The solute carrier (SLC) complement of the human genome: phylogenetic classification reveals four major families

Solute carriers (SLCs) is the largest group of transporters, embracing transporters for inorganic ions, amino acids, neurotransmitters, sugars, purines and fatty acids among other substrates. We mined the finished assembly of the human genome using Hidden Markov Models (HMMs) obtaining a total of 384 unique SLC sequences. Detailed clustering and phylogenetic analysis of the entire SLC family showed that 15 of the families place into four large phylogenetic clusters with the largest containing eight SLC families, suggesting that many of the distinct families of SLCs have a common evolutionary origin. This study represents the first overall genomic roadmap of the SLCs providing large sequence sets and clarifies the phylogenetic relationships among the families of the second largest group of membrane proteins.     

Cytotoxicity of lipid-free apolipoprotein B

To investigate the effect of apolipoprotein B (apoB) on cell viability, we used lipid-free apoB as a model for denatured apoB. Lipid-free apoB had cytotoxicity to J774 macrophages, CHO cells and HepG2 cells, whereas apoB bound to low density lipoprotein (LDL) and lipid-free apolipoprotein A-I had no effect on cell viability. Lipid-free apoB induced apoptosis in J774 macrophages assessed by caspase-3 activation and annexin V binding. LDL receptor, heparan sulfate proteoglycans, and class A scavenger receptor were involved in the binding/uptake of lipid-free apoB, but lipid-free apoB binding/uptake by the cells did not correlate with cytotoxicity. Lipid-free apoB disrupted the lipid bilayer of large unilamellar vesicles containing calcein. We evaluated the interaction between apoB and cellular membrane by monitoring the change in intracellular Ca²⁺ concentration using Fura-2, and found that lipid-free apoB rapidly disrupted the cellular membrane in the absence or presence of the inhibitors for cellular binding/uptake mediated by the receptors. Therefore, it is suggested that lipid-free apoB induces cell death by disturbance of the plasma membrane. In addition to other lipid component in modified LDL, apoB itself has an ability to induce apoptosis and plays a crucial role in the development of atherosclerotic lesions.     

Inference for constrained estimation of tumor size distributions

SUMMARY: In order to develop better treatment and screening programs for cancer prevention programs, it is important to be able to understand the natural history of the disease and what factors affect its progression. We focus on a particular framework first outlined by Kimmel and Flehinger (1991, Biometrics, 47, 987-1004) and in particular one of their limiting scenarios for analysis. Using an equivalence with a binary regression model, we characterize the nonparametric maximum likelihood estimation procedure for estimation of the tumor size distribution function and give associated asymptotic results. Extensions to semiparametric models and missing data are also described. Application to data from two cancer studies is used to illustrate the finite-sample behavior of the procedure.     

The Activity of the Peroxidase System in the Course of Stress-Induced CAM Development

The activity of the peroxidase system in Mesembryanthemum crystallinum L. plants in relation to the shift from C₃ to CAM photosynthesis was studied. In detached leaves of the fourth and fifth stories treated with NaCl (0.3 M), a rapid (after 30 min) transient induction of the ionically bound peroxidase (the first maximum) was observed followed by a second weak increase in the enzyme activity (90 min after salt treatment). In the leaves of intact plants, which received a longer treatment with NaCl, a two-phase change in the enzyme activity was also observed. It was most pronounced at the early stages of the NaCl-induced plant shift from C₃ to CAM photosynthesis. In this case, in both detached and intact leaves of juvenile plants, the activity of soluble peroxidase was at a low steady-state level. The situation changed dramatically when M. crystallinum plants transitioned to the reproductive developmental phase and photosynthesis switched from C₃ to CAM. The time dependence of the activities of both peroxidase types, the soluble ones in particular, was characterized by marked diurnal oscillations (light–dark), which coincided with the fluctuations of the total titratable acidity. In this case, the activity of the soluble enzyme was several orders of magnitude higher than the activity of the ionically bound peroxidase, even though the optimum pH for both isoforms was similar (pH 5.0). Three acid isoforms of soluble peroxidases, which operated more actively when the cytoplasm had a higher acidity, were distinguished by isoelectrofocusing. Their activity increased under salinity. Alkaline and neutral components were predominant in more than 30 molecular forms of the soluble peroxidase detected. We concluded that the operation of the peroxidase system changed substantially when plants shifted from the juvenile to the reproductive state and switched from C₃ to CAM photosynthesis: the activity of stress-induced ionically bound peroxidase was drastically inhibited with a concurrent increase in the activity of soluble peroxidase and a change in the spectrum of its molecular forms.     

Foundations of Security for Hash Chains in Ad Hoc Networks

Nodes in ad hoc networks generally transmit data at regular intervals over long periods of time. Recently, ad hoc network nodes have been built that run on little power and have very limited memory. Authentication is a significant challenge in ad hoc networks, even without considering size and power constraints. Expounding on idealized hashing, this paper examines lower bounds for ad hoc broadcast authentication for TESLA-like protocols. In particular, this paper explores idealized hashing for generating preimages of hash chains. Building on Bellare and Rogaways classical definition, a similar definition for families of hash chains is given. Using these idealized families of hash chain functions, this paper gives a time-space product (k² log ⁴ n) bit operation¹ lower-bound for optimal preimage hash chain generation for k constant. This bound holds where n is the total length of the hash chain and the hash function family is k-wise independent. These last results follow as corollaries to a lower bound of Coppersmith and Jakobsson.A preliminary version of this paper appeared at MWN 2003: Workshop on Mobile and Wireless Networks, (a workshop of the 23rd ICDCS), 743–748, Ivan Stojmenovic and Jingyuan Zhang Editors. IEEE Press.Phillip G. Bradford (ACM) is on the faculty in Computer Science at the University of Alabama. He was visiting faculty at Rutgers Business school and was a postdoc at the Max-Planck-Institute for Informatik. He earned his Ph.D. at Indiana University in Bloomington, his MS at The University of Kansas and his BS at Rutgers University. He has also had more than 4 years experience in industry.Olga V. Gavrylyako (ACMS) is a Ph.D. student at Computer Science Department of the University of Alabama. Her research interests include theoretical aspects of security for constrained devises, in particular security for ad hoc networks. Olga Gavrylyako received her Masters and Ph.D. degrees in Applied Mathematics from Kharkov State University, Ukraine.     

Grb7-SH2 domain dimerisation is affected by a single point mutation

Growth factor receptor bound protein 7 (Grb7) is an adaptor protein that is co-overexpressed and forms a tight complex with the ErbB2 receptor in a number of breast tumours and breast cancer cell lines. The interaction of Grb7 with the ErbB2 receptor is mediated via its Src homology 2 (SH2) domain. Whilst most SH2 domains exist as monomers, recently reported studies have suggested that the Grb7-SH2 domain exists as a homodimer. The self-association properties of the Grb7-SH2 domain were therefore studied using sedimentation equilibrium ultracentrifugation. Analysis of the data demonstrated that the Grb7-SH2 domain is dimeric with a dissociation constant of approximately 11 M. We also demonstrate, using size-exclusion chromatography, that mutation of phenylalanine 511 to an arginine produces a monomeric form of the Grb7-SH2 domain. This mutation represents the first step in the engineering of a Grb7-SH2 domain with good solution properties for further biophysical and structural investigation.     

Plant-water relations and the fibre saturation point

This review is about the behaviour of water in cell walls. The aim is to introduce to biologists the concept of the fibre saturation point (FSP), and the related research of material scientists and engineers on the thermodynamics and chemistry of water in timber and wood. In the review, we first summarise what the FSP is, why it is important and how the FSP is routinely used by engineers and material scientists to estimate the volume fractions of solid, liquid and gas phases in bulk timber. We then show that the FSP can be intuitively understood using equilibrium thermodynamics. That analysis shows that the FSP is based on the concept that a certain (and repeatable) amount of water is chemically bound to cellulose and other substances in wood. That water, sometimes called bound water, exists in a water-cell wall mixture. The noted physical chemist and wood scientist, A. J. Stamm, called this mixture a 'solid solution'. In timber, the 'solid solution' is considered a separate phase from adjacent water in either a pure liquid phase or a vapour phase. Following that, we examine the FSP and wood-water dynamics at the molecular and cellular level. Despite differences between timber and living trees, we conclude that the FSP-based framework long used by material scientists and engineers is likely to be useful to biologists.     

Quantitation of repetitive epitopes in glycosaminoglycans immobilized on hydrophobic membranes treated with cationic detergents

Glycosaminoglycans (GAGs) are linear carbohydrate polymers containing repetitive sequences of differently sulfated uronic acid and glycosamine residues that are recognized by antibodies raised against proteoglycans. We have developed a method to demonstrate such repetitive sequence motifs in isolated GAG chains immobilized on hydrophobic membranes derivatized with cationic detergents. Six monoclonal antibodies directed against Cs (2B6, 3B3, Cs56, and 1B5), Hs (HepSS), and Ks (5D4) were used to detect native and chondroitinase-generated epitopes in the immobilized GAGs. All antibodies, except 1B5, were able to detect epitopes in both proteoglycans and isolated GAGs. Type of detergent and buffer composition affected the accessibility and the retention of immobilized GAGs. The epitope density, i.e., the number of repetitive epitopes per GAG mass, was estimated as the ratio between antibody (epitope) and Alcian blue (mass) staining measured simultaneously. The epitope profiles, using six antibodies, were different for each sample (CsA, CsC, Ds, Hs, intact cartilage, and human serum). The epitope profile may be used as a structural characteristic of a GAG population. Electrophoretic separation of GAGs based on their glucuronic/ioduronic acid content and O-sulfate/N-sulfate ratio was performed using a diethylene glycol-diaminobutanol agarose gel. The electrophoretic populations were characterized by immunoblotting to detergent-treated membranes.