The Evolution and Origin of Animal Toll-Like Receptor Signaling Pathway Revealed by Network-Level Molecular Evolutionary Analyses

Genes carry out their biological functions through pathways in complex networks consisting of many interacting molecules. Studies on the effect of network architecture on the evolution of individual proteins will provide valuable information for understanding the origin and evolution as well as functional conservation of signaling pathways. However, the relationship between the network architecture and the individual protein sequence evolution is yet little known. In current study, we carried out network-level molecular evolution analysis on TLR (Toll-like receptor ) signaling pathway, which plays an important role in innate immunity in insects and mammals, and we found that: 1) The selection constraint of genes was negatively correlated with its position along TLR signaling pathway; 2) all genes in TLR signaling pathway were highly conserved and underwent strong purifying selection; 3) the distribution of selective pressure along the pathway was driven by differential nonsynonymous substitution levels; 4) The TLR signaling pathway might present in a common ancestor of sponges and eumetazoa, and evolve via the TLR, IKK, IκB and NF-κB genes underwent duplication events as well as adaptor molecular enlargement, and gene structure and conservation motif of NF-κB genes shifted in their evolutionary history. Our results will improve our understanding on the evolutionary history of animal TLR signaling pathway as well as the relationship between the network architecture and the sequences evolution of individual protein.     

A comparative study of mammalian diversification pattern

Although mammals have long been regarded as a successful radiation, the diversification pattern among the clades is still poorly known. Higher-level phylogenies are conflicting and comprehensive comparative analyses are still lacking. Using a recently published supermatrix encompassing nearly all extant mammalian families and a novel comparative likelihood approach (MEDUSA), the diversification pattern of mammalian groups was examined. Both order- and family-level phylogenetic analyses revealed the rapid radiation of Boreoeutheria and Euaustralidelphia in the early mammalian history. The observation of a diversification burst within Boreoeutheria at approximately 100 My supports the Long Fuse model in elucidating placental diversification progress, and the rapid radiation of Euaustralidelphia suggests an important role of biogeographic dispersal events in triggering early Australian marsupial rapid radiation. Diversification analyses based on family-level diversity tree revealed seven additional clades with exceptional diversification rate shifts, six of which represent accelerations in net diversification rate as compared to the background pattern. The shifts gave origin to the clades Muridae+Cricetidae, Bovidae+Moschidae+Cervidae, Simiiformes, Echimyidae, Odontoceti (excluding Physeteridae+Kogiidae+Platanistidae), Macropodidae, and Vespertilionidae. Moderate to high extinction rates from background and boreoeutherian diversification patterns indicate the important role of turnovers in shaping the heterogeneous taxonomic richness observed among extant mammalian groups. Furthermore, the present results emphasize the key role of extinction on erasing unusual diversification signals, and suggest that further studies are needed to clarify the historical radiation of some mammalian groups for which MEDUSA did not detect exceptional diversification rates.     

Human decidua-derived mesenchymal stromal cells differentiate into hepatic-like cells and form functional three-dimensional structures

Background aimsPreviously, we have shown that human decidua-derived mesenchymal stromal cells (DMSC) are mesenchymal stromal cells (MSC) with a clonal differentiation capacity for the three embryonic layers. The endodermal capacity of DMSC was revealed by differentiation into pulmonary cells. In this study, we examined the hepatic differentiation of DMSC.MethodsDMSC were cultured in hepatic differentiation media or co-cultured with murine liver homogenate and analyzed with phenotypic, molecular and functional tests.Results and ConclusionsDMSC in hepatic differentiation media changed their fibroblast morphology to a hepatocyte-like morphology and later formed a 3-dimensional (3-D) structure or hepatosphere. Moreover, the hepatocyte-like cells and the hepatospheres expressed liver-specific markers such as synthesis of albumin (ALB), hepatocyte growth factor receptor (HGFR), α-fetoprotein (AFP) and cytokeratin-18 (CK-18), and exhibited hepatic functions including glycogen storage capacity and indocyanine green (ICG) uptake/secretion. Human DMSC co-cultured with murine liver tissue homogenate in a non-contact in vitro system showed hepatic differentiation, as evidenced by expression of AFP and ALB genes. The switch in the expression of these two genes resembled liver development. Indeed, the decrease in AFP and increase in ALB expression throughout the co-culture were consistent with the expression pattern observed during normal liver organogenesis in the embryo. Interestingly, AFP and ALB expression was significantly higher when DMSC were co-cultured with injured liver tissue, indicating that DMSC respond differently under normal and pathologic micro-environmental conditions. In conclusion, DMSC-derived hepatospheres and DMSC co-cultured with liver homogenate could be suitable in vitro models for toxicologic, developmental and pre-clinical hepatic regeneration studies.     

中国跃蛃属(石蛃目,石蛃科)一新种记述

记述采自江苏南京跃蛃属1新种,老山跃蛃Pedetontinus laoshanensis sp.nov.,通过扩增其线粒体CO Ⅰ基因,与中国已知跃蛹属其它物种进行遗传距离比较,并构建系统发生树,发现其与天目跃蛹P.tianmuensis和武当跃蛹较为接近,这也更加支持了基于形态证据的系统发生关系.并提供了跃蛃属已知19种的检索表.老山跃蛹,新种Pedetontinus laoshanensis sp.nov.(图1～17)体长7.0～9.0mm,复眼长/宽为0.99 ～1.00,中连线/长为0.50 ～0.55,复眼近中连线具浅色白斑,阳基侧突为1+6型,阳茎基节/端节为2.4,阳茎和阳基侧突位于第Ⅸ肢基片的1/2,产卵管初级型,其长略超第Ⅸ腹节的刺突端刺.前产卵管,分49 ～ 50节,后产卵管,分47 ～ 50节.该物种CO Ⅰ基因信息见GenBank No.EU699175～ EU 699177.新种与泰山跃蛹P.songi、天目跃蛃P.tianmuensis和武当跃蛃P.wudangensis相似,但复眼中连线/长、阳茎基节/端节、阳茎和阳基侧突位置、产卵管分节具明显区别.基于CO Ⅰ基因序列构建BI、MP和NJ系统发生树均有效证明老山跃蛃P.laoshanensis为单系群.基于K2p模型,新种与中国跃蛹属其它物种的遗传距离比较,与天目跃蛃P.tianmuensis遗传距离最小9.7％,与栾川跃蛃P.luanchuanensis 遗传距离最大12.1％.结合形态和分子数据证明该物种的有效性.正模♂,江苏南京老山(32°07′N,118°36′E;海拔145m),2004-08-01,李鹏、张加勇采,编号ZJNUSB050.词源:新种种名源自采集地地名.     

Mitochondrial phylogeography and population history of finless porpoises in Sino‐Japanese waters

Phylogeographical patterns of intraspecific variation can provide insights into the population‐level processes responsible for speciation and yield information useful for conservation purposes. In the present study, three hundred and forty‐five base pairs of the mitochondrial DNA control region were sequenced to analyse the genetic diversity, population structure and history, and phylogeography of finless porpoises (Neophocaena phocaenoides) in Chinese and Japanese waters of the North Pacific. Nucleotide and haplotype diversities were 0.44% and 0.79 ± 0.01 for Chinese and Japanese waters, respectively, but varied significantly among populations. Analysis of molecular variance showed a high level of genetic structure between populations (Φ_ST = 0.61, P < 0.001; F_ST = 0.52, P < 0.001). Eleven of 18 haplotypes were restricted to a single population, common haplotypes were found in two to four populations, but no haplotype was found throughout Sino‐Japanese waters, suggesting multiple colonization events followed by limited gene flow. The inferred age of demographic expansion was from the end stage of the last ice age to the Holocene. No obvious phylogeographical pattern was revealed, including between saline and fresh water populations. A low level of genetic diversity for each population and high among‐population differentiation in haplotype frequency were revealed, which suggest a role for random genetic drift, recent demographic bottlenecks, and reduced or limited gene flow in these populations. Some conservation considerations, with special reference to the unique Yangtze population, are discussed. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 193–204.     

Growth-promoting effects of a bacterium on raphidophytes and other phytoplankton

On 29 April 2003, a Heterosigma akashiwo bloom (9.5 × 10⁴ cells mL⁻¹) associated with a fish kill (>10⁴ dead fishes estimated from aerial surveys) was observed offshore of Bulls Bay, McLellanville, South Carolina, USA. To assess a potential cause of this bloom event, we investigated the bacterial diversity and algal/bacterial interactions in the bloom microbial community. Thirty-five bacterial strains were isolated and screened for algicidal or algal growth-promoting activities. One strain (BBB25) had significant growth-promoting effects on all 7 algal species tested: three raphidophytes (Heterosigma akashiwo, Chattonella subsalsa, Fibrocapsa japonica), two diatoms (Chaetoceros neogracile, Nitzschia sp.), a cryptophyte (Cryptomonas sp.), and a chlorophyte, Ankistrodesmus sp. This strain (BBB25) is a Gram-positive, rod-shaped spore-forming bacterium. Partial 16S rDNA gene sequence and morphological characters indicated that BBB25 is related closely to the genus Bacillus. The general nature of the algal response indicates that the growth-promoting effects of BBB25 are not specific to H. akashiwo, and suggests potentially widespread effects. Since the presence or relative abundance of the other algal species was not assessed during the bloom initiation period, the selective stimulatory effect on H. akashiwo bloom formation in Bulls Bay is unknown. These results demonstrate, however, the potential for bacterial species to play a regulatory role in bloom formation.     

Changes in Expression of Manganese Superoxide Dismutase,Copper and Zinc Superoxide Dismutase and Catalase in Brachionus calyciflorus during the Aging Process

Rotifers are useful model organisms for aging research, owing to their small body size (0.1–1 mm), short lifespan (6–14 days) and the relative easy in which aging and senescence phenotypes can be measured. Recent studies have shown that antioxidants can extend the lifespan of rotifers. In this paper, we analyzed changes in the mRNA expression level of genes encoding the antioxidants manganese superoxide dismutase (MnSOD), copper and zinc SOD (CuZnSOD) and catalase (CAT) during rotifer aging to clarify the function of these enzymes in this process. We also investigated the effects of common life-prolonging methods [dietary restriction (DR) and resveratrol] on the mRNA expression level of these genes. The results showed that the mRNA expression level of MnSOD decreased with aging, whereas that of CuZnSOD increased. The mRNA expression of CAT did not change significantly. This suggests that the ability to eliminate reactive oxygen species (ROS) in the mitochondria reduces with aging, thus aggravating the damaging effect of ROS on the mitochondria. DR significantly increased the mRNA expression level of MnSOD, CuZnSOD and CAT, which might explain why DR is able to extend rotifer lifespan. Although resveratrol also increased the mRNA expression level of MnSOD, it had significant inhibitory effects on the mRNA expression of CuZnSOD and CAT. In short, mRNA expression levels of CAT, MnSOD and CuZnSOD are likely to reflect the ability of mitochondria to eliminate ROS and delay the aging process.     

鲸类二次水生生境适应Epac1和Epac2基因的分子进化

心率即心脏跳动的速度,不仅反映了心脏的功能,还与寿命的长短及能量代谢有关。与大多数陆生哺乳动物相比,鲸类心率显著降低。降低的心率有助于鲸类寿命的延长及能量的高效利用,便于其适应极端的海洋环境,而这一适应的分子机制尚不清楚。鉴于此,本研究采用基于最大似然法的枝模型、枝位点模型结合蛋白质功能差异分析等方法,对控制心率的环状腺苷酸结合蛋白（Epac1 和Epac2）基因进行适应性探究。分析结果表明,Epac1在长寿鲸类即须鲸类和抹香鲸（Physeter macrocephalus）组合进化支中检测到加速进化过程,且枝位点模型在须鲸类祖先支中检测到的强烈的正选择位点均位于功能重要的催化区;另外,该蛋白质在鲸类中还发生了显著的功能修饰（θ=0.5296 ± 0.1300;P<0.001）。对Epac2进行相同的分析发现,该基因在寿命长达200年之久的弓头鲸（Balaena mysticetus）中检测到的正选择位点同样位于功能重要的催化区。上述结果提示Epac1和Epac2在鲸类中均产生了适应性进化,这一方面可能有助于鲸类心率降低,另一方面也可能与其较长的寿命及高效的能量利用有关。     

Crinkled employs wingless pathway for wing development in Tribolium castaneum

Crinkled is associated with embryonic denticle formation and auditory organ development in Drosophila melanogaster. However, the functions of Crinkled have not been fully investigated. Additionally, the genes that participate in the Crinkled pathway are unknown. Phylogenetic analysis indicates that crinkled exhibits a one‐to‐one orthologous relationship in insects. In Tribolium castaneum, the crinkled gene is 6,498 bp in length and consists of six exons. Crinkled expression peaked during two phases in Tribolium: late embryonic and pupal stages. High levels of crinkled mRNA were detected in the fat body, head, epidermis, ovary, and accessory gland of late adults. Knockdown of crinkled using RNA interference (RNAi) severely affected wing morphogenesis in T. castaneum. We further showed that crinkled silencing reduced forked expression through wingless and shaven‐baby, and RNAi of forked phenocopied the effects of crinkled knockdown in T. castaneum. This study investigated the development role of crinkled in postembryonic stages and indicated that forked mediates the functions of crinkled during wing morphogenesis in T. castaneum.