) is a sister clade of Lobatae. Inferred divergence ages within this clade and the Cerris–Ilex clade are generally younger than could be expected from the fossil record, indicating that morphological differentiation pre-dates genetic isolation in this clade.

Association between serotonin Cumulative Genetic Score and the Behavioral Approach System (BAS): Moderation by early life environment

The present study investigates if genetic variation in the serotonergic system interacts with early adversity to predict changes in the Behavioral Approach System (BAS), a system that taps into reward processing. In a sample of community adults (N=236) the influence of single serotonergic candidate polymorphisms on BAS was analyzed, we also examined the aggregate contribution of these genetic variants by creating a Cumulative Genetic Score (CGS). A CGS quantifies an individual’s cumulative risk by aggregating the number of risk alleles across the candidate polymorphisms. After individual gene analysis, three candidate genes rs7305115 (TPH2), rs6311 (HTR2A), and rs6295 (HTR1A) were combined into the CGS. There were no significant interactions between individual candidate polymorphisms and childhood adversity, but the CGS interacted with childhood adversity to explain a significant amount of variance (11.6%) in the BAS. Findings suggest that genetic variations in the serotonergic system in combination with childhood adversity contribute to individual differences in reward sensitivity.

Overly simplistic substitution models obscure green plant phylogeny.

Phylogenetic analysis is an increasingly common and valuable component of plant science. Knowledge of the phylogenetic relationships between plant groups is a prerequisite for understanding the origin and evolution of important plant features, and phylogenetic analysis of individual genes and gene families provides fundamental insights into how those genes and their functions evolved. However, despite an active research community exploring and improving phylogenetic methods, the analytical methods commonly used, and the phylogenetic results they produce, are accorded far more confidence than they warrant. In this opinion article, I emphasise that important parts of the green plant phylogeny are inconsistently resolved and I argue that the lack of consistency arises due to inadequate modelling of changes in the substitution process.

Enhancing crop resilience to combined abiotic and biotic stress through the dissection of physiological and molecular crosstalk.

Plants growing in their natural habitats are often challenged simultaneously by multiple stress factors, both abiotic and biotic. Research has so far been limited to responses to individual stresses, and understanding of adaptation to combinatorial stress is limited, but indicative of non-additive interactions. Omics data analysis and functional characterization of individual genes has revealed a convergence of signaling pathways for abiotic and biotic stress adaptation. Taking into account that most data originate from imposition of individual stress factors, this review summarizes these findings in a physiological context, following the pathogenesis timeline and highlighting potential differential interactions occurring between abiotic and biotic stress signaling across the different cellular compartments and at the whole plant level. Potential effects of abiotic stress on resistance components such as extracellular receptor proteins, R-genes and systemic acquired resistance will be elaborated, as well as crosstalk at the levels of hormone, reactive oxygen species, and redox signaling. Breeding targets and strategies are proposed focusing on either manipulation and deployment of individual common regulators such as transcription factors or pyramiding of non- (negatively) interacting components such as R-genes with abiotic stress resistance genes. We propose that dissection of broad spectrum stress tolerance conferred by priming chemicals may provide an insight on stress cross regulation and additional candidate genes for improving crop performance under combined stress. Validation of the proposed strategies in lab and field experiments is a first step toward the goal of achieving tolerance to combinatorial stress in crops.

The tissue-specific transcriptomic landscape of the mid-gestational mouse embryo.

Differential gene expression is a prerequisite for the formation of multiple cell types from the fertilized egg during embryogenesis. Understanding the gene regulatory networks controlling cellular differentiation requires the identification of crucial differentially expressed control genes and, ideally, the determination of the complete transcriptomes of each individual cell type. Here, we have analyzed the transcriptomes of six major tissues dissected from mid-gestational (TS12) mouse embryos. Approximately one billion reads derived by RNA-seq analysis provided extended transcript lengths, novel first exons and alternative transcripts of known genes. We have identified 1375 genes showing tissue-specific expression, providing gene signatures for each of the six tissues. In addition, we have identified 1403 novel putative long noncoding RNA gene loci, 439 of which show differential expression. Our analysis provides the first complete transcriptome data for the mouse embryo. It offers a rich data source for the analysis of individual genes and gene regulatory networks controlling mid-gestational development.

Co-expression network analysis reveals immune response pathways important for pathogenesis of Chlamydial pelvic inflammatory disease (PID). (HUM8P.329)

Abstract Processes driving development of immune pathology after Chlamydia trachomatis infection are poorly understood. To provide insight into the pathways that may be underappreciated by individual gene analysis, weighted gene co-expression network analysis was performed to identify network modules using blood transcriptional profiles of women with chlamydial PID (N=15) and asymptomatically infected women (N=84). Modules, defined as centrally connected genes, that were significantly associated with chlamydial PID were further accessed via Ingenuity Pathway analysis. Type I and type II interferon (IFN) signaling pathways were significantly up regulated in women with chlamydial PID. Up regulation of both of these pathways has been detected in the transcriptomes of patients with active tuberculosis, suggesting a parallel role in PID. Up regulation of aryl hydrocarbon receptor, agranulocyte/granulocyte adhesion and diapedesis pathways was also noted, while EIF2/EIF4, mTOR and ILK signaling, granzyme A/B signaling, cross talk between dendritic cells and natural killer cells, signaling in T helper cells and T cell receptor pathways were down-regulated. Pathways likely to contribute to immunopathogenesis, including migration of leukocytes and inflammation were activated in chlamydial PID, while those involved in cell growth/proliferation and clearance of infected cells were decreased. Bioinformatics provides a new avenue to improve understanding of chlamydial disease mechanisms.