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PubMed1978

Systemic structural analysis of the electroencephalogram of depressed patients. General principles and preliminary results of an international collaborative study.

In previous articles, evidence has been presented which supports the hypothesis that detectable neurophysiological changes occur in the course of affective disorders, mainly of a depressive type. The scope of the present report has been to expand the previous investigation to comprise variables not hitherto taken into account and to present a new approach to the analysis of EEG in psychiatry. This new approach, a systemic structural analysis, follows the concepts borrowed from the general system theory, and is based on the assumption that brain activity can be regarded as a type of hierarchical system. Hints about the theoretical principles beyond a systemic structural analysis of EEG are given, and the point is stressed that possible correlations between, e.g., neurophysiological and clinical variables must be south starting from characteristics which are at a comparable level of integration in both realms. The preliminary findings of an international collaborative study of depressive syndromes are presented. 45 patients suffering from depressive syndromes of different aetiology and of varying severity participated in the study. These were rated by means of a rating scale which permitted a division for further analysis into subgroups according to the main symptomatology. The results show that characteristic neurofunctional structures can be identified which correspond to various symptomatological patterns. The occurrence of pronounced interhemispheric differences in electrical activity, related to the severity of the depressive syndrome, has also found further support in the results of this present investigation.

Adult↗

PubMed1991

Human von Willebrand factor gene and pseudogene: structural analysis and differentiation by polymerase chain reaction.

Structural analysis of the von Willebrand factor gene located on chromosome 12 is complicated by the presence of a partial unprocessed pseudogene on chromosome 22q11-13. The structures of the von Willebrand factor pseudogene and corresponding segment of the gene were determined, and methods were developed for the rapid differentiation of von Willebrand factor gene and pseudogene sequences. The pseudogene is 21-29 kilobases in length and corresponds to 12 exons (exons 23-34) of the von Willebrand factor gene. Approximately 21 kilobases of the gene and pseudogene were sequenced, including the 5' boundary of the pseudogene. The 3' boundary of the pseudogene lies within an 8-kb region corresponding to intron 34 of the gene. The presence of splice site and nonsense mutations suggests that the pseudogene cannot yield functional transcripts. The pseudogene has diverged approximately 3.1% in nucleotide sequence from the gene. This suggests a recent evolutionary origin approximately 19-29 million years ago, near the time of divergence of humans and apes from monkeys. Several repetitive sequences were identified, including 4 Alu, one Line-1, and several short simple sequence repeats. Several of these simple repeats differ in length between the gene and pseudogene and provide useful markers for distinguishing these loci. Sequence differences between the gene and pseudogene were exploited to design oligonucleotide primers for use in the polymerase chain reaction to selectivity amplify sequences corresponding to exons 23-34 from either the von Willebrand factor gene or the pseudogene. This method is useful for the analysis of gene defects in patients with von Willebrand disease, without interference from homologous sequences in the pseudogene.

Amino Acid Sequence↗

PubMed1989

Comparative structural analysis of staphylococcal enterotoxins A and E.

Structural analysis of staphylococcal enterotoxins A and E, two functionally and serologically related proteins, has been carried out using circular dichroism, and tryptophan fluorescence quantum yield and quenching. Secondary structures derived from the far-UV circular dichroic spectra revealed that both enterotoxins are in predominantly beta-sheets/beta-turn structures (80-85%). Staphylococcal enterotoxin A has significantly higher alpha-helical content (10.0%) than staphylococcal enterotoxin E (6.5%). Tryptophan fluorescence spectra of both enterotoxins showed maxima at approximately 342 nm, indicating that the fluorescent tryptophan residues are in polar environments. However, the tryptophan fluorescence quantum yields indicated that tryptophan residues are approximately 41% more fluorescent in staphylococcal enterotoxin A than in staphylococcal enterotoxin E. Tryptophan fluorescence quenching by a surface quencher, I-, and a neutral quencher, acrylamide, indicated that at least 1 of the 2 tryptophan residues in both staphylococcal enterotoxins A and E is located on the outer surface of the proteins. This tryptophan residue is in significantly different environments in the two enterotoxins. Six antigenic sites are predicted from the hydrophilicity and secondary structure information; at least four sites are identical. In general, staphylococcal enterotoxins A and E have some structural similarities which are compatible with their common biological activities.

Acrylamide↗

PubMed1989

Secondary structure analysis of adenovirus tripartite leader.

RNA secondary structure analysis was performed to understand the translation function of the adenovirus tripartite leader, a 200-nucleotide 5' noncoding region found on all late viral mRNAs. The tripartite leader facilitates the translation of viral mRNAs at late but not early times after infection and eliminates the normal requirement for the eukaryotic initiation factor 4F or cap binding protein complex. Secondary structures were determined by probing 5' or 3' end-labeled tripartite leader RNAs under nondenaturing conditions with various single strand-specific nucleases, and the information was used to generate a potential model structure. The resulting structure is attractive since it may explain the unusual translation behavior conferred by the tripartite leader. We demonstrate that the first leader segment is predominantly single-stranded, a property consistent with the ability to enhance translation and provide independence from cap binding protein complex. In contrast, the remaining two leader segments form a moderately stable base-paired structure, except for a large hairpin loop. To confirm these findings, the secondary structure of the tripartite leader was also probed when it was attached to a large segment of a messenger RNA and was found to be very similar to that of the individual leader RNA. These findings suggest several possible mechanisms to account for the translation activity of the tripartite leader.

Adenoviridae↗

PubMed1988

[Syndrome assessment using a generalized interaction structure analysis].

The concept of conventional interaction-structure-analysis (ISA) consists of comparing and analyzing two groups of variables. In the present paper this concept is thus generalized that more than two groups of variables can be analyzed. Data from depression research are analyzed by forming three groups of symptoms. The discussion expounds on strategies of data analysis with generalized ISA (GISA).

Attitude to Death↗

PubMed1989

[The effects on upper first molars by the face-bow construction. Consideration of utilizing the strain gauge method and the computer method of structural analysis].

The present study was undertaken for the purpose of detecting the influence on upper first molars by the dynamic behavior originated in face-bow construction. Tests were made at occipital pull and cervical pull face-bows utilizing strain gauge method and the computer method of structural analysis. As for the occipital pull face-bow, a short outer-bow 35 mm frontward of a tube was bent 30 degrees upward and be pulled in that direction. As for the cervical pull face-bow, a medium outer-bow flash to tube, parallel to the inner-bow was pulled from 20 degrees downward. These two types of face-bows were divided into 4 types, those with loops at the back end (WL) and to those without loops (NL). In the strain gauge method, the force and moment to tubes was measured and compared with the values obtained from theoretical analysis. And in the structural analysis, the data of deflection was compared with each other. Those results indicated that 1. face-bow shows a different force to the molars and a different phase of deflection, according to the difference of it's force concentrative section. 2. the larger the deflection, the larger the deviation of forces on molars from theoretical values. 3. the way of setting loops against the direction of pull alters the phase of deflection of face-bow and the force on molars. 4. existance of loops at inner-bow affects as follows: (1) Reduction of moment of each type of face-bow. (2) Reduction of vertical force at occipital pull face-bow and it's increase at cervical pull face-bow. (3) Resistance for deflection of face-bows in the case of tractive force for closing loops.

Dental Stress Analysis↗

PubMed1985

Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: a technique for RNA structure analysis using chemical probes and reverse transcriptase.

The structure of the intervening sequence (IVS) of the Tetrahymena rRNA precursor mediates cleavage-ligation reactions that result in pre-rRNA splicing and IVS cyclization. We have developed a method for RNA structure analysis and applied it to the circular form of the IVS RNA. The native RNA was treated with dimethyl sulfate or diethyl pyrocarbonate to modify bases not involved in secondary or tertiary interactions. The RNA was then used as a template for reverse transcription. Elongation of synthetic oligodeoxynucleotide primers was found to stop (or pause) one nucleotide prior to 1-methyladenosine, 3-methylcytidine, and 7-ethoxycarbonyladenosine residues. The detection of 1-methyladenosine is particularly useful for locating single-stranded regions. After chemical cleavage of the RNA, 7-methylguanosine also could be detected. In general, the sites of modification were consistent with a previous model of the secondary structure of the linear form of the IVS RNA, a model based on enzymatic cleavage data, free energy calculations, and phylogenetic comparison. Thus, IVS RNA autocyclization does not involve major rearrangements of the secondary structure, although there is evidence for a conformational change in one region of the molecule. The methods described here should be of general use for obtaining information about structure far from the ends of RNA molecules.

Animals↗

PubMed1985

[Principles of self-adjusting staining of sections of cerebral cortex for automatic structural analysis].

The development of methods of an automatic structural analysis which uses modern methods of image processing has put forward requirements to standardize the staining of the preparations studied. However, the examination of autopsy material of the human brain shows that the standard procedure of staining does not always lead to standard results. The author presents a formalized description of changes in the quality of preparation staining at different stages, which is based on the measurement of distributions of the mean gradients of the section image obtained with the help of the textural analysis system TAS produced by Leitz. The procedure of adaptive staining based on this description is proposed, which will help to compensate for differences in tinctural properties of different samples of autopsy material.

Cerebral Cortex↗

PubMed1985

Secondary structure analysis of apolipoprotein II mRNA using enzymatic probes and reverse transcriptase. Evaluation of primer extension for high resolution structure mapping of mRNA.

Primer extension has been employed to locate sites of cleavage made in apolipoprotein II (apo-II) mRNA by structure-specific nucleases. This approach permits structural analysis of specific mRNAs within a complex population. Electrophoretic analysis of cDNAs synthesized from T1 RNase-treated and mock-treated apo-II mRNA revealed that most cleavage sites can be mapped with single nucleotide accuracy. However, some T1 RNase-dependent cDNAs demonstrated mobilities corresponding to one nucleotide longer than the mRNA template, suggesting that reverse transcriptase can add a single nucleotide to full-length cDNAs in a template-independent reaction. This approach has been used to map double-stranded and single-stranded accessible domains of the 3' noncoding region of apo-II mRNA with cobra venom, T1, and S1 ribonucleases. Cleavage profiles of apo-II mRNA renatured under a variety of buffer and temperature conditions were identical and in no case was overlap observed between sites of cleavage by double strand- and single strand-specific enzymes. These results suggest that apo-II mRNA possesses a predominant, stable secondary structure. A computer-generated structure model, consistent with these nuclease cleavage data, is presented. In addition to the analysis of mRNA higher order structure in mixed RNA populations, this approach also appears suitable for the analysis of protein-mRNA interactions. Termination sites of incomplete cDNAs produced when untreated or mock-treated RNA is used as a template for primer extension were also mapped. This analysis revealed an over-representation of termination at the dinucleotides CA and CU, suggesting that termination of some incomplete apo-II cDNAs is related to primary and not secondary structure. Such sequence dependence could reflect in vivo degradation by an endogenous cytidine-specific nuclease.

Animals↗

PubMed1990

Structural analysis of a 64-kDa major structural protein of human cytomegalovirus (Towne): identification of a phosphorylation site and comparison to pp65 of HCMV (AD169).

The major 64-kDa structural protein of human cytomegalovirus (pp64) was isolated from a guanidinium chloride extract of the virions and dense bodies of HCMV (Towne) by reverse-phase HPLC. Purified pp64 was reduced and alkylated followed by digestion with trypsin. The molecular mass of each of the tryptic peptides was determined by fast atom bombardment/mass spectrometry and compared with the predicted molecular mass of the fragments deduced from the corresponding DNA-derived peptide sequence of pp65 from HCMV (AD169). Microsequence analysis was employed to confirm selected peptides. Results of protein sequence analysis of pp64 from HCMV (Towne) are in complete agreement with the DNA-derived protein sequence of pp65 predicted for HCMV (AD169) with the following exceptions and modifications. The protein isolated from HCMV (Towne) was found to contain an Ala at position 448 instead of Ser448 reported for the protein from HCMV (AD169). We also identified Ser472 as a site of phosphorylation in pp64 from HCMV (Towne). Finally, on the basis of the sequence of HCMV (AD169) DNA fragment encoding the matrix protein and on S1 nuclease protection analysis, it has been predicted that one version of the matrix protein (possibly the lower matrix protein, Mr 65K) is encoded by an mRNA that is formed through splicing of a short intron. However, we have obtained peptides that contain sequences spanning through the splice-junction region, suggesting that in HCMV (Towne), the matrix protein is encoded by an unspliced message.

Amino Acid Sequence↗

PubMed1992

Syntactic structure analysis of the arrangement of nuclei in dysplastic epithelium of colorectal adenomatous polyps.

In search of new objective classifiers of the degree of dysplasia in colorectal adenomatous polyps, we conducted syntactic structure analysis on hematoxylin-eosin-stained tissue sections of 59 colorectal adenomas. The adenomas were subjectively graded as showing mild (n = 20), moderate (n = 20) or severe (n = 19) dysplasia in a double-blind examination by two pathologists. Using an interactive video-overlay measuring system, a minimum spanning tree was computed in 10 fields per specimen according to a strict measurement protocol. From each minimum spanning tree, such features as total line length, length of line segments, total number of points and number of points with one, two, three or four neighbors were derived. Simple descriptive statistics of these minimum spanning tree features were used to analyze differences between the three grades of dysplasia. Univariate analysis indicated that most of the variables used were suitable for discriminating between mild and moderate as well as between mild and severe grades of dysplasia. Only median minimum line length also showed significant differences between moderate and severe dysplasia. By means of a jackknifed stepwise discriminant analysis, an overall correct classification of mild versus moderate and severe dysplasia of 81.4% was achieved. It is concluded that syntactic structure analysis may have additional value in describing, in an objective and rapid way, the morphologic changes of dysplasia in colorectal adenomatous polyps.

Adenoma↗

PubMed1991

Computer-assisted structural analysis of oligosaccharides using CASPER.

The computer program CASPER for structural analysis has been tested on some oligosaccharides. The program is shown to predict the correct structure of five linear or branched tri- to hexasaccharides using information on components and linkage positions and NMR chemical shifts. Theoligosaccharides are either reducting or methyl glycosides.

Carbohydrate Conformation↗

PubMed1992

Syntactic structure analysis in invasive breast cancer: analysis of reproducibility, biologic background, and prognostic value.

The reproducibility, biologic background, and prognostic value of syntactic structure analysis were studied in a group of 94 patients with invasive primary breast cancer. Using an interactive digitizing video overlay system, the centers of malignant breast cancer nuclei were marked in the five (subjectively) most cellular fields of vision for each case at a final magnification of X1,200, and the corresponding minimum spanning tree was composed for each field. From each minimum spanning tree, 10 syntactic structure features were derived; subsequently, the mean, standard deviation, minimum, and maximum values of the five fields analyzed were calculated for further statistical analysis. Forty statistics thus were available for each case. The reproducibility of repeatedly measuring the same field (independent of nuclearity) and the same patient twice by the same or different observers was good for most of the syntactic structure features. When comparing the statistics of the syntactic structure features with other established prognosticators, correlations were found with (in this order) standard deviation and mean nuclear area (expressing nuclear differentiation), volume percentage epithelium (expressing architectural differentiation), and mitotic activity index. In univariate survival analysis several syntactic structure statistics yielded prognostic significance, the best being the maximum of the number of nuclei with two neighbors (P = .002; Mantel-Cox test, 12.4). Multivariate analysis revealed that syntactic structure features did not provide additional prognostic values with regard to each other. However, they did show additional prognostic values with regard to the multivariate prognostic index (currently one of the best prognosticators in breast cancer), which combines the mitotic activity index, lymph node status, and tumor size. Measurement of syntactic structure features could therefore contribute to an improved prediction of prognosis of breast cancer patients. In conclusion, syntactic structure analysis is a simple, fast, and highly reproducible technique that shows prognostic value in invasive breast cancer and also has important prognostic value with regard to the well-established and prognostically strong morphometric features. It seems to be a promising new method of analyzing tissue architecture in breast cancer and perhaps in many other tumors.

Breast Neoplasms↗

PubMed1978

The covalent structure of bovine liver rhodanese. Isolation and partial structural analysis of cyanogen bromide fragements and the complete sequence of the enzyme.

Cyanogen bromide fragments from reduced and carboxymethylated rhodanese have been isolated by gel filtration and ion exchange chromatography on columns of Sephadex G-50 and sulfoethyl-Sephadex C-25, respectively. Partial or complete structural analysis of these fragments has permitted the ordering in sequence of all eleven of the nonaligned tryptic peptides from citraconylated, S-carboxymethylcysteinyl-rhodanese and has thus provided the complete covalent structure of the enzyme. Rhodanese is a single polypeptide of 293 residues and the molecule weight calculated from the covalent structural analysis is about 32,900. The cysteinyl residue implicated in the catalytic function of rhodanese is at position 247. In some preparations of the enzyme the NH2-terminal dipeptide Val-His is missing and the sequence begins with the glutamine at position 3. The rhodanese thus obtained contains 291 amino acid residues and possesses full enzymic activity. X-ray crystallographic analysis of rhodanese has shown that the halves of the molecule (Domains I and II) are nearly identical in conformation. Comparative analysis of the sequences in Domains I and II containing residues with conformationally equivalent alpha C atoms has revealed some degree of homology between the halves of the rhodanese polypeptide. Nethertheless, the structural equivalence of the rhodanese domains is reflected much more by their similarity in tertiary structural than by their sequence homology, even when the sequence comparisons are optimized with reference to the crystallographic results.

Amino Acid Sequence↗

PubMed1988

A computer-assisted structural analysis of regular polysaccharides on the basis of 13C-n.m.r. data.

A computerised approach to the structural analysis of unbranched regular polysaccharides is described, which is based on an evaluation of the 13C-n.m.r. spectra for all possible primary structures within the additive scheme starting from the chemical shifts of the 13C resonances of the constituent monosaccharides and the average values of the glycosylation effects. The analysis reveals a structure (or structures), the evaluated spectrum of which resembles most closely that observed. The approach has been verified by using a series of bacterial polysaccharides of known structure and, in combination with methylation analysis data, for the determination of the presently unknown structures of the O-specific polysaccharides from Salmonella arizonae O59 and O63, and Proteus hauseri O19.

Carbohydrate Conformation↗

PubMed1990

In vitro secondary structure analysis of mRNA from lacZ translation initiation mutants.

mRNA secondary structure can be an important determinant of the efficiency of translation initiation. To study the effect of secondary structure on translation initiation, in vitro secondary structure analysis was performed on 32 lacZ RNA transcripts that differ in their in vivo translation initiation efficiencies because of mutations. We have shown that well-translated RNA has a relatively unstructured translation initiation region in vitro. In contrast, the translation initiation region of many of the poorly translated RNA transcripts is involved in a stem-loop structure. Mutations that decrease the in vitro stability of the stem-loop increase the frequency of translation initiation. The sequences responsible for forming this stem-loop structure were localized to a small region of RNA. The results confirm some of the previous predictions of the RNA secondary structure of the mutant RNAs based on computer modeling, but they disagree with some of the predicted long-range interactions.

Base Composition↗

PubMed1991

Genetic and structural analysis of G protein alpha subunit regulatory domains.

Genetic and structural analysis of the alpha chain polypeptides of heterotrimeric G proteins defines functional domains for GTP/GDP binding, GTPase activity, effector activation, receptor contact and beta gamma subunit complex regulation. The conservation in sequence comprising the GDP/GTP binding and GTPase domains among G protein alpha subunits readily allows common mutations to be made for the design of mutant polypeptides that function as constitutive active or dominant negative alpha chains when expressed in different cell types. Organization of the effector activation, receptor and beta gamma contact domains is similar in the primary sequence of the different alpha subunit polypeptides relative to the GTP/GDP binding domain sequences. Mutation within common motifs of the different G protein alpha chain polypeptides have similar functional consequences. Thus, what has been learned with the Gs and Gi proteins and the regulation of adenylyl cyclase can be directly applied to the analysis of newly identified G proteins and their coupling to receptors and regulation of putative effector enzymes.

Adenosine Diphosphate Ribose↗

PubMed1992

Catalytic center of cyclodextrin glycosyltransferase derived from X-ray structure analysis combined with site-directed mutagenesis.

An X-ray structure analysis of a crystal of mutant Asp229----Ala of cyclodextrin glycosyltransferase from Bacillus circulans (Ec 2.4.1.19) that had been shortly exposed to beta-cyclodextrin showed density corresponding to a maltose bound at the catalytic center. The crystal structure was refined to an R-factor of 18.7% at 2.5-A resolution. The catalytic center is defined by homology with the structurally known alpha-amylases and by the observation that mutants Asp229----Ala and Asp328----Ala are almost inactive. By model building, the density-defined maltose was extended to a full beta-cyclodextrin, which then indicated the general locations of seven subsites for glucosyl units. The catalytically competent residues Asp229, Glu257, and Asp328 are at the reducing end of the density-defined maltose. In the unligated wild-type structure, Glu257 and Asp328 form a 2.6-A hydrogen bond between their carboxylates in an arrangement that resembles those of the catalytically competent carboxylates in acid proteases. Presumably, the first catalytic step is an attack of the proton between Glu257 and Asp328 on the oxygen of the glycosidic bond.

Bacillus↗