Complete convergence of randomly weighted END sequences and its application.
Ontology highlight
ABSTRACT:
SUBMITTER: Li P
PROVIDER: S-EPMC5547198 | biostudies-other | 2017
REPOSITORIES: biostudies-other
Similar Datasets
Project description:Deep sequencing of urine specimens detects two BK polyomavirus genotypes post-hematopoietic stem cell transplantation
| PRJEB29464 | ENA
Project description:Overlapping fragments of genomic RNA spanning 6963 nucleotides from 5' end of spike (S) protein gene to 3' end of nucleocapsid (N) protein gene of turkey coronavirus (TCoV) were amplified by reverse-transcription-polymerase chain reaction (RT-PCR). The primers were derived from the corresponding sequences of infectious bronchitis virus (IBV). The PCR products were cloned and sequenced and their nucleic acid structure and similarity to published sequences of other coronaviruses were analyzed. Sequencing and subsequent analysis revealed 9 open reading frames (ORFs) representing the entire S protein gene, tricistronic gene 3, membrane (M) protein gene, bicistronic gene 5, and N protein gene in the order of 5'-3'. The overall nucleic acid structures of these encoding regions of TCoV were very similar to the homologous regions of IBV. The consensus transcription-regulating sequence (TRS) of IBV, CT(T/G)AACAA, was highly conserved in TCoV genome at the levels of nucleotide sequence and location in regarding to the initiation codon of individual genes. Pair-wise comparison of gene 3, M gene, gene 5, or N gene sequences with their counterparts of IBV revealed high levels (82.1-92.0%) of similarity. Phylogenetic analysis based on the deduced amino acid sequences of S, M, or N protein demonstrated that TCoV was clustered within the same genomic lineage as the IBV strains while all the other mammalian coronaviruses were grouped into separate clusters corresponding to antigenic groups I or II. There were substantial differences of S protein sequence between TCoV and IBV with only 33.8-33.9% of similarity.
| S-EPMC7114097 | biostudies-literature
Project description:Many genome walking methods based on polymerase chain reaction (PCR) are available, including those with and without restriction enzyme modification. Nevertheless, these methods suffer from low reproducibility, inefficiency, and non-specificity. Here, we present a traceable and efficient PCR strategy: randomly broken fragment PCR with 5' end-directed adaptor for genome walking. The genome is first fragmented randomly. After blunting ends, the fragments are ligated to the 5' end-directed adaptors. Semi-nested PCR is then performed. Thus, we can obtain an unknown sequence by cloning the fragments of interest, followed by sequencing. This method effectively bypasses the above-mentioned obstacles and offers the advances: 1) genome fragmentation without using restriction enzymes; 2) enhancement of primer specificity and the prevention of self-ligation between the adaptors by employing a 5' end-directed adaptor. All of the steps in this new method are straightforward, and the unknown sequence can be definitively obtained by merely applying the method once.
| S-EPMC3857568 | biostudies-literature
Project description:Introns are well known for their high variation not only in length but also in base sequence. The evolution of intron sequences has aroused broad interest in the past decades. However, very little is known about the evolutionary pattern of introns due to the lack of efficient analytical method. In this study, we designed 2 evolutionary models, that is, mutation-and-deletion (MD) and mutation-and-insertion (MI), to simulate intron evolution using randomly generated and mutated bases by referencing to the phylogenetic tree constructed using 14 chordate introns from TF4 (transcription factor-like protein 4) gene. A comparison of attributes between model-generated sequences and chordate introns showed that the MD model with proper parameter settings could generate sequences that have attributes matchable to chordate introns, whereas the MI model with any parameter settings failed in doing so. These data suggest that the surveyed chordate introns have evolved from a long ancestral sequence through gradual reduction in length. The established methodology provides an effective measure to study the evolutionary pattern of intron sequences from organisms of various taxonomic groups. (C++ scripts of MD and MI models are available upon request.).
| S-EPMC6990610 | biostudies-literature
Project description:The extent of horizontal gene transfer (HGT) among marine pelagic prokaryotes and the role that HGT may have played in their adaptation to this particular environment remain open questions. This is partly due to the paucity of cultured species and genomic information for many widespread groups of marine bacteria and archaea. Molecular studies have revealed a large diversity and relative abundance of marine planktonic archaea, in particular of Thaumarchaeota (also known as group I Crenarchaeota) and Euryarchaeota of groups II and III, but only one species (the thaumarchaeote Candidatus Nitrosopumilus maritimus) has been isolated in pure culture so far. Therefore, metagenomics remains the most powerful approach to study these environmental groups. To investigate the impact of HGT in marine archaea, we carried out detailed phylogenetic analyses of all open reading frames of 21 archaeal 16S rRNA gene-containing fosmids and, to extend our analysis to other genomic regions, also of fosmid-end sequences of 12 774 fosmids from three different deep-sea locations (South Atlantic and Adriatic Sea at 1000 m depth, and Ionian Sea at 3000 m depth). We found high HGT rates in both marine planktonic Thaumarchaeota and Euryarchaeota, with remarkable converging values estimated from complete-fosmid and fosmid-end sequence analysis (25 and 21% of the genes, respectively). Most HGTs came from bacterial donors (mainly from Proteobacteria, Firmicutes and Chloroflexi) but also from other archaea and eukaryotes. Phylogenetic analyses showed that in most cases HGTs are shared by several representatives of the studied groups, implying that they are ancient and have been conserved over relatively long evolutionary periods. This, together with the functions carried out by these acquired genes (mostly related to energy metabolism and transport of metabolites across membranes), suggests that HGT has played an important role in the adaptation of these archaea to the cold and nutrient-depleted deep marine environment.
| S-EPMC3146271 | biostudies-literature
Project description:The association between maternal age of onset of dementia and amyloid deposition (measured by in vivo positron emission tomography (PET) imaging) in cognitively normal older offspring is of interest. In a regression model for amyloid, special methods are required due to the random right censoring of the covariate of maternal age of onset of dementia. Prior literature has proposed methods to address the problem of censoring due to assay limit of detection, but not random censoring. We propose imputation methods and a survival regression method that do not require parametric assumptions about the distribution of the censored covariate. Existing imputation methods address missing covariates, but not right censored covariates. In simulation studies, we compare these methods to the simple, but inefficient complete case analysis, and to thresholding approaches. We apply the methods to the Alzheimer's study.
| S-EPMC5319605 | biostudies-literature
Project description:The concept of f-lacunary statistical convergence which is, in fact, a generalization of lacunary statistical convergence, has been introduced recently by Bhardwaj and Dhawan (Abstr. Appl. Anal. 2016:9365037, 2016). The main object of this paper is to prove Korovkin type approximation theorems using the notion of f-lacunary statistical convergence. A relationship between the newly established Korovkin type approximation theorems via f-lacunary statistical convergence, the classical Korovkin theorems and their lacunary statistical analogs has been studied. A new concept of f-lacunary statistical convergence of degree β (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$0 < \beta< 1$\end{document}0<β<1) has also been introduced, and as an application a corresponding Korovkin type theorem is established.
| S-EPMC6208621 | biostudies-other
Project description:True colour vision requires comparing the responses of different spectral classes of photoreceptors. In insects, there is a wealth of data available on the physiology of photoreceptors and on colour-dependent behaviour, but less is known about the neural mechanisms that link the two. The available information in bees indicates a diversity of colour opponent neurons in the visual optic ganglia that significantly exceeds that known in humans and other primates. Here, we present a simple mathematical model for colour processing in the optic lobes of bees to explore how this diversity might arise. We found that the model can reproduce the physiological spectral tuning curves of the 22 neurons that have been described so far. Moreover, the distribution of the presynaptic weights in the model suggests that colour-coding neurons are likely to be wired up to the receptor inputs randomly. The perceptual distances in our random synaptic weight model are in agreement with behavioural observations. Our results support the idea that the insect nervous system might adopt partially random wiring of neurons for colour processing.
| S-EPMC6554269 | biostudies-literature
Project description:Human antibody light and heavey chain, IgG1 light and heavy chain digested by Asp-N, Chymotrypsin, Trypsin
2016-06-07 | MSV000079801 | MassIVE
Project description:BackgroundMetagenome shotgun sequencing presents opportunities to identify organisms that may prevent or promote disease. The analysis of sample diversity is achieved by taxonomic identification of metagenomic reads followed by generating an abundance profile. Numerous tools have been developed based on different design principles. Tools achieving high precision can lack sensitivity in some applications. Conversely, tools with high sensitivity can suffer from low precision and require long computation time.MethodsIn this paper, we present WEVOTE (WEighted VOting Taxonomic idEntification), a method that classifies metagenome shotgun sequencing DNA reads based on an ensemble of existing methods using k-mer-based, marker-based, and naive-similarity based approaches. Our evaluation on fourteen benchmarking datasets shows that WEVOTE improves the classification precision by reducing false positive annotations while preserving a high level of sensitivity.ConclusionsWEVOTE is an efficient and automated tool that combines multiple individual taxonomic identification methods to produce more precise and sensitive microbial profiles. WEVOTE is developed primarily to identify reads generated by MetaGenome Shotgun sequencing. It is expandable and has the potential to incorporate additional tools to produce a more accurate taxonomic profile. WEVOTE was implemented using C++ and shell scripting and is available at www.github.com/aametwally/WEVOTE.
| S-EPMC5040256 | biostudies-literature