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At least 649 records · Page 36Linked to original sources
PubMed2003

High-level expression of porcine liver cytochrome P-450 reductase catalytic domain in Escherichia coli by modulating the predicted local secondary structure of mRNA.

A direct expression system for the solubilized catalytic domains of NADPH-cytochrome P-450 reductase (sCPR) from rat (RsCPR) and porcine (PsCPR) in Escherichia coli cells was constructed using the expression plasmid pCWori(+). PsCPR was minimally expressed, whereas RsCPR was highly expressed. Replacement of the nucleotides encoding Thr(60)Ser(61)Ser(62) in PsCPR with those for Ala(60)Pro(61)Pro(62) in RsCPR markedly increased the expression level of the protein. The local secondary structures of the mRNAs, which were predicted with the prediction program GeneBee (http://www.genebee.msu.su), suggested that the intramolecular double strand between the ribosome binding site (RBS) and the Thr(60)Ser(61)Ser(62) codons in PsCPR, and/or the base-pairing at the initiation codon of the mRNAs significantly affected protein expression. Silent mutations were systematically introduced into the codons for Thr(58) and Thr(60)Ser(61) in PsCPR to modulate the local secondary structure of the mRNA. The expression level of the silently mutated PsCPR suggests that the expression level of PsCPR depends on the stability of the local structure at the RBS in the mRNA. A high-level expression system for wild-type PsCPR was constructed by introducing silent mutations at the codons for Thr(60)Ser(61) in PsCPR. The purified PsCPR showed the characteristic absorption spectral changes of sCPR after reduction with NADPH. The yield of purified PsCPR from 1 liter of culture fluid was 45.8 mg. These results substantiate that the introduction of silent mutations in the section of the gene encoding the N-terminal region of the protein based on the predicted local secondary structure of the mRNA at the RBS is a useful approach to control and increase the expression level of heterologous proteins in E. coli cells.

Amino Acid Sequence↗
PubMed2000

First laboratory observation of freely propagating electrostatic waves produced by intense, localized field structures

Freely propagating electrostatic waves (free modes) are observed to be produced by intense, localized field structures in laboratory measurements performed in an unmagnetized plasma in a state of strong Langmuir turbulence. The freely traveling waves conform to the Langmuir dispersion relation and have an average frequency which is approximately 11% higher than the average frequency of the localized field structures. The observations are consistent with the predictions of strong Langmuir turbulence theory.

Journal Article↗
PubMed2006

Rnall: an efficient algorithm for predicting RNA local secondary structural landscape in genomes.

BACKGROUND: The information of RNA local secondary structures (LSSs) can help retrieve biologically important motifs and study functions of RNA molecules. Most of the current RNA secondary structure prediction tools are not suitable for RNA LSS prediction on the genome scale due to high computational complexity. METHODS: We developed a new computer package Rnall based on a dynamic programming technique, which scans an RNA sequence with a sliding window and extracts all RNA LSSs with sizes no larger than the window size using the nearest neighbor thermodynamic parameters. The worst case running time of Rnall is O(W(3)L), where W is the window size and L is the query sequence length. In practice we observed a running time of O(W(2)L). We further introduced the concept of energy landscape for illustrating RNA LSS, which may facilitate RNA motif mining on the genomic scale. RESULTS: Rnall shows better prediction accuracy than two other prediction tools Lfold and Quickfold. Rnall is also applied to scan for RNA LSSs in three genomes, and the prediction maps well with known RNA motifs. CONCLUSIONS: Rnall is designed for RNA LSS prediction and together with the energy landscape, it has unique features that could be used for RNA structural motif mining. Rnall is freely available for download at http://digbio.missouri.edu/~wanx/Rnall or http://www.sysbio.muohio.edu/Rnall.

Algorithms↗
PubMed1983

Melting of local ordered structures in yeast 5S ribosomal RNA in aqueous salts.

Equilibrium and kinetics of thermal melting of yeast 5S ribosomal RNA in aqueous NaCl with or without Mg2+ were investigated by differential thermal melting and temperature jump methods. Two peaks (1 and 2) and a shoulder were observed in each of melting curves at ionic strength I=0.002-0.5 and linearity between each of melting temperatures T1m and T2m and log I was found at I=0.01-0.5 in the Mg2+-free solution. The local structures were found to be stabilized considerably by Mg2+. The temperature jump measurements gave the kinetic melting curve of the structure 1 at I=0.03 without Mg2+ or with 0.5 mM Mg2+. The kinetic Tm coincided well with the corresponding static Tm. For the structure 1, various parameters were calculated from the kinetic data, which indicated a double helical character of the structure 1. In terms of the values of Tm, G-C content, and enthalpy change of the transition of the structure 1 or 2, appropriateness of each of the secondary structure models of eukaryotic 5S RNA proposed previously was discussed.

Hot Temperature↗
PubMed1993

Automatic derivation of substructures yields novel structural building blocks in globular proteins.

Because the general problem of predicting the tertiary structure of a globular protein from its sequence is so difficult, researchers have tried to predict regular substructures, known as secondary structures, of proteins. Knowledge of the position of these structures in the sequence can significantly constrain the possible conformations of the protein. Traditional protein secondary structures are alpha-helices, beta-sheets, and coil. Secondary structure prediction programs have been developed, based upon several different algorithms. Such systems, despite their varied natures, are noted for their universal limit on prediction accuracy of about 65%. A possible cause for this limit is that traditional secondary structure classes are only a coarse characterization of local structure in proteins. This work presents the results of an alternative approach where local structure classes in proteins are derived using neural network and clustering techniques. These give a set of local structure categories, which we call Structural Building Blocks (SBBs), based upon the data itself, rather than a priori categories imposed upon the data. Analysis of SBBs shows that these categories are general classifications, and that they account for recognized helical and strand regions, as well as novel categories such as N- and C-caps of helices and strands.

Cluster Analysis↗
PubMed1996

Local genetic structure within two rookeries of Chelonia mydas (the green turtle).

We used multilocus minisatellite DNA fingerprinting to examine the local genetic structure within nesting populations of green turtles (Chelonia mydas) in Tortuguero, Costa Rica and Melbourne, Florida, USA. In the Tortuguero population, there was a significant negative correlation between genetic similarity of pairs of nesting females and the distance between their nest sites both within years (r2 = 0.273; P < 0.001) and between years (r2 = 0.578; P < 0.001). Of the 122 female pairs scored for Tortuguero, 12.3 per cent had genetic similarity values resembling those of mother-offspring pairs. In the Melbourne population, however, no relationship between genetic similarity and distance was found (r2 = 0.017; P = 0.075). The distance-related genetic structure of the Tortuguero population indicates that these females exhibit low levels of dispersal from natal sites, and that nestmates return independently to nest near their natal sites. The lack of a similar structure in the Melbourne population suggests that females from this population may not return to natal sites with comparable precision. High levels of mortality among nests, hatchlings or maturing turtles produced in the Melbourne rookery may also be responsible for the absence of distance-related local genetic structure.

Animals↗
PubMed1994

Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures.

Analyzing nucleic acid structures in a comparable manner has become increasingly important as the number of solved structures has increased. This paper presents the concepts, mathematics, theorems, and proofs that form the basis of a new program to analyze three-dimensional DNA and RNA structures. The approach taken here provides numerical data in accordance with guidelines set at a 1988 EMBO workshop. Mathematical definitions are provided for all local structural parameters described in the guidelines. The definitions satisfy the guideline requirements while preserving the original physical intuition of the parameters. In particular, the rotational parameters are true rotations based on a simple physical model (net rotation at constant angular velocity), not Euler angles or angles between vectors and planes as is the case with other approaches. As a result, the mathematical definitions are symmetrical with the property that a 5 degrees tilt is the same as a 5 degrees roll and a 5 degrees twist, except that the rotations take place about different axes. In other approaches, a 5 degrees tilt can mean a different amount of net rotation than a 5 degrees roll or a 5 degrees twist. A second unique feature of the mathematics is that it explicitly incorporates the concept of a pivot point, which is the point about which a base in a base-pair rotates as it buckles, propeller twists, and opens. Pivot points enable one to model the physical motion of bases more accurately. As a result, they greatly reduce and/or eliminate the statistical correlations between rotational and translational parameters that arise as mathematically induced artifacts in other approaches. This paper, together with the statistical analysis in the companion paper for determining the locations of the pivot points, provides everything needed to understand the output of the program as it relates to individual structures.

Base Composition↗
PubMed1991

An ectopic copy of the Drosophila ftz associated SAR neither reorganizes local chromatin structure nor hinders elution of a chromatin fragment from isolated nuclei.

In vitro assays using detergent extracted nuclei allow the operational definition of SARs--specific sequences in the chromosome which are thought to interact with a structural matrix or scaffold. This interaction results in the formation of large stable protein-DNA complexes. We have used P-element transformation to introduce a characterized SAR into the Drosophila genome. The standard assay, which uses detergent extracted nuclei, shows that the ectopic SAR is indeed bound to the scaffold. However, in unextracted nuclei, a chromatin fragment containing the SAR sequence is eluted from the nucleus as readily as a fragment which lacks an SAR. Furthermore, an analysis of the accessibility of the neighbouring chromosomal restriction sites in unextracted nuclei indicates that the introduction of this ectopic SAR does not influence the local structure of chromatin. We conclude that the ectopic SAR site is not attached to a nuclear scaffold or matrix in vivo.

Animals↗
PubMed2002

Molecular cloning, gene localization, and structure of human cyclin B3.

Here we describe the molecular cloning of human cyclin B3, its localization, and its structure. It is localized in the subcentromeric region of the X chromosome, still not completely sequenced by the Human Genome Project. This cyclin B3 is unusually large for a mitotic cyclin. Its mRNAs were found in all tissues and were particularly abundant in testis. At least three splice variants were found in the ORF and three variants in the 5'UTR.

Alternative Splicing↗
PubMed1978

Malignant giant cell tumor of bone. Fine structure and localization of acid phosphatase.

The fine structure of the different cell types constituting a primary malignant giant cell tumor of bone has been studied and the localization of acid phosphatase in relation to the subcellular organelles been demonstrated. Three distinct cell types with characteristic ultrastructural features were observed: giant cells, fibroblast-like cells, and cells with abundant lipid inclusions and mitochondria. Certain differences were noted between these three cell types and their counterparts in benign giant cell tumors of bone (described in a separate report). The enzyme histochemical and morphological data suggested that the giant cells in the malignant tumor might possess a more active and expansive lysosomal apparatus than corresponding cells in the benign variant.

Acid Phosphatase↗
PubMed1995

Drastic influence of a single heme axial ligand replacement on the thermostability of cytochrome c3.

The thermostability of wild type Desulfovibrio vulgaris Hildenborough tetraheme cytochrome c3 and its H22M, H25M, H35M and H70M mutants was studied by circular dichroism technique in the far UV and Soret regions. It was shown that wild type cytochrome is extremely thermostable and retains structural and functional properties up to 110 degrees C. Mutations do not change overall secondary structure and local structure of the hemes vicinity. All mutants are much more unstable to heat denaturation than the wild type cytochrome. Point mutation (His/Met replacement) results in extraordinary 30-45 degrees C decrease in the protein thermostability depending on the mutation. We may conclude therefore that the heme region is important not only for the functional properties of the cytochrome but also for the overall protein thermostability.

Circular Dichroism↗
PubMed2003

Energy transduction optical sensor in skeletal myosin.

The skeletal myosin cross-bridge in dynamic association with actin is the unitary energy transducer in muscle, converting free energy from ATP hydrolysis into contractile force. Myosin's conserved ATP-sensitive tryptophan (AST) is an energy transduction optical sensor signaling transduction-related transient conformation change by modulating its fluorescence intensity amplitude and relaxation rate. Recently introduced techniques have provided the means of observing the time-resolved intensity decay from this single residue in the native protein to elucidate the mechanism of its ATP sensitivity. AST signal characteristics could be derived from local protein structure by a scenario involving interactions with excited-state tryptophan. This investigation suggests the very different possibility that hypochromism induced in the tryptophan absorption band, a ground-state effect, is a significant structural effector of optical transduction sensing. This possibility makes feasible the interpretation of the transient AST optical signal in terms of dynamical protein structure, thereby raising the empirical signal to the level of a structural determinant. Using the crystallographically based geometry from several myosin structures, the maximum calculated AST hypochromism is <10% to be compared with the value of approximately 30% observed here experimentally. Rationalizing the discrepancy invites further investigation of S1 dynamical structure local to the AST during transduction.

Actins↗
PubMedDate not supplied

Narrative skills of children with communication impairments.

BACKGROUND: Narrative assessment is sensitive to the communication impairments of children with specific language impairment and those with autistic spectrum disorders. Although both groups of children tend to show deficits in narrative, it is unclear whether these deficits are qualitatively different and how language and pragmatic ability may impact on narrative competence. Comparing these two groups of children with children who exhibit pragmatic language impairment without autism may help to clarify these issues. AIMS: This study explored the relationship between structural language ability and pragmatic competence in narrative in children with communication impairments and typically developing children. METHODS AND PROCEDURES: Diagnostic status was determined using the Children's Communication Checklist. All children were asked to generate a narrative to the wordless picture book Frog, Where are You? (Mayer 1969). Narratives were analysed according to their global structure, local linguistic structure and the child's ability to provide evaluative comments, especially about mental or emotional states. OUTCOMES AND RESULTS: No group differences were seen in global structure or evaluation. Children with specific language impairment and autistic disorder made more syntactic errors, and children with autism were significantly more likely to provide ambiguous references in the story. No significant relationships were evident between the Children's Communication Checklist and narrative measures. The complexity of language used was related to evaluation in the clinical groups. CONCLUSIONS: Narrative is a good way of assessing linguistic ability in older children with communication impairments. Core language abilities rather than pragmatic skill or diagnostic status are likely to influence narrative development.

Autistic Disorder↗
PubMed2006

Local alcohol prohibition, police presence and serious injury in isolated Alaska Native villages.

AIMS: To consider the effects of alcohol prohibition and police presence upon serious injury in isolated Alaska Native villages. DESIGN: We compared rates of injury attributed to assault, self-harm, motor vehicle collisions and 'other causes' between villages with or without local prohibition and between villages with or without local police. Negative binomial regression was used to assess the relative effects of prohibition and police presence upon serious injury rates net of potential confounders. PARTICIPANTS: A total of 132 isolated Alaska Native villages between the years 1991 through 2000. MEASUREMENTS; Serious injury was measured using Alaska Trauma Registry and Alaska Bureau of Vital Statistics death certificate records. Local option election records were used to classify cases as occurring in wet or dry villages and police deployment records were used to classify cases as occurring in villages with or without local police. Village-level statistics from the 1990 and 2000 US censuses were used in the negative binomial regression analyses. FINDINGS: Villages that prohibited alcohol had lower age-adjusted rates of serious injury resulting from assault, motor vehicle collisions and 'other causes'. Dry villages with a local police presence had a lower age-adjusted rate of serious injury caused by assault. Controlling for the relative effects of village isolation, access to alcohol markets and local demographic structures, local prohibition was associated with lower rates of assault injuries and 'other causes' injuries while local police presence was associated with lower rates of assault injuries. CONCLUSIONS: Residents of isolated Alaska Native villages are safer when they prohibit alcohol. A local police presence in dry villages provides further reduction of the incidence of assault.

Accidents↗
PubMed2004

Systematic analysis of large screening sets in drug discovery.

Each year large pharmaceutical companies produce massive amounts of primary screening data for lead discovery. To make better use of the vast amount of information in pharmaceutical databases, companies have begun to scrutinize the lead generation stage to ensure that more and better qualified lead series enter the downstream optimization and development stages. This article describes computational techniques for end to end analysis of large drug discovery screening sets. The analysis proceeds in three stages: In stage 1 the initial screening set is filtered to remove compounds that are unsuitable as lead compounds. In stage 2 local structural neighborhoods around active compound classes are identified, including similar but inactive compounds. In stage 3 the structure-activity relationships within local structural neighborhoods are analyzed. These processes are illustrated by analyzing two large, publicly available databases.

Algorithms↗
PubMed2004

LOCnet and LOCtarget: sub-cellular localization for structural genomics targets.

LOCtarget is a web server and database that predicts and annotates sub-cellular localization for structural genomics targets; LOCnet is one of the methods used in LOCtarget that can predict sub-cellular localization for all eukaryotic and prokaryotic proteins. Targets are taken from the central registration database for structural genomics, namely, TargetDB. LOCtarget predicts localization through a combination of four different methods: known nuclear localization signals (PredictNLS), homology-based transfer of experimental annotations (LOChom), inference through automatic text analysis of SWISS-PROT keywords (LOCkey) and de novo prediction through a system of neural networks (LOCnet). Additionally, we report predictions from SignalP. The final prediction is based on the method with the highest confidence. The web server can be used to predict sub-cellular localization of proteins from their amino acid sequence. The LOCtarget database currently contains localization predictions for all eukaryotic proteins from TargetDB and is updated every week. The server is available at http://www.rostlab.org/services/LOCtarget/.

Databases, Genetic↗
PubMed1991

Differential induction of structural changes in the simian virus 40 origin of replication by T antigen.

The ATP-dependent binding of the simian virus 40 (SV40) large tumor antigen (T antigen) to the SV40 origin of replication (ori) results in the structural distortion of two critical elements within flanking regions of ori and the untwisting of the DNA helix. We examined the effect of changes in temperature, ATP concentration, and other reaction parameters on the generation of these DNA structural changes. We found that induction of the two localized structural transitions were highly and differentially sensitive to reaction conditions. Significant distortion of the early palindrome element, shown previously to result from DNA melting, required low levels of ATP (10 to 30 microM) but temperatures above 25 degrees C. Distortion of the AT tract occurred at low temperatures (5 degrees C) but required relatively high concentrations of ATP (greater than 300 microM). Thus, T antigen can induce structural changes within one critical element of ori without generating significant structural distortion within the second element. The response of ori untwisting to reaction conditions generally increased in parallel with or fell intermediate between the inductions of localized structural transitions. We suggest that ori untwisting and localized structural distortions are interdependent consequences of T-antigen binding to ori. These results suggest a model for the structural events occurring during the initial steps of SV40 DNA replication.

Adenosine Triphosphate↗
PubMed2005

Recursive estimation of 3D motion and surface structure from local affine flow parameters.

A recursive structure from motion algorithm based on optical flow measurements taken from an image sequence is described. It provides estimates of surface normals in addition to 3D motion and depth. The measurements are affine motion parameters which approximate the local flow fields associated with near-planar surface patches in the scene. These are integrated over time to give estimates of the 3D parameters using an extended Kalman filter. This also estimates the camera focal length and, so, the 3D estimates are metric. The use of parametric measurements means that the algorithm is computationally less demanding than previous optical flow approaches and the recursive filter builds in a degree of noise robustness. Results of experiments on synthetic and real image sequences demonstrate that the algorithm performs well.

Algorithms↗