Using P-Stat, BMDP and SPSS for a cross-products factor analysis

The major disadvantage of the Q factor analysis with Euclidean distances described by Tanner and Koning [Comput. Progr. Biomed. 12 (1980) 201-202] is the considerable editing required. An alternative procedure with commercially distributed software, and with cross-products in place of Euclidean distances is described. This procedure does not require any editing.     

An off-line system for in-time analysis of cardiac catheterization data and for establishment of a cardiological database for retrospective studies.

The system described may be divided in two major parts: (i) automatic analysis of cardiac catheterization data running off-line on a Siemens 305 computer; (ii) storage and retrieval of the results from these analyses and additional data from related departments (thoracic surgery, internal medicine and clinical physiology) in a cardiological database on an IBM 370/155 computer. The first part is described with special regard to (i) operation and control during the phases of data collection, pre-processing, processing and storage of results; (ii) the presentation of the results in a complete and readable form and (iii) the modular design of the software. The results of an evaluation of the computer methods versus manual methods are also presented. The second part has been described with regard to the type of data entered in the cardiological database. The structure of the database and the programs used for storage and retrieval have not been described in detail in the present publication.     

An improved method for mRNA isolation and characterization of in vitro translation products by Western blotting

A method is described for isolation of messenger RNA (mRNA) from a rather intractable tissue source, calf stomach. The use of additional RNase inhibitors, vanadyl ribonucleoside complexes and proteinase K, which are used in conjunction with the guanidine thiocyanate/CsCl ultracentrifugation procedure traditionally employed for isolation of mRNA, is described. These modifications make the procedure universally applicable to a wide variety of tissues and cell types. The validity of the procedure is demonstrated by isolation of biologically active full-length preprochymosin mRNA. The integrity of the mRNA is measured by in vitro translation, Northern blot analysis, Southern blot analysis of preprochymosin cDNA using synthetic oligodeoxynucleotide probes and immunospecific identification of in vitro translation products using a modification of the Western blot which is described in this report.     

Ernest L. Eliel: a life of purpose, determination, and integrity

A concise biography of Ernest L. Eliel is presented. The highlights of Eliel's scientific achievements are described, beginning with his Ph.D. thesis research performed under the supervision of Professor Harold Snyder (University of Illinois) and continuing as a faculty member at Notre Dame (synthesis of nonracemic C(6)H(5)CHDCH(3); kinetic method of conformational analysis; equilibrium and NMR methods of conformational analysis); and at the University of North Carolina (conformational analysis of heterocyclic compounds; enantioselective synthesis). Eliel's professional career as a teacher, textbook author, and major figure in the American Chemical Society are discussed. His philosophies of life, science, and chemistry are described by a series of poignant quotations.     

Systematic position of the enigmatic African cycad moths: an integrative approach to a nearly century old problem (Lepidoptera: Geometridae,Diptychini)

The systematic position and hierarchical level of the moth taxon Diptychini Janse (Lepidoptera: Geometridae), the cycad moths, has remained controversial. This is partly due to their unique morphological and biological characteristics. To study the systematics, comprehensive molecular analyses of eight genes, in total 6157 bp, were carried out. We used Bayesian inference to construct phylogenetic trees. The first analysis (46 Geometridae and 7 non‐Geometridae taxa, representing all recently recognised Geometridae subfamilies) demonstrated that the Diptychini belong to the Geometridae subfamily Ennominae. The second analysis, focused on the Ennominae (70 taxa, representing 28 of 30 recently recognised Ennominae tribes worldwide), found that the Diptychini are nested well within the Ennominae; it is monophyletic and associated with the complex of southern Hemisphere Nacophorini, refuting many of the earlier hypotheses about Diptychini relationships. The Diptychini are considered tentatively valid at the tribe level, but relationships with the Nacophorini and the Lithinini need further research. The molecular findings were evaluated from a morphological point of view, which are mostly in agreement with the molecular results. The Diptychini genera are illustrated and characterised using morphological and life‐history traits. Within the Diptychini, three genera are considered valid. Durbana Warren (described in 1904) is proposed as a junior synonym of Veniliodes Warren (described in 1894) ( n.syn. ). Monotypic Larentioides Prout is combined with the tribe Lithinini ( n.comb .). Homonymy of Diptychini Mirza (described in 1991) (Pisces: Cyprinidae, Schizothoracinae) with Diptychini Janse (described in 1933) (Lepidoptera: Geometridae, Ennominae) is noted, the former requiring a replacement name.     

Simultaneous analysis of multiple fluorescence decay curves by Laplace transforms. Deconvolution with reference or excitation profiles

The properties and potentials of the noniterative Laplace deconvolution (LAP2) (M. Ameloot and H. Hendrickx, Biophys. J. 44 (1983) 27) are further investigated. It is shown that LAP2 is exact and that no extrapolations have to be calculated or assumed for the data measured in the actual time window if the impulse response function of the investigated system can be described by a sum of exponentials. The formulas for the LAP2 deconvolution against the measured decay of a reference compound instead of the recorded excitation profile are derived. The procedure for the simultaneous analysis of multiple fluorescence decay curves by LAP2 is described in detail. This global analysis allows one to link any decay parameter, is fast and compares favorably with the nonlinear least-squares iterative reconvolution methods. Because of its short computation time the global analysis by LAP2 provides an efficient way to analyze the fluorescence decay surface in terms of decay associated spectra.     

Characterization and determination of neuropeptides by high-performance liquid chromatography and radioimmunoassay

A method is described for the separation and analysis of a variety of neuropeptides using reversed-phase high-performance liquid chromatography coupled with radioimmunoassay. The solvent system (an acetonitrile gradient containing 0.08% trifluoroacetic acid) allows UV detection at 206 nm, gives good resolution and, by being volatile, is readily compatible with radioimmunoassay. Three applications of the method are described: (a) thyrotropin releasing hormone immunoreactivity in the rat brain has been characterized; (b) ACTH immunoreactivity in the rat pituitary pars intermedia has been resolved into its component peptides; (c) degradation of luteinizing hormone releasing hormone in vitro has been followed.     

Micromethod of ultracentrifugation in cesium chloride]

The micromethod of ultracentrifugation in cesium chloride is described. Band destributions have been analysed by the direct scanning of microtubes with the differential doublewave micro-spectrophotometer at 260 nm. The 10(-8)-10(-9) g of DNA or ribosomes are enough for one analysis, tube volume is 2 mul. The method described permits the simultaneous centrifugation of several probe scores. The error of the beyoant density determination is 0.001 g/sm3 relatively internal standard. DNA's from 5 types of Acetabularia were analysed by the developed technique.     

Programming for the DNA analysis of FCM data on an IBM microcomputer

The analysis of data generated on a flow cytometer (FCM) is often performed on a computer obtained especially for dedicated use with the flow cytometer. This computer component can be expensive and also presents the FCM user with the added burden of mastering specialized programming language or of accepting the secret analytical processes of protected proprietary program routines. We believe that the evolution of more accurate and efficient FCM analyses that have the power to consider complex signal distributions can be assisted by the availability of analysis programs written in languages common to many users. DNA analysis routines written for a relatively inexpensive microcomputer (IBM PC/XT) in Basic and Pascal are described here. The routines can automatically process multiple FCM data files and can provide high-resolution graphic hardcopy. A foreground/background utilization is also described that allows the computer to be available for other uses in the laboratory.     

Determination of asparagine and glutamine in polypeptides using bis(I,I-trifluoroacetoxy)iodobenzene

A simple yet accurate method is described by which the numbers of asparagine and glutamine residues in polypeptides can be determined. The method involves difference analysis of the aspartic acid and glutamic acid contents of the polypeptide after acid hydrolysis (in 6 n HCl), without and with prior treatment of the sample with bis(I,I-trifluoroacetoxy)iodobenzene. Under the conditions described, this reagent quantitatively converts the carboxamide residues to the corresponding amines, which are eluted near (and interfere with the estimation of) the lysine peak on conventional ion-exchange amino acid analysis. During the carboxamide conversion, certain amino acid residues sensitive to oxidation are partially or completely destroyed and cannot be accurately determined.     

An ion-exchange chromatography procedure for the isolation and concentration of basic amino acids and polyamines from complex biological samples prior to high-performance liquid chromatography.

The original objective of this study was to develop a selective and sensitive method for the analysis and quantification of basic amino acids from biological samples via reversed-phase high-performance liquid chromatography. Using various previously described techniques for the separation of amino acids, we were unsuccessful in measuring levels of histidine, arginine, ornithine, and lysine in biological samples due to the presence of interfering compounds. A "cleanup" procedure for the isolation of the basic amino acids using a weakly acidic cation exchange resin, Biorex-70 (Bio-Rad), is described in detail. Upon separation from the bulk of the neutral and acidic amino acids, the basic amino acids were subjected to precolumn fluorescence derivatization using 9-fluorenylmethyl chloroformate (FMOC) and the fluorescent derivatives were separated by RP-HPLC. The advantages of this method over previously described amino acid analysis techniques are (i) isolation and stable recovery (greater than 95%) of the desired basic amino acids, (ii) sensitivity of detection (low pmol range), (iii) complete resolution of derivatized amino acids via HPLC, (iv) limited amount of sample required for analysis, and (v) samples readily concentrated by lyophilization or rotoevaporating. This ion-exchange cleanup procedure was also adapted for the analysis of polyamines in concentrated culture media samples and proved additionally advantageous by eliminating the use of costly C-18 extraction columns required by previously described techniques.     

Analysis of ellagitannins and conjugates of ellagic acid and quercetin in raspberry fruits by LC-MSn

The use of gradient reversed phase HPLC with diode array and MS(n) detection for the analysis of ellagitannins, ellagic acid conjugates and quercetin conjugates in raspberries (Rubus idaeus L.) is described. MS(n) is a particularly powerful tool for the analysis of trace levels of natural products in impure extracts as interpretation of fragmentation patterns, coupled in some instances with knowledge of HPLC retention properties, can facilitate the partial identification of components when reference compounds are unavailable.     

Fluorescent Pseudomonas species categorized by using polymerase chain reaction (PCR)/restriction fragment analysis of 16S rDNA

A rapid procedure for the identification of fluorescent pseudomonads, based on the polymerase chain reaction (PCR) and restriction fragment analysis of 16S rDNA genes is described. Thirty-one strains belonging to 10 different Pseudomonas species of the Pseudomonas fluorescens rRNA branch were characterized. Amplified rDNA was digested with 13 different restriction endonucleases. The combined data from restriction analysis enabled the definition of 17 different 16S rDNA genotypes. All type strains belonging to different species were differentiated. The good correlation between grouping obtained using restriction analysis with other molecular classification criteria demonstrates the value of the described method to characterize rapidly fluorescent Pseudomonas strains at the species level.     

Root-specific expression of a Zea mays gene encoding a novel glycine-rich protein,zmGRP3

The isolation and characterization of a cDNA clone from Zea mays coding for a novel glycine-rich protein (GRP) is described. The corresponding 1.4 kb mRNA accumulates exclusively in roots (primary, lateral seminal and crown roots) of young maize seedlings, following developmentally specific patterns. In agreement with previously described GRPs from other plant species the derived protein sequence exhibits a hydrophobic domain at the N-terminal region followed by repeated glycine-rich motifs. Genomic Southern analysis indicates that the zmGRP3 gene is present in the maize genome as one or two copies or at a low copy number.     

Plant communities in broad-leaved deciduous forests in Hordaland county, Western Norway

The vegetation of broad-leaved deciduous forests in Hordaland, Western Norway is described with regards to species composition and structure. The investigation is based on phytosociological analyses of native forest stands dominated by Corylus avellana, Fraxinus excelsior, Ulmus glabra , or Tilia cordata. Two-way-indicator analysis (TWINSPAN) and correspondence analysis (CA) are used to distinguish different vegetation types and assess possible gradients in the vegetation data. The vegetation types are discussed in relation to equivalent forest communities and to syntaxonomical units. Two forest types are described at the first hierarchical TWINSPAN level: 1) A hygrophilous and slightly thermophilous Fraxinus excelsior-Cirriphyllum piliferum forest characterised by an open tree canopy, a dense field layer of tall herbs and ferns, and a high cover of bryophytes. 2) A thermophilous and less hygrophilous Corylus avellana-Brachypodium sylvaticum forest characterised by a dense tree layer, a more open field layer with larger elements of small herbs, and a somewhat lower bryophyte cover. The CA analysis clearly separates the samples from the first TWINSPAN division along the first ordination axis. Five forest types have been described at the second hierarchical level, mainly associated with differences in mesotrophic and eutrophic species, but there is clearly a gradient structure in the species composition between these plant communities. In relation to syntaxonomy, the first TWINSPAN division supports the separation of the west Norwegian broad-leaved deciduous forests into a hygrophilous plant community, the Eurhynchio-Fraxinetum (Blom 1982) Øvstedal 1985 and a drier and more thermophilous community, the Primulo-Ulmetum (Blom 1982) Øvstedal 1985.     

Multivariate data analysis in empirical research. A look on the bright side

The interpretive benefits of employing multivariate analysis methods on experimental data with more than one dependent variable are described heuristically and illustrated on a set of data from a simply designed experiment in physiological psychology. Multivariate analysis of variance (MANOVA) is performed on the 9 dependent variables contained in the sample data and on the four composites derived from a principal components analysis (PCA) of the variability of the nine. A linear discriminant analysis (LDA) is conducted following both MANOVA results, and 5 methods of determining the "important" dependent variables in the experimental-control group difference are presented and discussed in terms of the data at hand.     

Reaction of tobacco mosaic virus with a thiol-containing imidoester and a possible application to X-ray diffraction analysis

The synthesis of the imidoester methyl 3-mercaptopropionimidate is described; this reacts selectively with the amino groups of proteins. It is intended that the additional thiol groups thereby introduced should serve as points of attachment for heavy atoms and allow the preparation of isomorphous derivatives (at chemically identifiable sites) for X-ray diffraction analysis. Specific reaction of the imidoester with one of the two lysine residues of the protein subunit of intact tobacco mosaic virus is described.     

HPLC quantification of uncarine D and the anti-plasmodial activity of alkaloids from leaves of Mitragyna inermis (Willd.) O. Kuntze

An efficient system for the analysis of the total alkaloids extracted from leaves of Mitragyna inermis (Willd.) O. Kuntze (Rubiaceae) by HPLC using a reversed-phase column is described. The chromatographic conditions allowed the separation of indole and oxindole alkaloids in leaf extracts, and the quantification of uncarine D in samples collected in Burkina Faso and Mali. The HPLC method described was validated for its specificity, linearity and precision using an internal standard (naphthalene). The concentrations of uncarine D in various extracts were compared with their in vitro anti-plasmodial activity. The anti-proliferative activity on chloroquine-resistant strain (W2) of Plasmodium falciparum was not correlated with the concentration of uncarine D in leaves.     

Simple protocols for NMR analysis of the enantiomeric purity of chiral diols

A three-component chiral derivatization protocol for determining the enantiopurity of chiral diols by (1)H NMR spectroscopic analysis is described here. The present approach involves the derivatization of 1,2- 1,3- and 1,4-diols with 2-formylphenylboronic acid and enantiopure alpha-methylbenzylamine. This method affords a mixture of diastereoisomeric iminoboronate esters whose ratio can be determined by integration of well-resolved diastereotopic resonances in their (1)H NMR spectra, thus enabling the determination of the enantiopurity of the parent diol. The protocol as described takes less than 90 min to complete.     

Characterization of loaded liposomes by size exclusion chromatography

This review focuses on the use of conventional (SEC) and high performance (HPSEC) size exclusion chromatography for the analysis of liposomes. The suitability of both techniques is examined regarding the field of liposome applications. The potentiality of conventional SEC is strongly improved by using a HPLC system associated to gel columns with a size selectivity range allowing liposome characterization in addition to particle fractionation. Practical aspects of size exclusion chromatography are described and a methodology based on HPSEC coupled to multidetection modes for on-line analysis of liposomes via label or substance encapsulation is presented. Examples of conventional SEC and HPSEC applications are described which concern polydispersity, size and encapsulation stability, bilayer permeabilization, liposome formation and reconstitution, incorporation of amphiphilic molecules. Size exclusion chromatography is a simple and powerful technique for investigation of encapsulation, insertion/interaction of substances from small solutes (ions, surfactants, drugs, etc.) up to large molecules (proteins, peptides and nucleic acids) in liposomes.