oalib
Search Results: 1 - 10 of 100 matches for " "
All listed articles are free for downloading (OA Articles)
Page 1 /100
Display every page Item
Functional analysis of an intergenic non-coding sequence within mce1 operon of M.tuberculosis
Monika Joon, Shipra Bhatia, Rashmi Pasricha, Mridula Bose, Vani Brahmachari
BMC Microbiology , 2010, DOI: 10.1186/1471-2180-10-128
Abstract: We predicted putative promoter activity of the 200 base pairs of non-coding, intergenic region between Rv0166 and Rv0167 in silico using MEME software and designate it as intergenic promoter, IGPr. We demonstrate both promoter activity and a putative negative regulatory function of this fragment by reporter assays carried out in the surrogate host M.smegmatis. We find that the repressive elements not only control the native promoter but also repress a heterologous promoter of M.smegmatis. The higher activity of the intergenic promoter in a clinical isolate in comparison with the wild type sequence from M.tuberculosis H37Rv could be correlated with a point mutation within the negative element. We have mapped two transcription start sites for mce1 operon both of which are utilized in M.tuberculosis H37Rv as well as the clinical isolate VPCI591. Our studies show that the promoter activity in the non-coding region is relevant not only in reporter gene expression but also in the expression of mce1 operon in M. tuberculosis cells grown in synthetic medium.The mce operon of M.tuberculosis H37Rv potentially can be transcribed from two promoters P1 and P2, former mapping upstream of Rv0166 and the latter in the non-coding intergenic region between Rv0166 and Rv0167. The transcription initiation from P1 results in a transcript with Rv0166 while that from P2 will be without it. The sequences between the translation start site of Rv0167 and the promoter P2 have a negative regulatory role, as point mutation within the sequence leads to enhanced activity of P2 as well as a heterologous promoter from M.smegmatis. The mutation detected in the clinical isolate VPCI591 therefore behaves like a gain-of-function mutation.Tuberculosis causes approximately two million deaths annually and it has been estimated that around two billion people are currently infected with the causative organism, Mycobacterium tuberculosis [1]. Attempts to understand the molecular basis of pathogenesis in tube
The effect of the environment on the P1/P2 period ratio for kink oscillations of coronal loops  [PDF]
B. Orza,I. Ballai,R. Jain,K. Murawski
Physics , 2011, DOI: 10.1051/0004-6361/201117957
Abstract: The P1/P2 period ratio of transversal loop oscillations is currently used for the diagnostics of longitudinal structuring of coronal loops as its deviation from 2 is intrinsically connected to the density scale-height along coronal loops and/or the sub-resolution structure of the magnetic field. The same technique can be applied not only to coronal structures, but also to other oscillating magnetic structures. The oscillations in magnetic structures are described by differential equations whose coefficients depend on the longitudinal structure of the plasma. Using a variational principle written for the transversal component of the velocity vector, developed earlier by McEwan et al. (2008), we investigate how the different temperature of the environment compared to the temperature of the magnetic structure will influence the P1/P2 ratio for typical coronal and prominence conditions. The possible changes are translated into quantities that are used in the process of remote plasma diagnostics in the solar atmosphere.
Characterization of sequences downstream from transcriptional start site ofRhizobium meliloti nifHDK promoter
Yunfeng Gao,Tong Wu,Jiabi Zhu,Guanqiao Yu,Shanjiong Shen
Science China Life Sciences , 1997, DOI: 10.1007/BF02882051
Abstract: In freeliving state, the nifHDK promoter P1 ofRhizbium meliloti is induced in response to microaerobiosis and expressed to a high level, while the fixABCX promoter P2 is not. The sequences upstream from both P1 and P2 share extended homology (about 85%), which are about 160 bp in length, but the sequences downstream of the respective transcriptional start site are different. When the downstream sequence (DS) of P2 was replaced by the corresponding fragment from+ 17 to + 61 of P1, the expression of P2 is greatly increased under freeliving condition by lowering the oxygen tension, and the activity of P2 promoter can also be significantly enhanced inE. coli by the NifA protein. The difference between the DS regions of P1 and P2 promoter resulted in different expressions of P1 and P2 promoter under freeliving microaerobic condition and inE. coli. The expression of P2 does not depend on the downstream sequences from the promoter element during symbiosis. Primer extension experiments identified the transcriptional start site of P2. Transcription from P2 was not changed when P2 promoter region was inserted by P1 DS. Under symbiotic conditions, levels of expression of P2 were independent of the P1 DS region. It indicates that the regulations of P2 under symbiotic conditions are different from those under freeliving conditions.
Numerical wave propagation for the triangular $P1_{DG}$-$P2$ finite element pair  [PDF]
C. J. Cotter
Mathematics , 2010, DOI: 10.1016/j.jcp.2010.12.024
Abstract: Inertia-gravity mode and Rossby mode dispersion properties are examined for discretisations of the linearized rotating shallow-water equations using the $P1_{DG}$-$P2$ finite element pair on arbitrary triangulations in planar geometry. A discrete Helmholtz decomposition of the functions in the velocity space based on potentials taken from the pressure space is used to provide a complete description of the numerical wave propagation for the discretised equations. In the $f$-plane case, this decomposition is used to obtain decoupled equations for the geostrophic modes, the inertia-gravity modes, and the inertial oscillations. As has been noticed previously, the geostrophic modes are steady. The Helmholtz decomposition is used to show that the resulting inertia-gravity wave equation is third-order accurate in space. In general the \pdgp finite element pair is second-order accurate, so this leads to very accurate wave propagation. It is further shown that the only spurious modes supported by this discretisation are spurious inertial oscillations which have frequency $f$, and which do not propagate. The Helmholtz decomposition also allows a simple derivation of the quasi-geostrophic limit of the discretised $P1_{DG}$-$P2$ equations in the $\beta$-plane case, resulting in a Rossby wave equation which is also third-order accurate.
Binding of activator SyrM to the site ofnodD3 P1 region ofRhizobium meliloti
Hui Xiao,Shanjiong Shen,Jiabi Zhu
Science China Life Sciences , 1998, DOI: 10.1007/BF02882721
Abstract: The nodD3 gene ofRhizobium meliloti is transcribed via promoter P1 or P2. Gel retardation assay showed binding of SyrM to the P1 upstream region of nodD3. DNaseI footprint analysis demonstrated that the binding site of SyrM in nodD3 P1 region consists of two inverted repeat sequences arranged in tandem. SyrM seems to bind to DNA in the form of dimer or tetramer and requires the two inverted repeat sequences for binding.
类猪圆环病毒2型因子P1和P2诱导PK-15细胞凋亡的研究  [PDF]
温立斌,何孔旺,杨汉春,王玉然,李广东,惠孝鑫
华北农学报 , 2008, DOI: 10.7668/hbnxb.2008.06.019
Abstract: 为了研究类猪圆环病毒2型因子P1和P2体外诱导的细胞凋亡作用,将P1和P2分子克隆分别转染PK-15细胞。结果表明,用透射电镜可以观察到P1和P2诱导PK-15细胞出现凋亡的典型形态学变化。
Analysis of the downstream region of nodD3 P1 promoter by deletion and complementation tests in Sinorhizobium meliloti
Di Chen,Yanjie Liu,Jiabi Zhu,Shanjiong Shen,Guanqiao Yu
Science China Life Sciences , 2003, DOI: 10.1360/03yc9018
Abstract: In Sinorhizobium meliloti, the nodD3 gene is transcriptionally controlled by two promoters, P1 and P2. Under P1, there is a 660 bp sequence including a small open reading frame, ORF2, followed by the nodD3 coding region. Genetic analysis using the different deletions on the 3’ ends of P1 downstream sequence showed that the downstream sequence +1–+125nt is essential for P1 expression. Complementation, mutations and nodulation tests demonstrated that the ORF2 auto-represses P1 expression, while the P1 downstream sequence +1–+125nt counteracts it.
Two previously proposed P1/P2-differentiating and nine novel polymorphisms at the A4GALT (Pk) locus do not correlate with the presence of the P1 blood group antigen
?sa Hellberg, M Alan Chester, Martin L Olsson
BMC Genetics , 2005, DOI: 10.1186/1471-2156-6-49
Abstract: P1 (n = 18) and P2 (n = 9) samples from donors of mainly Swedish descent were analysed by direct sequencing of PCR-amplified 5'- and 3'-fragments surrounding the Pk coding region. Seventy-eight P1 and P2 samples were investigated with PCR using allele-specific primers (ASP) for two polymorphisms previously proposed as P2-related genetic markers (-551_-550insC, -160A>G). Haplotype analysis of single nucleotide polymorphisms was also performed with PCR-ASP. In ~1.5 kbp of the 3'-untranslated region one new insertion and four new substitutions compared to a GenBank sequence (AL049757) were found. In addition to the polymorphisms at positions -550 and -160, one insertion, two deletions and one substitution were found in ~1.0 kbp of the 5'-upstream region. All 20 P2 samples investigated with PCR-ASP were homozygous for -550insC. However, so were 18 of the 58 P1 samples investigated. Both the 20 P2 and the 18 P1 samples were also homozygous for -160G.The proposed P2-specific polymorphisms, -551_-550insC and -160G, found in P2 samples in a Japanese study were found here in homozygous form in both P1 and P2 donors. Since P2 is the null allele in the P blood group system it is difficult to envision how these mutations would cause the P2 phenotype. None of the novel polymorphisms reported in this study correlated with P1/P2 status and the P1/p mystery remains unsolved.The P-related blood groups include four antigens that are predominantly of glycolipid nature and occur in related biosynthetic pathways [1].The GLOB blood group system [International Society of Blood Transfusion (ISBT) number 028] comprises the P antigen and the GLOB collection (ISBT number 209) includes the Pk antigen and also LKE that is not discussed further here [2]. The P1 antigen is assigned to ISBT system number 003. Five phenotypes depending on the presence or absence of the three antigens, P1, P and Pk, are known (Table 1). The presence of all three antigens results in the P1 phenotype but absence of th
Sequencing and promoter analysis of the nifENXorf3orf5fdxAnifQ operon from Azospirillum brasilense Sp7
Potrich, D.P.;Bressel, T.A.;Schrank, I.S.;Passaglia, L.M.P.;
Brazilian Journal of Medical and Biological Research , 2001, DOI: 10.1590/S0100-879X2001001100003
Abstract: a 40-kb dna region containing the major cluster of nif genes has been isolated from the azospirillum brasilense sp7 genome. in this region three nif operons have been identified: nifhdkorf1y, nifenxorf3orf5fdxanifq and orf2nifusvorf4. the operons containing nifenx and nifusv genes are separated from the structural nifhdkorf1y operon by about 5 kb and 10 kb, respectively. the present study shows the sequence analysis of the 6045-bp dna region containing the nifenx genes. the deduced amino acid sequences from the open reading frames were compared to the nif gene products of other diazotrophic bacteria and indicate the presence of seven orfs, all reading in the same direction as that of the nifhdkorf1y operon. consensus s54 and nifa-binding sites are present only in the promoter region upstream of the nife gene. this promoter is activated by nifa protein and is approximately two-times less active than the nifh promoter, as indicated by the ?-galactosidase assays. this result suggests the differential expression of the nif genes and their respective products in azospirillum.
Sequencing and promoter analysis of the nifENXorf3orf5fdxAnifQ operon from Azospirillum brasilense Sp7  [cached]
Potrich D.P.,Bressel T.A.,Schrank I.S.,Passaglia L.M.P.
Brazilian Journal of Medical and Biological Research , 2001,
Abstract: A 40-kb DNA region containing the major cluster of nif genes has been isolated from the Azospirillum brasilense Sp7 genome. In this region three nif operons have been identified: nifHDKorf1Y, nifENXorf3orf5fdxAnifQ and orf2nifUSVorf4. The operons containing nifENX and nifUSV genes are separated from the structural nifHDKorf1Y operon by about 5 kb and 10 kb, respectively. The present study shows the sequence analysis of the 6045-bp DNA region containing the nifENX genes. The deduced amino acid sequences from the open reading frames were compared to the nif gene products of other diazotrophic bacteria and indicate the presence of seven ORFs, all reading in the same direction as that of the nifHDKorf1Y operon. Consensus sigma54 and NifA-binding sites are present only in the promoter region upstream of the nifE gene. This promoter is activated by NifA protein and is approximately two-times less active than the nifH promoter, as indicated by the -galactosidase assays. This result suggests the differential expression of the nif genes and their respective products in Azospirillum.
Page 1 /100
Display every page Item


Home
Copyright © 2008-2017 Open Access Library. All rights reserved.