Complete Mitochondrial Genome Sequences of the South American and the Australian Lungfish: Testing of the Phylogenetic Performance of Mitochondrial Data Sets for Phylogenetic Problems in Tetrapod Relationships

We determined the complete nucleotide sequences (16403 and 16572 base pairs, respectively) of the mitochondrial genomes of the South American lungfish, Lepidosiren paradoxa, and the Australian lungfish, Neoceratodus forsteri (Sarcopterygii, Dipnoi). The mitochondrial DNA sequences were established in an effort to resolve the debated evolutionary positions of the lungfish and the coelacanth relative to land vertebrates. Previous molecular phylogenetic studies based on complete mtDNA sequences, including only the African lungfish, Protopterus dolloi, sequence were able to strongly reject the traditional textbook hypothesis that coelacanths are the closest relatives of land vertebrates. However, these studies were unable to statistically significantly distinguish between the two remaining scenarios: lungfish as the closest relatives to land vertebrates and lungfish and coelacanths jointly as their sister group (Cao et al. 1998; Zardoya et al. 1998; Zardoya and Meyer 1997a). Lungfish, coelacanths, and the fish ancestors of the tetrapod lineage all originated within a short time window of about 20 million years, back in the early Devonian (about 380 to 400 million years ago). This short divergence time makes the determination of the phylogenetic relationships among these three lineages difficult. In this study, we attempted to break the long evolutionary branch of lungfish, in an effort to better resolve the phylogenetic relationships among the three extant sarcopterygian lineages. The gene order of the mitochondrial genomes of the South American and Australian lungfish conforms to the consensus gene order among gnathostome vertebrates. The phylogenetic analyses of the complete set of mitochondrial proteins (without ND6) suggest that the lungfish are the closest relatives of the tetrapods, although the support in favor of this scenario is not statistically significant. The two other smaller data sets (tRNA and rRNA genes) give inconsistent results depending on the different reconstruction methods applied and cannot significantly rule out any of the three alternative hypotheses. Nuclear protein-coding genes, which might be better phylogenetic markers for this question, support the lungfish–tetrapod sister-group relationship (Brinkmann et al. 2004).This article contains online supplementary material.Reviewing Editor: Dr. Rafael Zardoya     

A Hybrid Approach of Gene Sets and Single Genes for the Prediction of Survival Risks with Gene Expression Data

Accumulated biological knowledge is often encoded as gene sets, collections of genes associated with similar biological functions or pathways. The use of gene sets in the analyses of high-throughput gene expression data has been intensively studied and applied in clinical research. However, the main interest remains in finding modules of biological knowledge, or corresponding gene sets, significantly associated with disease conditions. Risk prediction from censored survival times using gene sets hasn’t been well studied. In this work, we propose a hybrid method that uses both single gene and gene set information together to predict patient survival risks from gene expression profiles. In the proposed method, gene sets provide context-level information that is poorly reflected by single genes. Complementarily, single genes help to supplement incomplete information of gene sets due to our imperfect biomedical knowledge. Through the tests over multiple data sets of cancer and trauma injury, the proposed method showed robust and improved performance compared with the conventional approaches with only single genes or gene sets solely. Additionally, we examined the prediction result in the trauma injury data, and showed that the modules of biological knowledge used in the prediction by the proposed method were highly interpretable in biology. A wide range of survival prediction problems in clinical genomics is expected to benefit from the use of biological knowledge.     

Arthropod Phylogenetics in Light of Three Novel Millipede (Myriapoda: Diplopoda) Mitochondrial Genomes with Comments on the Appropriateness of Mitochondrial Genome Sequence Data for Inferring Deep Level Relationships

Background

Arthropods are the most diverse group of eukaryotic organisms, but their phylogenetic relationships are poorly understood. Herein, we describe three mitochondrial genomes representing orders of millipedes for which complete genomes had not been characterized. Newly sequenced genomes are combined with existing data to characterize the protein coding regions of myriapods and to attempt to reconstruct the evolutionary relationships within the Myriapoda and Arthropoda.

Results

The newly sequenced genomes are similar to previously characterized millipede sequences in terms of synteny and length. Unique translocations occurred within the newly sequenced taxa, including one half of the Appalachioria falcifera genome, which is inverted with respect to other millipede genomes. Across myriapods, amino acid conservation levels are highly dependent on the gene region. Additionally, individual loci varied in the level of amino acid conservation. Overall, most gene regions showed low levels of conservation at many sites. Attempts to reconstruct the evolutionary relationships suffered from questionable relationships and low support values. Analyses of phylogenetic informativeness show the lack of signal deep in the trees (i.e., genes evolve too quickly). As a result, the myriapod tree resembles previously published results but lacks convincing support, and, within the arthropod tree, well established groups were recovered as polyphyletic.

Conclusions

The novel genome sequences described herein provide useful genomic information concerning millipede groups that had not been investigated. Taken together with existing sequences, the variety of compositions and evolution of myriapod mitochondrial genomes are shown to be more complex than previously thought. Unfortunately, the use of mitochondrial protein-coding regions in deep arthropod phylogenetics appears problematic, a result consistent with previously published studies. Lack of phylogenetic signal renders the resulting tree topologies as suspect. As such, these data are likely inappropriate for investigating such ancient relationships.     

Slow Mitochondrial COI Sequence Evolution at the Base of the Metazoan Tree and Its Implications for DNA Barcoding

The evolution rates of mtDNA in early metazoans hold important implications for DNA barcoding. Here, we present a comprehensive analysis of intra- and interspecific COI variabilities in Porifera and Cnidaria (separately as Anthozoa, Hydrozoa, and Scyphozoa) using a data set of 619 sequences from 224 species. We found variation within and between species to be much lower in Porifera and Anthozoa compared to Medusozoa (Hydrozoa and Scyphozoa), which has divergences similar to typical metazoans. Given that recent evidence has shown that fungi also exhibit limited COI divergence, slow-evolving mtDNA is likely to be plesiomorphic for the Metazoa. Higher rates of evolution could have originated independently in Medusozoa and Bilateria or been acquired in the Cnidaria + Bilateria clade and lost in the Anthozoa. Low identification success and substantial overlap between intra- and interspecific COI distances render the Anthozoa unsuitable for DNA barcoding. Caution is also advised for Porifera and Hydrozoa because of relatively low identification success rates as even threshold divergence that maximizes the “barcoding gap” does not improve identification success. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Limitations of Metazoan 18S rRNA Sequence Data: Implications for Reconstructing a Phylogeny of the Animal Kingdom and Inferring the Reality of the Cambrian Explosion

We document the phylogenetic behavior of the 18S rRNA molecule in 67 taxa from 28 metazoan phyla and assess the effects of among-site rate variation on reconstructing phylogenies of the animal kingdom. This empirical assessment was undertaken to clarify further the limits of resolution of the 18S rRNA gene as a phylogenetic marker and to address the question of whether 18S rRNA phylogenies can be used as a source of evidence to infer the reality of a Cambrian explosion. A notable degree of among-site rate variation exists between different regions of the 18S rRNA molecule, as well as within all classes of secondary structure. There is a significant negative correlation between inferred number of nucleotide substitutions and phylogenetic information, as well as with the degree of substitutional saturation within the molecule. Base compositional differences both within and between taxa exist and, in certain lineages, may be associated with long branches and phylogenetic position. Importantly, excluding sites with different degrees of nucleotide substitution significantly influences the topology and degree of resolution of maximum-parsimony phylogenies as well as neighbor-joining phylogenies (corrected and uncorrected for among-site rate variation) reconstructed at the metazoan scale. Together, these data indicate that the 18S rRNA molecule is an unsuitable candidate for reconstructing the evolutionary history of all metazoan phyla, and that the polytomies, i.e., unresolved nodes within 18S rRNA phylogenies, cannot be used as a single or reliable source of evidence to support the hypothesis of a Cambrian explosion. Received: 9 December 1997 / Accepted: 23 March 1998     

Phylogenetic Relationships among Holarctic Populations of Chironomus entis and Chironomus plumosus in View of Possible Horisontal Transfer of Mitochondrial Genes

In eight Holarctic populations of two typical chironomid sibling species of the plumosus group, Chironomus entisandChironomus plumosus, nucleotide sequences of mitochondrial (cytb) and nuclear (gb2b) gene regions were examined. The phylogenetic trees reflecting the evolutionary histories of the nuclear and mitochondrial markers exhibited significant differences. On the tree based on the nuclear gene sequences the populations clustered according to their species affiliation, whereas on the tree based on the mitochondrial gene sequences the populations were grouped according to their geographic position. This discrepancy is probably explained by mitochondrial gene flow between sympatric species with incomplete reproductive isolation (sibling species). Based on our results together with the earlier data on nuclear and mitochondrial gene sequences of some other species from the phylogenetic group plumosus, a scheme of phylogenetic relationships within this group is proposed. This scheme is in many ways different from the traditional view on the evolutionary relationships among species of the plumosus group.     

胃癌侵袭转移相关基因研究进展

胃癌死亡率居高不下的原因主要在于广泛的侵袭和转移。恶性肿瘤的侵袭和转移是一个受多因素调控、多种基因参与的多步骤、多阶段、连续复杂的主动过程,很多机制现在还不清楚。但是目前很多研究表明肿瘤间质中的血管生成和细胞外基质的降解是恶性肿瘤侵袭和转移的重要步骤。随着分子生物技术的飞速发展,对这两个步骤基因水平上的研究已成为热点,并发现了例如血管内皮生长因子、基质金属蛋白酶多种基因通过不同方式调控肿瘤血管生成和细胞外基质降解,从而导致胃癌的侵袭和转移。     

A Molecular Phylogeny of the Tiger Beetles (Cicindelidae): Congruence of Mitochondrial and Nuclear rDNA Data Sets

As a basis for comparative studies in the family Cicindelidae (tiger beetles), a phylogenetic hypothesis for major groups was established based on molecular data, focusing on the taxa of the New World. Two markers, mitochondrial 16S rRNA and nuclear 18S rRNA, were sequenced for a total of 912 nucleotides and 30 taxa. All Cicindelidae were inferred to be a monophyletic group by the presence of a segment in the 5′ region of the 18S rDNA which is predicted to fold into a single stem-loop structure not present in the outgroup. The total number of variable and potentially informative positions was smaller in the 18S data set, but their higher internal consistency resulted in a strong phylogenetic signal. Inferred relationships were stable over a wide range of alignment parameters, but the inclusion of alignment-sensitive positions and presumptive gap characters added substantially to the resolution and overall support of the tree. Both data sets were in general congruence. The combined evidence suggests that relationships in Cicindelidae as currently recognized have to be reconsidered. No convincing evidence could be found for the traditional subdivision into two subfamilies, Cicindelinae and Collyrinae. The latter is embedded within the Cicindelinae and clearly not the sister to all other cicindelids. Most of the current tribes and subtribes, particularly in the Megacephalini, are paraphyletic groups, whereas monophyly of the large tribe Cicindelini is well supported by the molecular data.     

Genetic Analyses of ENDOTHIA PARASITICA: Linkage Data for Four Single Genes and Three Vegetative Compatibility Types

The loci cre, met and ts segregate independently in Endothia parasitica. The phenotype brown (br) seems to be determined by an allele at or very near the cre locus. The vegetative compatibility types (v-c) 5 and 39 are determined by different alleles at a locus that is not linked to cre, met or ts. Analysis of two crosses of v-c 5 strains by v-c 10 strains provides evidence that these two v-c groups are different at 5 or more v-c loci.     

Deregulation of Genes Related to Iron and Mitochondrial Metabolism in Refractory Anemia with Ring Sideroblasts

The presence of SF3B1 gene mutations is a hallmark of refractory anemia with ring sideroblasts (RARS). However, the mechanisms responsible for iron accumulation that characterize the Myelodysplastic Syndrome with ring sideroblasts (MDS-RS) are not completely understood. In order to gain insight in the molecular basis of MDS-RS, an integrative study of the expression and mutational status of genes related to iron and mitochondrial metabolism was carried out. A total of 231 low-risk MDS patients and 81 controls were studied. Gene expression analysis revealed that iron metabolism and mitochondrial function had the highest number of genes deregulated in RARS patients compared to controls and the refractory cytopenias with unilineage dysplasia (RCUD). Thus mitochondrial transporters SLC25 (SLC25A37 and SLC25A38) and ALAD genes were over-expressed in RARS. Moreover, significant differences were observed between patients with SF3B1 mutations and patients without the mutations. The deregulation of genes involved in iron and mitochondrial metabolism provides new insights in our knowledge of MDS-RS. New variants that could be involved in the pathogenesis of these diseases have been identified.     

Likelihood-Based Modeling and Analysis of Data Underdispersed Relative to the Poisson Distribution

By using a generalization of the Poisson process, distributions can be constructed that show appropriate amounts of underdispersion relative to the Poisson distribution that may be apparent from observed data. These are then used to examine the differences between the distributions of numbers of fetal implants in mice corresponding to different doses of the herbicide 2,4,5-T.     

三个拟南芥NAC同源基因突变体的ABA响应及下游基因表达分析

在获得拟南芥NAC同源基因(NAC019、NAC055和NAC072)双突变体和三突变体纯系的基础上,进一步分析它们对ABA响应的生理差异及其ABA诱导相关下游基因的表达变化,深入探讨它们与ABA响应的关系。结果表明,在种子绿胚建成的过程中,NAC055和NAC072基因与ABA响应相关;在根生长方面,三者在ABA响应中作用不明显。经ABA处理后,突变体nac072和nac055nac072与野生型比较,RAB18、RD29A和RD29B基因表达上调显著,推测在ABA响应的基因表达调控过程中,NAC072和NAC055起负调控协同作用,而NAC019则发挥拮抗作用。     

四个与小鼠摄食、摄水量及蛋白质代谢相关基因的功能研究

目的　通过对小鼠摄食、摄水量及蛋白质代谢相关基因的功能研究 ,为今后的营养学和营养疾病学的分子生物学水平研究提供一定的依据。方法　利用反义核酸技术与动物行为学实验方法相结合 ,从动物整体水平上研究与动物膳食和营养代谢相关的基因功能。从课题组以往研究得到的摄食量与对照组有显著差异的基因中选出 4个 ,用BALB c小鼠进行实验。结果　实验结果表明 :D1、Pe和Tr实验组小鼠的摄食量、摄水量与对照组有明显的差异 ,D1和Tr实验组的蛋白质代谢与对照组有明显的差异。D1实验组小鼠的摄食量和摄水量明显高于对照组并呈下降趋势 ,但其表观消化率小于对照组 ,说明其蛋白质代谢功能有所下降 ;Tr实验组小鼠的摄食量和摄水量也明显高于对照组但呈上升趋势 ,其表观消化率大于对照组 ,说明其蛋白质代谢功能有所上升。结论　预测D1基因可能与促进营养代谢功能有关 ,Tr基因可能与抑制营养代谢功能有关。D1、Pe和Tr与移动、痛觉、记忆等其他行为学有相关性 ,P3与其他行为学无相关性。     

Common Single Nucleotide Polymorphisms in Genes Related to Immune Function and Risk of Papillary Thyroid Cancer

Accumulating evidence suggests that alterations in immune function may be important in the etiology of papillary thyroid cancer (PTC). To identify genetic markers in immune-related pathways, we evaluated 3,985 tag single nucleotide polymorphisms (SNPs) in 230 candidate gene regions (adhesion-extravasation-migration, arachidonic acid metabolism/eicosanoid signaling, complement and coagulation cascade, cytokine signaling, innate pathogen detection and antimicrobials, leukocyte signaling, TNF/NF-kB pathway or other) in a case-control study of 344 PTC cases and 452 controls. We used logistic regression models to estimate odds ratios (OR) and calculate one degree of freedom P values of linear trend (P_SNP-trend) for the association between genotype (common homozygous, heterozygous, variant homozygous) and risk of PTC. To correct for multiple comparisons, we applied the false discovery rate method (FDR). Gene region- and pathway-level associations (P_Region and P_Pathway) were assessed by combining individual P_SNP-trend values using the adaptive rank truncated product method. Two SNPs (rs6115, rs6112) in the SERPINA5 gene were significantly associated with risk of PTC (P_SNP-FDR/P_SNP-trend = 0.02/6×10⁻⁶ and P_SNP-FDR/P_SNP-trend = 0.04/2×10⁻⁵, respectively). These associations were independent of a history of autoimmune thyroiditis (OR = 6.4; 95% confidence interval: 3.0–13.4). At the gene region level, SERPINA5 was suggestively associated with risk of PTC (P_Region-FDR/P_Region =0.07/0.0003). Overall, the complement and coagulation cascade pathway was the most significant pathway (P_Pathway = 0.02) associated with PTC risk largely due to the strong effect of SERPINA5. Our results require replication but suggest that the SERPINA5 gene, which codes for the protein C inhibitor involved in many biological processes including inflammation, may be a new susceptibility locus for PTC.