Evolution of the serum resistance-associated SRA gene in African trypanosomes

Serum resistance-associated (SRA) protein, a protein unique for Trypanosoma brucei rhodesiense, is responsible for resistance of this parasite to the lysis by normal human serum (NHS) and is a vital molecular marker to distinguish this species from other African trypanosomes. We cloned and sequenced the SRA basic copy (SRAbc) gene from T. b. rhodesiense and related species and found that this gene is confined to the subgenus Trypanozoon. The average 82% identity among the sequenced SRAbc genes indicates that they may have a common origin and are highly conserved. Since SRAbc coexists in the T. b. rhodesiense genome with SRA, we propose that SRAbc might be the ‘donor VSG’, which after duplication became inserted into the expression site by recombination. Under natural selection, SRAbc could reform into SRA following mosaic formation. Supported by National Natural Science Foundation of China (Grant Nos. 30570245, 30670275), Changjiang Scholars and Innovative Research Team in University (Grant No. DPCKSCU/IRT0447), International Foundation for Science of Sweden (Grant No. B/4318-1), Grant Agency of the Czech Republic (Grant No. Z60220518) and Education Foundation of the Czech Republic (Grant No. 2B06129)     

Engineering <Emphasis Type="Italic">Deinococcus radiodurans</Emphasis> into biosensor to monitor radioactivity and genotoxicity in environment

Based on a genetically modified radioresistant bacteria Deinococcus radiodurans, we constructed a real time whole cell biosensor to monitor radioactivity and genotoxicity in highly radioactive environment. The enhanced green fluorescence protein （eGFP） was fused to the promoter of the crucial DNA damage-inducible recA gene from D. radiodurans, and the consequent DNA fragment （PrecA-egfp） carried by plasmid was introduced into D. radiodurans R1 strain to obtain the biosensor strain DRG300. This engineered strain can express eGFP protein and generate fluorescence in induction of the recA gene promoter. Based on the correlation between fluorescence intensity and protein expression level in live D. radiodurans cells, we discovered that the fluorescence induction of strain DRG300 responds in a remarkable dose-dependent manner when treated with DNA damage sources such as gamma radiation and mitomycin C. It is encouraging to find the widely detective range and high sensitivity of this reconstructed strain comparing with other whole cell biosensors in former reports. These results suggest that the strain DRG300 is a potential whole cell biosensor to construct a detective system to monitor the biological hazards of radioactive and toxic pollutants in environment in real time.     

Photodegradation of <Emphasis Type="Italic">N</Emphasis>-nitrosodiethylamine in water with UV irradiation

The direct photolysis of N-nitrosodiethylamine （NDEA） in water with ultraviolet （UV） irradiation was investigated. Results showed that NDEA could be completely degraded under the direct UV irradiation. The effects of the experimental conditions, including the initial concentration of NDEA, humic acid and solution pH, were studied. The degradation products of NDEA were identified and quantified with gas chromatography-mass spectrometry （GC-MS） and high performance liquid chromatography （HPLC）. It was confirmed that methylamine （MA）, dimethylamine （DMA）, ethylamine （EA）, diethylamine （DEA）, NO2^- and NO3^- were the main degradation products. The photolysis degradation mechanism of NDEA was also discussed. As a result of N-N bond fission, NDEA was degraded by direct UV irradiation.     

Microstructure and structural color in wing scales of butterfly Thaumantis diores

The butterfly Thaumantis diores is a species in the Northeast of China. There are two kinds of scales on its wings, which overlap like roof tiles and completely cover the membrane. The SEM results showed that only Type-I scales play a key role in forming the blue structural color. Type-II scales have black chemical color. The cross section micro-configuration of scales is achieved by using the transmission electron microscopy (TEM). The brilliant blue generated through the multilayer microstructure is explained by the photonic crystal reason. The multilayer microstructure of the ridges is optimized to 1D Bragg stack for simulation. The reflectivity of the wing is measured by a spectrometer, and the experimental graph accord with the simulation curves basically. When this species fly, the wing’s color and brightness can change because of the transform between structural color and chemical color. The bionic color-changing design and the significance of this effect in video stealth or other fields are discussed at the end of the paper. Supported by Fok Ying Tong Education Foundation (Grant No. 101020), the Natural Science Foundation of China (Grant No. 30570235, 50635030), National Basic Research of China (Grant No. 2007CB616913) and Key Project of the Ministry of Education (Grant No. 105059)     

The evolutionary foundation of genomic imprinting in lower vertebrates

In mammals,genomic imprinting confers developmental asymmetry and complementation on the parental genomes and makes both parental genomes essential for complete development.Genomic imprinting is,therefore,the first regulatory step of genome-wide gene expression of embryogenesis and thought to be the epigenetic foundation of bisexual reproduction.However,how the genomic imprinting is originated,established and maintained during vertebrate evolution remains unknown.Because no endogenous imprinting gene has be...     

On the horizon of Protopteryx and the early vertebrate fossil assemblages of the Jehol Biota

Protopteryx, a monotypic fossil bird discovered from the Sichakou basin in Fengning, Hebei, is the most primitive enantiornithine currently known. The bird-bearing strata do not contain the index fossils of the Yixian Formation in western Liaoning; the fish and bird fossils have more primitive features than the related forms found in the Yixian Formation, and the conchostracans are those usually distributed in the Dabeigou and Dadianzi formations in northern Hebei. Besides, the Protopteryx-bearing strata underlie the deposits bearing the index fossils of the Yixian Formation in the neighboring basin. Thus, it could be confirmed that the horizon of Protopteryx should be lower than the Yixian Formation, and Is approximately equivalent to the Dadianzi Formation in northern Hebei. This is the lowest horizon of the known fossil birds in China and Mesozoic enantiornithine birds in the world. Accompanying Protopteryx, there are other birds, acipenseriform fishes, salamanders, and mammals, which compose the Peipiaosteus fengningensis-Protopteryx fengningensis assemblage. This new assemblage traces the vertebrate evolution history of the Jehol Biota back to 130.7 Ma before. It is suggested that the demarcation of the Jehol Biota should be based on the large-scale tectonic-sedimentary cycles, and Peipiaosteus, instead of Lycoptera, could be taken as the vertebrate representative of the Jehol Biota.     

Bayesian mixed models and divergence time estimation of Chinese cavefishes （Cyprinidae： Sinocyclocheilus）

The genus Sinocyclocheilus is distributed in Yun-Gui Plateau and its surrounding region only, within more than 10 cave species showing different degrees of degeneration of eyes and pigmentaUon with wonderful adaptations. To present, published morphological and molecular phylogenetic hypotheses of Slnocyclocheilus from prior works are very different and the relationships within the genus are still far from clear. We obtained the sequences of cytochrome b （cyt b） and NADH dehydrogenase subunlt 4 （ND4） of 34 species within Sinocyclocheilus, which represent the most dense taxon sampling to date. We performed Bayesian mixed models analyses with this data set. Under this phylogenetic framework, we estimated the divergence times of recovered clades using different methods under relaxed molecular clock. Our phyloegentic results supported the monophyly of Sinocyclocheilus and showed that this genus could be subdivided into 6 major clades. In addition, an earlier finding demonstrating the polyphyletlc of cave species and the most basal position of S. jii was corroborated. Relaxed divergence-time estimation suggested that Sinocyclocheilus originated at the late Miocene, about 11 million years ago （Ma）, which is older than what have been assumed.     

The internal structure of Early Cambrian fossil embryo <Emphasis Type="Italic">Olivooides</Emphasis> revealed in the light of Synchrotron X-ray Tomographic Microscopy

Countless fossil embryo Olivooides and the hatched larvae, juveniles and adults （the latter two kinds are Punctatus） are recovered by means of acid maceration from the fine-crystalline to medium-crystalline phosphatic limestone and phosphatic micrite of Early Cambrian Kuanchuanpu Formation at the Shizhonggou section, near Kuanchuanpu Village, Ningqiang County, Shaanxi Province, China. Using the technique of Synchrotron X-ray Tomographic Microscopy, the 3D internal structure of Ofivooides and Punctatus is reconstructed. The morphological and statistic analyses are also given to the stellae structure of Ofivooides and Punctatus, which indicates that this structure is a result of adaptive evolution to a lifestyle of fast-attaching after hatching, probably with the function of mucilage secretion. The internal structure of Punctatus is described and discussed. The ovum-like structure, a common internal feature of Punctatus, is considered as the taphonomic structure, rather than eggs or other biological structure. This structure is thought to be formed after the burial of the animal and before or during the mineralization. The original internal structure of Punctatus is assumed to be tabulae-filled, with soft body grown on them.     

S 100A8 mediates the activation of P65/HLA- B/S 100A8/BCL-2/Caspase-9 （-3） pathway in laryngeal carcinogenesis

S100 calcium binding protein A8 （S100A8）, a possible novel member of NF-kappa B signal pathway in laryngeal squamous cell carcinoma （LSCC）, interacts with human leukocyte antigen B （HLA-B） which carries an NF-kappa B binding site within the enhancer A. The objective of this study was to explore the molecular mechanism of S100A8 in laryngeal carcinogenesis. RT-PCR, Western blotting and immunohistochemistry staining were applied to evaluate the expression levels of IKKα, P65, REL-B, S100A8, APAF-1 and BCL-2 genes. The signal transduction passway in which S100A8 might participate was explored by RNA interference. Flow cytometry, TUNEL assay and cell invasion in vitro were used to detect the biological behavior of Hep2 cells induced by S100A8 gene. Our results showed that high expression of S100A8 was related to tumorigenesis in LSCC and negatively correlated with the degree of differentiation, indicating that S100A8 gene could inhibit apoptosis and promote metastasis in LSCC. Additionally, the suppression of S100A8 by RNA interference down-regulated BCL-2 but not APAF-1, P65 and IKKα, while, the suppression of P65 could significantly down-regulate the expression of S100A8 gene. In conclusion, S100A8 plays an important role in P65/HLA-B/S100A8/BCL-2/Caspase-9 （-3） pathway in laryngeal carcinoma.     

Estimating divergence times among subfamilies in Nymphalidae

The mitochondrial cytochrome oxidase subunit Ⅰ （COⅠ） gene and the nuclear elongation factor 1α （EF-1α） gene were sequenced from 13 species of Nymphalidae. Phylogenetic trees of Nymphalidae, which is the largest family in butterflies, were constructed based on the sequences determined from 13 species sequenced in our laboratory and an additional 43 species obtained from GenBank using the maximum likelihood （ML） and Bayesian methods. Relative-rate tests between lineages in these phylogenetic trees were performed. On the basis of the results of the relative-rate tests and fossil information of Satyrinae, Nymphalinae and Biblidinae, the average divergence times among the subfamilies are estimated as 44.2-87.1 million years ago （Ma）. These results will be helpful for better understanding of the origin and evolution of this family, as well as the divergence time of butterflies and other complex taxa.     

Synergistic defensive mechanism of phytochelatins and antioxidative enzymes in <Emphasis Type="Italic">Brassica chinensis</Emphasis> L. against Cd stress

Brassica chinensis L. was chosen and exposed to different concentrations of Cd exposure to evaluate its Cd-accumulating capacity and its potential cellular defensive mechanisms. Cd accumulation in the shoots and roots of B. chinensis was up to 1348.3±461.8 and 3761.0±795.0 mg per killogram of dry weight, respectively, under 200 μmol/L of Cd exposure. Increasing Cd accumulation in the plant was accompanied by rapid accumulation of phytochelatins （PCs）, and the sequestration of Cd by PCs provided a primary cellular mechanism for Cd detoxification and tolerance of B. chinensis. Furthermore, malondialdehyde formation, hydrogen peroxide content and antioxidative enzyme activities such as superoxide dismutase, catalase, guaiacol peroxidase and ascorbate peroxidase were observed in the shoots of Cd-stressed B. chinensis. Increasing enzyme activities in response to concentrations of 5 to 50 μmol/L Cd showed an efficient defense against oxidative stress, suggesting that the antioxidative system was a secondary defensive mechanism. These resulted in reduced free Cd damage and enhanced Cd accumulation and tolerance. Glutathione plays a pivotal role in these two detoxification pathways. In general, these results suggested that PCs and the antioxidative system are synergistic in combatting Cd-induced oxidative stress and that they play important roles in Cd detoxification of B. chinensis, and also give a deep understanding of the natural defensive mechanisms in plants under heavy metal stress.     

Effect of the contact distance on transport properties of an orsanic molecular device

Using a spatially symmetric phenyldithiolate molecule sandwiched between two gold electrodes as model system and through shifting one electrode from symmetric contact site to form asymmetric contact, we investigated the properties of electronic transport in such a device by the first-principles. It was found that the/（G ）-V characteristics of a device show significant asymmetry and the magnitudes of current and conductance depend remarkably on the variation of molecule-metal distance at one of the two contacts. Namely, an asymmetric contact would lead to the weak rectifying effects on the current-voltage characteristics of a molecular device. The analysis shows that the HOMO is responsible for the resonant tunneling and its shift due to the charging of the device while the bias voltage is the intrinsic origin of asymmetric/（G）- Vcharacteristics.     

dr1127： A novel gene of Deinococcus radiodurans responsible for oxidative stress

The functional analysis of dr1127,a novel gene in Deinococcus radiodurans was performed in this pa-per. The dr1127 gene was found occasionally in our microarray and 2-DE gel experiments. Mutation of the dr1127 gene decreased the γ-radiation and H2O2 resistance of D. radiodurans,and weakened the scavenging abilities of cell extracts for free radicals (superoxide anion,hydrogen peroxide,and hy-droxyl radical). Further oxidative damage assays demonstrated that the purified DR1127 protein of D. radiodurans could bind to double stranded DNA in vitro and protect DNA from oxidative damage in this way. These results suggest that the dr1127 gene is an important gene that can maintain γ-radiation and oxidative resistance in D. radiodurans and may take part in the oxidative stress process.     

Modified fiber qualities of the transgenic cotton expressing a silkworm fibroin gene

A silkworm gene for fibroin was introduced into the upland cotton WC line by Agrobacterium-mediated transformation. PCR detection for fibroin, nptII and gus genes, Kanamycin (Km)-resistance analysis and GUS-histochemical assay were conducted on 30 regenerated plants from 9 callus lines, and 17 positive plants were obtained by these 5 screening methods. By Km-resistance analysis and PCR for fibroin, 6 homozygous lines in T₃ were obtained. Southern blot and Northern bolt demonstrated that the fibroin gene was inserted into the genome of these 6 lines, stably inherited and expressed. Compared to the control, the surface structure of mature fiber in the 6 lines was significantly distorted and an increased number of convolution was observed by scanning electron microscopy (SEM). Fiber quality traits analysis indicated that fiber elongation of the 6 homozygous lines was all increased and fiber strength of 3 lines was enhanced. These results indicated that fibroin expression influenced cotton fiber structure and quality, suggesting that fibroin has great potential for improving cotton fiber quality by genetic engineering. Supported by National High Technology Research and Development Program of China (Grant No. 2006AA100105), Science & Technology Pillar Program of Jiangsu Province (Grant No. BE2008310) and Programme of Introducing Talents of Discipline to Universities (Grant No. B08025) Contributed equally to this work     

Inductive transfer learning for unlabeled target-domain via hybrid regularization

Recent years have witnessed an increasing interest in transfer learning. This paper deals with the classification problem that the target-domain with a different distribution from the source-domain is totally unlabeled, and aims to build an inductive model for unseen data. Firstly, we analyze the problem of class ratio drift in the previous work of transductive transfer learning, and propose to use a normalization method to move towards the desired class ratio. Furthermore, we develop a hybrid regularization framework for inductive transfer learning. It considers three factors, including the distribution geometry of the target-domain by manifold regularization, the entropy value of prediction probability by entropy regularization, and the class prior by expectation regularization. This framework is used to adapt the inductive model learnt from the source-domain to the target-domain. Finally, the experiments on the real-world text data show the effectiveness of our inductive method of transfer learning. Meanwhile, it can handle unseen test points.