Peptide recognition by PTB and PDZ domains

Protein tyrosine binding (PTB) and ‘post synaptic density disc-large zo-1’ (PDZ) domains bind to short peptidic ligands by augmentation of one of the domain's β sheets and other recognition mechanisms. The two domain classes have a superficial resemblance to each other, even though no sequential homology exists. The structural bases of the interactions are well understood for the domains now experimentally determined, and ligand—target pairs can probably be identified in favorable cases by analogy with the known domains. For both PTB and PDZ classes, functional activities are still not fully defined: it is possible that these domain classes, along with pleckstrin homology domains, have multiple roles.     

A note on the brine shrimp Artemia in Tuz Lake (Turkey)

Population density, fecundity andreproduction period of Artemia sp. in TuzLake, Turkey, beside environmental factors, such as oxygen,temperature, salinity, pH and electrical conductivity werestudied during 1993 and 1994.Artemia sp. occurred at two stations at the coast.Overwintering cysts hatched in early May, when the population was composed of 90% metanauplii (93%at Y4 and 99% at Y5) and few adult females. Peak abundanceoccurred in late May, at 106to 114 ind.m^–3.     

The importance of intraspecific competition in a Littorina littorea population in the Wadden Sea

Two field experiments were carried out totest whether effects of intraspecific competition ina Littorina littorea population can be detectedin a short-term investigation. Different size classesof L. littorea showed no significant differencein preferences when offered four kinds of eitherpossible food or substrata (Fucus vesiculosus,Ulva lactuca, Carcinus maenas, brick).Large and medium winkles preferred Fucusvesiculosus, followed by Ulva lactuca. Deadshore crabs (Carcinus maenas) were the leastpreferred objects for all size classes. On the firstday of the experiment bricks were more attractive tosmall littorines than to larger ones. Considering allfour days, the same ranking occurred for all sizeclasses: Fucus vesiculosus > Ulvalactuca > brick > Carcinus maenas. The reactionofjuveniles to increased densities was examined using anin situ caging experiment on a mussel bed. Meshsize of the cages allowed adult densities to beincreased while juveniles could escape by passingthrough the meshes. However, there was no significantemigration of small winkles even from cages with 10 to20 times natural density of large individuals. Ofgreater importance was the original number of winklesat the site. The available resources on the musselbeds appear to be sufficient to maintain a highpopulation density. Intraspecific competition does notseem to play a major role in this L. littorea-population.     

Molecular Diversity and Evolution of bla TEM Genes Encoding β-Lactamases Resistant to Clavulanic Acid in Clinical E. coli

The molecular diversity of inhibitor-resistant TEM (IRT) enzymes was explored using a strategy which involved DNA amplification by polymerase chain reaction (PCR), analysis of restriction fragment length polymorphism (RFLP), and direct nucleotide sequencing. The study of plasmid-borne genes from 27 strains, resistant to amoxicillin and β-lactamase-inhibitor combinations, identified mutations resulting in amino acid change at positions 69, 244, 275, and 276 known to be associated with the IRT phenotype and a mutation at nucleotide position 162 in the promoter region. These mutations were found to lie on two different gene sequences, described here as ``TEM-1B like' and ``TEM-2 like' restriction linkage groups. Further analysis, of nucleotide sequences of promoter and coding regions of the β-lactamases, confirmed that a given mutation causing IRT phenotype could be associated with two different gene sequence frameworks and two different causal mutations could lie on identical gene sequence framework. These data argue in favor of convergent phenotypic evolution of IRT enzymes under the selective pressure imposed by the intensive clinical use of β-lactam–β-lactamase inhibitor combinations. Received: 18 March 1996 / Accepted: 15 July 1996     

The Human Obesity Gene Map: The 1996 Update

An update of the human obesity gene map up to October 1996 is presented. Evidence from Mendelian disorders exhibiting obesity as a clinical feature, single-gene mutation rodent models, quantitative trait loci uncovered in crossbreeding experiments with mouse, rat, and pig models, association and case-control studies with candidate genes, and linkage studies with genes and other markers is reviewed. All chromosomal locations of the animal loci are converted into human genome locations based on syntenic relationships between the genomes. A complete listing of all these loci reveals that only 4 of the 24 human chromosomes are not yet represented, i.e., 9, 18, 21, and Y. Several chromosome arms are characterized by the presence of several putative loci. The following arms include at least three such loci: 1p, 1q, 3p, 4q, 6p, 7q, 8p, 8q, 11p, 11q, 15q, 20q, and Xq. Studies with negative association and linkage results are also reviewed.     

Effects of seed size, planting density and planting pattern on the severity of silver scurf (Helminthosporium solani) and black scurf (Rhizoctonia solani) diseases of potatoes

The effects of different seed sizes, planting densities and planting patterns on the transmission of silver scurf (Helminthosporium solani) and black scurf (Rhizoctonia solani) diseases of potatoes were examined in five field experiments with cv. Estima in 1991–93.
In all experiments, silver scurf was more severe with increase in seed size and planting density. At high planting density, silver scurf was less severe from a square planting pattern than from planting in wide rows. The incidence of black scurf also tended to increase with increase in seed size and was increased markedly high planting density.     

Larmor frequency selective model free analysis of protein NMR relaxation

Summary The Lipari-Szabo dynamical formalism is extended by setting the time constants of the Lorentzian terms to and . This analysis is compared to the earlier proposed three-parameter extended model free formalism with regard to the range of equivalence and the advantages of the simplified two-parameter (S _inff ^sup2 ,S _infH ^sup2 ) and (S _inff ^sup2 ,S _infN ^sup2 ) representations. Spectral density components are calculated and compared to those obtained from the spectral density analysis formalism. Protein relaxation data, commonly analyzed in terms of the two-parameter representation, may correspond to a dynamically heterogeneous behaviour that is more appropriately represented in terms of a fast limit order parameter and a second, lower frequency order parameter.     

Mapping of the spectral density function of a Cα−Hα bond vector from NMR relaxation rates of a 13C-labelled α-carbon in motilin

Summary The peptide hormone motilin was synthesised with a ¹³C-enriched -carbon in the leucine at position 10. In aqueous solution, six different relaxation rates were measured for the ¹³C–H fragment as a function of temperature and with and without the addition of 30% (v/v) of the cosolvent d ₂-1,1,1,3,3,3-hexafluoro-2-propanol (HFP). The relaxation rates were analysed employing the spectral density mapping technique introduced by Peng and Wagner [(1992) J. Magn. Reson., 98, 308–322] and using the model-free approach by Lipari and Szabo [(1982) J. Am. Chem. Soc., 104, 4546–4570]. The fit to various models of dynamics was also considered. Different procedures to evaluate the overall rotational correlation time were compared. A single exponential time correlation function was found to give a good fit to the measured spectral densities only for motilin in 30% (v/v) HFP at low temperatures, whereas at high temperatures in this solvent, and in D₂O at all temperatures, none of the considered models gave an acceptable fit. A new empirical spectral density function was tested and found to accurately fit the experimental spectral density mapping points. The application of spectral density mapping based on NMR relaxation data for specific ¹³C–¹H vector is shown to be a highly useful method to study biomolecular dynamics. Advantages are high sensitivity, high precision and uniform sampling of the spectral density function over the frequency range.Abbreviations CD circular dichroism - NOE nuclear Overhauser enhancement - NOESY two-dimensional NOE spectroscopy - INEPT insensitive nuclei enhanced by polarisation transfer - DANTE delays alternating with nutations for tailored excitation - WALTZ-16 wideband, alternating phase, low-power technique for zero residual splitting - FID Free induction decay - ppm parts per million - TSPA 3-trimethylsilyl-(3,3,2,2-d)-propionic acid - HFP d ₂-1,1,1,3,3,3-hexafluoro-2-propanol - CPMG Carr-Purcell-Meiboom-Gill - TFD time-resolved fluorescence depolarisation - CSA chemical shift anisotropy Partly presented at the symposium Dynamics and Function of Biomolecules, Szeged, Hungary, July 31–August 2, 1993.     

Resolving genetic relationships with microsatellite markers: a parentage testing system for the swallow Hirundo rustica

Eight polymorphic microsatellite markers from the swallow were isolated and characterized. Extraordinary variability was revealed at the HrU6 locus with 45 different alleles scored among 46 unrelated individuals. The probability that the same genotype combination would occur in two random and unrelated individuals at six selected loci was as low as 1.3 × 10^-8 and the combined exclusion probability was 0.9996. Stable Mendelian inheritance was observed in about 1000 meioses. No significant linkage was revealed and for almost all combinations of marker-pairs, linkage closer than 5 cM could be excluded. At two loci, null (nonamplifying) alleles were encountered. Thirteen (30%) extra-pair offspring were identified in 5 (56%) broods when applying the marker set on a nearly complete swallow colony. We were able to identify a single male from the other families in the colony as the most likely father for nine of the 13 extra-pair offspring.     

Changes in cytoplasmic and lysosomal enzyme activities in cultured rat heart cells: The relationship to cell differentiation and cell population in culture

Summary Postnatal rat heart cells in culture enriched with respect to muscle cells were obtained by either high density seeding or by the replating technique. [³H]Thymidine incorporation to DNA and the enzymatic pattern of cytoplasmic and lysosomal enzymes have been studied as a function of the culture’s age, of seeding density, and replating. It was shown that (a) replating maintains predominance of myocyte population for at least 2 wk in culture; (b) heavy seeding density allows homogeneous myocyte population for the 1st wk in culture; and (c) the enzyme profile of the culture may serve as an indicator for the type of cell population in culture and its state of differentiation. This study was done as partial fulfilment of the M.Sc. thesis in Biochemistry (SY). Supported by grants from The Chief Scientist, Ministry of Health, State of Israel; The Ministry of Education and Sciences, State of Niedersachssen (FRG); and The Foundation for Heart Research from Mr. and Mrs. D. Vidal-Madjar, Paris, France.