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1.
Vladimir Makarenkov Alix Boc Jingxin Xie Pedro Peres-Neto François-Joseph Lapointe Pierre Legendre 《BMC evolutionary biology》2010,10(1):250
Background
Non-parametric bootstrapping is a widely-used statistical procedure for assessing confidence of model parameters based on the empirical distribution of the observed data [1] and, as such, it has become a common method for assessing tree confidence in phylogenetics [2]. Traditional non-parametric bootstrapping does not weigh each tree inferred from resampled (i.e., pseudo-replicated) sequences. Hence, the quality of these trees is not taken into account when computing bootstrap scores associated with the clades of the original phylogeny. As a consequence, traditionally, the trees with different bootstrap support or those providing a different fit to the corresponding pseudo-replicated sequences (the fit quality can be expressed through the LS, ML or parsimony score) contribute in the same way to the computation of the bootstrap support of the original phylogeny. 相似文献2.
Background
There exist many segmentation techniques for genomic sequences, and the segmentations can also be based on many different biological features. We show how to evaluate and compare the quality of segmentations obtained by different techniques and alternative biological features. 相似文献3.
Background
The automated annotation of biological sequences (protein, DNA) relies on the computation of hits (predicted features) on the sequences using various algorithms. Public databases of biological sequences provide a wealth of biological "knowledge", for example manually validated annotations (features) that are located on the sequences, but mining the sequence annotations and especially the predicted and curated features requires dedicated tools. Due to the heterogeneity and diversity of the biological information, it is difficult to handle redundancy, frequent updates, taxonomic information and "private" data together with computational algorithms in a common workflow. 相似文献4.
Andrew Butterfield Vivek Vedagiri Edward Lang Cath Lawrence Matthew J Wakefield Alexander Isaev Gavin A Huttley 《BMC bioinformatics》2004,5(1):1
Background
Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the conserved portions of sequences – ignoring the biological significance of sequence differences. A suite of sophisticated likelihood based statistical models from the field of molecular evolution provides the basis for extracting the information from the full distribution of sequence variation. The number of different problems to which phylogeny-based maximum likelihood calculations can be applied is extensive. Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation. 相似文献5.
Background
Joint alignment and secondary structure prediction of two RNA sequences can significantly improve the accuracy of the structural predictions. Methods addressing this problem, however, are forced to employ constraints that reduce computation by restricting the alignments and/or structures (i.e. folds) that are permissible. In this paper, a new methodology is presented for the purpose of establishing alignment constraints based on nucleotide alignment and insertion posterior probabilities. Using a hidden Markov model, posterior probabilities of alignment and insertion are computed for all possible pairings of nucleotide positions from the two sequences. These alignment and insertion posterior probabilities are additively combined to obtain probabilities of co-incidence for nucleotide position pairs. A suitable alignment constraint is obtained by thresholding the co-incidence probabilities. The constraint is integrated with Dynalign, a free energy minimization algorithm for joint alignment and secondary structure prediction. The resulting method is benchmarked against the previous version of Dynalign and against other programs for pairwise RNA structure prediction. 相似文献6.
Background
The rapid burgeoning of available protein data makes the use of clustering within families of proteins increasingly important. The challenge is to identify subfamilies of evolutionarily related sequences. This identification reveals phylogenetic relationships, which provide prior knowledge to help researchers understand biological phenomena. A good evolutionary model is essential to achieve a clustering that reflects the biological reality, and an accurate estimate of protein sequence similarity is crucial to the building of such a model. Most existing algorithms estimate this similarity using techniques that are not necessarily biologically plausible, especially for hard-to-align sequences such as proteins with different domain structures, which cause many difficulties for the alignment-dependent algorithms. In this paper, we propose a novel similarity measure based on matching amino acid subsequences. This measure, named SMS for Substitution Matching Similarity, is especially designed for application to non-aligned protein sequences. It allows us to develop a new alignment-free algorithm, named CLUSS, for clustering protein families. To the best of our knowledge, this is the first alignment-free algorithm for clustering protein sequences. Unlike other clustering algorithms, CLUSS is effective on both alignable and non-alignable protein families. In the rest of the paper, we use the term "phylogenetic" in the sense of "relatedness of biological functions". 相似文献7.
Application of NIR Spectroscopy Coupled with PLS Regression for Quantification of Total Polyphenol Contents from the Fruit and Aerial Parts of Citrullus colocynthis 下载免费PDF全文
Tania S. Rizvi Fazal Mabood Liaqat Ali Mohammed Al‐Broumi Hamida K.M. Al Rabani Javid Hussain Farah Jabeen Suryyia Manzoor Ahmed Al‐Harrasi 《Phytochemical analysis : PCA》2018,29(1):16-22
Introduction
Citrullus colocynthis (L.) Schrad is extensively used to treat diabetes, obesity, fever, cancer, amenorrhea, jaundice, leukemia, rheumatism, and respiratory diseases. Chemical studies have indicated the presence of several cucurbitacins, flavones, and other polyphenols in this plant. These phytochemical constituents are responsible for the interesting antioxidant and other biological activities of C. colocynthis.Objective
In the present study, for the first time, near infrared (NIR) spectroscopy coupled with partial least square (PLS) regression analysis was used to quantify the polyphenolic phytochemicals of C. colocynthis.Methodology
The fruit and aerial parts of the C. colocynthis were extracted individually in methanol followed by fractionation in n‐hexane, chloroform, ethyl acetate, n‐butanol, and water. Near infrared (NIR) spectra were obtained in absorption mode in the wavelength range 700–2500 nm. The PLS regression model was then built from the obtained spectral data to quantify the total polyphenol contents in the selected plant samples.Results
The PLS regression model obtained had a R2 value of 99% with a 0.98 correlationship value and a good prediction with a root mean square error of prediction (RMSEP) value of 1.89% and correlation of 0.98. These results were further confirmed through UV–vis spectroscopy and it is found that the ethyl acetate fraction has the maximum value for polyphenol contents (101.7 mg/100 g; NIR, 100.4 mg/100 g; UV–vis).Conclusions
The polyphenolic phytochemicals of the fruit and aerial parts of C. colocynthis have been quantified successfully by using multivariate analysis in a non‐destructive, economical, precise, and highly sensitive method, which uses very simple sample preparation. Copyright © 2017 John Wiley & Sons, Ltd. 相似文献8.
N. Nayan A.S.M. Sonnenberg W.H. Hendriks J.W. Cone 《Journal of applied microbiology》2018,125(2):468-479
Aim
In this study, the biological variation for improvement of the nutritive value of wheat straw by 12 Ceriporiopsis subvermispora, 10 Pleurotus eryngii and 10 Lentinula edodes strains was assessed. Screening of the best performing strains within each species was made based on the in vitro degradability of fungal‐treated wheat straw.Methods and Results
Wheat straw was inoculated with each strain for 7 weeks of solid state fermentation. Weekly samples were evaluated for in vitro gas production (IVGP) in buffered rumen fluid for 72 h. Out of the 32 fungal strains studied, 17 strains showed a significantly higher (P < 0·05) IVGP compared to the control after 7 weeks (227·7 ml g?1 OM). The three best Ceriporiopsis subvermispora strains showed a mean IVGP of 297·0 ml g?1 OM, while the three best P. eryngii and L. edodes strains showed a mean IVGP of 257·8 and 291·5 ml g?1 OM, respectively.Conclusion
Ceriporiopsis subvermispora strains show an overall high potential to improve the ruminal degradability of wheat straw, followed by L. edodes and P. eryngii strains.Significance and Impact of the Study
Large variation exists within and among different fungal species in the valorization of wheat straw, which offers opportunities to improve the fungal genotype by breeding. 相似文献9.
Biotic interactions influence the projected distribution of a specialist mammal under climate change
Brooke L. Bateman Jeremy VanDerWal Stephen E. Williams Christopher N. Johnson 《Diversity & distributions》2012,18(9):861-872
Aim
To measure the effects of including biotic interactions on climate‐based species distribution models (SDMs) used to predict distribution shifts under climate change. We evaluated the performance of distribution models for an endangered marsupial, the northern bettong (Bettongia tropica), comparing models that used only climate variables with models that also took into account biotic interactions.Location
North‐east Queensland, Australia.Methods
We developed separate climate‐based distribution models for the northern bettong, its two main resources and a competitor species. We then constructed models for the northern bettong by including climate suitability estimates for the resources and competitor as additional predictor variables to make climate + resource and climate + resource + competition models. We projected these models onto seven future climate scenarios and compared predictions of northern bettong distribution made by these differently structured models, using a ‘global’ metric, the I similarity statistic, to measure overlap in distribution and a ‘local’ metric to identify where predictions differed significantly.Results
Inclusion of food resource biotic interactions improved model performance. Over moderate climate changes, up to 3.0 °C of warming, the climate‐only model for the northern bettong gave similar predictions of distribution to the more complex models including interactions, with differences only at the margins of predicted distributions. For climate changes beyond 3.0 °C, model predictions diverged significantly. The interactive model predicted less contraction of distribution than the simpler climate‐only model.Main conclusions
Distribution models that account for interactions with other species, in particular direct resources, improve model predictions in the present‐day climate. For larger climate changes, shifts in distribution of interacting species cause predictions of interactive models to diverge from climate‐only models. Incorporating interactions with other species in SDMs may be needed for long‐term prediction of changes in distribution of species under climate change, particularly for specialized species strongly dependent on a small number of biotic interactions. 相似文献10.
T. Yasuda M. Waki K. Kuroda D. Hanajima Y. Fukumoto T. Yamagishi Y. Suwa K. Suzuki 《Journal of applied microbiology》2013,114(3):746-761
Aims
To investigate community shifts of amoA‐encoding archaea (AEA) and ammonia‐oxidizing bacteria (AOB) in biofilter under nitrogen accumulation process.Methods and Results
A laboratory‐scale rockwool biofilter with an irrigated water circulation system was operated for 436 days with ammonia loading rates of 49–63 NH3 g m?3 day?1. The AEA and AOB communities were investigated by denaturing gradient gel electrophoresis, sequencing and real‐time PCR analysis based on amoA genes. The results indicated that changes in abundance and community compositions occurred in a different manner between archaeal and bacterial amoA during the operation. However, both microbial community structures mainly varied when free ammonia (FA) concentrations in circulation water were increasing, which caused a temporal decline in reactor performance. Dominant amoA sequences after this transition were related to Thaumarchaeotal Group I.1b, Nitrosomonas europaea lineages and one subcluster within Nitrosospira sp. cluster 3, for archaea and bacteria, respectively.Conclusions
The specific FA in circulation water seems to be the important factor, which relates to the AOB and AEA community shifts in the biofilter besides ammonium and pH.Significance and Impact of the Study
One of the key factors for regulating AEA and AOB communities was proposed that is useful for optimizing biofiltration technology. 相似文献11.
Background
A central goal of Systems Biology is to model and analyze biological signaling pathways that interact with one another to form complex networks. Here we introduce Qualitative networks, an extension of Boolean networks. With this framework, we use formal verification methods to check whether a model is consistent with the laboratory experimental observations on which it is based. If the model does not conform to the data, we suggest a revised model and the new hypotheses are tested in-silico. 相似文献12.
Gordon Blackshields Fabian Sievers Weifeng Shi Andreas Wilm Desmond G Higgins 《Algorithms for molecular biology : AMB》2010,5(1):21
Background
The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs of sequences. This requires memory and time proportional to N 2 for N sequences. When N grows larger than 10,000 or so, this becomes increasingly prohibitive and can form a significant barrier to carrying out very large multiple alignments. 相似文献13.
Lake-Ee Quek Christoph Wittmann Lars K Nielsen Jens O Krömer 《Microbial cell factories》2009,8(1):25-15
Background
The quantitative analysis of metabolic fluxes, i.e., in vivo activities of intracellular enzymes and pathways, provides key information on biological systems in systems biology and metabolic engineering. It is based on a comprehensive approach combining (i) tracer cultivation on 13C substrates, (ii) 13C labelling analysis by mass spectrometry and (iii) mathematical modelling for experimental design, data processing, flux calculation and statistics. Whereas the cultivation and the analytical part is fairly advanced, a lack of appropriate modelling software solutions for all modelling aspects in flux studies is limiting the application of metabolic flux analysis. 相似文献14.
Background
Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. 相似文献15.
Background
Modern-day proteins were selected during long evolutionary history as descendants of ancient life forms. In silico reconstruction of such ancestral protein sequences facilitates our understanding of evolutionary processes, protein classification and biological function. Additionally, reconstructed ancestral protein sequences could serve to fill in sequence space thus aiding remote homology inference. 相似文献16.
Robert Hasterok Joanna Dulawa Glyn Jenkins Mike Leggett Tim Langdon 《BMC biotechnology》2006,6(1):20-5
Background
A modification of a standard method of fluorescence in situ hybridisation (FISH) is described, by which a combination of several substrates and probes on single microscope slides enables more accurate comparisons of the distribution and abundance of chromosomal sequences and improves the relatively low throughput of standard FISH methods. 相似文献17.
Timur Shtatland Daniel Guettler Misha Kossodo Misha Pivovarov Ralph Weissleder 《BMC bioinformatics》2007,8(1):280
Background
Peptides are important molecules with diverse biological functions and biomedical uses. To date, there does not exist a single, searchable archive for peptide sequences or associated biological data. Rather, peptide sequences still have to be mined from abstracts and full-length articles, and/or obtained from the fragmented public sources. 相似文献18.
Cong Zeng Yangxin Tang Martin Vastrade Neil E. Coughlan Ting Zhang Yongjiu Cai Karine Van Doninck Deliang Li 《Diversity & distributions》2023,29(3):364-378
Aim
To date, few studies have examined the phylogenetics of Corbicula clams in their native range and the environmental parameters influencing their distribution, although this could provide great insights into the biological adaptation and invasion dynamics of Corbicula clams. We sought to identify the genetic lineages of native Corbicula clams and elucidate the environmental factors shaping the distributions of identified lineages.Location
China, mainly the Yangtze River Basin.Methods
The alignment comprised 558 COI sequences including samples from China and 222 COI sequences from published studies. This dataset was used to generate phylogenetic trees and compare population diversity. We used dbRDA method to assess the relationship between these COI data and environmental factors measured to identify the important factors affecting Corbicula's distribution.Results
The COI phylogenetic tree delineated the monophyly of 3 major COI clades and 77 distinct COI haplotypes in the Yangtze River Basin. The invasive lineage C/S (FW17) was not identified in our sampling in China, while invasive lineages A/R (FW5 = Hap6), B (FW1 = Hap17) and Rlc (FW4 = Hap43) were identified, abundant and widely distributed in the middle and lower reaches of Yangtze River. Focusing on populations from Yangtze River Basin, both the COI haplotype and nucleotide diversity in the lakes along the Yangtze River increased with longitude, except for the river mouth population. The AMOVA tests showed significant differentiation between the middle and lower reaches of the Yangtze River and among populations. The dbRDA results suggested that the parameter chloride explained most of the spatial COI haplotype distribution variation in the Yangtze River Basin, with the three invasive lineages tolerating broad fluctuations of salinity (chloride levels ranging from 4 to 60 mg/L).Conclusions
The Corbicula COI haplotypes found within the Yangtze River Basin had distinct distribution preferences, with the invasive androgenetic lineages being the most abundant and widely distributed. Genetic diversity was higher in this native region than in invaded areas in Europe and America, while it decreased with increasing distance from the river mouth. Salinity appeared to be the main environmental factor shaping the COI haplotype distribution of Corbicula lineages within their native range. 相似文献19.
Karina Reiter Christoph Plutzar Dietmar Moser Philipp Semenchuk Karl-Heinz Erb Franz Essl Andreas Gattringer Helmut Haberl Fridolin Krausmann Bernd Lenzner Johannes Wessely Sarah Matej Robin Pouteau Stefan Dullinger 《Global Ecology and Biogeography》2023,32(6):855-866
Aim
Land use is the most pervasive driver of biodiversity loss. Predicting its impact on species richness (SR) is often based on indicators of habitat loss. However, the degradation of habitats, especially through land-use intensification, also affects species. Here, we evaluate whether an integrative metric of land-use intensity, the human appropriation of net primary production, is correlated with the decline of SR in used landscapes across the globe.Location
Global.Time period
Present.Major taxa studied
Birds, mammals and amphibians.Methods
Based on species range maps (spatial resolution: 20 km × 20 km) and an area-of-habitat approach, we calibrated a “species–energy model” by correlating the SR of three groups of vertebrates with net primary production and biogeographical covariables in “wilderness” areas (i.e., those where available energy is assumed to be still at pristine levels). We used this model to project the difference between pristine SR and the SR corresponding to the energy remaining in used landscapes (i.e., SR loss expected owing to human energy extraction outside wilderness areas). We validated the projected species loss by comparison with the realized and impending loss reconstructed from habitat conversion and documented by national Red Lists.Results
Species–energy models largely explained landscape-scale variation of mapped SR in wilderness areas (adjusted R2-values: 0.79–0.93). Model-based projections of SR loss were lower, on average, than reconstructed and documented ones, but the spatial patterns were correlated significantly, with stronger correlation in mammals (Pearson's r = 0.68) than in amphibians (r = 0.60) and birds (r = 0.57).Main conclusions
Our results suggest that the human appropriation of net primary production is a useful indicator of heterotrophic species loss in used landscapes, hence we recommend its inclusion in models based on species–area relationships to improve predictions of land-use-driven biodiversity loss. 相似文献20.
Fate of Escherichia coli O145 present naturally in bovine slurry applied to vegetables before harvest,after washing and simulated wholesale and retail distribution 下载免费PDF全文
M.L. Hutchison D. Harrison J.F. Heath J.M. Monaghan 《Journal of applied microbiology》2017,123(6):1597-1606