Prediction of nucleosome occupancy in Saccharomyces cerevisiae using position-correlation scoring function

Knowledge of the detailed organization of nucleosomes across genomes and the mechanisms of nucleosome positioning is critical for the understanding of gene regulation and expression. In the present work, the bias of 4-mer frequency in nucleosome and linker sequences of the S. cerevisiae genome was analyzed statistically. A novel position-correlation scoring function algorithm based on the bias of 4-mer frequency in linker sequences was presented to distinguish nucleosome vs linker sequences. Five-fold cross-validation demonstrated that the algorithm achieved a good performance with mean area under the receiver operator characteristics curve of 0.981. Next, the algorithm was used to predict nucleosome occupancy throughout the S. cerevisiae genome and relatively high correlation coefficients with experiment maps of nucleosome positioning were obtained. Besides, the distinct nucleosome depleted regions in the vicinity of regulatory sites were confirmed. The results suggest that intrinsic DNA sequence preferences in linker regions have a significant impact on the nucleosome occupancy.     

Modification of the Micro Arc-oxidized Ti Surface for Implant Applications

Surface treatments applied to titanium and its alloys for implant applications are important for the development of bio properties.In this study,first an oxide layer was formed on the surface of the titanium plate by micro arc oxidation,and then both calcium phosphate and calcium phosphate/chitosan accumulation were performed for different samples by the sol-gel method.FE-SEM/EDS examinations,XRD,FTIR and thermal analysis were performed for these micro arc-oxidized,cal-cium phosphate-coated and calcium phosphate/chitosan-coated surfaces.The surface roughnesses for these surfaces were measured between 10 μm and 100 μm,suitable for bone development on the surface.The effect of chitosan addition on the calcium phosphate-coated surface on apatite formation ability and antibacterial properties was investigated.Although the addition of chitosan slows down the formation of apatite,it ensured that the coating had antibacterial properties.The calcium phosphate/chitosan biocomposite obtained can be recommended for dental and orthopedic implants.     

Characterizing genomic variation of Arabidopsis thaliana: the roles of geography and climate

Arabidopsis thaliana inhabits diverse climates and exhibits varied phenology across its range. Although A. thaliana is an extremely well‐studied model species, the relationship between geography, growing season climate and its genetic variation is poorly characterized. We used redundancy analysis (RDA) to quantify the association of genomic variation [214 051 single nucleotide polymorphisms (SNPs)] with geography and climate among 1003 accessions collected from 447 locations in Eurasia. We identified climate variables most correlated with genomic variation, which may be important selective gradients related to local adaptation across the species range. Climate variation among sites of origin explained slightly more genomic variation than geographical distance. Large‐scale spatial gradients and early spring temperatures explained the most genomic variation, while growing season and summer conditions explained the most after controlling for spatial structure. SNP variation in Scandinavia showed the greatest climate structure among regions, possibly because of relatively consistent phenology and life history of populations in this region. Climate variation explained more variation among nonsynonymous SNPs than expected by chance, suggesting that much of the climatic structure of SNP correlations is due to changes in coding sequence that may underlie local adaptation.     

A new biocatalyst: Penicillin G acylase immobilized in sol-gel micro-particles with magnetic properties

The present work focuses on the development and basic characterization of a new magnetic biocatalyst, namely penicillin G acylase (PGA), immobilized in sol-gel matrices with magnetic properties, ultimately aimed for application in cephalexin (CEX) synthesis. A mechanically stable carrier, based on porous xerogels silica matrixes starting from tetramethoxysilane (TMOS), was prepared leading to micro-carriers with medium sized particles of 30 μm, as determined by scanning electron microscopy. An immobilization yield of 95–100% and a recovered activity of 50–65% at 37°C, as determined by penicillin G (PG) hydrolysis (pH STAT method), were observed. These results clearly exceed those reported in a previous work on PGA immobilization in sol-gel, where only 10% of activity was recovered. The values of activity were kept constant for 6 months. Immobilized PGA (682 U/g_{dry weight}) retained high specific activity throughout ten consecutive runs for PG hydrolysis, suggesting adequate biocatalyst stability. The CEX synthesis was performed at 14°C, using the free and immobilized PGA in aqueous medium. Phenylglycine methyl ester was used as acyl donor at 90 mM and 7-aminodeacetoxycephalosporanic acid was the limiting substrate at 30 mM. The CEX stoichiometric yield after 1-h reaction was close to 68% (23 mM CEX/h) and 65% (19 mM CEX/h), respectively.     

Are fingernail lead levels a reliable biomarker of lead internal dose?

BackgroundPotentially toxic elements, such as lead, can bioaccumulate and alter human physiology. Human biomonitoring is an essential tool to evaluate chemical exposures in different biological matrices (blood, urine, saliva, nails, and hair). Of these biological matrices, nails are favorable for their ease of sampling, transport and storage. The aim of this study was to investigate possible correlations between blood lead levels (BLL) and washed and non-washed fingernail lead levels (FLL) in 55 adults living in a lead-contaminated area.MethodVenous blood and fingernail (thumbs and forefingers) samples were collected. Nails from the left hand were washed with Triton X-100 (0.5 % m/v) and HNO₃ solution, while nails from the right hand were not submitted to the pre-analytical procedures. Samples were analyzed by graphite furnace atomic absorption spectrometry, and pairwise correlations were used to correlate lead concentrations between BLL and FLL; nails from fingers of the same hand and between washed and unwashed fingernails. Principal component analysis was performed and scatter diagrams were plotted to investigate correlations.ResultsA non-significant positive correlation was found between BLL and washed forefinger nails lead (r = 0.219, p = 0.112) and between BLL and thumbnail lead levels (r = 0.182, p = 0.191). Comparison of fingernails from the same hand (thumb and forefinger), showed that lead concentrations of non-washed nails varied widely, even on analyses of transversal fragments from the same nail. Lead levels in non-washed forefinger nails were not correlated with non-washed thumbnails (r = 0.169, p = 0.219). Conversely, washed thumb and forefinger nails were found to be correlated (r = 0.39, p = 0.003). Washed and non-washed nails were also found to be correlated (p < 0.0001).ConclusionIn conclusion, the results showed that non-washed nails are not a reliable biomarker for lead exposure. Although washing nails before analysis may reduce external contamination, the correlation of lead concentrations between fingers is poor for fingernail lead levels to serve as an internal dose biomarker to lead exposure. In addition, levels in washed nails were not significantly correlated with blood lead levels. Fingernail lead levels seem to serve as an indicator of lead exposure sources in contact with the individual, but not as a reliable biomarker of internal dose.     

Matrix analysis to model the invasion of alligatorweed (Alternanthera philoxeroides) on Kentucky lakes

Aims Alligatorweed (Alternanthera philoxeroides (Mart.) Griseb.) is an invasive species indigenous to South America. With its rapid invasion of southeastern US waterways, understanding the invasiveness of this plant species is critical for providing possible mechanisms of prevention for resource managers. The aim of this project is to use a matrix model to study the invasion dynamics of alligatorweed under both terrestrial and aquatic environments. The use of this model allows for a deeper understanding of the invasiveness and life history–stage structure of alligatorweed. In particular, matrix analysis can further test the hypothesis that certain life stages of alligatorweed might be more sensitive to control and management.Methods A greenhouse experiment was conducted to study the spread of alligatorweed under both aquatic and terrestrial environments. Utilizing the growth data obtained during the summer of 2010, matrix analysis was used to model the growth of alligatorweed for six different treatments. Transition matrices were generated based on plant measurements taken at different life stages defined by the number of leaves or nodes. These matrices are population projection models whose eigenvalues represent the growth rate of alligatorweed. A high growth rate is a key feature of successful invaders. Residuals were calculated and sensitivity analysis was performed to test the accuracy of the model and importance of each life stage over the entire life cycle of alligatorweed.Important findings The results of this study indicate that in the aquatic habitat, plants at their early life cycle stage are most sensitive to potential control measures. Conversely, in the terrestrial habitat, the most sensitive stage of alligatorweed is at its late life cycle stage, characterized with large-sized plants, thus suggesting the best timing for management and eradication of this invasive species.     

荧光量子点的生物合成方法研究进展

作为一种新型纳米材料,荧光量子点的合成方法大致可分为物理法、化学法和生物合成法。生物合成方法因其绿色、环保、产物生物相容性好而备受关注。本文通过对国内外荧光量子点生物合成方法的资料研究,以细菌、真菌、其它生物机体、生物辅助等角度对生物合成荧光量子点的方法进行归纳总结,并着重对基于微生物的合成方法进行了分类。在探讨微生物合成机理的基础上,对生物合成法的未来方向提出展望。     

陕北黄土丘陵区撂荒群落土壤养分与地上生物量空间异质性

应用地统计学方法,研究了群落尺度上陕北黄土丘陵区不同演替阶段猪毛蒿、长芒草和达乌里胡枝子3种撂荒群落土壤全氮、全磷和地上生物量的空间异质性.利用基于距离矩阵的Mantel偏相关方法分析了群落地上生物量与土壤全氮、全磷在不同尺度上的相互关系,分析了土壤全氮、全磷及群落自身的空间过程对群落地上生物量空间分布的解释程度.结果表明:(1)猪毛蒿、长芒草和达乌里胡枝子3种群落土壤全氮含量空间自相关性较差,而全磷自相关性较好,不同深度的土壤全氮含量其空间异质性大小也有所差别.3种群落0～20cm全氮的空间变异性大小为:达乌里胡枝子〉长芒草〉猪毛蒿群落;20～40cm为:长芒草〉达乌里胡枝子〉猪毛蒿群落.即土壤表层全氮含量为撂荒年限越长空间变异性越大,而亚表层全氮含量则是演替中期空间异质性较大,演替前后期较小.3种群落0～20cm、20～40cm全磷含量也是演替中期空间异质性较大,而前后期较小.(2)3种群落地上生物量空间自相关性以长芒草群落为最小,并且空间异质性大小为猪毛蒿〉达乌里胡枝子〉长芒草群落;猪毛蒿群落地上生物量与土壤全氮在小尺度上(0.71m)为显著正相关,与全磷相关性也较好,为负相关,在19.80～20.51m尺度上与全磷为显著负相关.达乌里胡枝子群落地上生物量与全磷在7.07～20.51m尺度上为显著正相关,在小尺度上(0.71m)正相关性也较好.长芒草群落地上生物量与土壤全氮、全磷相关性在各个尺度上都不显著,只在小尺度上与全氮负相关性较好.(3)土壤氮和磷,对达乌里胡枝子群落地上生物量的解释较好,约为19.59%,猪毛蒿次之,长芒草群落最小.群落本身的空间过程对猪毛蒿群落的解释程度最高,约为5.42%,其次为达乌里胡枝子,长芒草最小. m)为显著正相关,与全磷相关性也较好,为负相关,在19.80～20.51 尺度上与全磷为显著负相关.达乌里胡枝子群落地上生物量与全磷在7.07～20.51m尺度上为显著正相关,在小尺度上(0.71m)正相关性也较好.长芒草群落地上生物量与土壤全氮、全磷相关性在各个尺度上都不显著,只在小尺度上与全氮负相关性较好.(3)土壤氮和磷,对达乌里胡枝子群落地上生物量的解释较好,约为19.59%,猪毛蒿次之,长芒草群落最小.群落本身的空间过程对猪毛蒿群落的解释程度最高,约为5.42%,其次为达乌里胡枝子,长芒草最小. m)为显著正相关,与全磷相关性也较好,为负相关,在19.80～20.51 尺度上与全磷为显著负相关.达乌里胡枝子群落地上生物量与全磷在7.07～20.51m尺度上为显著正相关,在小尺度上(0.71m)正相关性也较好.长芒草群落地上生物量与土壤全氮、全磷相关性在各个尺度上都不显著,只在小尺度上与全氮负相关性较好.(3)土壤氮和磷,对达乌里胡枝子群落地上生物量的解释较好,约为19.59%,猪毛蒿次之,长芒草群落最小.群落本身的空间过程对猪毛蒿群落的解释程度最高,约为5.42%,其次为达乌里胡枝子,长芒草最小. m)为显著正相关,与全磷相关性也较好,为负相关,在19.80～20.51 尺度上与全磷为显著负相关.达乌里胡枝子群落地上生物量与全磷在7.07～20.51m尺度上为显著正相关,在小尺度上( .71m)正相关性也较好.长芒草群落地上生物量与土壤全氮、全磷相关性在各个尺度上都不显著,只在小尺度上与全氮负相关性较好.(3)土壤氮和磷,对达乌里胡枝子群落地上生物量的解释较好,约为19.59%,猪毛蒿次之,长芒草群落最小.群落本身的空间过程对猪毛蒿群落的解释程度最高,约为5.42%,其次为达乌里胡枝子,长芒草最小. m)为显著正相关,与全磷相关性也较好,为负相关,在19.80～20.51 尺度上与全磷为显著负相关.达乌里胡枝子群落地上生物量与全磷在7.07～20.51m尺度上为显著正相关,在小尺度上( .71m)正相关性也较好.长芒草群落地上生物量与土壤全氮、全磷相关性在各个尺度上都不显著,只在小尺度上与全氮负相关性较好.(3)土壤氮和磷,对达乌里胡枝子群落地上生物量的解释较好,约为19.59%,猪毛蒿次之,长芒草群落最小.群落本身的空间过程对猪毛蒿群落的解释程度最高,约为5.42%,其次为达乌里胡枝子,长芒草最小. m)为显著正相关,与全磷相关性也较好,为负相关,在19.80～20.51 尺度上与全磷为显著负相关.达乌里胡枝子群落地上生物量与全磷在7.07～20.51m尺度上为显著正相关,在小尺度上( .71m)正相关性也较好.长芒草群落地上生物量与土壤全氮、全磷相关性在各个尺度上都不显著,只在小尺度上与全氮负相关性较好.(3)土壤氮和磷,对达乌里胡枝子群落地上生物量的解释较好,约为19.59%,猪毛蒿次之,长芒草群落最小.群落本身的空间过程对猪毛蒿群落的解释程度最高,约为5.42%,其次为达乌里胡枝子,长芒草最小. m)为显著正相关,与全磷相关性也较好,为负相关,在19.80～20.51 尺度上与全磷为显著负相关.达乌里胡枝子群落地上生物量与全磷在7.07～20.51m尺度上为显著正相关,在小尺度上( .71m)正相关性也较好.长芒草群落地上生物量与土壤全氮、全磷相关性在各个尺度上都不显著,只在小尺度上与全氮负相关性较好.(3)土壤氮和磷,对达乌里胡枝子群落地上生物量的解释较好,约为19.59%,猪毛蒿次之,长芒草群落最小.群落本身的空间过程对猪毛蒿群落的解释程度最高,约为5.42%,其次为达乌里胡枝子,长芒草最小. m)为显著正相关,与全磷相关性也较好,为负相关,在19.80～20.51 尺度上与全磷为显著负相关.达乌里胡枝子群落地上生物量与全磷在7.07～20.51m尺度上为显著正相关,在小尺度上( .71m)正相关性也较好.长芒草群落地上生物量与土壤全氮、全磷相关性在     

Phylogenetic analysis of non-stereotyped behavioural sequences with a successive event-pairing method

A new method is proposed which uses transitions among acts in non-stereotyped behavioural sequences as phylogenetic characters. This method is derived from the event-pairing method designed for the phylogenetic study of developmental sequences and from ethological analyses of transition matrices. It is applied to study the phylogenetic relationships within a well-known group, the presocial Zetoborinae cockroaches. The analysis is carried out with three data sets: a behavioural data set with transitions among acts in behavioural dyadic sequences, together with morphological and molecular data sets. Non-stereotyped behaviour proved to be phylogenetically informative and to display low homoplasy. This new method opens an avenue for studying the evolution of behaviour in the framework of phylogenetic analysis, which was restricted until now to the study of stereotyped sequences and/or isolated features involved in courting or building activities.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 853–867.