Identification of preferred protein interactions by phage-display of the human Src homology-3 proteome

We have determined the human genome to contain 296 different Src homology-3 (SH3) domains and cloned them into a phage-display vector. This provided a powerful and unbiased system for simultaneous assaying of the complete human SH3 proteome for the strongest binding to target proteins of interest, without the limitations posed by short linear peptide ligands or confounding variables of more indirect methods for protein interaction screening. Studies involving three ligand proteins, human immunodeficiency virus-1 Nef, p21-activated kinase (PAK)2 and ADAM15, showed previously reported as well as novel SH3 partners with nanomolar affinities specific for them. This argues that SH3 domains may have a more dominant role in directing cellular protein interactions than has been assumed. Besides showing potentially important new SH3-directed interactions, these studies also led to the discovery of novel signalling proteins, such as the PAK2-binding adaptor protein POSH2 and the ADAM15-binding sorting nexin family member SNX30.     

Mobile gene cassettes: a fundamental resource for bacterial evolution

Horizontal gene transfer increases genetic diversity in prokaryotes to a degree not allowed by the limitations of reproduction by binary fission. The integron/gene cassette system is one of the most recently characterized examples of a system that facilitates horizontal gene transfer. This system, discovered in the context of multidrug resistance, is recognized in a clinical context for its role in allowing pathogens to adapt to the widespread use of antibiotics. Recent studies suggest that gene cassettes are common and encode functions relevant to many adaptive traits. To estimate the diversity of mobile cassettes in a natural environment, a molecular technique was developed to provide representative distributions of cassette populations at points within a sampling area. Subsequently, statistical methods analogous to those used for calculating species diversity were employed to assess the diversity of gene cassettes within the sample area in addition to gaining an estimate of cassette pool size. Results indicated that the number of cassettes within a 5x10-m sample area was large and that the overall mobile cassette metagenome was likely to be orders of magnitude larger again. Accordingly, gene cassettes appear to be capable of mobilizing a significant genetic resource and consequently have a substantial impact on bacterial adaptability.     

Minimal mutation of the cytoplasmic tail inhibits the ability of E-cadherin to activate Rac but not phosphatidylinositol 3-kinase: direct evidence of a role for cadherin-activated Rac signaling in adhesion and contact formation

Classic cadherins are adhesion-activated cell signaling receptors. In particular, homophilic cadherin ligation can directly activate Rho family GTPases and phosphatidylinositol 3-kinase (PI3-kinase), signaling molecules with the capacity to support the morphogenetic effects of these adhesion molecules during development and disease. However, the molecular basis for cadherin signaling has not been elucidated, nor is its precise contribution to cadherin function yet understood. One attractive hypothesis is that cadherin-activated signaling participates in stabilizing adhesive contacts (Yap, A. S., and Kovacs, E. M. (2003) J. Cell Biol. 160, 11-16). We now report that minimal mutation of the cadherin cytoplasmic tail to uncouple binding of p120-ctn ablated the ability of E-cadherin to activate Rac. This was accompanied by profound defects in the capacity of cells to establish stable adhesive contacts, defects that were rescued by sustained Rac signaling. These data provide direct evidence for a role of cadherin-activated Rac signaling in contact formation and adhesive stabilization. In contrast, cadherin-activated PI3-kinase signaling was not affected by loss of p120-ctn binding. The molecular requirements for E-cadherin to activate Rac signaling thus appear distinct from those that stimulate PI3-kinase, and we postulate that p120-ctn may play a central role in the E-cadherin-Rac signaling pathway.     

Offspring of male and female parents with thalidomide embryopathy: birth defects and functional anomalies

BACKGROUND: The aim of the study was to evaluate congenital malformations and functional anomalies in the offspring of Swedish parents with thalidomide embryopathy (TE). METHODS: Sixty-four children (29 girls, 35 boys) with ages ranging from 0-18 years, born to 34 Swedish parents (14 women, 20 men) with TE, were studied. Data on malformations and dysfunction were collected from medical records at maternity and child healthcare units, delivery units, hospitals, outpatient clinics and schools. RESULTS: Five children had both a mother and father with TE, 23 had a mother suffering from TE, and in 36 children the father had TE. One girl had a major malformation consisting of pulmonary stenosis, and single cases of minor physical features and positional deformities were observed. One boy had autism. Four children were born preterm, all to a TE mother. One child died within 24 hr after birth. Seven spontaneous abortions were registered, five of them in TE mothers. The cesarian section rate was 39% among the TE mothers, compared to 14% among the non-TE mothers. CONCLUSIONS: Malformations or functional anomalies similar to those typical for TE were not found in this group of children born to Swedish parents with TE. Cesarian sections were more frequently performed in TE mothers, partly because of pelvic and uterine malformations.     

Determination of melagatran, a novel, direct thrombin inhibitor, in human plasma and urine by liquid chromatography-mass spectrometry

Analytical methods for the determination of melagatran (H 319/68) in biological samples by liquid chromatography (LC)-positive electrospray ionization mass spectrometry using multiple reaction monitoring are described. Melagatran in plasma was isolated by solid-phase extraction on octylsilica, either in separate extraction tubes or in 96-well plates. Absolute recovery of melagatran from plasma was >92%. Melagatran and the internal standard, H 319/68 D2 13C2, were separated from other sample components by LC utilizing a C18 stationary phase and a mobile phase comprising 35% acetonitrile and 0.08% formic acid in 0.0013 mol/l ammonium acetate solution. After dilution, urine was injected directly onto the LC column and subjected to gradient LC. The relative standard deviation was 1-5% for concentrations above the limit of quantification, which was estimated for plasma at 10 or 25 nmol/l for sample volumes of 500 or 200 microl, respectively, and 100 nmol/l for urine.     

Histamine immunohistochemistry is superior to the conventional heparin-based routine staining methodology for investigations of human skin mast cells

Summary Conventional studies of mast cells are limited by methodological restrictions such as a selective fixative-dependent routine staining blockage. This is thought to depend on the biochemical differences of the mast cell granule contents suggesting a cellular heterogeneity. Investigations of human mast cells, using routine methods, also suffer from the problem of a low signal-to-noise ratio.In the present study, normal human skin was used to compare an immunohistochemical method for histamine with two recommended mast-cell fixatives and a new commercial fixative in combination with three routine stains. Mast cells were found throughout the dermis with all the routine stains used. However, immunohistochemistry gave profoundly better results. Small structures, such as thin cytoplasmatic extensions and single granules, were readily detectable. Double-staining (immunohistochemistry followed by routine staining) revealed differences in staining capacity. All immunoreactive cells were not stained by routine stains and sometimes the opposite was also seen. This supports earlier reported evidence of heterogeneity, not only between skin and intestinal mast cells but also among skin mast cells themselves. Furthermore, by focusing on histamine, instead of heparin, we probably overcame the problems of the selective fixative-dependent routine staining blockage. Finally, the immunofluorescence technique provides a high signal-to-noise ratio and is an excellent method for making high-quality microphotographs of human mast cells.In conclusion, we have found histamine immunohistochemistry (a) to be easy to perform, (b) to show cytoplasmic details better of the, sometimes, dendritic-type mast cells, (c) to result in a higher signal-to-noise ratio, i.e. a better detectability, resulting in a higher number of cells being evident, and (d) to reveal the presence of histamine, instead of heparin, thus being more relevant to all kinds of histamine-related scientific endeavours. However, routine methods occasionally revealed single cells not visualized by the histamine immunohistochemistry.     

Two-and three-dimensional HCN experiments for correlating base and sugar resonances in 15N, 13C-labeled RNA oligonucleotides

Summary New 2D and 3D ¹H-¹³C-¹⁵N triple resonance experiments are presented which allow unambiguous assignments of intranucleotide H1'-H8(H6) connectivities in ¹³C-and ¹⁵N-labeled RNA oligonucleotides. Two slightly different experiments employing double INEPT forward and back coherence transfers are optimized to obtain the H1'-C1'-N9/N1 and H8/H6-C8/C6-N9/N1 connectivities, respectively. The correlation of H1' protons to glycosidic nitrogens N9/N1 is obtained in a nonselective fashion. To correlate H8/H6 with their respective glycosidic nitrogens, selective ¹³C-refocusing and ¹⁵N-inversion pulses are applied to optimize the magnetization transfers along the desired pathway. The approach employs the heteronuclear one-bond spin-spin interactions and allows the 2D ¹H-¹⁵N and 3D¹H-¹³C-¹⁵N chemical shift correlation of nuclei along and adjacent to the glycosidic bond. Since the intranucleotide correlations obtained are based exclusively on through-bond scalar interactions, these experiments resolve the ambiguity of intra-and internucleotide H1'-H8(H6) assignments obtained from the 2D NOESY spectra. These experiments are applied to a 30-base RNA oligonucleotide which contains the binding site for Rev protein from HIV.     

Investigation of sucrose synthase from rice for the synthesis of various nucleotide sugars and saccharides

The unique character of the plant glucosyltransferase sucrosesynthase, to catalyse in vitro the synthesis and cleavage ofsucrose under appropriate conditions, can be exploited for theenzymatic synthesis of carbohydrates. The present paper describesthe potential utilization of sucrose synthase from rice forthe enzymatic synthesis of activated sugars and saccharides.In the cleavage reaction of sucrose, the nucleoside diphosphatescan be used in the order UDP > TDP > ADP > CDP >GDP to obtain the corresponding activated glucoses. In batchreactions, >90% conversion of UDP and TDP could be achieved.Substituting different di- and trisaccharides for sucrose inthe cleavage reaction with UDP 2-deoxysucrose was the most promisingsubstrate. Sucrose synthase was combined with UDP-galactose4'-epimerase and ß1–4 galactosyltransferaseto synthesize N-acetyllactosamine with in situ regenerationof UDP-glucose. In the synthesis reaction of sucrose synthase,different donor (UDP-sugars) and acceptor substrates were investigated.UDP-N-acetylglucosamine and UDP-xylose could be used in combinationwith fructose as acceptor. D-Xylulose, D-tagatose, D-lyxose,D-psicose, L-sorbose, D-mannose, L-arabinose, 1, 6 anhydroglucose,lactulose, raffinose and isomaltulose can serve as acceptorsfor UDP-glucose. N-acetyllactosamine nucleotide sugars saccharides sucrose synthase