The R- and AR-indices： Complementing the h-index

Based on the foundation laid by the h-index we introduce and study the R- and AR-indices. These new indices eliminate some of the disadvantages of the h-index, especially when they are used in combina-tion with the h-index. The R-index measures the h-core’s citation intensity, while AR goes one step further and takes the age of publications into account. This allows for an index that can actually in-crease and decrease over time. We propose the pair (h, AR) as a meaningful indicator for research evaluation. We further prove a relation characterizing the h-index in the power law model.     

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.     

Southern rice black-streaked dwarf virus: A new proposed <Emphasis Type="Italic">Fijivirus</Emphasis> species in the family <Emphasis Type="Italic">Reoviridae</Emphasis>

For the past several years, a novel dwarf disease has been observed on rice （Oryza sativa） in some regions of Guangdong Province and Hainan Province, southern China. Infected plants showed stunting, dark leaf and small enations on stem and leaf back. Typical Fijivirus viroplasma containing crystalline arrayed spherical virons approximately 70--75 nm in diameter and tubular structures were detected in ultrathin sections by an electron microscope in parenchyma phloem cells of the infected plants. The virus was transmitted to rice seedlings by white-backed planthoppers, Sogatella furcifera （Hemiptera： Delphacidae）, collected in the diseased fields. Analysis of dsRNA extracts from infected plants revealed ten linear segments, which were similar to the electrophoretic profile of Rice black-streaked dwarf virus （RBSDV）. RT-PCR with a single primer which matched to a linker sequence ligated to both 3＇ ends of the viral genomic dsRNAs resulted in amplification of genome segments 9 （S9） and 10 （S10） cDNA products. The complete nucleotide sequences of S9 and S10 were obtained from clones of the RT-PCR amplicon exhibited characteristic properties of Fijivirus including low GC content （34.5% and 35.6%）, genus conserved 5＇ and 3＇ termini sequences and similar genome organization. Blast searches indicated that the sequences of S9 and S10 shared 68.8%--74.9% and 67.1% --77.4% nucleotide identities with those of viruses in the Fijivirus group 2, respectively. These values were similar to those among other viruses in the Fijivirus group 2 and considerably lower than those among RBSDV isolates. Phylogenetic trees based on S9 and S10 nucleotide sequences and their putative amino acid sequences showed that this virus represented a separate branch among other Fijiviruses. The virus was also detected by a nested RT-PCR assay in corn （Zea mays）, barnyard grass （Echinochloa crusgalll）, Juncellus serotinus and flaccidgrass （Pennisetum flaccidum） in and/or adjacent to the infected rice fields. I     

Studies of new EST-SSRs derived from Gossypium barbadense

Existing cotton EST-SSR markers are mostly derived from Gossypium arboreum and Gossypium hir-sutum, but EST-SSR markers from Gossypium barbadense are scarce. One hundred and nineteen EST-SSRs were developed based on 98 unique ESTs from a cDNA library constructed in our laboratory using developing fibers from G. barbadense cv. Pima3-79. Among the SSRs, trinucleotide AAG appeared at a high frequency of 11.76%. 36 accessions (consisting of 13 diploids of the A genome, 11 diploids of the D genome and 12 allotetraploids of the AD genome) were employed to test new EST-SSRs. 76 EST-SSRs were successfully amplified, and 313 polymorphic fragments were yielded, with an average of 4.11 fragments per primer pair. The PIC ranged from 0.17 to 0.95 with an average of 0.53. Based on Jaccard’s genetic similarity coefficient, these 36 accessions were clustered into three groups. 21 EST-SSRs exhibited polymorphisms in BC1 population ((Emian22 × Pima3-79) × Emian22), 24 polymor- phic loci were generated, while 22 of the 24 polymorphic loci were integrated with our interspecific BC1 backbone genetic linkage map, and anchored in 12 chromosomes. This study effectively proved that EST-SSRs from G. barbadense are valuable for genetic diversity analysis and genetic mapping.     

Effects of cadmium, 17β-estradiol and their interaction in the male Chinese loach （Misgurnus anguillicaudatus）

To assess the interaction effect between cadmium (Cd) and 17-estradiol (E2),male Chinese loaches (Misgurnus anguillicaudatus) were exposed to E2 (1 g/L) and Cd (50 or 500 g/L) alone and in combination using a semi-static waterborne exposure system.The effects of E2 on the accumulation and distribution of Cd,as well as the effects of Cd on vitellogenin (Vtg) synthesis induced by E2,were investigated.Cd mainly accumulated in the kidneys,liver,intestines,and gills,with little amounts in muscles,bones,and gonads.Co-exposure with E2 did not change the main targets for Cd.E2 could induce Vtg synthesis in male Chinese loaches,and co-exposure with 50 or 500 g/L Cd could inhibit the Vtg induced by 1 g/L E2.Compared with the results reported in the literature,it can be concluded that factors such as fish species,Cd dosage,and manner of exposure might make contributions to the interaction between Cd and E2.Our results also suggested that male Chinese loaches are susceptible to Cd,and can be recommended as a potential sentinel species to study the ecotoxicology of heavy metals.     

Formation of ζ phase in Cu-Ge peritectic alloys

Rapid growth behavior of ζ phase has been investigated in the undercooling experiments of Cu-14%Ge, Cu-15%Ge, Cu-18.5%Ge and Cu-22%Ge alloys. Alloys of the four compositions obtain the maximum undercoolings of 202 K（0.17TL）, 245 K（0.20TL）, 223 K（0.20TL） and 176 K（0.17TL）, respectively. As the content of Ge increases, the microstructural transition of ＂a（Cu） dendrite ＋ ζ＂ peritectic phase → ζ＂ peritectic phase →, ζ dendrite ＋ （ε＋ζ） eutectic＂ takes place in the alloy at small undercooling, while the microstructural transition of ＂fragmented α （Cu）dendrite ＋ ζ peritectic phase →, ζ peritectic phase →ζ dendrite ＋ ε phase＂ happens in the alloy at large undercooling. EDS analysis of the Ge content in peritectic phase indicates that undercooling enlarges the solid solubility of ζ rdendrite, which leads to a decrease in the Ge content in ζ phase as undercooling increases. In the Cu-18.5%Ge alloy composed of ζ peritectic phase, the Ge content in ζ phase increases when undercooling increases, which is due to the restraint of the Ge enrichment on the grain boundaries by high undercooling effect.     

Primary Study on Phytodegradation of Bisphenol A by Elodea nuttallii

In a microcosm system where Elodea nuttallii and Bisphenol A （BPA） coexist, with the help of Liquid chromatography-mass spectrometer （LC-MS） and gas chromatography-mass spectrometer （GC-MS）, the dynamics of phytodegradation of BPA with concentration 1-20 mg/L and the products of phytodegradation was studied. Antioxidation activity and phospholipids fatty acids were measured to evaluate the effects of BPA on E.nuttallii. The results showed that the half life period of phytodegradation of BPA was less than 15 days. 2-（4-hydroxypheny）-2-（3,4-o-dihydroxypheny） propane and 2, 2-bis（4-hydroxypheny） propyl alcohol were identified to be as two possible products of BPA. The peroxidase （POD） activity of E.nuttallii decreased by 50% to 100% compared with that controlled at the end of the experiment. The fatty acid methanol esters （FAMEs） changed obviously too. It showed that oxidation stress and membrane damage would be the two effcting aspects of BPA on E.nuttallii.     

B-Valued Dyadic Derivative

The principles of the new maximal operator H＊ we defined are discussed. We prove that it is bounded from martingale Hardy-Lorentz L^Xp.q[0,1） to the Lorentz L^Xp.q[0,1） for 1/2〈 p〈∞, 0〈~ q ≤ ∞, where X is any Banach space. When the Banach space X has the RN property, the sequence dnHnf converges to f a.e. Meanwhile the convergence in L^Xp norm for 1≤p〈∞ is a consequence of that the family functions K （n∈N） is an approximate identity.     

Molecular identification and phylosenetic position of Cuora yunnanensis

The Yunnan box turtle （Cuora yunnanensis, Boulenger, 1906）, which has drawn much attention in conservation biology, was regarded as extinct since it was previously known only from 12 specimens collected in Yunnan, China, before 1908. Recently, live specimens have been discovered which are suggested to be C. yunnanensis. To determine whether the newly discovered specimens are really C. yunnanensis, we have established a molecular phylogeny, with a 1725-bp fragment of mitochondrial DNA, using samples from three live individuals of C. yunnanensis, together with sequence data from a museum specimen of C. yunnanensis （MNHN 1907.10） and other members of the genus Cuora. We found that the three newly discovered individuals and the old museum specimen of C. yunnanensis are very similar both in morphology and in mitochondrial DNA sequence, suggesting that the three new individuals are the very C. yunnanensis, and thus the species is not extinct. Our phylogenetic analysis also demonstrates that C. yunnanensis is not of recent hybrid origin, but rather represents a distinct evolutionary lineage.     

Carboxymethytl Pachymaram Up-Regulates Dendritic Cell＇s Function in Hepatitis B Virus Transgenic Mice

The effect of carboxymethytl pachymaram (CMP) on the function of dendritic cells(DCs) derived from spleens of hepatitis B virus transgenic mice are studied in vitro. The phenotypes of DCs are tested by flow cytometry (FCM), cytokines measured by ELISA. The expression of DCs’ phenotypes in HBV transgenic mice are low (CD80⁺CD11c⁺:59.12±11.53 vs 9.60±4.53, p<0.01; CD80⁺ MHC-II⁺: 44.86±12.31 vs 9.80±5.72, p<0.01, normal mice vs HBV transgenic mice), the ability of DCs stimulating T lymphocytes proliferation decreases (0.37±0.11 vs 0.20±0.11, p<0.05, normal mice vs HBV transgenic mice), levels of IL-12 and IFN-γ decrease whereas the level of IL-10 increases; CMP can enhance DCs’ ability of stimulating T lymphocytes proliferation, facilitate the secretion of IL-12 and IFN-γ, inhibit the secretion of IL-10, thus up regulates DCs function. The results show a good prospective use of CMP on the treatment of chronic hepatitis B. Biography: HOU Anji (1963–), male, Ph.D. candidate, Associate professor, research direction: clinical virology.     

Investigation of charge transfer complexes formed between 3,3＇-dimethylbenzidine （o-toluidine） donor and DDQ, p-chloranil and TCNQ as π-acceptors

Charge-transfer (CT) complex of o-toluidine (o-tol) with the π-acceptor tetrachloro-p-benzoquinone (p-chloranil; CHL) has been synthesized and characterized, along with the products of the elimination reaction of o-toluidine (o-tol) with 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ) and 7,7,8,8-tetracyanoquinodimethane (TCNQ). Their properties and structures have been investigated using electronic absorption and IR spectroscopy as well as elemental analyses of the isolated compounds. The o-tol/p-CHL CT complex is shown to consist of a CHL⁻ radical anion and o-tol⁺ radical cation. The formations of all three compounds result in the appearance of new UV-Vis spectral bands that peaked in intensity at a stoichiometric ratio of 1:1. ¹H-NMR and mass spectra were used to confirm the formation of the o-tol/DDQ and o-tol/TCNQ products. The new 7,8-dicyano-7′,8′-o-toluidilequino-dimethane and 2,3-dichloro-5-cyano-6-o-toluidil-p-benzoquinone products resulted from the rapid reaction of o-tol with TCNQ and DDQ, respectively. Thermogravimetric studies showed that the CT-complex decomposes in three steps whereas the new compounds decompose in a single step. Thermodynamic parameters were computed from the thermal decomposition data.     

Mutagenesis of Ser24 of Cytochrome b559 α Subunit Affects PSII Acitivies in Chlamydomonas reinhardtii

In order to study the functions of cytochrome b559 (Cyt b559) in photosystem two (PSII) activity, mutant S24F of Chlamydomonas reinhardtii was constructed using site directed mutagenesis, in which Serine24 (Ser24) locating downstream of Histidine23 (His23) in α subunit of Cyt b559 was replaced by Phenylalanine (Phe). Physiological and biochemical analysis showed that mutant S24F could be grown photoautotrophically or photoheterotrophically. However, their growth rate was slower either on HSM or TAP medium than that of the control; Analysis of PSII activity revealed that its oxygen evolution was about 71% of wild type (WT); The Photochemical efficiency of PSII (Fv/Fm) of S24F was reduced 0.23 compared with WT; S24F was more sensitive to strong light irradiance than the wild type; Furthermore, SDS-PAGE and Western-blotting analysis indicated that the expression levels of α subunit of Cyt b559, LHCII and PsbO of S24F were a little less than those of the wild type. Overall, these data suggests that Ser24 plays a significant role in making Cyt b559 structure maintain PSII complex activity of oxygen evolution although it is not directly bound to heme group.     

Synthesis,characterization and photoluminescence of aluminum <Emphasis Type="Italic">N</Emphasis>-aryloxo functionalized <Emphasis Type="Italic">β</Emphasis>-ketoiminate complexes

The synthesis, characterization and luminescent properties of aluminum complexes containing a dianionic N-aryloxo functionalized β-ketoiminate ligand are presented. 4-(2-Hydroxy-5-R-phenyl)imino-2-pentanone (R = Me, L¹H₂; R = tert-butyl, L²H₂) ligands reacted with AlEt₃ in tetrahydrofuran to give the aluminum complexes (L¹AlEt)₂ (1) and (L²AlEt)₂ (2) in reasonable isolated yields. X-ray diffraction revealed that complexes 1 and 2 have solvent-free centrosymmetric dimeric structures, and each aluminum center has distorted trigonal bipyramidal geometry. At room temperature, complexes 1 and 2 exhibit blue photoluminescence in acetonitrile with maximum emission wavelengths of 419 and 413 nm, respectively.     

Molecular cloning, expression and biochemical property analysis of AtKP1, a kinesin gene from Arabidopsis thaliana

Kinesins are common in a variety of eukaryotic cells with diverse functions. A cDNA encoding a member of the Kinesin-14B subfamily is obtained using 3＇-RACE technology and named AtKP1 （for Arabidopsis kinesin protein 1）. This cDNA has a maximum open reading frame of 3.3 kb encoding a polypeptide of 1087 aa. Protein domain analysis shows that AtKP1 contains the motor domain and the calponin homology domain in the central and amino-terminal regions, respectively. The carboxyl-terminal region with 202 aa residues is diverse from other known kinesins. Northern blot analysis shows that AtKP1 is widely expressed at a higher level in seedlings than in mature plants. 2808 bp of the AtKP1 promoter region is cloned and fused to GUS. GUS expression driven by the AtKP1 promoter region shows that AtKP1 is mainly expressed in vasculature of young organs and young leaf trichomes, indicating that AtKP1 may participate in the differentiation or development of Arabidopsis thaliana vascular bundles and trichomes. A truncated AtKP1 protein containing the putative motor domain is expressed in E. coil and affinity-purified. In vitro characterizations indicate that the polypeptide has nucleotide-dependent microtubule-binding ability and microtubule-stimulated ATPase activity.     

Functional analysis of the sbcD （dr1921 ） gene of the extremely radioresistant bacterium Deinococcus radiodurans

In eukaryotes, the Mre11-Rad50-Nbs1 (MRN) complex, which resides at the crossroads of DNA repair and checkpoint signaling, rapidly forms prominent foci at damage sites following double-strand break (DSB) induction. This complex carries out the initial processing of the DSB ends. Mutations in the genes that encode components of this complex result in DNA-damage hypersensitivity, genomic in- stability, telomere shortening, and aberrant meiosis. Therefore, the MR proteins are highly conserved during evolution. The bacterial orthologs of Mre11 and Rad50 are the SbcD and SbcC proteins, respec- tively. Deinococcus radiodurans, an extremely radioresistant bacterium, is able to mend hundreds of radiation-induced DSBs. The SbcD and SbcC proteins were identified as the products of the Dr1921 and Dr1922 genes. Disruption of the sbcD gene, by direct reverse-orientation insertional mutagenesis tech- nology, remarkably increases the cells’ sensitivity to various types of DNA damaging agents, such as ionizing radiation, ultraviolet irradiation, hydrogen peroxide, and mitomycin C. We also provide evidence that the drSbcD protein plays an important role in both growth and DNA repair in this organ- ism, especially in repair of DSBs generated after cellular exposure to 6000 Gy of IR. These results demonstrate that the drSbcD protein plays an important role in DSBs repair in D. radiodurans.     

A novel gene <Emphasis Type="Italic">R049</Emphasis> identified in uropathogenic <Emphasis Type="Italic">Escherichia coli</Emphasis> provides partial protection in mice from colonization

Uropathogenic Escherichia coli (UPEC) is the most common causative organism of human urinary tract infection (UTI). Several UPEC virulence factors have been identified, but more are yet to be found. We previously identified a novel 789-bp-long DNA fragment (named R049) in UPEC strain 132 using a suppressive subtractive hybridization technique. In the present study, we used genome walking to elongate the sequence of this fragment to obtain the whole gene sequence and examined the role of this gene product in generating protective immunity. Through bioinformatic analysis, we predicted that this gene is a 1311-bp open reading frame (ORF), which we designated ORF_R049 (GenBank accession No.: EF488001). We further constructed a prokaryotic expression system to express full recombinant R049 protein and isolated and purified the protein through IPTG induction and nickel affinity chromatography. Using mouse immunosera generated by the purified protein, we confirmed the natural expression and outer membrane localization of the protein in wild-type strain UPEC132 by Western blotting. To test the potential of this protein as a vaccine candidate, we immunized mice with the recombinant protein before challenging them with UPEC132 through the urinary tract. The results showed significantly reduced bacterial colonization in the urine and kidneys of the immunization group compared with the control group. However, the degree of renal pathological damage was not significantly improved in the immunized mice. Our study has identified a novel gene of UPEC which can generate protective immunity against UTI. This novel gene provides a promising new vaccine candidate.     

Identification of <Emphasis Type="Italic">Fallopia</Emphasis> species based on the chloroplast <Emphasis Type="Italic">mat</Emphasis>K gene sequences

In order to develop an efficient identification method for Fallopia plants and drugs, molecular analysis of the partial matK gene sequences was performed on 6 Fallopia species. Based on the matK sequences, a phylogenetic tree was constructed, which showed that different populations of inter- and intra-species could be specified and distinguished. The matK gene sequences of the 6 Fallopia species were all found to be of 1 271 bp in length, with some nucleotide variations throughout the entire sequences. The nucleotide difference at position 1 041 could distinguish F. denticulata from others, while specific nucleotide at position 1 154 became identification markers for F. aubertii. Moreover, four specific marker sites for F. multiflora var. ciliinerve at positions 216, 224, 1 060 and 1 179, seven for F. convolvulus at 318, 765, 772, 874, 936, 952 and 1 036, and seven for F. dentate alata at 111, 192, 366, 450, 457, 1 032 and 1 074 were also observed. By detecting the marker nucleotides and analyzing the phylogenetic relationship, the botanical origins of five inspected drugs were determined, suggesting that matK sequences can be used for authenticating Fallopia plants and drugs.     

Icariin suppresses bone resorption activity of rabbit osteoclasts in vitro

The effect of icariin on the bone resorption activity of rabbit osteoclasts is assessed in vitro. Osteoclasts were isolated from Japanese white rabbits and cultured on plates with a sterilized bone slice in each well. After treatment with icariin at various concentrations, the bone resorption activity of osteoclasts was evaluated by examining pit areas, superoxide anion (·O2-) generation, size and number of actin rings and intracellular calcium concentration [Ca2 ]i. As revealed by these data, icariin elicited continuous decline of [Ca2 ]i, making actin ring constricted and ·O2- generation decreased. These events resulted in smaller and fewer pits which indicate suppressed bone resorption activity of rabbit osteoclasts by icariin.     

Accurate localization and excision of genomic islands in four strains of <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> and <Emphasis Type="Italic">Pseudomonas fluorescens</Emphasis>

Mobile genomic islands (GIs) can be excised from the chromosome, then form a circular intermediate and be reintegrated into the chromosome by the GI internal integrase. Some mobile GIs can also be transferred into a new receptor cell by transformation, conjugation, or transduction. The action sites of the integrase are usually flanked direct repeats (DRs) of the GIs. Accurate localization of the flanking sequences is a precondition for determining the mobility of the GI. Mobile GIs are generally associated with transfer RNAs (tRNAs). Based on the correlation between flanking sequences and tRNA sequences, the flanking sequences of 11 putative mobile GIs in Pseudomonas aeruginosa PAO1, P. aeruginosa PA14, P. fluorescens Pf-5 and P. fluorescens Pf0-1 were identified. Among the 11 GIs, Pf0-1GI-1 is responsible for benzoate degradation. PAO1GI-1, Pf5GI-2, Pf5GI-3, and Pf5GI-4 were confirmed experimentally to be excised from a chromosome to form a circular intermediate. The action sites of the integrases are these GIs direct repeats. Due to distinct DRs, cutting sites for the internal integrase of PAO1GI-1, Pf5GI-2, Pf5GI-3 and Pf5GI-4 were determined outside the T-loop of the tRNA^Gly gene, outside the anticodon loop of the tRNA^Ser gene and tRNA^Lys gene, and at the asymmetric 3′-end of the tRNA^Leu gene, respectively. PAO1GI-1 and other mobile GIs may be transferred into many different strains that belong to different phyla because of the clear flanking sequences. This study describes basic information about the action sites of the integrases, assesses the mobility of GIs, and can help design and transfer mobile GIs to candidate strains.