Fabrication and Characterization of Large, Perfectly Periodic Arrays of Metallic Nanocups

Fabrication of plasmonic resonance devices composed of large arrays of highly ordered gold nanocups is presented. The nanostructures are generated from periodic photoresist templates created by interference lithography and subsequent reflow, deposition, and dislodging. The nanocups are hemispherical in shape and arranged in both rectangular and hexagonal arrays with periods of ~500?nm. Their ability to support surface plasmonic resonances is manifested experimentally by reflectance spectroscopy. Theoretical modeling to ascertain the plasmonic spectra of these nanostructures is performed. The computed spectra of the rectangular structure are in qualitative agreement with the measurements. A weaker correlation observed for the hexagonal structure is explained by its more intricate symmetry which complicates the spectral response.     

Synthesis and Functionalization of Nitrogen-doped Carbon Nanotube Cups with Gold Nanoparticles as Cork Stoppers

Nitrogen-doped carbon nanotubes consist of many cup-shaped graphitic compartments termed as nitrogen-doped carbon nanotube cups (NCNCs). These as-synthesized graphitic nanocups from chemical vapor deposition (CVD) method were stacked in a head-to-tail fashion held only through noncovalent interactions. Individual NCNCs can be isolated out of their stacking structure through a series of chemical and physical separation processes. First, as-synthesized NCNCs were oxidized in a mixture of strong acids to introduce oxygen-containing defects on the graphitic walls. The oxidized NCNCs were then processed using high-intensity probe-tip sonication which effectively separated the stacked NCNCs into individual graphitic nanocups. Owing to their abundant oxygen and nitrogen surface functionalities, the resulted individual NCNCs are highly hydrophilic and can be effectively functionalized with gold nanoparticles (GNPs), which preferentially fit in the opening of the cups as cork stoppers. These graphitic nanocups corked with GNPs may find promising applications as nanoscale containers and drug carriers.     

Formation of Self-organized Silver Nanocup-Type Structures and Their Plasmonic Absorption

The present work reports on the formation of extremely low volume, silver nanocup-type structures on the surface by annealing of ultra-thin silver film on quartz in inert environment. Atomic force microscopy studies together with scanning electron microscopy confirmed the formation of Ag nanocup-type structures at the surface. A basic physical model for the formation of nanocups in terms of buckling and Oswald ripening due to surface-induced morphological instability and diffusional mass transport under thermal treatment is demonstrated. Surface plasmon resonance absorptions of nanocup structures are studied and preliminary experiment for observing the surface-enhanced Raman scattering of fullerene C₇₀ molecules has been shown.     

基于数据挖掘分析ATP1A1基因在肾透明细胞癌中的表达及意义

目的:通过数据挖掘分析ATP1A1在肾透明细胞癌中的表达及意义。方法:通过Oncomine数据库检索关于ATP1A1的mRNA信息,采用The Human Protein Atlas分析ATP1A1蛋白在正常肾组织和肾透明细胞癌中表达情况,GEPIA网站中TCGA数据对ATP1A1低表达的肾透明细胞癌患者进行生存分析,Meth HC数据库分析ATP1A1甲基化水平和蛋白相互作用,利用String-DB数据分析ATP1A1与上下游蛋白的相互作用。结果:肾透明细胞癌(Clear cell Renal Cell Carcinoma,cc RCC)组织中ATP1A1的mRNA表达水平较正常对照组明显降低。免疫组化结果证实ATP1A1蛋白质表达变化与mRNA相似。TCGA数据中得出ATP1A1低表达患者的总体生存期明显短于高表达组患者。此外,ATP1A1基因启动子区在肾透明细胞癌中的甲基化水平明显高于正常肾组织中。同时,ATP1A1与ATP1B1、FXYD2、ATP1B2等蛋白可能存在相互作用。结论:大数据分析结果表明ATP1A1在肾透明细胞癌中低表达,并与其发生发展相关,可能作为其潜在的治疗靶点。     

A tree reconstruction method that is economical in the number of pairwise comparisons used

A fast method for reconstructing phylogenies from distance data is presented. The method is economical in the number of pairwise comparisons needed. It can be combined with a new phylogenetic alignment procedure to yield an algorithm that gives a complete history of a set of homologous sequences. The method is applicable to very large distance matrices. An auxiliary program was developed that simplifies large phylogenies without ignoring biologically essential features. A set of 213 globins from vertebrates, plants, and Vitreoscilla (a prokaryote) were analyzed using this method.      

Study on Ultrastructure and Localization of Acid Phosphatase of Gastrodia elata Cortical Cells in Their Digestive Process of Armillaria mellea

In order to study the mechanism of the digestive process of Armillaria mellea in Castrodia data, electron microscopy and cytochemical method for determination of acid phosphatase activity was employed. The provacuoles were formed by means of expanded or convoluted ER under the stimulation of cortical cells and large cells of Gastrodia data by Armillaria mellea. A product of acid phosphatase (lead phosphate deposits) occured on the tonoplast. The papillae were produced in the cell wall of cortex in Gastrodia data when Armillaria mellea penetrated into its cortex. Our results showed that the enzyme was not released from cell of Armillaria mellea. A number of small vacuoles in the cortical cells disappeared. At the same time, lead phosphate deposits on the Armillaria mellea hyphae wall were observed and than Armillaria mellea hyphae wall was going to be digested, and the hyphae lost their structure. The activity of Armillaria mellea hyphae was not observed in the large cell of Gastrodia data. A great deal of small vacuoles and mitochondria were produced, at the same time the renewable nuclei and nuclolar vacuoles etc. appeared in the large cells of Gastrodia data under the stimulation of Armillaria mellea.     

From a clinical observation of chronic wound microbiology to the elaboration of an anti-biofilm dressing: The PANSaBIO project strategy

The PANSaBIO project aims to evaluate the prevalence of biofilms on a large panel of chronic wounds (more than 100 samples) and relate its presence to the type and history of the wound and its microbiology. A large file computing all the data is under construction. Moreover, several strategies to prepare an innovative anti-biofilm dressing have been developed. On one hand, antimicrobial peptides were grafted to gelatin; the modified protein can be used to prepare an active dressing. Second, various antiseptics were entrapped in a gelatin gel. An adaptation was necessary to obtain the convenient mechanical properties of the gel. Then this preparation was turned to a dressing. A first generation of dressings efficient against biofilms of Pseudomonas aeruginosa and Staphylococus aureus is available today.     

Anatomy in Toledonia warenella n. sp. (Gastropoda: Opisthobranchia: Diaphanidae) visualized by three-dimensional reconstruction

Abstract. A new species in the cephalaspidean family Diaphanidae, Toledonia warenella n. sp., is described from New South Wales, Australia. Three-dimensional, computer-aided reconstructions of the anatomy, based on serial histological sections, show that T. warenella n. sp. has some features in common with other diaphanids, including lack of jaws, gizzard plates, or an operculum. A gill was not detected in the mantle cavity, which is dominated by large, triangular, opposed ciliary bands and a kidney with lobed edges. The buccal mass is large with thick, muscular walls, perhaps indicative of a suctorial feeding behavior. Comparison with other diaphanid genera was hindered by lack of detailed published anatomical data, but shell and radula morphology suggests a close relationship between the new species and the polar genera Toledonia and Bogasonia (members of Toledoniinae), and for this reason, it is provisionally included in Toledonia. The systematics of Diaphanidae are addressed in the light of the anatomical data presented here.     

Spatial autocorrelation as a tool for identifying the geographical patterns of aphid annual abundance

Abstract 1 A spatial autocorrelation analysis was undertaken to investigate the spatial structure of annual abundance for the pest aphid Myzus persicae collected in suction traps distributed across north‐west Europe. 2 The analysis was applied at two different scales. The Moran index was used to estimate the degree of spatial autocorrelation at all sites within the study area (global level). The contributions of each site to the global index were identified by the use of a local indicator of spatial autocorrelation (LISA). A hierarchical cluster analysis was undertaken to highlight differences between groups of resulting correlograms. 3 Similarity between traps was shown to occur over large geographical distances, suggesting an impact of phenomena such as climatic gradients or land use types. 4 The presence of outliers and zones of similarity (hot‐spots) and of dissimilarity (cold‐spots) were identified indicating a strong impact of local effects. 5 Several groups of traps characterized by similarities in their local spatial structure (correlograms, value of Moran's I_i) also had similar values for land use variables (the area occupied by agricultural zones, forest and sea). 6 It is concluded that trap data can provide information about Myzus persicae that is representative of large geographical areas. Thus, trap data can be used to estimate the aerial abundance of this species, even if the suction traps are not regularly and densely distributed.     

Phytosociological studies at malham tarn moss and fen,Yorkshire, England

Summary During a field course the vegetation of the extensive mire complex on the west side of Malham Tarn was examined. 84 relevés were collected, with 210 taxa in total. This data set has been ‘structured’ by classical phytosociological techniques. It is suggested that it approaches the maximum size of data-set which can be handled in this way, especially if the data are not all collected by one person. Ordination of the quadrats was carried out but gave little insight into the data despite the use of non-centred as well as centred principal components analysis. Numerical classification of the quadrats using minimumvariance cluster analysis was shown to produce a structure interpretable in ecological terms. A classification of the taxa was carried out by the same method and a ‘rearranged’ table was drawn up using the results of the two classifications. A relocation technique was applied at an appropriate cluster level but little was felt to be gained from this. The use of ‘two-way’ minimum-variance cluster analysis for the rapid production of re-arranged tables is recommended for large data-sets. In addition the vegetational units recognised in the data are described and discussed. The authors wish to thank Miss D. R. Clowes, Mr. P. Gladders, Mr. A. R. Hall, Mr. R. N. Lentell, and Mr. J. E. Young for assistance in the collection of the data, and Mrs. M. E. Pettit and Mrs. S. Peglar for assistance in the data processing.     

An ancient autosomal haplotype bearing a rare achromatopsia-causing founder mutation is shared among Arab Muslims and Oriental Jews

Numerous cultural aspects, mainly based on historical records, suggest a common origin of the Middle-Eastern Arab Muslim and Jewish populations. This is supported, to some extent, by Y-chromosome haplogroup analysis of Middle-Eastern and European samples. Up to date, no genomic regions that are shared among Arab Muslim and Jewish chromosomes and are unique to these populations have been reported. Here, we report of a rare achromatopsia-causing CNGA3 mutation (c.1585G>A) presents in both Arab Muslim and Oriental Jewish patients. A haplotype analysis of c.1585G>A-bearing chromosomes from Middle Eastern and European origins revealed a shared Muslim–Jewish haplotype, which is different from those detected in European patients, indicating a recurrent mutation stratified by a Jewish–Muslim founder effect. Comprehensive whole-genome haplotype analysis using 250 K single nucleotide polymorphism arrays revealed a large homozygous region of ~11 Mbp shared by both Arab Muslim and Oriental Jewish chromosomes. A subsequent microsatellite analysis of a 21.5 cM interval including CNGA3 and the adjacent chromosome 2 centromere revealed a unique and extremely rare haplotype associated with the c.1585G>A mutation. The age of the shared c.1585G>A mutation was calculated using the microsatellite genotyping data to be about 200 generations ago. A similar analysis of mutation age based on the Arab Muslim data alone showed that the mutation was unlikely to be the product of a recent gene flow event. The data present here demonstrate a large (11 Mbp) genomic region that is likely to originate from an ancient common ancestor of Middle-Eastern Arab Muslims and Jews who lived approximately 5,000 years ago.     

Population heteromorphisms of Ag-stained nucleolus organizer regions (NORs) in the acrocentric chromosomes of East Indians

Summary The nucleolar organizer regions (NORs) of acrocentric chromosomes in 70 normal East Indians were examined by Ag-staining (NSG) and acridine orange reverse banding (RFA) techniques. The Ag-stainability of NORs was variable from one individual to another but characteristics were constant within each individual. The average modal number of Agpositive NORs per individual was eight. A racial difference in the expression of NORs is suggested. to study the heteromorphism of NORs, the NSG technique was found to be more useful than RFA. Furthermore, it is concluded that there is no direct relationship between a heteromorphism of NORs identified by NSG and that identified by the RFA technique. Quantitative data on these differences is provided. In addition NOR-regions are classified into five sizes namely; very large, large, medium, small, and very small using subjectively defined criteria.     

Distribution and faunal associations of benthic invertebrates at Lake Turkana,Kenya

The benthic environment and fauna of Lake Turkana were studied during 1978–1979 to determine distribution patterns and associations of benthic invertebrates. Lake Turkana is a large, closed-basin, alkaline lake, located in northern Kenya.Detailed environmental information is currently only available for substrate variations throughout Lake Turkana. Water chemistry and other data are currently inadequate to evaluate their effects on the distribution of Lake Turkana benthic invertebrates. Three weak faunal-substrate associations were discovered at Turkana. A littoral, soft bottom association (large standing crop) is dominated by the corixid Micronecta sp. and the ostracod Hemicypris kliei. A littoral, rocky bottom association, also with a large standing crop, is dominated by various gastropods and insects. A profundal, muddy bottom association, with a very small standing crop, is dominated by the ostracods Hemicypris intermedia and Sclerocypris cf. clavularis and several gastropod and chironomid species.     

Conformational stability and thermodynamic characterization of homotetrameric Plasmodium falciparum beta-ketoacyl-ACP reductase

The conformational stability of the homotetrameric Plasmodium falciparum beta-ketoacyl-ACP reductase (FabG) was determined by guanidinium chloride-induced isothermal and thermal denaturation. The reversible unfolding transitions were monitored by intrinsic fluorescence, circular dichroism (CD) spectroscopy and by measuring the enzyme activity of FabG. The denaturation profiles were analyzed to obtain the thermodynamic parameters associated with unfolding of the protein. The data confirm the simple A(4) <--> 4A model of unfolding, based on the corroboration of CD data by fluorescence transition and similar Delta G estimation for denaturation curves obtained at four different concentration of the FabG. Denaturation is well described by the linear extrapolation model for denaturant-protein interactions. In addition, the conformational stability (Delta G(s)) as well as the Delta C(p) for the protein unfolding is quite high, 22.68 kcal/mole and 5.83 kcal/(mole K), respectively, which may be a reflection of the relatively large size of the tetrameric molecule (Mr 120, 000) and a large buried hydrophobic core in the folded protein. This study provides a prototype for determining conformational stability of other members of the short-chain alcohol dehydrogenase/reductase superfamily of proteins to which PfFabG belongs.     

An improved treatment of data for estimation of molecular weights by sephadex gel filtration

A method for analysis of elution data of proteins, obtained from Sephadex gel filtration experiments, is described. The relevant elution data from seven different proteins, with known molecular weights and Stoke's radii, were fitted into various equations relating elution parameters and molecular size parameters. It was observed that polynomial relationships represented elution data for proteins with a much greater degree of precision than linear equations. The validity of this procedure was also checked by analysing gel filtration data available in the literature and it was concluded that a better fit was obtained using polynomial relationships, provided a sufficiently large number of experimental points were available for numerical analysis. Using this method, values of 320,000 ± 7000 for the molecular weight, and (60 ± 0.4) × 10^?8 cm for the Stoke's radius of Neurospora NAD-specific glutamate dehydrogenase were calculated.     

Aromatization of testosterone in large and small bovine luteal cells. Conflicting results between radioimmunoassay and cocrystallization data

The ability of isolated large or small bovine luteal cells to synthesize estradiol-17β was tested by incubations in the absence or in the presence of exogenous testosterone.Using a specific radioimmunoassay, no synthesis of estradiol-17β could be detected in the small or large luteal cells after incubation in the absence of testosterone. However, after incubation in the presence of exogenous unlabelled testosterone, radioimmunoassay data suggested the existence in the large but not the small luteal cells of synthesis of estradiol-17β. However, the results obtained by measuring the conversion of ³H-testosterone to ³H-estradiol-17β by cocrystallization with unlabelled estradiol-17β failed to confirm the presence of aromatase in the large cells. These data indicate that aromatization in large and small bovine luteal cells is probably negligible. Moreover, they cast serious doubt on studies of aromatization in luteal tissue based on radioimmunoassay data only.     

An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme

The divide-and-conquer strategy is commonly used for protein structure determination, but its applications to high-resolution structure determination of RNAs have been limited. Here, we introduce an integrative approach based on the divide-and-conquer strategy that was undertaken to determine the solution structure of an RNA model system, the Neurospora VS ribozyme. NMR and SAXS studies were conducted on a minimal trans VS ribozyme as well as several isolated subdomains. A multi-step procedure was used for structure determination that first involved pairing refined NMR structures with SAXS data to obtain structural subensembles of the various subdomains. These subdomain structures were then assembled to build a large set of structural models of the ribozyme, which was subsequently filtered using SAXS data. The resulting NMR-SAXS structural ensemble shares several similarities with the reported crystal structures of the VS ribozyme. However, a local structural difference is observed that affects the global fold by shifting the relative orientation of the two three-way junctions. Thus, this finding highlights a global conformational change associated with substrate binding in the VS ribozyme that is likely critical for its enzymatic activity. Structural studies of other large RNAs should benefit from similar integrative approaches that allow conformational sampling of assembled fragments.     

Diet and activity in black howler monkeys (<Emphasis Type="Italic">Alouatta pigra</Emphasis>) in southern Belize: does degree of frugivory influence activity level?

This study reports on the diet and activity budgets of Central American black howling monkeys (Alouatta pigra) at Monkey River, Belize. This is a previously unstudied population, close to the southern boundary of the species range, and it provides comparative data on A. pigra from a new study site. Both diet and activity are within the ranges reported for other A.pigra sites and for mantled howlers (A. palliata). No age-sex differences could be discerned in either diet or activity, though monthly variation was apparent. The monkeys switch from consuming leaves 86% of the time in January to March to consuming 67% fruit in April to July. This difference was statistically significant, and provided the opportunity to compare activity levels of the monkeys over two dietary periods, one characterized primarily by folivory, the other by frugivory. Howlers are often seen as a relatively inactive species, something that is associated with a low quality, folivorous diet. However, A. pigra have been described as being as frugivorous as possible and as folivorous as necessary. Yet, despite the opportunistic consumption of large quantities of high-energy foods, A. pigra has been observed as conforming to the howler lifestyle, resting as much as 80% of the day. The data in this paper support both of these reports. Black howlers at Monkey River Belize are typically inactive, maintaining high levels of inactivity even during months characterized by frugivory, suggesting that diet is more flexible and varied than is behavior and calling into question the assumption that howler inactivity is due to the digestion of large quantities of leaves.