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PubMed2004

AANT: the Amino Acid-Nucleotide Interaction Database.

We have created an Amino Acid-Nucleotide Interaction Database (AANT; http://aant.icmb.utexas. edu/) that categorizes all amino acid-nucleotide interactions from experimentally determined protein-nucleic acid structures, and provides users with a graphic interface for visualizing these interactions in aggregate. AANT accomplishes this by extracting individual amino acid-nucleotide interactions from structures in the Protein Data Bank, combining and superimposing these interactions into multiple structure files (e.g. 20 amino acids x 5 nucleotides) and grouping structurally similar interactions into more readily identifiable clusters. Using the Chime web browser plug-in, users can view 3D representations of the superimpositions and clusters. The unique collection and representation of data on amino acid-nucleotide interactions facilitates understanding the specificity of protein-nucleic acid interactions at a more fundamental level, and allows comparison of otherwise extremely disparate sets of structures. Moreover, by modularly representing the fundamental interactions that govern binding specificity it may prove possible to better engineer nucleic acid binding proteins.

Amino Acids↗

PubMed2005

Canine hepatic neuroendocrine carcinoma: an immunohistochemical and electron microscopic study.

Ten dogs with neuroendocrine carcinoma of the liver were selected for inclusion in the study. Clinical signs were anorexia (7), vomiting (5), polydipsia/polyuria (3), icterus (2), lethargy (2), weight loss (2), paresis (1), ataxia (1), weakness (1), collapse (1), and urinary tract infection (1). Hematologic and biochemical abnormalities included anemia (2/8), leukocytosis (4/8), high liver enzyme activity (serum alkaline phosphatase, 7/9; alanine transaminase, 7/9; aspartate transaminase, 8/9), and high total bilirubin (6/9). Grossly, the tumors were diffuse, involving all liver lobes in six dogs, and two dogs had various-sized nodules in addition to diffuse involvement. Histologically, there were eight tumors with solid or trabecular pattern (group A), one tumor with cords or rows of neoplastic cells (group B), and one tumor with multiple rosette-like structures (group C). Immunohistochemical studies revealed that all 10 neoplasms were positive for at least one of the endocrine markers used: neuron-specific enolase (NSE; 8/10), synaptophysin (5/10), and chromogranin-A (3/10). A panel of NSE, chromagranin-A, and synaptophysin detected 100% of the tumors in our series. Electron microscopy confirmed the diagnosis by the presence of intracytoplasmic neurosecretory granules in the two examined cases. Our results show that neuroendocrine markers commonly used in humans can be used for the diagnosis of hepatic neuroendocrine carcinoma in dogs, preferably a panel of synaptophysin, chromagranin-A, and NSE because chromogranin-A alone is not as useful in dogs as in humans.

Animals↗

PubMed2000

Solution NMR evidence for a cis Tyr-Ala peptide group in the structure of [Pro93Ala] bovine pancreatic ribonuclease A.

Proline peptide group isomerization can result in kinetic barriers in protein folding. In particular, the cis proline peptide conformation at Tyr92-Pro93 of bovine pancreatic ribonuclease A (RNase A) has been proposed to be crucial for chain folding initiation. Mutation of this proline-93 to alanine results in an RNase A molecule, P93A, that exhibits unfolding/refolding kinetics consistent with a cis Tyr92-Ala93 peptide group conformation in the folded structure (Dodge RW, Scheraga HA, 1996, Biochemistry 35:1548-1559). Here, we describe the analysis of backbone proton resonance assignments for P93A together with nuclear Overhauser effect data that provide spectroscopic evidence for a type VI beta-bend conformation with a cis Tyr92-Ala93 peptide group in the folded structure. This is in contrast to the reported X-ray crystal structure of [Pro93Gly]-RNase A (Schultz LW, Hargraves SR, Klink TA, Raines RT, 1998, Protein Sci 7:1620-1625), in which Tyr92-Gly93 forms a type-II beta-bend with a trans peptide group conformation. While a glycine residue at position 93 accommodates a type-II bend (with a positive value of phi93), RNase A molecules with either proline or alanine residues at this position appear to require a cis peptide group with a type-VI beta-bend for proper folding. These results support the view that a cis Pro93 conformation is crucial for proper folding of wild-type RNase A.

Amino Acid Sequence↗

PubMed2004

Bioisosterism: quantitation of structure and property effects.

The powerful concept of bioisosterism is presented as a method for selecting molecular groups for drug design and lead-compound development. Three group-structure characteristics are described for this purpose. The E-State value for an attached atom is used as a measure of electrotopological group impact. The volume of the group is estimated from counts of sigma, pi, and lone-pair n electrons, as embodied in the valence and simple connectivity delta values for atoms in the group. Polarity is described in terms of the polarity index Q(v). Specific examples are given for commonly used groups. Parameter spaces encoding these three attributes are presented as examples that may be used to guide bioisostere selection in late-stage drug-design procedures. The method presented here is of practical value in the decision processes of molecular modification.

Biodiversity↗

PubMed1984

Xenopus laevis 18S ribosomal RNA: experimental determination of secondary structural elements, and locations of methyl groups in the secondary structure model.

18S ribosomal RNA from X. laevis was subjected to partial digestion with ribonucleases A or T1 under a variety of conditions, and base-paired fragments were isolated. Sequence analysis of the fragments enabled five base-paired secondary structural elements of the 18S RNA to be established. Four of these elements (covering bases 221-256, 713-757, 1494-1555 and 1669-1779) confirm our previous secondary structure predictions, whereas the fifth (comprising bases 1103-1125) represents a phylogenetically conserved "switch" structure, which can also form in prokaryotic 16S RNA. The results are incorporated into a refined model of the 18S RNA secondary structure, which also includes the locations of the many methyl groups in X. laevis 18S RNA. In general the methyl groups occur in non-helical regions, at hairpin loop ends, or at helix boundaries and imperfections. One large cluster of 2'-O-methyl groups occurs in a region of complicated secondary structure in the 5'-one third of the molecule.

Animals↗

PubMed1975

Some characteristics of schizophrenics and their parents.

This study was designed to test four hypotheses: (a) parents of schizophrenics constitute a discrete group amongst the parents of psychiatric patients with regard to aspects of their construing; (b) schizophrenics can be differentiated from other psychiatric patients by aspects of their construing; (c) the construing of parents of psychiatric patients is related to that of their disturbed children; and (d) parents of schizophrenics differ from parents of other psychiatric patients in their personality and attitudes. An experimental group of parents of acute schizophrenics and a control group of parents of acute non-schizophrenic psychiatric patients were given a battery of psychological tests, and their hospitalized children completed a shortened battery. There was some confirmation of each hypothesis. Both experimental groups structured supplied, but not their own personal, constructs more abnormally than the corresponding control groups, and showed more deviant sexual identification, though this latter was a function of social class. The parents' structuring of supplied constructs was related to that of their children. There were also some differences in personality between the groups of parents.

Adolescent↗

PubMed2006

Solid memory: structural preferences in group 2 dihalide monomers, dimers, and solids.

The link between structural preferences in the monomers, dimers, and extended solid-state structures of the group 2 dihalides (MX(2): M = Be, Mg, Ca, Sr, Ba and X = F, Cl, Br, I) is examined theoretically. The question posed is how well are geometric properties of the gas-phase MX(2) monomers and lower order oligomers "remembered" in the corresponding MX(2) solids. Significant links between the bending in the MX(2) monomers and the D(2)(h)()/C(3)(v)() M(2)X(4) dimer structures are identified. At the B3LYP computational level, the monomers that are bent prefer the C(3)(v)() triply bridged geometry, while the rigid linear molecules prefer a D(2)(h)() doubly bridged structure. Quasilinear or floppy monomers show, in general, only a weak preference for either the D(2)(h)() or the C(3)(v)() dimer structure. A frontier orbital perspective, looking at the interaction of monomer units as led by a donor-acceptor interaction, proves to be a useful way to think about the monomer-oligomer relationships. There is also a relationship between the structural trends in these two (MX(2) and M(2)X(4)) series of molecular structures and the prevalent structure types in the group 2 dihalide solids. The most bent monomers condense to form the high coordination number fluorite and PbCl(2) structure types. The rigidly linear monomers condense to form extended solids with low coordination numbers, 4 or 6. The reasons for these correlations are explored.

Journal Article↗

PubMed2005

Tandem mass spectrometry characteristics of polyester anions and cations formed by electrospray ionization.

Electrospray ionization of polyesters composed of isophthalic acid and neopentyl glycol produces carboxylate anions in negative mode and mainly sodium ion adducts in positive mode. A tandem mass spectrometry (MS/MS) study of these ions in a quadrupole ion trap shows that the collisionally activated dissociation pathways of the anions are simpler than those of the corresponding cations. Charge-remote fragmentations predominate in both cases, but the spectra obtained in negative mode are devoid of the complicating cation exchange observed in positive mode. MS/MS of the Na(+) adducts gives rise to a greater number of fragments but not necessarily more structural information. In either positive or negative mode, polyester oligomers with different end groups fragment by similar mechanisms. The observed fragments are consistent with rearrangements initiated by the end groups. Single-stage ESI mass spectra also are more complex in positive mode because of extensive H/Na substitutions; this is also true for matrix-assisted laser desorption ionization (MALDI) mass spectra. Hence, formation and analysis of anions might be the method of choice for determining block length, end group structure and copolymer sequence, provided the polyester contains at least one carboxylic acid end group that is ionizable to anions.

Anions↗

PubMed2002

Distributed Web-supported radiology clerkship for the required clinical clerkship year of medical school: development, implementation, and evaluation.

RATIONALE AND OBJECTIVES: The authors performed this study to develop, implement, and evaluate a new radiology clerkship for the required clinical clerkship year of medical school. MATERIALS AND METHODS: A mandatory radiology clerkship experience was added to the required clinical clerkships as a series of 10 independent half-day teaching sessions. These sessions were distributed as one session per existing clerkship throughout the year. To provide continuity and organization, Web-based curriculum materials were designed and implemented as a component of the radiology clerkship. The new clerkship was evaluated with observations, pretest and posttest measures with a control group, structured and unstructured student and faculty surveys, and individual and small group interviews. RESULTS: The clerkship was successfully developed and implemented. Ninety-five students have completed the clerkship. Their mean posttest score (84.8) was significantly higher than their mean pretest score (58.8, P < .001) and the mean control group score (59.7, P < .001). Students rarely used the Web site. Disadvantages of the distributed clerkship were identified. CONCLUSION: A radiology clerkship distributed among existing clerkships is feasible but has many disadvantages. Students greatly prefer live instruction, and Web-based educational materials are more valuable to faculty and administrators than to students.

Attitude↗

PubMed2003

Thermolytic carbonates for potential 5'-hydroxyl protection of deoxyribonucleosides.

Thermolytic groups structurally related to well-studied heat-sensitive phosphate/thiophosphate protecting groups have been evaluated for 5'-hydroxyl protection of deoxyribonucleosides as carbonates and for potential use in solid-phase oligonucleotide synthesis. The spatial arrangement of selected functional groups forming an asymmetric nucleosidic 5'-O-carbonic acid ester has been designed to enable heat-induced cyclodecarbonation reactions, which would result in the release of carbon dioxide and the generation of a nucleosidic 5'-hydroxyl group. The nucleosidic 5'-O-carbonates 3-8, 10-15, and 19-21 were prepared and were isolated in yields ranging from 45 to 83%. Thermolytic deprotection of these carbonates is preferably performed in aqueous organic solvent at 90 degrees C under near neutral conditions. The rates of carbonate deprotection are dependent on the nucleophilicity of the functional group involved in the postulated cyclodecarbonation reaction and on solvent polarity. Deprotection kinetics increase according to the following order: 4 < 5 < 10 < 6 < 12 < 7 < 13 < 8 < 14 congruent with 19-21 and CCl4 < dioxane < MeCN < t-BuOH < MeCN:phosphate buffer (3:1 v/v, pH 7.0) < EtOH:phosphate buffer (1:1 v/v, pH 7.0). Complete thermolytic deprotection of carbonates 7, 8, 13, and 14 is achieved within 20 min to 2 h under optimal conditions in phosphate buffer-MeCN. The 2-(2-pyridyl)amino-1-phenylethyl and 2-[N-methyl-N-(2-pyridyl)]aminoethyl groups are particularly promising for 5'-hydroxyl protection of deoxyribonucleosides as thermolytic carbonates.

Carbonates↗

PubMed1976

Selection in reference to biological groups. V. Analysis of full-sib groups.

Previous studies in this series have dealt with the consequences of truncation selection operating with respect to random groups within which geno-full-sib group structure. The objective is to compare the results of individual and group selection as these methods operate on populations of random versus typic interaction may exist. The present study deal with a non-random, full-sib groups. In almost all comparisons individual selection is found to be qualitatively and quantitatively superior when used in conjunction with full-sib groups. This is due to the fact that the change in gene frequency for full-sib groups is a function of both direct and associate effects, whereas with random groups it is a function of direct effects only. With regard to group selection the efficiency is invariably superior when selection operates on non-random, full-sib rather than random groups.

Genetics, Population↗

PubMed1999

Evidence-based nephrology.

Systematic reviews and meta-analyses are the best approaches available for summarizing the available evidence concerning the efficacy of therapies. Although the renal field has been slow to use these techniques, they are being used increasingly. In March 1997, the Cochrane Renal Group was formed, and this group aims to produce and maintain up to date systematic reviews of the evidence on the effectiveness of therapies used to treat patients with renal diseases. This group is part of the Cochrane Collaboration which is an international structure grouping collaborators together, with the aim of preparing, maintaining and disseminating systematic reviews of the effects of health care in all areas of medicine.

Clinical Trials as Topic↗

PubMedDate not supplied

Human testis vitamin D binding protein involved in infertility.

Immunoglobulin G (IgG) fraction was prepared from a serum obtained from an infertile woman containing antisperm antibodies that induced head-to-head agglutination of human sperm. The antibodies in the IgG fraction interacted with a 60-kD protein found in human testes determined by Western blot. The 60-kD protein was purified from human testis by isoelectric focusing (IEF), affinity chromatography on blue sepharose column, and preparative electrophoresis with electroelution. The purified 60-kD protein migrated as a single homogeneous band when analyzed by SDS-PAGE. The amino acid sequence of the N-terminus was determined. The initial 10 amino acid residues were identical to the human serum vitamin D binding protein (VDBP). Polyclonal antibodies were raised against the 60-kD protein. The polyclonal anti-60-kD antibodies and the anti-VDBP antibodies obtained from a commercial source immobilized human sperm in vitro. The interacting antigens were located on the postacrosomal region and midpiece of human sperm, as determined by an immunofluorescence method. The IgG fraction prepared from the serum of an infertile woman interacted with the human testis 60-kD protein but failed to stain serum VDBP. The results suggest that the 60-kD and VDBP are related proteins but not identical entities and that the 60-kD protein contains a unique structural group lacking in serum VDBP. Production of antibodies against the unique structure of the 60-kD protein may be the cause of the infertility.

Antibodies↗

PubMed2004

Timing variations in music performance: musical communication, perceptual compensation, and/or motor control?

A perceptual performance paradigm was designed to disentangle the timing variations in music performance that are due to perceptual compensation, motor control, and musical communication. First, pianists perceptually adjusted the interonset intervals of three excerpts so that they sounded regular. These adjustments deviated systematically from regularity, highlighting two sources of perceptual biases in time perception: rhythmic grouping and a psychoacoustic intensity effect. Then the participants performed the excerpts on the piano in the same regular way. The intensity effect disappeared, and some variations due to motor constraints were observed in relation to rhythmic groups. Finally, the participants performed the excerpts musically. Variations due to musical communication involved additional group-final lengthening that reflected the hierarchical grouping structure of the excerpts. These results underline the nuclear role of grouping in musical time perception and production.

Adult↗

PubMed1990

Genotoxic effects observed in workers occupationally exposed to organic solvents.

The aim of this work is to analyse chromosome aberrations and cell cycle kinetics in workers occupationally exposed to organic solvents, which contain benzene among other agents. In the exposed group structural chromosome aberrations were found in 2%, while in the control group in 0.9% of analysed metaphases. Detailed band localization of breakpoints in chromosomes of patients in both groups is presented. No significant differences in cell cycle kinetics in individual members of exposed and control groups were found.

Adult↗

PubMed2005

Altered transcapillary escape of albumin and microalbuminuria reflects two different pathogenetic mechanisms.

We studied the following in normo- and microalbuminuric hypertensive type 2 diabetic patients: 1) transcapillary escape rate of albumin (TERalb) and 2) expression of mRNA slit diaphragm and podocyte proteins in renal biopsies. Normoalbuminuric subjects had renal cancer, and kidney biopsy was performed during surgery. TERalb was evaluated by clearance of (125)I-albumin. Real-time PCR of mRNA slit diaphragm was measured in kidney specimens. Albumin excretion rate (AER) was by definition lower in normoalbuminuric subjects than in microalbuminuric subjects with typical diabetic glomerulopathy (group 1), in microalbuminuric subjects with normal or near-normal glomerular structure (group 2), and in microalbuminuric subjects with atypical diabetic nephropathy (group 3). This classification was based on light microscopy analysis of renal tissue. TERalb (%/h) was similar in normoalbuminuric and microalbuminuric group 1, 2, and 3 diabetic patients (medians: 14.1 vs. 14.4 vs. 15.7 vs. 14.9, respectively) (ANOVA, NS). mRNA expression of slit diaphragm proteins CD2AP, FAT, Actn 4, NPHS1, and NPHS2 was higher in normoalbuminuric patients than in microalbuminuric patients (groups 1, 2, and 3) (ANOVA, P < 0.001). All diabetic patients had greater carotid artery intimal thickness than normal control subjects using ultrasound technique (ANOVA, P < 0.01). In conclusion, the present study suggests that microalbuminuria identifies a subgroup of hypertensive type 2 diabetic patients who have altered mRNA expression of slit diaphragm and podocyte proteins, even before glomerular structure shows abnormalities using light microscopy analysis. On the contrary, altered TERalb and increased carotid artery intimal thickness are shown by all hypertensive type 2 diabetic patients, both with normal and altered patterns of AER.

Adult↗

PubMed1994

A comparative database of group I intron structures.

We have created a database of comparatively derived group I intron secondary structure diagrams. This collection currently contains a broad sampling of phylogenetically and structurally similar and diverse structures from over 200 publicly available intron sequences. As more group I introns are sequenced and added to the database, we anticipate minor refinements in these secondary structure diagrams. These diagrams are directly accessible by computer as well as from the authors.

Base Sequence↗

PubMed2000

Structural analysis of polymer end groups by electrospray ionization high-energy collision-induced dissociation tandem mass spectrometry

Chemical structures of polymer end groups play an important role in determining the functional properties of a polymeric system. We present a mass spectrometric method for determining end group structures. Polymeric ions are produced by electrospray ionization (ESI), and they are subject to source fragmentation in the ESI interface region to produce low-mass fragment ions. A series of source-fragment ions containing various numbers of monomer units are selected for high-energy collision-induced dissociation (CID) in a sector/time-of-flight tandem mass spectrometer. It is shown that high-energy CID spectra of source-induced fragment ions are very informative for end group structure characterization. By comparing the CID spectra of fragment ions with those of known chemicals, it is possible to unambiguously identify the end group structures. The utility of this technique is illustrated for the analysis of two poly(ethylene glycol)-based slow-releasing drugs where detailed structural characterization is of significance for drug formulation, quality control, and regulatory approval. Practical issues related to the application of this method are discussed.

Journal Article↗