Influence of main site factors on Fraxinus mandshurica (Oleaceae) plantation

the investigation was carried out on 10-year-old plantation of Fraxinus mandshurica in Mao抏r Mountain Experimental Station of Northeast Forest University. Tree height (H), diameter at breast height (D1.3) and the increment of tree height in 5 years (H5), the thickness of humus layer, as well as the soil moisture were measured for the plantation and the growth indexes (H, D1.3, H5) for different site conditions were analyzed. The results showed that main site factors influencing the growth of Fraxinus mandshurica were soil moisture, gradient and location of slope in order. The growth of Fraxinus mandshurica was better on the middle- or up-slope site than on the down-slope site. Soil moisture and late frost caused by terrain are the main reasons that limit the growth of Fraxinus mandshurica plantation.

QUANTITATIVE ANALYSIS OF RELATIONSHIP BETWEEN ARMILLARIA ROOT ROT AND SITE FACTORS IN PINUS RADIATA PLANTATIONS

Incidence of Armillaria infection was quantified based on site factors in New Zealand Pinus radiata plantations.A linear multiple regression model was derived to predict infection levels of Armillaria root rot.Factors positivily associated with the infection were:previous vegetation（native bush,pine）;soil type（pumice）;landform （valley,gully,flat）and the interaction between them.This model could assist in management planning with regard to the predisposition of particular stand to Armillaria infection.Keywods:Armillaria root rot,Disease incidence,Site factors,Quantification,Pinus radiata.

Relationship between the productivity of Pinus brutia Ten. and site characters, the Taurus Mountains, Turkey

Turkish red pine is an important forest tree species because of its role in the ecosystem whose range includes many countries in the eastern Mediterranean basin.In addition,red pine is a preferred forest tree species due to rapid growth,usage in afforestation in arid areas and the production of non-wood forest products such as resin.The aim of the study was to examine the relationship between the productivity of red pine and ecosystem in the lower and middle belt of the Taurus Mountains,and to determine the interrelations between the productivity of red pine and ecosystem.Multivariate analyses(multiple regression analysis and artificial neural networks)were used to model the efficiency(biomass production)of red pine.From the multivariate analyses,a productivity model of the species was created with the slope,soil depth,and precipitation in the driest variables.A significant correlation was found between site index and site factors in the driest quarter.These variables had a statistically significant relationship with the site index in the multiple regression analysis.The forecast power of the model was 0.33.Of the methods used,the artificial neural network consisting of 2 L10 N(2 Layers 10 Neurons)had the highest margin of explanation(R^(2)=0.71)and the lowest margin of error.This model has the potential to open land aimed for afforestation studies with red pine in forestry areas.The results will shed light on afforestation studies to be carried out in the Western Mediterranean region and in similar ecosystems.

A stochastic based approach for a new site classification method:application to the Algerian seismic code

Building codes have widely considered the shear wave velocity to make a reliable subsoil seismic classification, based on the knowledge of the mechanical properties of material deposits down to bedrock. This approach has limitations because geophysical data are often very expensive to obtain. Recently, other alternatives have been proposed based on measurements of background noise and estimation of the H/V amplification curve. However, the use of this technique needs a regulatory framework before it can become a realistic site classification procedure. This paper proposes a new formulation for characterizing design sites in accordance with the Algerian seismic building code (RPA99/ver.2003), through transfer functions, by following a stochastic approach combined to a statistical study. For each soil type, the deterministic calculation of the average transfer function is performed over a wide sample of 1-D soil profiles, where the average shear wave (S-W) velocity, Vs, in soil layers is simulated using random field theory. Average transfer functions are also used to calculate average site factors and normalized acceleration response spectra to highlight the amplification potential of each site type, since frequency content of the transfer function is significantly similar to that of the H/V amplification curve. Comparison is done with the RPA99/ver.2003 and Eurocode8 (EC8) design response spectra, respectively. In the absence of geophysical data, the proposed classification approach together with micro-tremor measures can be used toward a better soil classification.

Site correction of ground motion in Fujian area

On the basis of the interpretation of the highresolution satellite remote sensing images, in combination with the data of engineering geological exploration and shear-wave velocity testing, the site category-zoning map of FJ area with the scale of 1：200,000 is generated according to the site classification standard of ＂Code for Seismic design of Buildings＂ of China （GB50011 2010）. By the method of Probabilistic Seismic Hazard Analysis, we obtain bedrock seismic ground motion parameters of five recurrent periods （50, 200, 500, 1000, and 2500 a） of FJ area. By using the 617 typical soil layer structures of the site classifications in FJ area, we build seismic response models of soil layers and make seismic response analysis, then obtain the statistic sample space of site amplification factors, which possess reasonable distribution and sufficient data. Considering the distribution characteristics of The Quaternary Strata in FJ area, according to the statistic zoning （mountains and coastal areas respectively） and site classifications as well as the level of bedrock importing ground motion, the site magnification-factors of ground motion in FJ area are obtained by classification statistics.

Studying the depth-dependent variation of site magnification factor in Dongchuan by earthquakes observed in borehole

The digital seismometers with high accuracy are installed at depths of -200 m, -100 m in borehole and on the surface in Dongchuan. By analysis of spectra ratio, the local events (with epicentral distances between 8.5 km and 95 km, magnitudes ML = 1.3-5.1) recorded are used to calculate site magnification factor at different depths (-100 m and surface) in Dongchuan. Comparing results with that at the depth of -200 m, the site magnification factors at three components of N-S, E-W and U-D corresponding to the depth of -100 m at 8 frequencies (f = 0.75, 1.0, 1.5, 2, 3, 4, 6, and 12 Hz) are 1.0-1.49 when 0.75 Hz- [less-than or equal to] f [less-than or equal to] 2 Hz and 0.47-0.99 when 2 Hz less than or equal f less than or equal 12 Hz. On the surface, site magnification factors at three components are all greater than 1, i.e. between 1.6 and 7.63. The correlation coefficients of site magnification factors for S wave and coda at the depth of -100 m and on surface are 0.82 and 0.81 when 0.75 Hz [less-than or equal to] f [less-than or equal to] 2 Hz, 0.47 and 0.45 when 2 Hz less than or equal f less than or equal 12 Hz, respectively.

Influencing Factors of the Elderly’s Preference for Sports Venues in a University of the North

From the aspects of time characteristics,spatial characteristics and subjective will of sports activities,the preference of sports venues for the elderly in colleges and universities is investigated through questionnaires and interviews,and further analysis and studies are conducted by using the abstract method and discrete selection model,so as to explore the factors affecting the preference of sports venues for the elderly in colleges and universities and their importance.The results show that the factors affecting preference of the elderly in colleges and universities for sports venues from high to low are site greening,site amenities,site shade facilities,site rest seats,site lighting facilities,site size,site fitness and leisure facilities,site walking distance and site quietness degree.Among them,the walking distance of the site is negatively correlated,and the quiet degree of the site has no significant effect,and the other 7 items are positively correlated.The research on the preference of sports venues for the elderly in colleges and universities is helpful to the location and construction of sports venues,so as to provide comfortable and satisfactory sports space for the elderly,which has important practical significance.

Nest Site Selection of Loggerhead and Leatherback Sea Turtles at the Eastern Coast of Inhaca Island, Mozambique

Nest site selection represents an important reproductive strategy for sea turtles as it can strongly affect the development and survival of the offsprings and the reproductive fitness of the adults. In this study we analyzed the nest site selection of loggerhead and leatherback turtles and the factors correlated with that selection at Inhaca Island. The spatial position of the nests was recorded during sea turtles nests monitoring and six nesting seasons were used. Satellite images of Inhaca were used to characterize some of the beach features that might be correlated with nest site selection. Nest distribution analysis revealed that loggerhead turtles tend to spread their nests along the entire beach, but a higher aggregation of nests was evident at the northern most section of the eastern coast. Leatherback turtles tend to nest in a restricted area, with approximately 40% nests at the central sections of the coast. Beach height was the physical variable significantly correlated to loggerhead＇s nest density （r = 0.309, N = 125, P 〈 0.01） while fin grain particles （specifically 0.125 mm grain size particles） （r = 0.399, N = 125, P 〈 0.01） and organic content （r = 0.218, N = 125, P 〈 0.05） were the variables significantly correlated to leatherback＇s nest density. No other factors investigated affected nest site selection of either species.

A combined statistical model for multiple motifs search

Transcription factor binding sites （TFBS） play key roles in genebior 6.8 wavelet expression and regulation. They are short sequence segments with definite structure and can be recognized by the corresponding transcription factors correctly. From the viewpoint of statistics, the candidates of TFBS should be quite different from the segments that are randomly combined together by nucleotide. This paper proposes a combined statistical model for finding over- represented short sequence segments in different kinds of data set. While the over-represented short sequence segment is described by position weight matrix, the nucleotide distribution at most sites of the segment should be far from the background nucleotide distribution. The central idea of this approach is to search for such kind of signals. This algorithm is tested on 3 data sets, including binding sites data set of cyclic AMP receptor protein in E.coli, PlantProm DB which is a non-redundant collection of proximal promoter sequences from different species, collection of the intergenic sequences of the whole genome of E.Coli. Even though the complexity of these three data sets is quite different, the results show that this model is rather general and sensible.

Bioinformatics Analysis of the Human TCF7L2 Gene Promoter Region

[Objectives]This study was conducted to investigate characteristics of the human TCF7 L2 gene promoter.[Methods]The 2000 bp sequence of the 5’regulatory region of the human TCF7 L2 gene was obtained from the UCSC genome database.The promoter,transcription factor binding sites,CpG islands,SNPs and so on were analyzed by a variety of online softwares.[Results]The bioinformatics analysis results showed there were at least 5 potential promoters in the positive-sense strand of the 2000 bp sequence,among which-242--192 bp,-853--803 bp might contain core promoters.A TATA box and a CpG island with a length of 499 bp were found.241,944 and 1035(positive-sense strand)transcription factor binding sites were predicted by the AliBaba2.1,PROMO and JASPAR softwares,respectively.207 common transcription factor binding sites in the conserved region of human and mouse homologous TCF7 L2 gene promoter were identified with CONREAL program,involving 66 kinds of transcription factors.Two SNPs were found in the promoter region.[Conclusions]The promoter of the human TCF7 L2 gene was analyzed by bioinformatics,and the promoter characteristics were obtained.

Systematic identification and annotation of multiple-variant compound effects at transcription factor binding sites in human genome

Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites （TFBSs） are one of the most important cis-regulatory elements. While multiple tools have been developed to assess functional effects of genetic variants at TFBSs, they usually assume that each variant works in isolation and neglect the potential ＂interference＂ among multiple variants within the same TFBS. In this study, we presented COPE-TFBS （Context-Oriented Predictor for variant Effect on Transcription Factor Binding Site）, a novel method that considers sequence context to accurately predict variant effects on TFBSs. We systematically re-analyzed the sequencing data from both the 1000 Genomes Project and the Genotype-Tissue Expression （GTEx） Project via COPE-TFBS, and identified numbers of novel TFBSs, transformed TFBSs and discordantly annotated TFBSs resulting from multiple variants, further highlighting the necessity of sequence context in accurately annotating genetic variants.

Structure-Based Prediction of Transcription Factor Binding Sites

Transcription Factors（TFs） are a very diverse family of DNA-binding proteins that play essential roles in the regulation of gene expression through binding to specific DNA sequences. They are considered as one of the prime drug targets since mutations and aberrant TF-DNA interactions are implicated in many diseases.Identification of TF-binding sites on a genomic scale represents a critical step in delineating transcription regulatory networks and remains a major goal in genomic annotations. Recent development of experimental high-throughput technologies has provided valuable information about TF-binding sites at genome scale under various physiological and developmental conditions. Computational approaches can provide a cost-effective alternative and complement the experimental methods by using the vast quantities of available sequence or structural information. In this review we focus on structure-based prediction of transcription factor binding sites. In addition to its potential in genomescale predictions, structure-based approaches can help us better understand the TF-DNA interaction mechanisms and the evolution of transcription factors and their target binding sites. The success of structure-based methods also bears a translational impact on targeted drug design in medicine and biotechnology.

Nucleosomal Context of Binding Sites Influences Transcription Factor Binding Affinity and Gene Regulation

Transcription factor （TF） binding to its DNA target site plays an essential role in gene regulation. The location, orientation and spacing of transcription factor binding sites （TFBSs） also affect regulatory function of the TF. However, how nucleosomal context of TFBSs influences TF binding and subsequent gene regulation remains to be elucidated. Using genome-wide nucleosome positioning and TF binding data in budding yeast, we found that binding affinities of TFs to DNA tend to decrease with increasing nucleosome occupancy of the associated binding sites. We further demonstrated that nucleosomal context of binding sites is correlated with gene regulation of the corresponding TF. Nucleosome-depleted TFBSs are linked to high gene activity and low expression noise, whereas nucleosome-covered TFBSs are associated with low gene activity and high expression noise. Moreover, nucleosome-covered TFBSs tend to disrupt coexpression of the corresponding TF target genes. We conclude that nucleosomal context of binding sites influences TF binding affinity, subsequently affecting the regulation of TFs on their target genes. This emphasizes the need to include nucleosomal context of TFBSs in modeling gene regulation.

TrFAST: A Tool to Predict Signaling Pathway-specific Transcription Factor Binding Sites

Recent advances in the development of high-throughput tools have significantly revolutionized our understanding of molecular mech- anisms underlying normal and dysfunctional biological processes. Here we present a novel computational tool, transcription factor search and analysis tool （TrFAST）, which was developed for the in silico analysis of transcription factor binding sites （TFBSs） of sig- naling pathway-specific TFs. TrFAST facilitates searching as well as comparative analysis of regulatory motifs through an exact pattern matching algorithm followed by the graphical representation of matched binding sites in multiple sequences up to 50 kb in length. TrFAST is proficient in reducing the number of comparisons by the exact pattern matching strategy. In contrast to the pre-existing tools that find TFBS in a single sequence, TrFAST seeks out the desired pattern in multiple sequences simultaneously. It counts the GC con- tent within the given multiple sequence data set and assembles the combinational details of consensus sequence（s） located at these regions, thereby generating a visual display based on the abundance of unique pattern. Comparative regulatory region analysis of multi- ple orthologous sequences simultaneously enhances the features of TrFAST and provides a significant insight into study of conservation of non-coding cis-regulatory elements. TrFAST is freely available at http：//www.fi-pk.com/trfast.html.

Identification of Conserved Regulatory Elements in Mammalian Promoter Regions:A Case Study Using the PCK1 Promoter

A systematic phylogenetic footprinting approach was performed to identify conserved transcription factor binding sites （TFBSs） in mammalian promoter regions using human, mouse and rat sequence alignments. We found that the score distributions of most binding site models did not follow the Gaussian distribution required by many statistical methods. Therefore, we performed an empirical test to establish the optimal threshold for each model. We gauged our computational predictions by comparing with previously known TFBSs in the PCK1 gene promoter of the cytosolic isoform of phosphoenolpyruvate carboxykinase, and achieved a sensitivity of 75% and a specificity of approximately 32% Almost all known sites overlapped with predicted sites, and several new putative TFBSs were also identified. We validated a predicted SP1 binding site in the control of PCK1 transcription using gel shift and reporter assays. Finally, we applied our computational approach to the prediction of putative TFBSs within the promoter regions of all available RefSeq genes. Our full set of TFBS predictions is freely available at http：//bfgl.anri.barc.usda.gov/tfbsConsSites.

Differential signaling regulatory networks governing hormone refractory prostate cancers

To understand the organization of the biological networks that might potentially govern the pathogenesis of hormone refractory prostate cancer （HRPC）, we investigated the transcriptional circuitry and signaling in androgen-dependent 22Rvl and MDA PCa 2b cells, androgen- and estrogen-dependent LNCaP cells, and androgen-independent DU 145 and PC-3 prostate cancer （PCa） cell lines. We used microarray analyses, quantitative real-time PCR, pathway prediction analyses, and determination of Transcription Factor Binding Site （TFBS） signatures to dissect HRPC regulatory networks. We generated graphical representations of global topology and local network motifs that might be important in prostate carcinogenesis. Many important putative biomarker ＇target hubs＇ were identified in the current study including AP-1, NF-KB, EGFR, ERK1/2, JNK, p38 MAPK, TGF beta, VEGF, PDGF, CD44, Akt, PI3K, NOTCH1, CASP1, MMP2 and AR. Our results suggest that complex cellular events including autoregulation, feedback loops and cross-talk might govern progression from early lesion to clinically diagnosed PCa, as well as metastatic potential of pre-existent high-grade prostate intraepithelial neoplasia （HG-PIN） and/or advancement to HRPC. The identification of TFBS signatures for TCF/LEF, SOX9 and ELK1 in the regulatory elements suggests additional biomarkers for the potential development of chemopreventive/therapeutic strategies against PCa. Taken together, in this study, we have identified putative biomarker ＇target hubs＇ in the architecture of PCa signaling networks, and investigated TFBS signatures that might enhance our understanding of key regulatory nodes in the progression and pathogenesis of HRPC.