scholarly journals Characterization of promoters in archaeal genomes based on DNA structural parameters

2021 ◽  
Author(s):  
Gustavo Martinez ◽  
Sharmilee Sarkar ◽  
Aditya Kumar ◽  
Ernesto Perez-Rueda ◽  
Scheila Silva
Keyword(s):  
Structural Analysis ◽  
Structural Parameters ◽  
Sequence Divergence ◽  
Structural Features ◽  
Gene Organization ◽  
Tata Box ◽  
Upstream Region ◽  
Promoter Sequences ◽  
Novel Method ◽  
Eukaryotic Organisms

The transcription machinery of archaea can be roughly classified as a simplified version of eukaryotic organisms. The basal transcription factor machinery binds to the TATA-box found around 28 nucleotides upstream of the transcription start site; however, some transcription units lack a clear TATA-box and still have TBP/TFB binding over them. This apparent absence of conserved sequences could be a consequence of sequence divergence associated with the upstream region, operonic and gene organization. Furthermore, earlier studies have found that a structural analysis gains more information compared to a simple sequence inspection. In this work, we evaluated and coded 3630 archaeal promoter sequences of three organisms, Haloferax volcanii, Thermococcus kodakarensis, and Sulfolobus solfataricus into DNA duplex stability, enthalpy, curvature, and bendability parameters. We also split our dataset into conserved TATA and degenerated TATA promoters in order to identify differences among these two classes of promoters. The structural analysis reveals variations in archaeal promoters’ architecture, i.e., a distinctive signal is observed in the TFB, TBP, and TFE binding sites independently of these being TATA-conserved or TATA-degenerated. In addition, the promoter encountering method was validated with upstream regions of 13 other archaea, suggesting that there might be promoter sequences among them. Therefore, we suggest a novel method for locating promoters within the genome of archaea based on energetic/structural features.

A Study of the Anchor Effect Based on Structural Parameters of Flexible Pressurized Anchor and Pressure from Surrounding Rock

2011 ◽  
Vol 71-78 ◽  
pp. 4634-4637
Author(s):  
Tian Lin Cui ◽  
Jing Kun Pi ◽  
Yong Hui Liu ◽  
Zhen Hua He
Keyword(s):  
Structural Parameters ◽  
Structural Features ◽  
Surrounding Rock ◽  
Design Parameters ◽  
Optimized Design ◽  
Anchor Effect ◽  
The Finite Element Method ◽  
Anchor System ◽  
New Type ◽  
Stress Relation

In order to optimize the design of flexible pressurized anchor, this paper gives a further analysis on structural features of the new type of flexible pressurized anchor and carries out a contact analysis on anchor system by using the finite element method. It calculates as well as researches the contact stress relation of interactional anchor rod and surrounding rock under the circumstance of anchoring, obtaining the law of all major design parameters of anchor rod structure and pressure from surrounding rock influencing the anchoring performance and arriving at the conclusion that the anchor rod is adapted to various conditions of surrounding rock. They not only serve as important references for optimized design and application of anchor rod, but also provide a basis for the experiment of new type of anchor rod.

QSAR AND PHARMACOPHORE MODELING OF 4-ARYLTHIENO [3, 2-d] PYRIMIDINE DERIVATIVES AGAINST ADENOSINE RECEPTOR OF PARKINSON'S DISEASE

2010 ◽  
Vol 09 (06) ◽  
pp. 975-991 ◽  
Author(s):  
SHIEK S. S. J. AHMED ◽  
A. AHAMEETHUNISA ◽  
WINKINS SANTOSH
Keyword(s):  
Structural Parameters ◽  
Pharmacophore Model ◽  
Structural Features ◽  
Pharmacophore Modeling ◽  
Hydrogen Bond Donor ◽  
Pyrimidine Derivatives ◽  
Antagonist Activity ◽  
Qsar Studies ◽  
Adenosine A1 ◽  
Adenosine A2a

A series of 47, 4-arylthieno[3, 2-d] pyrimidine derivatives was subjected to quantitative structure-antiparkinson activity relationships (QSAR) studies to evaluate the antagonist activity towards both adenosine A1 and adenosine A2A targets in Parkinson's drug discovery. QSAR models were derived with the aid of genetic function approximation (GFA) technique using descriptors to make connections between structural parameters and antiparkinson's activity followed by ADMET analysis and pharmacophore model generation. QSAR model was assessed using a test set of 12 compounds for A1 (r2 pred = 0.961), (q2 = 0.912) and 12 compounds for A2a (r2 pred = 0.914), (q2 = 0.781) receptor. The results revealed the significant role of DIPOLE MAG, CHI-V-3-P, WIENER, AREA, SC-2 and PHI-MAG descriptors in the antiparkinson activity of the studied compounds against adenosine A1 and adenosine A2A receptors. Subsequent, ADMET analysis shows 28 compounds can be the better candidates of drug and execution of pharmacophore model, explores the hydrogen bond donor, aromatic ring and hydrophobic groups are the key structural features for the antagonist activity.

scholarly journals NUMERICAL MODELING AND FULL-SCALE EXPERIMENTS OF GLUED WOODEN STRUCTURES JOINT DESTRUCTION ON CARBON-FIBER DOWEL PINS

2020 ◽  
Vol 16 (2) ◽  
pp. 101-112
Author(s):  
Mikhail Vodiannikov ◽  
Galina Kashevarova ◽  
Danil Starobogatov
Keyword(s):  
Numerical Modeling ◽  
Structural Analysis ◽  
Carbon Fiber ◽  
Structural Parameters ◽  
General Structure ◽  
Failure Process ◽  
Joint Destruction ◽  
Field Tests ◽  
Full Scale ◽  
Glued Laminated Timber

This paper presents the results of numerical modeling and full-scale experiments of the failure process of a glued laminated timber beam with rigid joint in the middle. All the connecting parts are made of carbon fiber. The structural analysis is done with the finite element method (ANSYS software). The nonlinear problem was solved. The contact interaction of the structural elements in the process of deformation and fracture, as well as orthotropy of the wood, the transversely isotropic properties of the plates, and the real diagrams of the deformation of carbon fiber dowel pins were taken into account. The influence of the structural parameters of the joint on the position of the most loaded dowel pin in the joint and the bearing capacity of the general structure are investigated. To verify the structural analysis results, field tests were carried out before destruction by a stepwise increasing load on a personally designed stand. The destruction of the structure occurred according to the forecast of the numerical model as a result of the mutual slip of the glued wood layers and the destruction of the polymer matrix of the glued dowel pins with the beginning of the formation of plastic joints and the formation of cracks in the wood at the junction.

scholarly journals Protein microcrystallography using synchrotron radiation

IUCrJ ◽  
2017 ◽  
Vol 4 (5) ◽  
pp. 529-539 ◽  
Author(s):  
Masaki Yamamoto ◽  
Kunio Hirata ◽  
Keitaro Yamashita ◽  
Kazuya Hasegawa ◽  
Go Ueno ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Data Collection ◽  
Diffraction Data ◽  
Structure Determination ◽  
Structural Features ◽  
X Ray ◽  
Data Collection Strategy ◽  
Technological Developments ◽  
Novel Method

The progress in X-ray microbeam applications using synchrotron radiation is beneficial to structure determination from macromolecular microcrystals such as smallin mesocrystals. However, the high intensity of microbeams causes severe radiation damage, which worsens both the statistical quality of diffraction data and their resolution, and in the worst cases results in the failure of structure determination. Even in the event of successful structure determination, site-specific damage can lead to the misinterpretation of structural features. In order to overcome this issue, technological developments in sample handling and delivery, data-collection strategy and data processing have been made. For a few crystals with dimensions of the order of 10 µm, an elegant two-step scanning strategy works well. For smaller samples, the development of a novel method to analyze multiple isomorphous microcrystals was motivated by the success of serial femtosecond crystallography with X-ray free-electron lasers. This method overcame the radiation-dose limit in diffraction data collection by using a sufficient number of crystals. Here, important technologies and the future prospects for microcrystallography are discussed.

Geology, Structural Analysis, and Paragenesis of the Arrow Uranium Deposit, Western Athabasca Basin, Saskatchewan, Canada: Implications for the Development of the Patterson Lake Corridor

2020 ◽  
Author(s):  
Sean Hillacre ◽  
Kevin Ansdell ◽  
Brian McEwan
Keyword(s):  
Structural Analysis ◽  
Uranium Deposit ◽  
Regional Scale ◽  
Structural Features ◽  
White Mica ◽  
Uranium Mineralization ◽  
Fault System ◽  
Thin Sections ◽  
Athabasca Basin ◽  
Quartz Veins

Abstract Recent significant discoveries of uranium mineralization in the southwestern Athabasca basin, northern Saskatchewan, Canada, have been associated with a series of geophysical conductors along a NE- to SW-trending structural zone, termed the Patterson Lake corridor. The Arrow deposit (indicated mineral resource: 256.6 Mlb U3O8; grade 4.03% U3O8) is along this trend, hosted exclusively in basement orthogneisses of the Taltson domain, and is the largest undeveloped uranium deposit in the basin. This study is the first detailed analysis of a deposit along this corridor and examines the relationships between the ductile framework and brittle reactivation of structures, mineral paragenesis, and uranium mineralization. Paragenetic information from hundreds of drill core samples and thin sections was integrated with structural analysis utilizing over 18,000 measurements of various structural features. The structural system at Arrow is interpreted as a partitioned, strike-slip–dominated, brittle-ductile fault system of complex Riedel-style geometry. The system developed along subvertical, NE- to SW-trending dextral high-strain zones formed syn- to post-D3 deformation, which were the focus of extensive premineralization metasomatism (quartz flooding, sericitization, chloritization), within the limb domain of a regional-scale fold structure. These zones evolved through post-Athabasca dextral and sinistral reactivation events, creating brittle fault linkages and dilation zones, allowing for hydrothermal fluid migration and resulting uraninite precipitation and associated alteration (white mica, chlorite, kaolinite, hematite, quartz veins). This study of the structural context of Arrow is important as it emphasizes that protracted reactivation of deep-seated structures and their subsidiaries was a fundamental control on uranium mineralization in the southwestern Athabasca basin.

Transcription of the ADH2 gene in Saccharomyces cerevisiae is limited by positive factors that bind competitively to its intact promoter region on multicopy plasmids

1987 ◽  
Vol 7 (3) ◽  
pp. 1233-1241
Author(s):  
M Irani ◽  
W E Taylor ◽  
E T Young
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Promoter Region ◽  
Glucose Repression ◽  
Regulatory Gene ◽  
Tata Box ◽  
Upstream Region ◽  
Competition Effect ◽  
Yeast Saccharomyces Cerevisiae ◽  
Upstream Activation Sequence ◽  
Activation Sequence

Transcription of the ADH2 gene in the yeast Saccharomyces cerevisiae was inhibited by excess copies of its own promoter region. This competition effect was promoter specific and required the upstream activation sequence of ADH2 as well as sequences 3' to the TATA box. Introducing excess copies of ADR1, an ADH2-specific regulatory gene, did not alleviate the competition that was observed in these circumstances during both constitutive and derepressed ADH2 expression. Excess copies of the upstream region did not release ADH2 from glucose repression, consistent with the view that ADH2 is regulated by positive trans-acting factors.

scholarly journals Triplet Analysis That Identifies Unpaired Regions of Functional RNAs

2011 ◽  
Vol 2011 ◽  
pp. 1-6
Author(s):  
Junji Kawakami ◽  
Yoshie Yamaguchi ◽  
Naoki Sugimoto
Keyword(s):  
Consensus Sequence ◽  
Structural Features ◽  
Analysis Method ◽  
Primary Sequence ◽  
Rna Sequences ◽  
Unpaired Region ◽  
Novel Method ◽  
Functional Rnas ◽  
Hiv 1

We developed a novel method for analyzing RNA sequences, deemed triplet analysis, and applied the method in anin vitroRNA selection experiment in which HIV-1 Tat was the target. Aptamers are nucleic acids that bind a desired target (bait), and to date, many aptamers have been identified byin vitroselection from enough concentrated libraries in which many RNAs had an obvious consensus primary sequence after sufficient cycles of the selection. Therefore, the higher-order structural features of the aptamers that are indispensable for interaction with the bait must be determined by additional investigation of the aptamers. In contrast, our triplet analysis enabled us to extract important information on functional primary and secondary structure from minimally concentrated RNA libraries. As a result, by using our method, an important unpaired region that is similar to the bulge of TAR was readily predicted from a partially concentrated library in which no consensus sequence was revealed by a conventional sequence analysis. Moreover, our analysis method may be used to assess a variety of structural motifs with desired function.

scholarly journals The Rhizobium leguminosarum bv. trifolii RosR: Transcriptional Regulator Involved in Exopolysaccharide Production

2007 ◽  
Vol 20 (7) ◽  
pp. 867-881 ◽  
Author(s):  
Monika Janczarek ◽  
Anna Skorupska
Keyword(s):  
Binding Site ◽  
Rhizobium Leguminosarum ◽  
Upstream Region ◽  
Regulatory Sequence ◽  
Lacz Gene ◽  
Sequence Motifs ◽  
Exopolysaccharide Production ◽  
Promoter Sequences ◽  
E Coli ◽  
Multiple Copies

The acidic exopolysaccharide is required for the establishment of symbiosis between the nitrogen-fixing bacterium Rhizobium leguminosarum bv. trifolii and clover. Here, we describe RosR protein from R. leguminosarum bv. trifolii 24.2, a homolog of transcriptional regulators belonging to the family of Ros/MucR proteins. R. leguminosarum bv. trifolii RosR possesses a characteristic Cys2His2 type zincfinger motif in its C-terminal domain. Recombinant (His)6RosR binds to an RosR-box sequence located upstream of rosR. Deletion analysis of the rosR upstream region resulted in identification of two -35 to -10 promoter sequences, two conserved inverted palindromic pentamers that resemble the cAMP-CRP binding site of Escherichia coli, inverted repeats identified as a RosR binding site, and other regulatory sequence motifs. When assayed in E. coli, a transcriptional fusion of the cAMP-CRP binding site containing the rosR upstream region and lacZ gene was moderately responsive to glucose. The sensitivity of the rosR promoter to glucose was not observed in E. coli ΔcyaA. A rosR frame-shift mutant of R. leguminosarum bv. trifolii formed dry, wrinkled colonies and induced nodules on clover, but did not fix nitrogen. In the rosR mutant, transcription of pssA-lacZ fusion was decreased, indicating positive regulation of the pssA gene by RosR. Multiple copies of rosR in R. leguminosarum bv. trifolii 24.2 increased exopolysaccharide production.

Cushioning properties of weft-knitted spacer fabrics

2017 ◽  
Vol 88 (14) ◽  
pp. 1628-1640 ◽  
Author(s):  
Tong Zhao ◽  
Hairu Long ◽  
Tianqi Yang ◽  
Yanping Liu
Keyword(s):  
Human Body ◽  
Structural Parameters ◽  
Testing Machine ◽  
Three Dimensional ◽  
Structural Features ◽  
Practical Significance ◽  
Absorption Energy ◽  
Yarn Diameter ◽  
Spacer Fabrics ◽  
Compression Resistance

Three-dimensional spacer fabrics which have a sandwich structure are formed in a single knitting process without any additional joining treatment. They consist of two separate multifilament outer layers connected by arrays of spacer monofilaments. This paper presents an experimental study on the relationships between the cushioning properties and structural parameters of weft-knitted spacer fabrics in order to lay a foundation for the development of seamless shaped impact protectors for human body impact protection. Sixteen spacer fabrics of different structural parameters were knitted on a computerized flat knitting machine and tested on a universal mechanical testing machine. The cushioning properties of the spacer fabrics were analyzed in terms of their structural features, compression stress–strain curves, energy absorption, and compression resilience. It was found that multifilament fineness, spacer yarn diameter, and spacer yarn pattern should be matching in order to form effective binding structures between the outer layers and spacer monofilaments. The results also showed that spacer fabrics knitted with a shorter spacer yarn span distance, coarser monofilaments, and higher spacer yarn density have better compression resistance and absorption energy but inferior compression resilience if their binding structures are effective. This study has practical significance in promoting the application of this type of fabric as a cushion material for human body protection.

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