Pathways and Networks-Based Analysis of Candidate Genes Associated with Nicotine Addiction

Nicotine is the addictive substance in tobacco and it has a broad impact on both the central and peripheral nervous systems. Over the past decades, an increasing number of genes potentially involved in nicotine addiction have been identified by different technical approaches. However, the molecular mechanisms underlying nicotine addiction remain largely unclear. Under such situation, a comprehensive analysis focusing on the overall functional characteristics of these genes, as well as how they interact with each other will provide us valuable information to understand nicotine addiction. In this study, we presented a systematic analysis on nicotine addiction-related genes to identify the major underlying biological themes. Functional analysis revealed that biological processes and biochemical pathways related to neurodevelopment, immune system and metabolism were significantly enriched in the nicotine addiction-related genes. By extracting the nicotine addiction-specific subnetwork, a number of novel genes associated with addiction were identified. Moreover, we constructed a schematic molecular network for nicotine addiction via integrating the pathways and network, providing an intuitional view to understand the development of nicotine addiction. Pathway and network analysis indicated that the biological processes related to nicotine addiction were complex. Results from our work may have important implications for understanding the molecular mechanism underlying nicotine addiction.     

Identification of Key Candidate Genes and Pathways of Candida albicans-Infected Human Umbilical Vein Endothelial Cells and Drug Screening

Indian Journal of Microbiology - Candida albicans is a common opportunistic pathogen that can cause serious infection by blood transmission. C. albicans enters the blood circulation and adheres to...     

Schizophrenia Gene Networks and Pathways and Their Applications for Novel Candidate Gene Selection

Background

Schizophrenia (SZ) is a heritable, complex mental disorder. We have seen limited success in finding causal genes for schizophrenia from numerous conventional studies. Protein interaction network and pathway-based analysis may provide us an alternative and effective approach to investigating the molecular mechanisms of schizophrenia.

Methodology/Principal Findings

We selected a list of schizophrenia candidate genes (SZGenes) using a multi-dimensional evidence-based approach. The global network properties of proteins encoded by these SZGenes were explored in the context of the human protein interactome while local network properties were investigated by comparing SZ-specific and cancer-specific networks that were extracted from the human interactome. Relative to cancer genes, we observed that SZGenes tend to have an intermediate degree and an intermediate efficiency on a perturbation spreading throughout the human interactome. This suggested that schizophrenia might have different pathological mechanisms from cancer even though both are complex diseases. We conducted pathway analysis using Ingenuity System and constructed the first schizophrenia molecular network (SMN) based on protein interaction networks, pathways and literature survey. We identified 24 pathways overrepresented in SZGenes and examined their interactions and crosstalk. We observed that these pathways were related to neurodevelopment, immune system, and retinoic X receptor (RXR). Our examination of SMN revealed that schizophrenia is a dynamic process caused by dysregulation of the multiple pathways. Finally, we applied the network/pathway approach to identify novel candidate genes, some of which could be verified by experiments.

Conclusions/Significance

This study provides the first comprehensive review of the network and pathway characteristics of schizophrenia candidate genes. Our preliminary results suggest that this systems biology approach might prove promising for selection of candidate genes for complex diseases. Our findings have important implications for the molecular mechanisms for schizophrenia and, potentially, other psychiatric disorders.     

Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

Genome-wide association studies have been successful in identifying genes involved in polygenic traits and are valuable for crop improvement. Tomato (Solanum lycopersicum) is a major crop and is highly appreciated worldwide for its health value. We used a core collection of 163 tomato accessions composed of S. lycopersicum, S. lycopersicum var cerasiforme, and Solanum pimpinellifolium to map loci controlling variation in fruit metabolites. Fruits were phenotyped for a broad range of metabolites, including amino acids, sugars, and ascorbate. In parallel, the accessions were genotyped with 5,995 single-nucleotide polymorphism markers spread over the whole genome. Genome-wide association analysis was conducted on a large set of metabolic traits that were stable over 2 years using a multilocus mixed model as a general method for mapping complex traits in structured populations and applied to tomato. We detected a total of 44 loci that were significantly associated with a total of 19 traits, including sucrose, ascorbate, malate, and citrate levels. These results not only provide a list of candidate loci to be functionally validated but also a powerful analytical approach for finding genetic variants that can be directly used for crop improvement and deciphering the genetic architecture of complex traits.In crops, linkage mapping has proved invaluable for detecting quantitative trait loci (QTLs) for traits of interest and to unravel their underlying genetic architecture. This approach is based on the analysis of the segregation of polymorphism between the parental lines and their progeny. However, one of the limitations of this approach is the reduced number of recombination events that occur per generation (for review, see Korte and Farlow, 2013). This leads to extended linkage blocks that reduce the accuracy of the linkage mapping. An alternative to linkage-based mapping studies is to perform linkage disequilibrium (LD) mapping in a population of theoretically unrelated individuals. The ancestral polymorphism segregating through this population (or panel) is far more informative compared with the polymorphism of the parental lines of the linkage mapping population (Mauricio, 2001). LD mapping, also known as genome-wide association (GWA), relies on the natural patterns of LD in the population investigated. The aim of GWA is to reveal trait-associated loci by taking advantage of the level of LD. Depending on the decay of LD, the mapping resolution can be narrowed from a large genomic portion where the level of LD is relatively high to a single marker when the LD level is very low.Following domestication, crops are prone to (1) increased levels of LD, (2) population structure (remote common ancestry of large groups of individuals), and (3) cryptic relatedness (the presence of close relatives in a sample of unrelated individuals; Riedelsheimer et al., 2012). Population structure and cryptic relatedness may lead to false-positive association in GWA studies (Astle and Balding, 2009), but their effect is now relatively well accounted for in mixed linear models (for review, see Sillanpää, 2011; Listgarten et al., 2012). The problem of high LD in GWA scans also must be taken into account: Segura et al. (2012) investigated this difficulty by proposing a multilocus mixed model (MLMM) that handles the confounding effect of background loci that may be present throughout the genome due to LD. This approach revealed multiple loci in LD and associated with sodium concentration in leaves in Arabidopsis (Arabidopsis thaliana), while previous methods failed to identify this complex pattern (Segura et al., 2012).In parallel, the development of cost-effective high-throughput sequencing technologies has identified increasingly dense variant loci necessary to conduct GWA scans, especially in model species such as rice (Oryza sativa) for agronomic traits (Huang et al., 2010) or maize (Zea mays) for drought tolerance (Lu et al., 2010; for review, see Soto-Cerda and Cloutier, 2012). However, GWA is not restricted to model species and is becoming increasingly widespread in nonmodel ones such as sunflower (Helianthus annuus; Mandel et al., 2013) and tomato (Solanum lycopersicum; Xu et al., 2013), where numerous associations have been successfully identified for traits related to plant architecture (branching in the case of sunflower) and fruit quality (e.g. fresh weight in tomato).Tomato is a crop of particular interest, as the fruit are an important source of fiber and nutrients in the human diet and a model for the study of fruit development (Giovannoni, 2001). Over the last two decades, numerous QTLs have been identified for traits such as fresh weight using linkage approaches (Frary et al., 2000; Zhang et al., 2012; Chakrabarti et al., 2013) but also for other fruit-related traits such as fruit ascorbic acid levels (Stevens et al., 2007), sensory and instrumental quality traits (Causse et al., 2002), sugar and organic acids (Fulton et al., 2002), and metabolic components (Schauer et al., 2008). Large tomato germplasm collections have been characterized at the molecular level using simple sequence repeat (Ranc et al., 2008) and single-nucleotide polymorphism (SNP) markers (Blanca et al., 2012; Shirasawa et al., 2013), giving insights into population structure, tomato evolutionary history, and the genetic architecture of traits of agronomic interest. These screens of nucleotide diversity were made possible (for review, see Bauchet and Causse, 2012) in the last couple of years due to the release of the tomato genome sequence (Tomato Genome Consortium, 2012) and derived genomic tools such as a high-density SNP genotyping array (Sim et al., 2012). The combination of large germplasm collections, high-throughput genomic tools, and traits of economic interest provide a framework to apply genome-wide association study (GWAS) in this species. In tomato, previous association studies have been limited to a targeted region (e.g. chromosome 2; Ranc et al., 2012), used low-density genome-wide-distributed SNP markers (Xu et al., 2013), or investigated a limited number of agronomic traits with low precision on the association panel (Shirasawa et al., 2013).Using tomato as a model, we aimed to investigate the genetic architecture of traits related to fruit metabolic composition at high resolution. To reach this objective, we carried out an investigation into LD patterns at the genome-wide scale and a GWA scan using the MLMM approach. We present results on the genetic architecture of fruit metabolic composition for metabolites such as organic acids, amino acids, sugars, and ascorbate in tomato.     

Differential Gene Repertoire in Mycobacterium ulcerans Identifies Candidate Genes for Patho-Adaptation

Background

Based on large genomic sequence polymorphisms, several haplotypes belonging to two major lineages of the human pathogen Mycobacterium ulcerans could be distinguished among patient isolates from various geographic origins. However, the biological relevance of insertional/deletional diversity is not understood.

Methodology

Using comparative genomics, we have investigated the genes located in regions of difference recently identified by DNA microarray based hybridisation analysis. The analysed regions of difference comprise ∼7% of the entire M. ulcerans genome.

Principal Findings

Several different mechanisms leading to loss of functional genes were identified, ranging from pseudogenization, caused by frame shift mutations or mobile genetic element interspersing, to large sequence polymorphisms. Four hot spot regions for genetic instability were unveiled. Altogether, 229 coding sequences were found to be differentially inactivated, constituting a repertoire of coding sequence variation in the rather monomorphic M. ulcerans.

Conclusions/Significance

The differential gene inactivation patterns associated with the M. ulcerans haplotypes identified candidate genes that may confer enhanced adaptation upon ablation of expression. A number of gene conversions confined to the classical lineage may contribute to particular virulence of this group comprising isolates from Africa and Australia. Identification of this spectrum of anti-virulence gene candidates expands our understanding of the pathogenicity and ecology of the emerging infectious disease Buruli ulcer.     

播散性浅表性光线性汗孔角化症DSAP1位点的精细定位和候选基因的突变检测

播散性浅表性光线性汗孔角化症(DSAP)是一种以多个浅表的角化性皮损,边缘轻微嵴状角化性隆起为特征的少见的慢性角化性皮肤病,呈常染色体显性遗传。以往的研究将该病基因定位于12q23．2—24．1区域(DSAP1)和15q25．1-26．1区域(DSAP2)。本研究对2个无关的六代DSAP家系进行了全基因组扫描和连锁分析,结果显示,这2个DSAP家系在D12窝4位点的最高累积LOD值为8．28(θ=0．00)。单倍型分析结果显示,这2个DSAP家系致病基因位于12q24．1-q24．2(D12S330和D12S354)之间8．0cM的区域内。该区域与DSAP1的致病区域部分重叠。对重叠区域内6个候选基因(CRY1,PWP1,ASCL4,PRDM4,KIAA0789和CMKLR1)的编码区进行序列分析,在DSAP病人中未发现突变位点。提示该6个候选基因可能与这2个DSAP家系的发病机理无关。     

Defining the Sequence Elements and Candidate Genes for the Coloboma Mutation

The chicken coloboma mutation exhibits features similar to human congenital developmental malformations such as ocular coloboma, cleft-palate, dwarfism, and polydactyly. The coloboma-associated region and encoded genes were investigated using advanced genomic, genetic, and gene expression technologies. Initially, the mutation was linked to a 990 kb region encoding 11 genes; the application of the genetic and genomic tools led to a reduction of the linked region to 176 kb and the elimination of 7 genes. Furthermore, bioinformatics analyses of capture array-next generation sequence data identified genetic elements including SNPs, insertions, deletions, gaps, chromosomal rearrangements, and miRNA binding sites within the introgressed causative region relative to the reference genome sequence. Coloboma-specific variants within exons, UTRs, and splice sites were studied for their contribution to the mutant phenotype. Our compiled results suggest three genes for future studies. The three candidate genes, SLC30A5 (a zinc transporter), CENPH (a centromere protein), and CDK7 (a cyclin-dependent kinase), are differentially expressed (compared to normal embryos) at stages and in tissues affected by the coloboma mutation. Of these genes, two (SLC30A5 and CENPH) are considered high-priority candidate based upon studies in other vertebrate model systems.     

利用来自多技术平台数据的候选基因挖掘食物抗氧化剂共同影响基因或通路

抗氧化剂通过调节机体基因表达发挥广泛的功能,基于多种技术平台的研究文献中蕴藏大量抗氧化剂可调控的基因.探索这些基因间的关系有助于阐明抗氧剂的共同作用机理,也有助于开发新的生物标记用于抗氧化剂筛选.选择维生素C、维生素E和视黄酸等3种典型抗氧化剂为研究对象,从highwire数据库检索文献提取与它们功能相关主要基因,利用DAVID在线GO分析工具和pathway express分析工具分析其相关的GO生物过程定义及基因通路.结果表明,这3种抗氧化剂共同可调控的基因有14个,每种抗氧化剂显著相关的GO生理过程定义及基因通路具有很多相似性,涉及细胞通讯、免疫、细胞凋亡、细胞周期和多种典型信号传导通路.粘着斑是这3种抗氧化剂共同影响的基因网络,说明这3种抗氧化剂可能通过这一信号通路系统调节细胞周期调控、细胞骨架组装、粘附、迁徙、运动能力、生长调节、生存、血管生成等多方面发挥了重要作用,并以此通路为靶标抑制肿瘤发生、发展及侵袭转移.     

Pathways of Uptake and Accumulation of Sugars in Tomato Fruit

The route of sucrose unloading from the conducting tissue, theregulation of sucrose hydrolysis and the uptake and subsequentmetabolism of sugars were investigated in the rapidly growingtomato fruit. During the first two weeks of fruit enlargement, the vacuoleaccounted for more than 85% of the protoplast volume and theintercellular space accounted for 20% of the fruit placentaltissue. The plasmodesmatal frequency was highest between phloemparenchyma cells and lowest between phloem sieve cells and phloemparenchyma. The total invertase activity was about 8 µmolglucose g^–1 d. wt min^–1 during the rapid growingperiod and increased six-fold at ripening. The wall-bound invertaseaccounted for less than 11% of the total activity. Invertaseactivity increased with increasing sucrose concentrations (upto 50 mM) in the incubation medium, but decreased at higherconcentrations. Sucrose synthase activity could only be detectedwhen fruit was older than 19 d. The uptake and metabolism of sugars by fruit cells were investigatedby incubation of fruit slices with ¹⁴C-sugars for 3 h. The uptakeof sucrose increased with the sucrose concentration up to 200mM. The rate of glucose uptake and its conversion to the ethanol-insolublefraction were higher than those of sucrose. The uptake of sucrosedid not compete with that of glucose or vice versa, providedthe osmotic potential of the incubation solution was maintainedconstant. The uptake of sucrose was not inhibited by metabolicinhibitors such as PCMBS, CCCP, sodium azide or vanadate. TheATPase activity in the fruit tissue was low. These findings did not identify conclusively the mode of sucroseunloading. However, the uptake of sugars by fruit cells is non-specificand does not appear to require a membrane carrier or plasmalemmaATPase to provide energy for sucrose uptake. Fruit, invertase, Lycopersicon esculentum, phloem unloading, plasmodesmata, sucrose     

Molecular Characterization of Five Porcine Candidate Genes for Drip Loss in Pork

Drip loss is the loss of fluid from a piece of meat without mechanical force and represents an important meat quality trait. Previous work revealed a quantitative trait locus (QTL) for drip loss in pork in an experimental Duroc x Piétrain (DUPI) F2 family on SSC 5. Based on functional data indicating their possible involvement in water holding capacity and their expression in skeletal muscle, we selected five positional candidates (ACO2, ADSL, CBY1, KCNJ4, PLA2AG6) out of 130 predicted genes in the QTL interval for further analysis. We performed a mutation analysis of all coding exons and discovered 204 polymorphisms. We genotyped 39 single nucleotide polymorphisms (SNPs) in 192 Piétrain pigs with extreme drip loss phenotypes and detected a possible association with drip loss for one non-coding SNP in the ADSL gene (ss107793818, p_raw = 0.021). Correspondingly, ADSL diplotypes were associated with drip loss and pH1 of M. longissimus dorsi. However, after correction for multiple testing, none of the tested SNPs were significantly associated with drip loss. One possible explanation for these results is that one of the QTL-alleles from the experimental DUPI family may be fixed or nearly fixed in the tested Piétrain population.