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PubMed2004

Direct optical resolution of the enantiomers of novel chiral tetrahedral metal clusters by HPLC on a cellulose tris-(3,5-dimethylphenylcarbamate) stationary phase.

The enantioseparation of seven novel chiral transition metal tetrahedral clusters has been achieved for the first time on cellulose derivatized with tris(3,5-dimethylphenylcarbamate) (CDMPC) as chiral stationary phase (CSP) and hexane containing different alcohols as modifiers as mobile phases. The effect of mobile-phase composition on enantioselectivity was studied, and the effect of structural variation of the solutes on their enantioseparation was also investigated. It was found that both the metal in the tetrahedral core and the ligand coordinated to the atom in the tetrahedral core had significant effects on the chromatographic behavior of the analytes.

Alcohols↗
PubMed2001

Structural changes induced by antineoplastic therapies: keys to evaluate tumor response to treatment.

The criteria to define therapeutic response in oncology are those proposed by Miller, characterized by four response categories (complete response, partial response, no change, progression of disease), and based upon both measurable and non-measurable (and otherwise assessable) morphological parameters in comparison with baseline and subsequently modified following the Response Evaluation Criteria In Solid Tumors. In addition to these classical morphological criteria, we review the predictive value of structural changes in the evaluation of response to antineoplastic therapies. The goal of the present review is to evaluate in detail structural variations (calcification, fibrosis, differentiation, necrosis, cavitation, vascularization, edema, and pseudocapsule formation) induced by therapy, and to ascertain their significance in terms of biological evolution of the neoplastic process.

Calcinosis↗
PubMed1997

ACTBP2 gene frequency distribution and sequencing of the allelic ladder and variants in the Japanese and Chinese populations.

The human beta-actin related pseudogene H-beta-Ac-psi-2 (ACTBP2) gene frequency distributions in the Japanese and Chinese Han populations were investigated and compared. Analysis was carried out by applying fluorescently labeled samples and a differently labeled sequenced allelic ladder within the same lanes in denaturing gels, followed by laser detection and automated analysis using Genescan software 672. The discrimination index and the heterozygosity index were calculated to be 0.993 and 0.916 in the Japanese population, and 0.993 and 0.944 in the Chinese Han population, respectively. No deviation from Hardy-Weinberg equilibrium was observed in these two populations. The allelic ladder, which ranged from 233 bp to 319 bp, was constructed from a combination of 23 regularly occurring alleles. The allelic ladder and 12 variants observed in 24 individuals in these two populations were sequenced. The variants could be divided into three types according to their structural variation characteristics. These variants differed from the alleles of the same repeats in the allelic ladder by the presence or absence of hexanucleotides in the central repeat regions, base deletions in the flanking regions, and base insertions in the repeat units.

Actins↗
PubMed1999

Sertoli and Leydig cells of the human testis express neurofilament triplet proteins.

Using RT-PCR, western blot and enzyme and fluorescence immunocytochemical techniques, the three isoforms of neurofilament proteins (NFPs), namely NF-L (NFP-68 kDa), NF-M (NFP-160 kDa) and NF-H (NFP-200 kDa) were found in Sertoli and Leydig cells of human testes. RT-PCR showed specific for the three NFP fragments in testicular tissue, in isolated seminiferous tubules and in isolated Leydig cells. In protein preparations from the same testicular components, western blot analysis detected bands with molecular weights characteristic for NF-H, NF-M and NF-L. Application of immunofluorescence and immunoenzyme methods on cryostat and paraffin sections resulted in differences in the staining pattern in Sertoli cells and Leydig cells. In these cells, the NFPs showed predominantly a perinuclear location from which bundles emerge that were directed towards the basal, apical and lateral extensions of the Sertoli cells as well as the periphery of Leydig cells. NF-H coexists with vimentin-type filaments as seen by dual staining and staining of consecutive serial sections of material embedded in paraffin. In Sertoli cells, vimentin and NF-H showed distinct dynamic changes depending on the stage of spermatogenesis and some structural variations of seminiferous tubules. Although in some tubules both vimentin and NF-H immunoreactivity was present at high levels, in the Sertoli cells from most individuals an inverse relationship in the staining intensity of vimentin and NF-H was observed. The strongest NF-H immunoreactivity was detected in Sertoli cells associated with stage 3 spermatids, whereas vimentin immunoreactivity was most abundant in association with stage 5 spermatids. The leydig cells did not show functional changes of the NFP immunoreactivity. The results obtained provide new evidence for the heterogeneous phenotype of human Sertoli cells and raise the question of their exact nature and origin.

Aged↗
PubMed2003

Tandem duplication of alkaline phosphatase genes and polymorphism in the intergenic sequence in Bombyx mori.

Alkaline phosphatases are ubiquitous in organisms from bacteria to human. Two alkaline phosphatase genes, Alp-m and Alp-s, were independently cloned from the silkworm Bombyx mori. They were mapped to a small DNA region and shown to be organized in tandem. Exon-intron structures of the two genes were highly conserved, with the exception of the second intron in Alp-m, which has no counterpart in Alp-s. The similarity between the nucleotide sequences of the exons of the two genes was strikingly high (60-79%), suggesting that Alp-m and Alp-s originated from a duplication of their common ancestor gene. The intergenic sequence between the two Alp genes shows length polymorphism in different B. mori strains, which can be explained by presence/absence of two putative insertion sequences. This structural variation suggests a possible scenario for the divergence of the two Alp genes after the duplication event.

Alkaline Phosphatase↗
PubMed2006

Spatio-temporal modelling and assessment of within-species phenological variability using thermal time methods.

Phenological observations of flowering date, budding date or senescence provide very valuable time series. They hold out the prospect for relating plant growth to environmental and climatic factors and hence for engendering a better understanding of plant physiology under natural conditions. The statistical establishment of associations between time series of phenological data and climatic factors provides a means of aiding forecasts of the biological impacts of future climatic change. However, it must be kept in mind that plant growth and behaviour vary spatially as well as temporally. Environmental, climatic and genetic diversity can give rise to spatially structured variation on a range of scales. The variations extend from large-scale geographical (clinal) trends, through medium-scale population and sub-population fluctuations, to micro-scale differentiation among neighbouring plants, where spatially close individuals are found to be genetically more alike than those some distance apart. We developed spatio-temporal phenological models that allow observations from multiple locations to be analysed simultaneously. We applied the models to the first-flowering dates of Prunus padus and Tilia cordata from localities as far apart as Norway and the Caucasus. Our growing-degree-day approach yielded a good fit to the available phenological data and yet involved only a small number of model parameters. It indicated that plants should display different sensitivities to temperature change according to their geographical location and the time of year at which they flower. For spring-flowering plants, we found strong temperature sensitivities for islands and archipelagos with oceanic climates, and low sensitivities in the interiors of continents.

Climate↗
PubMed2001

Human arylhydrocarbon receptor repressor (AHRR) gene: genomic structure and analysis of polymorphism in endometriosis.

The diversity of biological effects resulting from exposure to dioxin may reflect the ability of this environmental pollutant to alter gene expression by binding to the arylhydrocarbon receptor (AHR) gene and related genes. AHR function may be regulated by structural variations in AHR itself, in the AHR repressor (AHRR), in the AHR nuclear translocator (ARNT), or in AHR target molecules such as cytochrome P-4501A1 (CYP1A1) and glutathione S-transferase. Analysis of the genomic organization of AHRR revealed an open reading frame consisting of a 2094-bp mRNA encoded by ten exons. We found one novel polymorphism, a substitution of Ala by Pro at codon 185 (GCC to CCC), in exon 5 of the AHRR gene; among 108 healthy unrelated Japanese women, genotypes Ala/Ala, Ala/Pro, and Pro/Pro were represented, respectively, by 20 (18.5%), 49 (45.4%), and 39 (36.1%) individuals. We did not detect previously published polymorphisms of ARNT (D511N) or the CYP1A1 promoter (G-469A and C-459T) in our subjects, suggesting that these polymorphisms are rare in the Japanese population. No association was found between uterine endometriosis and any polymorphisms in the AHRR, AHR, ARNT, or CYP1A1 genes analyzed in the present study.

Aryl Hydrocarbon Receptor Nuclear Translocator↗
PubMed2005

Antibodies as drug carriers III: design of oligonucleotides with enhanced binding affinity for immunoglobulin G.

PURPOSE: To understand the structural requirements in designing epitope-bearing oligonucleotides with high antibody-binding affinity. METHODS: Binding affinity (KA) and stoichiometry (n) of dinitrophenyl (DNP)-derivatized model 27-mer oligonucleotides (ODNs), GGG(AAA)7GGG, to monoclonal anti-trinitrophenyl (TNP) antibodies were determined using isothermal titration calorimetry (ITC). Structural variations were made in the ODNs to assess the effects of antigenic valence, epitope density, inter-epitope linker length, and linker flexibility. Binding isotherms were fitted with a single binding-site model to obtain K(A) and n, from which changes in Gibbs free energy (deltaG(0)), entropy (deltaS(0)), and enthalpy (deltaH(0)) were derived. RESULTS: As expected, ligands displaying increased epitope density showed increases in K(A): for example, K(A) for (DNP)2-Cys is 3.3-fold greater than that for DNP-Lys. Introduction of multiple DNP groups via long and flexible linkers to one end of the 27-mer ODN resulted in a bivalent behavior with n value of 1. A bivalent ligand, derivatized at both ends with a long and flexible linker, failed to form an immune complex when hybridized to its antisense strand, presumably due to intercalation of the DNP moiety to the double strand. ODNs derivatized with flexible linkers exhibited a higher K(A) than those with a rigid linker. Ligands with flexible inter-epitope linkers measuring distances of 110, 60, and 40 angstroms yielded 13-, 30-, and 13-fold increases in K(A), respectively. The combination of these factors; namely, bivalence, flexible inter-epitope linkers, and optimal inter-epitope distance, resulted in an overall 66-fold increase in K(A). Thermodynamic analysis of binding indicates that the formation of high-affinity ODN-IgG complexes was a spontaneous and exothermic event, characterized by large negative deltaS degrees, deltaH degrees, and deltaG degrees values. CONCLUSIONS: All four strategies tested during this investigation, namely bivalence, epitope density, inter-epitope linker flexibility, and optimal inter-epitope distance, proved to be useful in improving the binding affinity of DNP-labeled ODNs to anti-TNP IgG. The final ODN design incorporating these strategies will be used in testing the systemic pharmacokinetic advantage gained from complexing such ODNs to IgG.

Binding Sites, Antibody↗
PubMedDate not supplied

Positron emission tomography measurement of tumor metabolism and growth: its expanding role in oncology.

This work highlights the explosion and evolution of positron emission tomography (PET) for use in oncology research and clinical practice. 2-Deoxy-2-[F-18]fluoro-D-glucose (FDG)-PET is important in the staging of cancer, estimation of prognosis, and for its ability to predict therapeutic outcome. A number of new imaging agents are under development and may find a place in oncology when studies prove their utility. This scientific overview includes a review of the development of a number of thymidine analogs, such as 18F-3'-deoxy-3'-fluorothymidine (FLT) and 18F-1-(2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl)-thymine (FMAU), including chemical structure variations; their application in a variety of tumors; and the role of various kinetic models for understanding cellular proliferation. The greatest unmet need for PET is in further developing and validating its use in the measurement of treatment response.

Cell Proliferation↗
PubMed2026

Comparative Genomics of Paenibacillus Secondary Metabolism: Unveiling the Putative Biosynthetic Gene Cluster for Paenialvins in Paenibacillus Alvei Strain 32.

In this study, we used comparative genomics and culture-based methods to investigate Biosynthetic Gene Clusters (BGCs) responsible for the production of antimicrobial peptides. Paenibacillus alvei strain 32 was isolated from a cystic fibrosis sputum. Its genome was sequenced using Illumina, showing a size of 6,584,590 bp with 239 contigs assembled in 26 scaffolds, an average coverage of 243X, and 6,832 coding sequences. ANI analysis and in silico DNA-DNA hybridization showed its affiliation inside Paenibacillus alvei, with a clear separation from other related strains, leading us to propose a distinct species-level genomic clade (genomospecies) within this group. AntiSMASH analysis predicted 22 putative BGCs in the genome of strain 32. Its culture supernatant exhibited inhibitory activity against Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA), Bacillus cereus, and Enterococcus faecalis. By comparing in silico BGC predictions with activities described in the literature, we propose that strain 32 harbours a specific 110-kb cluster (cluster 6.2) with five non-ribosomal peptide synthetase (NRPS) genes. These synthetases are predicted to direct the assembly of a 16-amino acid backbone that correlates with the structure of paenialvins, which are known anti-MRSA molecules. This study describes the putative biosynthetic pathway of the paenialvins and explains structural variations, bringing useful data on Paenibacillus secondary metabolism for future antibiotic development.

Paenibacillus alvei↗
PubMed1988

Supercritical fluid chromatography of glycosphingolipids.

Glucose polymers and three classes of glycosphingolipids were permethylated and studied by supercritical fluid chromatography using a DB-5 coated capillary columns and carbon dioxide as the mobile phase. Column restrictors were fabricated at each column tip as described by E.J. Guthrie and H.E. Schwartz (1986, J. Chromatogr. Sci. 24, 236). Sample elution was facilitated by a programmed increase in density and detection was by flame ionization. Compounds up to 3000 Da showed excellent resolution for structural variations in carbohydrate moieties and in alkane chain heterogeneity caused by the sphingoid or N-acyl alkane chain residues.

Chromatography↗
PubMed1992

Two-dimensional mapping of N-glycosidically linked asialo-oligosaccharides from glycoproteins as reductively pyridylaminated derivatives using dual separation modes of high-performance capillary electrophoresis.

N-Glycosidically linked oligosaccharides were released from glycoproteins by digestion with trypsin followed by hydrazinolysis and subsequently re-N-acetylated and reductively pyridylaminated. Derivatives of sialic acid-containing oligosaccharides were further desialylated with neuraminidase. The final derivatives of asialo-oligosaccharides were analyzed by capillary zone electrophoresis in two carriers, an acidic phosphate buffer and an alkaline borate buffer. The former carrier allowed direct zone electrophoresis as cationic immonium ions, accordingly size-dependent separation, whereas the latter realized indirect electrophoresis as anionic borate complexes, i.e., separation based on the structural variation in outermost monosaccharide residues. Two-dimensional plots of relative mobilities of the derivatives in these dual separation modes to reductively pyridylaminated glucose provided a good tool for identification of oligosaccharides.

Algorithms↗
PubMed1987

Ferredoxin-thioredoxin reductase, an iron-sulfur enzyme linking light to enzyme regulation in oxygenic photosynthesis: purification and properties of the enzyme from C3, C4, and cyanobacterial species.

Ferredoxin-thioredoxin reductase (FTR), an enzyme involved in the light regulation of chloroplast enzymes, was purified to homogeneity from leaves of spinach (a C3 plant) and corn (a C4 plant) and from cells of a cyanobacterium (Nostoc muscorum). The enzyme is a yellowish brown iron-sulfur protein, containing four nonheme iron and labile sulfide groups, that catalyzes the activation of NADP-malate dehydrogenase and fructose 1,6-bisphosphatase in the presence of ferredoxin and of thioredoxin m and f, respectively. FTR is synonymous with the protein earlier called ferralterin. FTR showed an Mr of about 30,000 (determined by sedimentation equilibrium ultracentrifugation, amino acid composition, gel filtration, and gradient gel electrophoresis) and was composed of two dissimilar subunits (as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis). One of the FTR subunits from each source was similar both in Mr (about 13,000) and immunological properties, while the other subunit (of variable molecular weight) was characteristic of a particular organism. The similar subunit contained a disulfide group that was rapidly reduced by a dithiol (dithiothreitol) but not by monothiols (2-mercaptoethanol or reduced glutathione). Homogeneous FTR formed a tight noncovalent complex with ferredoxin on affinity columns. The basis for the structural variation in the different FTR enzymes remains to be determined.

Chloroplast Thioredoxins↗
PubMed1989

Monoclonal antibodies to human A-I apolipoprotein and characterisation of cyanogen bromide fragments of apoA-I.

Several monoclonal antibodies to human A-I apolipoprotein were produced after immunising mice with pure delipidated apoA-I. These monoclonal antibodies were characterised for their ability to react with whole lipoproteins, apolipoproteins and fragments of apoA-I generated by cleavage with cyanogen bromide. The data suggest that production of monoclonal antibodies using apoA-I as antigen was influenced by two major epitopes subsequently localised to cyanogen bromide fragments 1 and 3, and have been designated antibodies 1----5 A-IB and 6----10 A-IB, respectively. Cyanogen bromide fragments were first purified to homogeneity before screening by competitive displacement or immunoblotting procedures. Definitive characterisation of one antibody series (1----5 A-IB) depended ultimately on Western blotting following isoelectric focusing of purified apoA-I fragments. This technique identified the epitope for these antibodies to fragment 1, an identification not fully concluded from competitive displacement studies. These studies have also revealed the presence of microheterogeneity in fragment 1 (as well as in fragment 4) of apoA-I, suggesting that structural variations in several regions may account for the polymorphism observed in this apolipoprotein.

Animals↗
PubMed1983

A new immunoglobulin marker.

In an examination of 16 human immunoglobulin lambda-light chains, one was found to have amino acid substitutions which have not previously been reported for the constant region of the lambda-chains. It involved in two positions: an arginine instead of lysine at position 130, and a leucine for glutamine at position 195 (Sh numbering (1) ). The structural variation is tentatively designated as "Is" marker.

Amino Acid Sequence↗
PubMed1986

Neurons of origin of striatonigral axons in the cat: connectivity and Golgi markers of somatodendritic architecture.

We identified adult cat striatonigral neurons and characterized their somatodendritic architecture by single- and double-labeling with connectivity and Golgi markers. Light and electron microscopic observations demonstrated two important structural variations among striatofugal neurons. First, striatonigral axons originate from multiple types of neurons. The principal striatonigral neurons are frequent throughout the caudate nucleus and putamen, have medium spherical or ovoidal cell bodies and form spine-laden distal dendrites. The 'accessory' striatonigral neurons are sparse in limited regions of the caudate nucleus and putamen, have large fusiform cell bodies and lack spinous processes. Second, the medium spiny striatonigral neurons exhibit a range of anatomical specializations. In some cases, these cells have folded nuclear envelopes. Some of these neurons have somatic and/or proximal dendritic as well as distal dendritic spines. We conclude that adult cat striatofugal neurons are morphologically heterogeneous in terms of regional locations, somatodendritic architecture and ultrastructure. These anatomical specializations may affect the origin and processing of synaptic inputs to the neostriatum to provide functionally different routes of neurotransmission through the basal ganglia.

Animals↗
PubMed1988

Studies on uptake of gamma-aminobutyric acid by mouse brain particles; toward the development of a model.

Several substances were studied for their effect on enhancement and/or inhibition of uptake of GABA into a mouse brain microsomal fraction (P3) at pH 7.3 in the presence and absence of buffer. These were diverse: Na+, K+, NH4+, Hg2+, Cl-, and HCO3-; beta-guanidinopropionic and L-2,3-diaminopropionic acids and 1,2-diaminoethane; pyridine and several methylated pyridines; chlorpromazine and ketamine; and melittin. Kinetic experiments tested these substances for competition with GABA and Na+. Assuming the GABA transporter to consist of a GABA recognition entity and a Na+- and Cl-dependent protein required for its activity, a minimal provisional model for the GABA uptake process is proposed that is consistent with all current data and with relevant observations in the literature. It accounts for the activational effects of proton removal on GABA uptake, the stoichiometry of 2 Na+ and 1 Cl- associated with uptake of one GABA molecule, and the types of inhibition of uptake shown by the substances listed above. Factors are considered that may be necessary to maintain the transporter in a GABA-receptive configuration and that allow it the freedom of movement to undergo the structural variations necessary for the transport process to take place at rates that may be regulated by environmental factors.

Animals↗
PubMed1990

Classification of muscle spindle afferents in the peroneus brevis muscle of the cat.

Muscle-spindle afferents are commonly classified according to their conduction velocity. Under certain conditions such classifications may not be feasible and another form of identification is required. In this study 5 tests, comprising either quantitative or qualitative criteria, have been evaluated as a means of classifying spindle afferents. The choice of these tests was made on the basis of predicted physiological differences arising from the structural variations in the endings. Prior conditioning of the spindles was found to enhance the distinction between the two types of afferent. All the tests generated similar identifications with a maximum of 10% of afferents being classified differently by any two tests.

Animals↗