Jumping and gliding rodents: Mitogenomic affinities of Pedetidae and Anomaluridae deduced from an RNA-Seq approach

An RNA-Seq strategy was used to obtain the complete set of protein-coding mitochondrial genes from two rodent taxa. Thanks to the next generation sequencing (NGS) 454 approach, we determined the complete mitochondrial DNA genome from Graphiurus kelleni (Mammalia: Rodentia: Gliridae) and partial mitogenome from Pedetes capensis (Pedetidae), and compared them with published rodent and outgroup mitogenomes. We finished the mitogenome sequencing by a series of amplicons using conserved PCR primers to fill the gaps corresponding to tRNA, rRNA and control regions. Phylogenetic analyses of the mitogenomes suggest a well-supported rodent phylogeny in agreement with nuclear gene trees. Pedetes groups with Anomalurus into the clade Anomaluromorpha, while Graphiurus branches within the squirrel-related clade. Moreover, Pedetes + Anomalurus branch with Castor into the mouse-related clade. Our study demonstrates the utility of NGS for obtaining new mitochondrial genomes as well as the importance of choosing adequate models of sequence evolution to infer the phylogeny of rodents.     

Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae

Hemocyanins are multimeric copper-containing hemolymph proteins involved in oxygen binding and transport in all major arthropod lineages. Most arachnids have seven primary subunits (encoded by paralogous genes a–g), which combine to form a 24-mer (4 × 6) quaternary structure. Within some spider lineages, however, hemocyanin evolution has been a dynamic process with extensive paralog duplication and loss. We have obtained hemocyanin gene sequences from numerous representatives of the spider infraorders Mygalomorphae and Araneomorphae in order to infer the evolution of the hemocyanin gene family and estimate spider relationships using these conserved loci. Our hemocyanin gene tree is largely consistent with the previous hypotheses of paralog relationships based on immunological studies, but reveals some discrepancies in which paralog types have been lost or duplicated in specific spider lineages. Analyses of concatenated hemocyanin sequences resolved deep nodes in the spider phylogeny and recovered a number of clades that are supported by other molecular studies, particularly for mygalomorph taxa. The concatenated data set is also used to estimate dates of higher-level spider divergences and suggests that the diversification of extant mygalomorphs preceded that of extant araneomorphs. Spiders are diverse in behavior and respiratory morphology, and our results are beneficial for comparative analyses of spider respiration. Lastly, the conserved hemocyanin sequences allow for the inference of spider relationships and ancient divergence dates.     

Phylogenetic analysis and positive-selection site detecting of vascular endothelial growth factor family in vertebrates

Vascular endothelial growth factor (VEGF), known to play an important role in vascular homeostasis, vascular integrity and angiogenesis, is little known about the evolutionary relationship of its five members especially the role of gene duplication and natural selection in the evolution of the VEGF family. In this study, seventy-five full-length cDNA sequences from 33 vertebrate species were extracted from the NCBI's GenBank, UniProt protein database and the Ensembl database. By phylogenetic analyses, we investigated the origin, conservation, and evolution of the VEGFs. Five VEGF family members in vertebrates might be formed by gene duplication. The inferred evolutionary transitions that separate members which belong to different gene clusters correlated with changes in functional properties. Selection analysis and protein structure analysis were combined to explain the relationship of the site-specific evolution in the vertebrate VEGF family. Eleven positive selection sites, one transmembrane region and the active sites were detected in this process.     

Stimulatory guanine nucleotide-binding protein and adenylate cyclase activities in Bio 14.6 cardiomyopathic hamsters at the hypertrophic stage

The Bio 14.6 cardiomyopathic Syrian hamster is an animal model of human idiopathic cardiomyopathy. The pathogenesis of the disease in this animal has not yet been clearly elucidated. It is well known that α- and β-adrenergic receptors are increased in the myocardium of this animal, but that isoprenaline does not produce an augmented response. We examined the activity of cardiac stimulatory GTP-binding protein (Gs), which couple with β-adrenergic receptors to stimulate adenylate cyclase, in Bio 14.6 cardiomyopathic hamsters at 90 and 160 days of age. The cardiac norepinephrine concentration was significantly increased in Bio 14.6 hamsters compared with control hamsters (F1B) at 90 days of age (1,739±120 vs 1,470±161 ng/g wet tissue weight, p<0.05). Cardiac forskolin-stimulated adenylate cyclase activities at 90 and 160 days of age were lower in the cardiomyopathic hamsters than in the F1B controls (90 days old: 98±24 vs 122±29 pmol/min/mg protein, p<0.05; 160 days old: 74±13 vs 124±28 pmol/min/mg protein, p<0.01). Cardiac Gs activities at 90 and 160 days of age were significantly lower in Bio 14.6 hamsters than those in F1B hamsters (90 days old: 204±42 vs 259±49 pmol/min/mg protein, p<0.05; 160 days old: 156±39 vs 211±60 pmol/min/mg protein, p<0.05). We thus demonstrated functional defects in cardiac Gs protein and adenylate cyclase activity in the Bio 14.6 cardiomyopathic hamsters at 90 to 160 days of age (the hypertrophic stage of cardiomyopathy). Such defects could be one possible mechanism preventing an enhanced response to β-adrenergic stimulation in this animal and could also contribute to myocardial decompensation in the late stage of cardiomyopathy.     

Pike and salmon as sister taxa: Detailed intraclade resolution and divergence time estimation of Esociformes + Salmoniformes based on whole mitochondrial genome sequences

The increasing number of taxa and loci in molecular phylogenetic studies of basal euteleosts has brought stability in a controversial area. A key emerging aspect to these studies is a sister Esociformes (pike) and Salmoniformes (salmon) relationship. We evaluate mitochondrial genome support for a sister Esociformes and Salmoniformes hypothesis by surveying many potential outgroups for these taxa, employing multiple phylogenetic approaches, and utilizing a thorough sampling scheme. Secondly, we conduct a simultaneous divergence time estimation and phylogenetic inference in a Bayesian framework with fossil calibrations focusing on relationships within Esociformes + Salmoniformes. Our dataset supports a sister relationship between Esociformes and Salmoniformes; however the nearest relatives of Esociformes + Salmoniformes are inconsistent among analyses. Within the order Esociformes, we advocate for a single family, Esocidae. Subfamily relationships within Salmonidae are poorly supported as Salmoninae sister to Thymallinae + Coregoninae.     

Mitochondrial genomic investigation of flatfish monophyly

We present the first study to use whole mitochondrial genome sequences to examine phylogenetic affinities of the flatfishes (Pleuronectiformes). Flatfishes have attracted attention in evolutionary biology since the early history of the field because understanding the evolutionary history and patterns of diversification of the group will shed light on the evolution of novel body plans. Because recent molecular studies based primarily on DNA sequences from nuclear loci have yielded conflicting results, it is important to examine phylogenetic signal in different genomes and genome regions. We aligned and analyzed mitochondrial genome sequences from thirty-nine pleuronectiforms including nine that are newly reported here, and sixty-six non-pleuronectiforms (twenty additional clade L taxa [Carangimorpha or Carangimorpharia] and forty-six secondary outgroup taxa). The analyses yield strong support for clade L and weak support for the monophyly of Pleuronectiformes. The suborder Pleuronectoidei receives moderate support, and as with other molecular studies the putatively basal lineage of Pleuronectiformes, the Psettodoidei is frequently not most closely related to other pleuronectiforms. Within the Pleuronectoidei, the basal lineages in the group are poorly resolved, however several flatfish subclades receive consistent support. The affinities of Lepidoblepharon and Citharoides among pleuronectoids are particularly uncertain with these data.     

牙周再生膜体外降解的实验研究

目的研究牙周再生膜在体外动态和静态降解体系中的降解性能。方法用聚乳酸乙醇酸制作的牙周再生膜在动态(降解介质流速为250μl/min)和静态两种降解体系中进行降解,分别在材料降解前的第0周和降解后的第1、2、4、6周测定牙周再生膜在体外动态和静态降解体系中的残存质量、平均分子量、弹性模量、孔隙率和渗透性的变化并对两种降解体系中的降解性能进行比较。结果降解过程中,牙周再生膜实验材料的质量随着降解的进行而不断损耗,残存的质量越来越少。实验材料的分子量随着降解的进行而不断减少。牙周再生膜的质量和分子量在静态降解体系中损失速度显著高于在动态降解体系(P<0.01);在两种实验条件下,牙周再生膜实验材料的弹性模量都是在第2周时开始上升,随后下降。材料的弹性模量在动态降解体系中较之静态降解体系能维持较长时间;无论在动态降解条件下,还是在静态降解条件下,实验材料的孔隙率都是从第2周时开始下降,而后逐渐增加。降解系统的状态对材料孔隙率变化的影响无显著差异(P>0.05);材料在静态降解体系中的渗透性显著高于动态降解体系(P<0.01)。材料在两种降解介质中的降解性能相似,但是在所测定的降解指标中,材料在人工唾液中的变化速度显著高于在PBS中的(0.01相似文献   

GTR1 is a jasmonic acid and jasmonoyl-l-isoleucine transporter in Arabidopsis thaliana

Jasmonates are major plant hormones involved in wounding responses. Systemic wounding responses are induced by an electrical signal derived from damaged leaves. After the signaling, jasmonic acid (JA) and jasmonoyl-l-isoleucine (JA-Ile) are translocated from wounded to undamaged leaves, but the molecular mechanism of the transport remains unclear. Here, we found that a JA-Ile transporter, GTR1, contributed to these translocations in Arabidopsis thaliana. GTR1 was expressed in and surrounding the leaf veins both of wounded and undamaged leaves. Less accumulations and translocation of JA and JA-Ile were observed in undamaged leaves of gtr1 at 30 min after wounding. Expressions of some genes related to wound responses were induced systemically in undamaged leaves of gtr1. These results suggested that GTR1 would be involved in the translocation of JA and JA-Ile in plant and may be contributed to correct positioning of JA and JA-Ile to attenuate an excessive wound response in undamaged leaves.     

High altitude adaptation of the schizothoracine fishes (Cyprinidae) revealed by the mitochondrial genome analyses

The schizothoracine fishes, also known as “mountain carps” are widely distributed in the Qinghai-Tibetan Plateau and its peripheral regions. Although they provide a prime example of high altitude adaptation, the phylogenetic relationships and the divergence times among these carp lineages are still controversial. Moreover, the genetic basis for high altitude adaptation is also poorly understood. In this study, we determined the mitochondrial genomes from two species of the schizothoracine fishes, representing a “morphologically primitive” clade and “morphologically specialized” clade, respectively. The phylogenetic tree and the divergence times were estimated within the evolutionary framework of the entire order Cypriniformes. Our results indicate a polyphylyetic relationship of the schizothoracine fishes and suggest two independent migration events into the Qinghai-Tibetan Plateau: one by the “morphologically primitive” clade in the Late Miocene and another by the “morphologically specialized” clade in the Eocene. Rapid speciation events of each clade from the Late Miocene to the Pliocene correspond to the timing of the geologic acceleration of the Qinghai-Tibetan Plateau. Interestingly, we found evidence for positive selection acting on the protein coding genes in the mitochondrial genomes of the “morphologically specialized” clade, implying a possible genetic basis for high altitude adaptation in this derived lineage of cypriniform fishes.