The efficacy of DNA barcoding in the classification,genetic differentiation,and biodiversity assessment of benthic macroinvertebrates

Macroinvertebrates have been recognized as key ecological indicators of aquatic environment and are the most commonly used approaches for water quality assessment. However, species identification of macroinvertebrates (especially of aquatic insects) proves to be very difficult due to the lack of taxonomic expertise in some regions and can become time‐consuming. In this study, we evaluated the feasibility of DNA barcoding for the classification of benthic macroinvertebrates and investigated the genetic differentiation in seven orders (Insecta: Ephemeroptera, Plecoptera, Trichoptera, Diptera, Hemiptera, Coleoptera, and Odonata) from four large transboundary rivers of northwest China and further explored its potential application to biodiversity assessment. A total of 1,144 COI sequences, belonging to 176 species, 112 genera, and 53 families were obtained and analyzed. The barcoding gap analysis showed that COI gene fragment yielded significant intra‐ and interspecific divergences and obvious barcoding gaps. NJ phylogenetic trees showed that all species group into monophyletic species clusters whether from the same population or not, except two species (Polypedilum. laetum and Polypedilum. bullum). The distance‐based (ABGD) and tree‐based (PTP and MPTP) methods were utilized for grouping specimens into Operational Taxonomic Units (OTUs) and delimiting species. The ABGD, PTP, and MPTP analysis were divided into 177 (p = .0599), 197, and 195 OTUs, respectively. The BIN analysis generated 186 different BINs. Overall, our study showed that DNA barcoding offers an effective framework for macroinvertebrate species identification and sheds new light on the biodiversity assessment of local macroinvertebrates. Also, the construction of DNA barcode reference library of benthic macroinvertebrates in Eurasian transboundary rivers provides a solid backup for bioassessment studies of freshwater habitats using modern high‐throughput technologies in the near future.     

DNA barcoding of genus Toxoptera Koch (Hemiptera: Aphididae): Identification and molecular phylogeny inferred from mitochondrial COI sequences

Abstract Identification of aphid species is always difficult due to the shortage of easily distinguishable morphological characters. Aphid genus Toxoptera consists of species with similar morphology and similar to Aphis in most morphological characters except the stridulatory apparatus. DNA barcodes with 1 145 bp sequences of partial mitochondrial cytochrome‐coxidase I (COI) genes were used for accurate identification of Toxoptera. Results indicated mean intraspecific sequence divergences were 1.33%, whereas mean interspecific divergences were greater at 8.29% (0.13% and 7.79% if T. aurantii 3 and T. aurantii 4 are cryptic species). Sixteen samples were distinguished to four species correctly by COI barcodes, which implied that DNA barcoding was successful in discrimination of aphid species with similar morphology. Phylogenetic relationships among species of this genus were tested based on this portion of COI sequences. Four species of Toxoptera assembled a clade with low support in maximum‐parsimony (MP) analysis, maximum‐likelihood (ML) analysis and Bayesian phylogenetic trees, the genus Toxoptera was not monophyletic, and there were two sister groups, such as T. citricidus and T. victoriae, and two clades of T. aurantii which probably presented cryptic species in the genus.     

APC/C(Cdc20) controls the ubiquitin-mediated degradation of p21 in prometaphase

During the G1/S transition, p21 proteolysis is mediated by Skp2; however, p21 reaccumulates in G2 and is degraded again in prometaphase. How p21 degradation is controlled in mitosis remains unexplored. We found that Cdc20 (an activator of the ubiquitin ligase APC/C) binds p21 in cultured cells and identified a D box motif in p21 necessary for APC/C(Cdc20)-mediated ubiquitylation of p21. Overexpression of Cdc20 or Skp2 destabilized wild-type p21; however, only Skp2, but not Cdc20, was able to destabilize a p21(D box) mutant. Silencing of Cdc20 induced an accumulation of p21, increased the fraction of p21 bound to Cdk1, and inhibited Cdk1 activity in p21(+/+) prometaphase cells, but not in p21(-/-) cells. Thus, in prometaphase Cdc20 positively regulates Cdk1 by mediating the degradation of p21. We propose that the APC/C(Cdc20)-mediated degradation of p21 contributes to the full activation of Cdk1 necessary for mitotic events and prevents mitotic slippage during spindle checkpoint activation.     

Demographic History and Genomic Response to Environmental Changes in a Rapid Radiation of Wild Rats

For organisms to survive and prosper in a harsh environment, particularly under rapid climate change, poses tremendous challenges. Recent studies have highlighted the continued loss of megafauna in terrestrial ecosystems and the subsequent surge of small mammals, such as rodents, bats, lagomorphs, and insectivores. However, the ecological partitioning of these animals will likely lead to large variation in their responses to environmental change. In the present study, we investigated the evolutionary history and genetic adaptations of white-bellied rats (Niviventer Marshall, 1976), which are widespread in the natural terrestrial ecosystems in Asia but also known as important zoonotic pathogen vectors and transmitters. The southeastern Qinghai-Tibet Plateau was inferred as the origin center of this genus, with parallel diversification in temperate and tropical niches. Demographic history analyses from mitochondrial and nuclear sequences of Niviventer demonstrated population size increases and range expansion for species in Southeast Asia, and habitat generalists elsewhere. Unexpectedly, population increases were seen in N. eha, which inhabits the highest elevation among Niviventer species. Genome scans of nuclear exons revealed that among the congeneric species, N. eha has the largest number of positively selected genes. Protein functions of these genes are mainly related to olfaction, taste, and tumor suppression. Extensive genetic modification presents a major strategy in response to global changes in these alpine species.     

大黄素降糖及改善脂质代谢的实验研究

目的:探讨大黄素对2型糖尿病模型db/db小鼠血糖及血脂水平的影响.方法:4周龄16只db/db雄性小鼠随机分为治疗组和对照组,每组8只;治疗组经灌胃每天给予100mg/kg大黄素;对照组灌胃给予相仿体积的生理盐水,开始10天每天算进食量,每周测空腹血糖及体重1次,连续干预8周,干预前及实验结束前1周测胰岛素耐量,干预结束后于颈动脉取血测血脂水平(HDLC、LDL-C、TG、TC).结果:①大黄素干预不影响db/db小鼠的进食量,与对照组比较,P＞0.05;②大黄素可显著减轻db/db小鼠体重,与对照组比较,P＜0.05;③大黄素可改善db/db小鼠胰岛素敏感性,降低小鼠的空腹血糖水平,与对照组比较,P＜0.05或P＜0.01;④大黄素可降低db/db小鼠血TG、TC、LDL-C水平,P＜0.01.结论:大黄素可有效地改善db/db小鼠的糖脂紊乱状态,其降糖及改善血脂代谢机制值得进一步深入研究.     

清得佳凝胶治疗烧伤创面的生物学作用

目的探讨清得佳凝胶治疗烧伤创面的效果及其意义。方法采用家兔皮肤创伤模型,将每只家兔的背部烧伤区域用2种不同颜色的记号笔分成二组:A组(n=9):为实验组(6个部位):常规方法清洁、消毒创口,使用清得佳凝胶涂抹;B组(n=9):为对照组(6个部位):使用常规的无菌敷料覆盖包扎创口。实验于第3、5、7、9天分别取各组皮肤组织进行切片,作组织病理学及免疫组织化学观察。结果1.HE观察结果:烧伤后第3天,A组与B组皮肤烧伤创面结构变化不明显;烧伤后第5天,A组表皮细胞变性坏死程度减轻,成纤维细胞增生,水肿减轻,而B组表皮细胞变性坏死减轻程度不明显,结缔组织胶原纤维变性坏死程度没有得到明显的改善;烧伤后第7天,A组表皮细胞生长良好,真皮组织水肿基本消失;而B组表皮细胞变性坏死程度开始出现减轻,可见部分上皮增生;烧伤后第9天,A组上皮及结缔组织结构基本接近正常,创面愈合情况较好。而B组以上结构出现改变,但愈合状况不是很理想,真皮组织轻、中度水肿,有少量的炎性细胞浸润。2.转化生长因子β1(transforming growth factor β1,TGF-β1)的表达:烧伤后第3天和第5天,A组成纤维细胞胞浆中可见一些棕黄色颗粒,TGF-β1表达较强;B组成纤维细胞胞浆中未见或少见棕黄色颗粒,TGF-β1无表达或表达很弱。烧伤后第7天和第9天,A组成纤维细胞胞浆中可见密集分布的棕黄色颗粒,TGF-β1表达强;B组成纤维细胞胞浆中可见少量的棕黄色颗粒,TGF-β1表达弱。结论清得佳凝胶是一种烧伤创面良好的外用药,能清除创面坏死组织,有利于烧伤创面愈合。     

Elevated O3 reduces the fitness of Bemisia tabaci via enhancement of the SA-dependent defense of the tomato plant

The effect of elevated O₃ on tomato plants of three different genotypes (wild-type, a jasmonic acid (JA) defense-enhanced genotype (35S) and a JA-deficient genotype (spr2)) grown in association with the whitefly Bemisia tabaci Gennadius biotype B was examined in the field in open-top chambers. We experimentally tested the hypothesis that elevated O₃ tends to reduce the nutrition of tomato plants, and to increase the SA-dependent pathway defenses and the secondary metabolites, and therefore decrease the population fitness of the whitefly. The results show that for all three tomato genotypes, elevated O₃ reduced the soluble sugars and free amino acids, increased the phenylalanine ammonia-lyase enzyme activity and the accumulated salicylic acid (SA), and up-regulated the pathogenesis-related protein (PR1), which is commonly considered to be the whitefly-resistance gene product involved in SA-dependent defense. Elevated O₃ did not affect the JA level in any of the three plant genotypes, but it increased the levels of some secondary metabolites, including total phenolics and condensed tannins. Elevated O₃ prolonged the developmental time of whiteflies fed on the three plant genotypes, and it also reduced the fecundity and the intrinsic rate of increase of whiteflies fed on either the 35S or the wild-type plants. These results suggest that elevated O₃ reduces the nutrition of tomato plants and enhances their SA content, relative PR mRNA expression and secondary metabolism, resulting in decreased fitness of whiteflies on these tomato plants.     

Molecular insights into the antifungal mechanism of bacilysin

Bacilysin is one of the simplest antimicrobial peptides and has drawn great attention for its excellent performance against Candida albicans. In this study, the antifungal mechanism of bacilysin was investigated. The target enzyme glucosamine-6-phosphate synthase (GFA) was expressed heterologously in Escherichia coli and its inhibition by bacilysin and derivatives was studied. It was concluded that bacilysin could be hydrolyzed by a proteinase of C. albicans, and that the released product, anticapsin, then inhibited the aminotransferase activity of GFA. This result was verified by molecular simulation, and the interaction mode of anticapsin with GFA was detailed, which provides data for the development of novel antifungal drugs. Transport of bacilysin into fungal cells was also simulated and it was shown that bacilysin is more readily transported into cells than anticapsin. Thus, our findings support a mechanism whereby bacilysin is transported into fungal pathogens, hydrolyzed to anticapsin, which then inhibits GFA.     

Pressure-induced metallization of condensed phase β-HMX under shock loadings via molecular dynamics simulations in conjunction with multi-scale shock technique

Thanks to the advances in grid technologies, we are able to propose here an evolution of our molecular simulator that, when moving to larger systems, instead of reducing the granularity of the dynamical treatment (as is often done in molecular dynamics studies of such systems) exploits the extra power of the grid approach to the end of preserving the detailed nature of theatomistic formulation of the interaction. Key steps of such evolution are: (1) the assemblage of the interaction based on a composition of the ab initio intramolecular data and a portable parameterization of the intermolecular potential linking ab initio evaluation of intramolecular potentials and the partitioning of molecular polarizability; (2) the exploitation of an efficient coordinated porting and running of molecular dynamics codes on the European grid distributed computing infrastructure. As a prototype case study, the N-methylacetamide dimer in vacuo has been considered and the formation of possible conformers is analyzed.