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PubMedDate not supplied

The automated analysis of rat sperm motility following subchronic epichlorohydrin administration: methodologic and statistical considerations.

The automated analysis of sperm motion endpoints is potentially useful in identifying male reproductive toxicants and ultimately in predicting fertility in humans. The present study was designed to evaluate the automated analysis of rat sperm motility characteristics following subchronic administration of epichlorohydrin. This type of validation is a prerequisite for inclusion of sperm motion measurements in the process of reproductive risk assessment. In the present studies videotapes were made of cauda epididymal spermatozoa from Long-Evans rats, both untreated and treated with epichlorohydrin. From analysis of videotapes of control epididymal spermatozoa, the relationship of various sperm motion endpoints and settings of the CellSoft computer-assisted sperm motion analysis system (Cryo Resources, Ltd., New York, NY) is described. Optimal settings of the system for analysis of rat spermatozoa are detailed. Employing data from both control and epichlorohydrin-treated animals, a statistical methodology is described that evaluates: (1) the distributions of CellSoft generated sperm motion endpoints, (2) the correlations between these endpoints, and (3) techniques for detection of dose-related effects.

Animals↗
PubMed2005

Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics.

MOTIVATION: The key to MS -based proteomics is peptide sequencing. The major challenge in peptide sequencing, whether library search or de novo, is to better infer statistical significance and better attain noise reduction. Since the noise in a spectrum depends on experimental conditions, the instrument used and many other factors, it cannot be predicted even if the peptide sequence is known. The characteristics of the noise can only be uncovered once a spectrum is given. We wish to overcome such issues. RESULTS: We designed RAId to identify peptides from their associated tandem mass spectrometry data. RAId performs a novel de novo sequencing followed by a search in a peptide library that we created. Through de novo sequencing, we establish the spectrum-specific background score statistics for the library search. When the database search fails to return significant hits, the top-ranking de novo sequences become potential candidates for new peptides that are not yet in the database. The use of spectrum-specific background statistics seems to enable RAId to perform well even when the spectral quality is marginal. Other important features of RAId include its potential in de novo sequencing alone and the ease of incorporating post-translational modifications.

Algorithms↗
PubMed1990

Randomization, statistics, and causal inference.

This paper reviews the role of statistics in causal inference. Special attention is given to the need for randomization to justify causal inferences from conventional statistics, and the need for random sampling to justify descriptive inferences. In most epidemiologic studies, randomization and random sampling play little or no role in the assembly of study cohorts. I therefore conclude that probabilistic interpretations of conventional statistics are rarely justified, and that such interpretations may encourage misinterpretation of nonrandomized studies. Possible remedies for this problem include deemphasizing inferential statistics in favor of data descriptors, and adopting statistical techniques based on more realistic probability models than those in common use.

Bayes Theorem↗
PubMed1996

Method development in liquid chromatography with a charged cyclodextrin additive for chiral resolution of rac-amlodipine utilising a central composite design.

A negatively charged derivative of beta-cyclodextrin, sulphobutyl ether-beta-cyclodextrin (SBE-beta-CD), was examined as a chiral mobile phase additive in reversed-phase high-performance liquid chromatography for the enantiomeric resolution of the calcium channel blocker rac-amlodipine. Theoretical and practical aspects are discussed for setting up a central composite design applicable to any analytical method. These include the correct location of factor points for maintaining orthogonality within the design and the augmentation of centrepoint experiments to allow a larger factor space by increasing the distance of axial star points. Optimised separation was achieved using a reverse-phase column with eluent comprising: acetonitrile (ACN)-potassium dihydrogen phosphate (pH 3.93) containing 2.66 mM SBE-beta-CD (26.5:73.5% v/v) at a flow rate of 1.0 ml/min. This yielded a Kaiser peak separation index, Pi = 0.96, at tR2 = 52 min with satisfactory reproducibility, relative standard deviation values: tR1, 0.39%; tR2, 0.47% (n = 5). These experimental results were in excellent agreement with those predicted by the SAS software package for a chromatographic response function model. Multiple regression analysis in four dimensions, with three response models based on Rs, Pi, and a function of Pi, produced response surfaces which revealed zones of optimum robustness and illustrated the interactions involved between the key chromatographic factors. Putative proposals for a mechanism involving the interaction of each of the positively charged enantiomers with the negatively charged cyclodextrin are also discussed. These examine the possibility of ion-pairing and inclusion phenomena to account for the excellent resolution observed.

Amlodipine↗
PubMed1995

NGF binding to the trk tyrosine kinase receptor requires the extracellular immunoglobulin-like domains.

Neurotrophins initiate their biological effects by activating members of the trk tyrosine kinase subfamily. The extracellular region of trk receptors is distinguished by several common structural features, including leucine-rich repeats, clusters of cysteine-rich domains, and two immunoglobulin-like domains. However, the receptor sequences required for ligand binding have not been localized. In order to define the domains involved in NGF binding, a series of chimeric receptors was constructed using cDNA sequences from rat trkA and trkB. The chimeric constructs were expressed after transient transfection in 293 cells and the expression of each receptor was verified by immunoprecipitation and immunoblot analysis. Equilibrium binding of transfected cells revealed that the two IgG domains of trkA are essential for NGF binding. The requirement for the two IgG domains was further confirmed by Scatchard analysis and affinity crosslinking with 125I-NGF. These results indicate that NGF binding is crucially dependent upon interactions with the IgG domains of the trkA receptor.

Base Sequence↗
PubMed1999

A method for evaluating phylogenetic relationship of alpha-satellite DNA suprachromosomal family by nucleotide frequency calculation.

The sequence similarity among chromosome-specific alpha-satellite DNA was quantitatively evaluated by a novel procedure: nucleotide frequency calculation. Tandem-arrayed repetitive DNA segments were aligned with unit length repeat, and the nucleotide frequency at each position was used to estimate the phylogenetic distance between repetitive DNA segments. The calculations for human and chimpanzee X chromosome alpha-satellites showed that the results were consistent with the known relationships of primates, indicating that the nucleotide frequency calculation worked effectively to estimate the distances between satellite arrays. Human chromosome-specific alpha-satellites had been grouped into three suprachromosomal families (I, II, and III), and in the current work the nucleotide frequency analysis has defined the quantitative distances between the chromosome-specific alpha-satellite DNA.

Animals↗
PubMed1996

Sequential assignments in uniformly 13C- and 15N-labelled RNAs: the HC(N,P) and HC(N,P)-CCH-TOCSY experiments.

An approach for the simultaneous acquisition of HCN and HCP as well as HCN-CCH-TOCSY and HCP-CCH-TOCSY triple resonance data sets for 13C-/15N-labelled RNAs is presented. The new HCN-CCH-TOCSY scheme unambiguously links all sugar resonances to the base nitrogen. In addition, simultaneous acquisition of HCN-CCH-TOCSY and HCP-CCH-TOCSY data sets provides sequential and base-type information in a single experiment, thereby saving data acquisition time as well as providing complementary data sets that are useful in clarifying ambiguous assignments. Virtually complete sequence-specific phosphate-ribose 1H, 31P, and base 15N1,9, assignments as well as partial 13C assignments could be obtained in a single experiment for a 0.5-mM sample of a 19-mer ribonucleotide.

Base Sequence↗
PubMed1991

Multivariate data analysis of NMR data.

Multivariate methods based on principal components (PCA and PLS) have been used to reduce NMR spectral information, to predict NMR parameters of complicated structures, and to relate shift data sets to dependent descriptors of biological significance. Noise reduction and elimination of instrumental artifacts are easily performed on 2D NMR data. Configurational classification of triterpenes and shift predictions in disubstituted benzenes can be obtained using PCA and PLS analysis. Finally, the shift predictions of tripeptides from descriptors of amino acids open the possibility of automatic analysis of multidimensional data of complex structures.

Amino Acid Sequence↗
PubMed2000

Frequency and markov chain analysis of amino-acid sequences of human tumour necrosis factor.

The amino-acid sequence of human tumour necrosis factor was measured according to two- and three-amino-acid sequences. The measured frequency and probability were compared with predicted frequency and probability. Of 232 two-amino-acid sequences in human tumour necrosis factor, 64 (27.586%) and 24 (10.345%) sequences can be explained by the predicted frequency and the predicted probability according to a purely random mechanism. Of 243 non-appeared two-amino-acid sequences in human tumour necrosis factor, 176 (72. 428%) and 42 (17.284%) sequences can be explained by the predicted frequency and the predicted probability according to a purely random mechanism. No measured Markov transition probability matches the predicted conditional probability. No more-than-two-amino-acid sequences can be explained by a purely random mechanism.

Amino Acid Sequence↗
PubMed2003

Palindromes in proteins.

Palindromes in DNA consist of nucleotides sequences that read the same from the 5'-end to the 3'-end, and its double helix is related by twofold axis. They occur in genomes of all organisms and have various functions. For example, restriction enzymes often recognize palindromic sequences of DNA. Palindromes in telomeres are crucial for initiation of replication. One can ask the questions, Do palindromes occur in protein, and if so, what function they play? We have searched the protein SWISSPROT database for palindromic sequences. A great number (26%) of different protein palindromes were found. One example of such protein is systemin, an 18-amino-acid-long peptide. It contains palindrome in its beta-sheet domain that interacts with palindromic fragment of DNA. The other palindrome containing protein is cellular human tumor suppressor p53. Oligonucleotide LTI-ITL has been observed in the crystal structure and is located close to a DNA recognizing domain. As the number of possible palindromic sequences of a given length is far much greater for proteins (20N) than for nucleic acids (4N), the study on their role seems to be an exciting challenge. Our results have clearly showed that palindromes are frequently occurring motives in proteins. Moreover, even very few examples that we have examined so far indicate the importance of further studies on protein palindromes.

Amino Acid Sequence↗
PubMed2005

Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards.

Partitioned Bayesian analyses of approximately 2.2 kb of nucleotide sequence data (mtDNA) were used to elucidate phylogenetic relationships among 30 scincid lizard genera. Few partitioned Bayesian analyses exist in the literature, resulting in a lack of methods to determine the appropriate number of and identity of partitions. Thus, a criterion, based on the Bayes factor, for selecting among competing partitioning strategies is proposed and tested. Improvements in both mean -lnL and estimated posterior probabilities were observed when specific models and parameter estimates were assumed for partitions of the total data set. This result is expected given that the 95% credible intervals of model parameter estimates for numerous partitions do not overlap and it reveals that different data partitions may evolve quite differently. We further demonstrate that how one partitions the data (by gene, codon position, etc.) is shown to be a greater concern than simply the overall number of partitions. Using the criterion of the 2 ln Bayes factor > 10, the phylogenetic analysis employing the largest number of partitions was decisively better than all other strategies. Strategies that partitioned the ND1 gene by codon position performed better than other partition strategies, regardless of the overall number of partitions. Scincidae, Acontinae, Lygosominae, east Asian and North American "Eumeces" + Neoseps; North African Eumeces, Scincus, and Scincopus, and a large group primarily from sub-Saharan Africa, Madagascar, and neighboring islands are monophyletic. Feylinia, a limbless group of previously uncertain relationships, is nested within a "scincine" clade from sub-Saharan Africa. We reject the hypothesis that the nearly limbless dibamids are derived from within the Scincidae, but cannot reject the hypothesis that they represent the sister taxon to skinks. Amphiglossus, Chalcides, the acontines Acontias and Typhlosaurus, and Scincinae are paraphyletic. The globally widespread "Eumeces" is polyphyletic and we make necessary taxonomic changes.

Animals↗
PubMed2004

Application of a new probabilistic model for recognizing complex patterns in glycans.

MOTIVATION: The study of carbohydrate sugar chains, or glycans, has been one of slow progress mainly due to the difficulty in establishing standard methods for analyzing their structures and biosynthesis. Glycans are generally tree structures that are more complex than linear DNA or protein sequences, and evidence shows that patterns in glycans may be present that spread across siblings and into further regions that are not limited by the edges in the actual tree structure itself. Current models were not able to capture such patterns. RESULTS: We have applied a new probabilistic model, called probabilistic sibling-dependent tree Markov model (PSTMM), which is able to inherently capture such complex patterns of glycans. Not only is the ability to capture such patterns important in itself, but this also implies that PSTMM is capable of performing multiple tree structure alignments efficiently. We prove through experimentation on actual glycan data that this new model is extremely useful for gaining insight into the hidden, complex patterns of glycans, which are so crucial for the development and functioning of higher level organisms. Furthermore, we also show that this model can be additionally utilized as an innovative approach to multiple tree alignment, which has not been applied to glycan chains before. This extension on the usage of PSTMM may be a major step forward for not only the structural analysis of glycans, but it may consequently prove useful for discovering clues into their function.

Algorithms↗
PubMed1998

New tools and resources for analysing protein structures and their interactions.

The determination of protein structures has furthered our understanding of how various proteins perform their functions. With the large number of structures currently available in the PDB, it is necessary to be able to easily study these proteins in detail. Here new software tools are presented which aim to facilitate this analysis; these include the PDBsum WWW site which provides a summary description of all PDB entries, the programs TOPS and NUCPLOT to plot schematic diagrams representing protein topology and DNA-binding interactions, SAS a WWW-based sequence-analysis tool incorporating structural data, and WWW servers for the analysis of protein-protein interfaces and analyses of over 300 haem-binding proteins.

Amino Acid Sequence↗
PubMedDate not supplied

A milestone in ribosomal crystallography: the construction of preliminary electron density maps at intermediate resolution.

Preliminary electron density maps of the large and the small ribosomal particles from halophilic and thermophilic sources, phased by the isomorphous replacement method, have been constructed at intermediate resolution. These maps contain features comparable in size with what is expected for the corresponding particles, and their packing arrangements are in accord with the schemes obtained by ab-initio procedures as well as with the motifs observed in thin sections of the crystals by electron microscopy. To phase higher resolution data, procedures are being developed for derivatization by specific labeling of the ribosomal particles at selected locations with rather small and dense clusters. Potential binding sites are being inserted either by site directed mutagenesis or by chemical modifications to facilitate cluster binding on the surface of the halophilic large and the thermophilic small ribosomal particles, which yield the crystals diffracting to highest resolution (2.9 and 7.3 A (1 A = 0.1 nm), respectively). For this purpose, the surface of these ribosomal particles is being characterized and procedures are being developed for quantitative detachment of selected ribosomal proteins and for their incorporation into core particles. The genes of these proteins are being cloned, sequenced, mutated to introduce reactive side groups, mainly cysteines, and overexpressed. In parallel, two in situ small and stable complexes were isolated from the halophilic ribosome. Procedures for their crystal production in large quantities are currently being developed. Models, reconstructed at low resolution from crystalline arrays of ribosomes and their large subunits, are being used for initial low-resolution phasing of the X-ray amplitudes. The interpretation of these models stimulated the design and the crystallization of complexes mimicking defined functional states of a higher quality than those obtained for isolated ribosomes. These models also inspired modelling experiments according to results of functional studies, performed elsewhere, focusing on the progression of nascent proteins.

Base Sequence↗