scholarly journals Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 188 ◽  
Author(s):  
Jacob Abel ◽  
Jan Mrázek
2010 ◽  
Vol 192 (14) ◽  
pp. 3763-3772 ◽  
Author(s):  
Jan Mrázek

ABSTRACT Regular spacing of short runs of A or T nucleotides in DNA sequences with a period close to the helical period of the DNA double helix has been associated with intrinsic DNA bending and nucleosome positioning in eukaryotes. Analogous periodic signals were also observed in prokaryotic genomes. While the exact role of this periodicity in prokaryotes is not known, it has been proposed to facilitate the DNA packaging in the prokaryotic nucleoid and/or to promote negative or positive supercoiling. We developed a methodology for assessments of intragenomic heterogeneity of these periodic patterns and applied it in analysis of 1,025 prokaryotic chromosomes. This technique allows more detailed analysis of sequence periodicity than previous methods where sequence periodicity was assessed in an integral form across the whole chromosome. We found that most genomes have the periodic signal confined to several chromosomal segments while most of the chromosome lacks a strong sequence periodicity. Moreover, there are significant differences among different prokaryotes in both the intensity and persistency of sequence periodicity related to DNA curvature. We proffer that the prokaryotic nucleoid consists of relatively rigid sections stabilized by short intrinsically bent DNA segments and characterized by locally strong periodic patterns alternating with regions featuring a weak periodic signal, which presumably permits higher structural flexibility. This model applies to most bacteria and archaea. In genomes with an exceptionally persistent periodic signal, highly expressed genes tend to concentrate in aperiodic sections, suggesting that structural heterogeneity of the nucleoid is related to local differences in transcriptional activity.


Author(s):  
Yong Li ◽  
Xiaojun Yang ◽  
Min Zuo ◽  
Qingyu Jin ◽  
Haisheng Li ◽  
...  

The real-time and dissemination characteristics of network information make net-mediated public opinion become more and more important food safety early warning resources, but the data of petabyte (PB) scale growth also bring great difficulties to the research and judgment of network public opinion, especially how to extract the event role of network public opinion from these data and analyze the sentiment tendency of public opinion comment. First, this article takes the public opinion of food safety network as the research point, and a BLSTM-CRF model for automatically marking the role of event is proposed by combining BLSTM and conditional random field organically. Second, the Attention mechanism based on vocabulary in the field of food safety is introduced, the distance-related sequence semantic features are extracted by BLSTM, and the emotional classification of sequence semantic features is realized by using CNN. A kind of Att-BLSTM-CNN model for the analysis of public opinion and emotional tendency in the field of food safety is proposed. Finally, based on the time series, this article combines the role extraction of food safety events and the analysis of emotional tendency and constructs a net-mediated public opinion early warning model in the field of food safety according to the heat of the event and the emotional intensity of the public to food safety public opinion events.


PLoS ONE ◽  
2013 ◽  
Vol 8 (4) ◽  
pp. e63068 ◽  
Author(s):  
Pablo Smircich ◽  
Diego Forteza ◽  
Najib M. El-Sayed ◽  
Beatriz Garat

1994 ◽  
Vol 13 (3) ◽  
pp. 377-385
Author(s):  
Johann Boos ◽  
Karl-Goswin Grosse-Erdmann ◽  
T. Leiger

1989 ◽  
Vol 9 (11) ◽  
pp. 5143-5153
Author(s):  
J T Bruder ◽  
P Hearing

We have identified a cellular enhancer-binding protein, present in nuclear extracts prepared from human and rodent cells, that binds to the adenovirus E1A enhancer element I sequence. The factor has been termed EF-1A, for enhancer-binding factor to the E1A core motif. EF-1A was found to bind to two adjacent, related sequence motifs in the E1A enhancer region (termed sites A and B). The binding of EF-1A to these adjacent sites, or to synthetic dimerized sites of either motif, was cooperative. The cooperative binding of EF-1A to these sites was not subject to strict spacing constraints. EF-1A also bound to related sequences upstream of the E1A enhancer region and in the polyomavirus and adenovirus E4 enhancer regions. The EF-1A-binding region in the E1A enhancer stimulated expression of a linked gene in human 293 cells when multimerized. Based on the contact sites for EF-1A binding determined by chemical interference assays, this protein appears to be distinct from any previously characterized nuclear binding protein.


1998 ◽  
Vol 16 (1) ◽  
pp. 41-50 ◽  
Author(s):  
Francisca Barceló ◽  
Francisco Gutiérrez ◽  
Ignasi Barjau ◽  
José Portugal
Keyword(s):  

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