Classification and naming of dyes, stains and fluorochromes.

A classification of dyes and other colorants is proposed, based on the chemical features responsible for their visibility and generally consonant with the writings of modern color chemists. The scheme differs in several respects from that of the Colour Index (CI), but it retains some traditional small groups of dyes that include biological stains. Natural dyes, recognized as a group in the CI, are placed with or near synthetic dyes with identical or similar chromophores. The new scheme also provides categories for dyes and fluorochromes that do not have places in the CI classification. Some CI categories, including lactones, aminoketones and hydroxyketones, are not recognized in this new scheme, which is adopted in the forthcoming 10th edition of Conn's Biological Stains: a Handbook of Dyes and Fluorochromes for Use in Biology and Medicine. Some rules are also set out for the spelling of trivial names, which has long been inconsistent in scientific literature. The ending '-ine' is used for compounds derived from organic bases (e.g., fuchsine and thionine, not fuchsin or thionin), and names ending in '-in' are for compounds that are not bases or their derivatives (e.g., eosin and phloxin, not eosine or phloxine). Initial capital letters are used only for words that are names of people or places (e.g., Nile blue or Congo red) and for the 'generic' components of CI application names (as in Acid yellow 36). Other words, including trade names that have fallen into common usage are not capitalized (e.g., alcian blue, biebrich scarlet, coomassie blue). The recommended spellings of some dyes differ from those commonly seen in vendors' catalogs and in biological publications, but they are generally consistent with English and American dictionaries, with recent writings in English by color chemists, and with the trivial names of other organic compounds.     

Biodecolorization of azo,anthraquinonic and triphenylmethane dyes by white-rot fungi and a laccase-secreting engineered strain

One laccase-secreting engineered strain and four white-rot fungi were tested for their capacity to decolorize nine dyes that could be classified as azo, anthraquinonic and triphenylmethane dyes. Trametes versicolor was the most efficient of the tested strains under these experimental conditions. Anthraquinonic dyes were decolorized more easily than the other two types. Small structural differences among the dyes could significantly affect decolorization. None of the strains showed lignin peroxidase or veratryl alcohol oxidase activity. None of the dyes were decolorized completely by laccase alone. It is likely that other phenoloxidases, such as Mn-dependent and versatile peroxidase, were also involved in decolorization of the dyes.     

Carbon from Cassava peel, an agricultural waste, as an adsorbent in the removal of dyes and metal ions from aqueous solution

Cassava (Manihot esculenta) is a short lived erect perennial shrub, planted vegetatively from hard wood stem cuttings. It is an important crop across a wide range of tropical environments and is a significant component of cropping systems. Cassava peel is an agricultural waste from the food processing industry. Activated carbons prepared from waste cassava peel employing physical and chemical methods were tested for their efficiency in the removal of dyes and metal ions from aqueous solution. While both of these were efficient as adsorbents for dyes and metal ions, the material impregnated with H₃PO₄ showed higher efficiency than the heat treated materials.     

Reassessment of type specimens of Cordyceps and its allies described by Dr. Yosio Kobayasi, preserved in the National Museum of Nature and Science. Part 2: Cordyceps (Elaphocordyceps) on Elaphomyces

Four holotype specimens of Cordyceps parasitic on Elaphomyces that were originally described by Dr. Yosio Kobayasi and Mr. Daisuke Shimizu were relocated, and TNS (National Museum of Nature and Science, Japan) registration numbers (TNS-F-number) were assigned: viz. Cordyceps minazukiensis (TNS-F-197989), C. ophioglossoides var. cuboides (TNS-F-230312), C. valvatistipitata (TNS-F-230284), and Cordyceps × jezoensoides (TNS-F-230286). Two specimens were selected as lectotypes: C. delicatistipitata (TNS-F-230293) and C. ophioglossoides f. alba (TNS-F-18223). Those taxa, except for Cordyceps × jezoensoides, have been treated as members of the genus Elaphocordyceps in the latest taxonomy. The new combination Elaphocordyceps × jezoënsoides (Kobayasi) is proposed. In addition, Elaphomyces asahimontanus Kobayasi, the host of Cordyceps delicatistipitata, is lectotypified (TNS-F-230293).     

植物几丁质酶的结构与功能、分类及进化

近年来对几丁质酶的研究越来越深入,资料也愈来愈多,有的植物几丁质酶除具有几丁质酶活性,还具有其它的活性,典型的几丁质酶由－N－端信号区,催化区和C－端延伸区组成,有的还有几丁质结合域,各项能域具有各自的功能,对植物几丁质酶的分类已经过多次改进,目前公认的分成4组9个亚组,有证据表明植物几丁质酶在进化过程中有遗传转座现象,但具有进化过程还有待进一步确证,对几丁质酶与其它一些蛋白的关系的了解有助于理解几丁质酶的起源和进化,由于几丁质酶具有独特的抗真菌特性,因而几丁质酶基因成为目前抗真菌基因工程研究的热之一。     

Morphological and molecular characterization of the name-bearing type species Rimaleptus binucleatus (Kahl, 1931), with a phylogenetic re-analysis of dileptid evolutionary history (Ciliophora: Litostomatea: Rhynchostomatia)

We collected Rimaleptus binucleatus from soil in the surroundings of the town of Ulsan, South Korea. Its morphology and 18S rRNA gene were studied using standard methods. This possibly widely distributed species is characterized by: (i) a size of about 170–400 × 20–65 μm; (ii) a narrowly to cylindrically dileptid body with proboscis occupying about 30–65% of body length; (iii) two dorsal contractile vacuoles; (iv) two size groups of rod-shaped extrusomes; and (v) about 18–29 ciliary rows, 4–6 of them anteriorly differentiated into a staggered dorsal brush. Phylogenetic analyses of five new rhynchostomatian 18S rRNA gene sequences supported monophylies of the orders Tracheliida and Dileptida, but revealed that the genera Rimaleptus and Pseudomonilicaryon are polyphyletic. Monophyly of genera with two macronuclear nodules was consistently rejected, but monophylies of dileptids with many scattered macronuclear nodules and of dileptids with moniliform macronucleus and multi-rowed dorsal brush could not be excluded by statistical topology tests. Nevertheless, phylogenetic network analyses indicated considerable conflict in the phylogenetic signal provided by the 18S rRNA gene to resolve unambiguously relationships among dileptid genera.     

Classification of trypanosomatids from fruits and seeds using morphological, biochemical and molecular markers revealed several genera among fruit isolates

Trypanosomatids are widespread in several plant families and although most isolates have been classified as Phytomonas, other trypanosomatid genera can also infect plants. In order to assess the natural occurrence of non-Phytomonas trypanosomatids in plants we characterized 21 new trypanosomatid cultures, 18 from fruits and three from seeds of 17 plant species. The trypanosomatids from fruit and seeds were compared in terms of morphological, growth, biochemical and molecular features. The high diversity among the isolates permitted the classification of the new flagellates into the genera Crithidia and Leptomonas as well as Phytomonas. The data showed that natural fruit infection with non-Phytomonas trypanosomatids is more common than usually thought, being detected in 43% of the fruit isolates.     

Comments on the Systematics and Classification of the Beavers (Rodentia, Castoridae)

The systematics of the beavers (Castoridae) are reviewed and definitions are presented for each subfamilial group. Four subfamilies are recognized: primitive Agnotocastorinae (divided into two tribes, Agnotocastorini and Anchitheriomyini); burrowing beavers, Palaeocastorinae; giant beavers, Castoroidinae (containing two tribes, Castoroidini and Trogontheriini); and the Castorinae. The agnotocastorines are viewed as the ancestral group for all later subfamilies. The Palaeocastorinae is viewed as a side-branch, not ancestral or closely related to any of the later subfamilies. The Castorinae and Castoroidinae may represent a distinct clade united by dental features.     

Phylogeny of the Baldratiina (Diptera: Cecidomyiidae) inferred from morphological, ecological and molecular data sources, and evolutionary patterns in plant-galler relationships

The phylogeny of the gall-midge subtribe Baldratiina (Diptera: Cecidomyiidae) was reconstructed from molecular (partial sequence of the mitochondrial 12S rDNA), morphological and ecological data sets, using 16 representative species of most of the genera. The morphological and ecological data were combined in a single character matrix and analyzed separately from the molecular data, resulting in an eco-morphological cladogram and a molecular cladogram. Attributes of galls and host associations were superimposed on the molecular cladogram in order to detect possible trends in the evolution of these traits. The cladograms resulting from the two independent analyses were statistically incongruent, although both provide evidence for the monophyly of the genera Baldratia and Careopalpis and the paraphyly of the genera Stefaniola and Izeniola. The results suggest a minor impact of the morphological characters traditionally used in the classification of the Baldratiina, whereas ecological data had a major impact on the phylogenetic inference. Mapping of gall and host attributes on the molecular cladogram suggests that multi-chambered stem galls constitute the ancestral state in the subtribe, with several subsequent shifts to leaf galls. It is concluded that in contrast to other studied groups of gall insects, related baldratiine species induce different types of galls, attesting to speciation driven by gall-type shifts at least as often as host shifts.     

The S-Distribution A Tool for Approximation and Classification of Univariate,Unimodal Probability Distributions

In many statistical applications a data set needs to be evaluated but there is no solid information about which probability distribution might be most appropriate. Typical solutions to this problems are: to make assumptions that facilitate mathematical treatment; to use a family of distribution functions that contains all relevant distributions as special cases; or, to employ nonparametric methods. All three solutions have disadvantages since assumptions are usually difficult to justify, families of distributions contain too many parameters to be of practical use, and nonparametric methods make it difficult to characterize data in a succinct quantitative form. The S-distribution introduced here is a compromise between the conflicting goals of simplicity in analysis and generality in scope. It is characterized by four parameters, one of which reflects its location, the second one its spread, and the remaining two its shape; transformation to a standard form reduces the number of free parameters to two. Cumulatives and densities are computed numerically in fractions of seconds, key features like quantiles and moments are easily obtained, and results can be presented in terms of parameter values. The S-distribution rather accurately models different distribution functions, including central and noncentral distributions, and thus competes in flexibility with some distribution families. As an approximation, the S-distribution provides a graphical method for demonstrating relationships between distributions, such as the relationships between central F, χ² and χ^?2 or central and noncentral t, χ^-1, and normal.     

The Probability Density Functions of the Contingency Coefficients,defined by KRAMER and PEARSON,in a 2-Dimensional Frequency Distribution of Grouped Bivariate Normal Variables. I

Two general measures for the degree of association in a contingency table are the contingency coefficients defined by PEARSON and KRAMER. In the case of a standardized bivariate normal distribution with correlation coefficient of the variables, whose realizations constitute the rows and columns of the table, the density functions of the two listed association measures are derived.     

多倍化--白刺属的系统分类、进化特征及应用前景

在回顾白刺属研究历史的基础上,根据白刺属种间染色体倍数特征并结合形态学、生物地理学等方面的研究文献,提出新的白刺属种间分类系统：二倍体组(2n=2x=24)和四倍体组(2n=4x=48)。多倍化(2x→4x)是白刺属内种间进化的基本特征。白刺属的起源中心可能是古地中海沿岸地区;中亚及我国西北地区是白刺属的现代分布中心。并指出将该属作为模式系统开展荒漠植物分子生态学研究的前景。     

云南大山包黑颈鹤自然保护区草甸植被的数量分类和排序

在法瑞学派样地调查法的基础上,采用双向指示种分析（TWINSPAN）和趋势对应分析（DCA）对大山包黑颈鹤自然保护区草甸植被进行数量分类和排序研究。调查样地包含114个物种,分属31科72属,其中禾本科（14种）、菊科（13种）、蓼科（8种）、石竹科（6种）、玄参科（6种）等科所含物种较多。经TWINSPAN分类,106个样地分为20个聚组,根据其指示种确定为20个群丛。样地DCA和物种DCA排序结果反映了植物群丛与指示种之间的一致关系,排序轴的生态学意义说明水分和海拔两个环境因子同时影响该区草甸植被的分布。     

Study on Construction,Expression, and Biological Activity of Recombinant Adenovirus of Neurturin

Abstract

Neurturin (NTN) can improve the function and delay the rate of degeneration of dopaminergic neurons in Parkinson's disease (PD). However, its method of delivery to the central nervous system has not been established. Adenoviral vectors have been widely applied in gene therapy because of their high-efficiency gene transfer, easy manipulation, and safety. We used replication-defective adenovirus type 5 (Ad5) to construct a recombinant viral vector encoding full-length human NTN (Ad-NTN) and amplified Ad-NTN and the control (Ad-lacZ) in HEK 293 cells. NTN-specific expression in the Ad-NTN-infected HEK 293 cells was detected by RT-PCR and the immunofluorescent assay. However, no NTN expression was detected in the Ad-lacZ-infected HEK 293 cells. After incubation with the Ad-NTN-infected conditioned medium (CM), the dorsal root ganglia of chicken embryos examined in vitro exhibited radial neurite outgrowth around the ganglia. However, incubation with the Ad-lacZ-infected or blank CM resulted in a short or absent nerve process and the growth of only a few fibroblasts. Our findings indicated that recombinant Ad-NTN was specifically expressed in the host cells, and the expressed NTN possessed biological activity.     

Classification and identification of the Burkholderia cepacia complex: Past, present and future

The Burkholderia cepacia complex is a group of closely related species with conflicting biological properties. Triggered by the devastating effect of pulmonary infections in cystic fibrosis patients, the scientific community generated an unusually large amount of taxonomic data for these bacteria during the past 15 years. This review presents the polyphasic, multilocus and genomic methodology used for the classification and identification of these bacteria. The current state-of-the-art demonstrates that present day taxonomists can replace traditional DNA-DNA hybridizations for species level demarcation and 16S rRNA sequence analysis for studying phylogeny by superior whole genome sequence-based parameters within the framework of polyphasic taxonomic studies.     

Opal phytoplankton assemblages of the Late Quaternary sapropel layers S5 and S7 from the southeastern Mediterranean Sea (“Meteor”-Cruise 40/4, Site 67)

Well-preserved opal planktic assemblages containing diatom and silicoflagellate species were discovered in the finely laminated sapropels S5 and S7 from Site 67, core GeoTüKL51 during “RV Meteor”-Cruise 40, Leg 4 (34° 48 N; 27° 17 E). The siliceous microflora, composed quasi-exclusively of warm water species, is here studied for taxonomy, stratigraphy and ecology, as well as for quantitative distribution. The diatom assemblage is very diverse and dominated by rhizosolenids, which are generally characteristic of stratified, oligotrophic waters. A significant shift to higher abundances of Pseudosoleniacalcar-avis is observed in the upper part of Sapropel S5, with a simultaneous decrease in the abundances of Thalassionema bacillaris/frauenfeldii,T.nitzschioides,T. oestrupii and Chaetoceros sp., which is probably due to nutrient - poor conditions in the surface waters.     

Influence of bicarbonate,sulfate, and electron donors on biological reduction of uranium and microbial community composition

A microcosm study was performed to investigate the effect of ethanol and acetate on uranium(VI) biological reduction and microbial community changes under various geochemical conditions. Each microcosm contained an uranium-contaminated sediment (up to 2.8 g U/kg) suspended in buffer with bicarbonate at concentrations of either 1 or 40 mM and sulfate at either 1.1 or 3.2 mM. Ethanol or acetate was used as an electron donor. Results indicate that ethanol yielded in significantly higher U(VI) reduction rates than acetate. A low bicarbonate concentration (1 mM) was favored for U(VI) bioreduction to occur in sediments, but high concentrations of bicarbonate (40 mM) and sulfate (3.2 mM) decreased the reduction rates of U(VI). Microbial communities were dominated by species from the Geothrix genus and Proteobacteria phylum in all microcosms. However, species in the Geobacteraceae family capable of reducing U(VI) were significantly enriched by ethanol and acetate in low-bicarbonate buffer. Ethanol increased the population of unclassified Desulfuromonales, while acetate increased the population of Desulfovibrio. Additionally, species in the Geobacteraceae family were not enriched in high-bicarbonate buffer, but the Geothrix and the unclassified Betaproteobacteria species were enriched. This study concludes that ethanol could be a better electron donor than acetate for reducing U(VI) under given experimental conditions, and electron donor and groundwater geochemistry alter microbial communities responsible for U(VI) reduction.     

Molecular phylogeny of the genus Gobio Cuvier, 1816 (Teleostei: Cyprinidae) and its contribution to taxonomy

The phylogenetic relationships among gudgeons that represent most nominal taxa within Gobio gobio sensu lato were examined by mitochondrial and nuclear genome sequencing. The molecular analyses confirmed the separate generic status of Gobio as a monophyletic group and revealed 15 Eurasian lineages divided into two main clades, the Northern European and the Ponto-Caspian. The validity of eleven nominal taxa as distinct species was confirmed, gudgeons from the Volga River basin were described as a new species G. volgensis, and three revealed phylogenetic lineages were submitted for a comprehensive revision as "species-in-waiting". The species G. gobio showed a wide range extending from the British Isles to the Black Sea coast and overlapped the areas of several other species. Four pure lineages were detected in the middle Danube River basin. The Crimean Peninsula was found to be a region with the occurrence of individuals of hybrid origin. This region will require special investigation to define species participating in hybridization events, and to establish further steps for the conservation of endemic native gudgeon species. A simple diagnostic method, based on different lengths of the PCR products, called "S7indel diagnostics" is presented for further taxonomic investigations in the genus Gobio.     

Isolation and characterization of Methanocorpusculum parvum,gen. nov., spec. nov., a new tungsten requiring,coccoid methanogen

A new mesophilic, monotrichously flagellated methane-producing coccus of 1m in diameter was isolated from an anaerobic sour whey digester, originally inoculated with sewage sludge. Growth and methane production were observed with H₂/CO₂, formate and — less effectively — with 2-propanol/CO₂. The isolate grew at temperatures between 15° C and 45° C with the optimum at around 37° C. Acetate, yeast extract and tungstate were required in the medium. Clarified rumen fluid stimulated growth.The DNA of the new methanogen has a G+C content of 48.5 mol%. Comparative 16 S rRNA oligonucleotide cataloguing allows to define the new isolate as a member of a new genus of the order Methanomicrobiales. Further evidence for this is provided by the antigenic crossreactivity with anti-S probes and by metabolic features.Because of its small size the new methanogen is named Methanocorpusculum parvum.This work was supported by a grant of the Deutsche Forschungsgemeinschaft DFG to J. W. and E. S. Immunologic studies were supported in part by grants No. DE-FGO2-84 R 13197 from the U.S. Department of Energy, and No. 261.81/82 from the North Atlantic Treaty Organization (NATO)     

Identification of the up-regulation of TP-alpha, collagen alpha-1(VI) chain, and S100A9 in esophageal squamous cell carcinoma by a proteomic method

Esophageal squamous cell carcinoma (ESCC) is one of the most common primary malignant tumor of digestive tract. However, the early diagnosis and molecular mechanisms that underlie tumor formation and progression have been progressed less. To identify new biomarkers for ESCC, we performed a comparative proteomic research. Isobaric tags for relative and absolute quantitation-based proteomic method was used to screen biomarkers between ESCC and normal. 802 non-redundant proteins were identified, 39 of which were differentially expressed with 1.5-fold difference (29 up-regulated and 10 down-regulated). Through Swiss-Prot and GO database, the location and function of differential proteins were analyzed, which are related to the biological processes of binding, cell structure, signal transduction, cell adhesion, etc. Among the differentially expressed proteins, TP-alpha, collagen alpha-1(VI) chain and S100A9 were verified to be upregulated in 77.19%, 75.44% and 59.65% of ESCC by immunohistochemistry and western-blot. Diagnostic value of these three proteins was validated. These results provide new insights into ESCC biology and potential diagnostic and therapeutic biomarkers, which suggest that TP-alpha, collagen alpha-1(VI) chain and S100A9 are potential biomarkers of ESCC, and may play an important role in tumorigenesis and development of ESCC.