bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA–carcinogen interaction: covalent DNA-adducts of benzo(a)pyrene 7, 8-dihydrodiol 9, 10-epoxides studied by biochemical and biophysical techniques
Authors: Gräslund Astrid , Jernström Bengt
Published: March 2009

Exposure to various chemicals, either due to occupation or lifestyle, is considered to be a major contributing factor to tumour formation in man (Higginson, 1969; Doll & Peto, 1981). An important and prevalent class of potent carcinogenic compounds present in the environment is polycyclic aromatic hydrocarbons (PAHs), which are found in various petroleum and combustion products derived from heat and power generation and motor vehicle exhausts (Baum, 1978). Furthermore, since PAHs are generally formed by pyrolysis of organic matters such as tobacco smoking and certain procedures of food preparation, the PAH exposure to humans is extensive
Biophysical processes in invertebrate photoreceptors: recent progress and a critical overview based on Limulus photoreceptors
Authors: Nagy Károly
Published: March 2009

Photoreceptor cells are special neurons which convert light to an electrical signal. The absorption of a photon by a rhodopsin molecule triggers a sequence of chemical processes leading to a change in the membrane voltage of the photoreceptor. The mechanism of this light-induced voltage change is different in vertebrates and invertebrates. Light causes a hyperpolarization in vertebrates, but a depolarization in invertebrate photoreceptors.
Transport across plant roots
Authors: Pitman M. G.
Published: March 2009

The plant root is a complex system that has evolved under the constraints of a number of functions. It is a pressure-probe that can penetrate the soil; it is a scavenger of nutrients that may be either tightly bound to soil particles or in low concentrations in the soil solution; it is an absorber of water from the soil. The tip of the root contains the region of dividing cells from which the root is formed, and is pushed through the soil by the extension of these cells some 10–20 times as they develop and differentiate.
Sensitivity amplification in biochemical systems
Authors: Goldbeter A. , Koshland D. E.
Published: March 2009

The sensitivity of biological systems to changes in environmental stimuli is connected with their regulatory properties. In order to achieve efficient control, these systems must respond to minute environmental variations by amplifying external stimuli to yield a significant response. To that end, biochemical systems have often evolved to a cascade organization in which the product of the nth reaction in a chain acts as a catalyst in subsequent transformations. The amplification properties of such cascades were first noticed in the process of blood clotting (MacFarlane, 1964, 1969) and visual excitation (Wald, 1965). Later on, a similar organization was noticed in hormonal control of metabolism (Bowness, 1964; Stadtman & Chock, 1977, 1978; Chock, Rhee & Stadtman, 1980).
Overexpression of integral membrane proteins for structural studies
Authors: Grisshammer R. , Tateu C. G.
Published: March 2009

Determination of the structure of integral membrane proteins is a challenging task that is essential to understand how fundamental biological processes (such as photosynthesis, respiration and solute translocation) function at the atomic level. Crystallisation of membrane proteins in 3D has led to the determination of four atomic resolution structures [photosynthetic reaction centres (Allenet al. 1987; Changet al. 1991; Deisenhofer & Michel, 1989; Ermleret al. 1994); porins (Cowanet al. 1992; Schirmeret al. 1995; Weisset al. 1991); prostaglandin H2synthase (Picotet al. 1994); light harvesting complex (McDermottet al. 1995)], and crystals of membrane proteins formed in the plane of the lipid bilayer (2D crystals) have produced two more structures [bacteriorhodopsin (Hendersonet al. 1990); light harvesting complex (Kühlbrandtet al. 1994)].
Charge transport of ion pumps on lipid bilayer membranes
Authors: Bamberg E. , Butt H.-J. , Eisenrauch A. , Fendler K.
Published: March 2009

Ion pumps create ion gradients across cell membranes while consuming light energy or chemical energy. The ion gradients are used by the corresponding cell types for passive-ion transport via ion channels or carriers or for accumulation of nutrients like sugar or amino acids via cotransport systems or antiporters.
Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMRspectroscopy
Authors: Brünger Axel T. , Nilges Michael
Published: March 2009

Macromolecular structure determination by X-ray crystallography and solution NMR spectroscopy has experienced unprecedented growth during the past decade.
The structure of branched DNA species
Authors: Lilley David M. J. , Clegg Robert M.
Published: March 2009

Branched DNA molecules provide a challenging set of structural problems. Operationally we define branched DNA species as molecules in which double helical segments are interrupted by abrupt discontinuities, and we draw together a number of different kinds of structure in the class, including helical junctions of different orders, and base bulges (Fig. 1).
The current state of high resolution scanning electron microscopy
Authors: Crewe A. V.
Published: March 2009

It has been known for many years that there are two distinct ways of designing an electron microscope.
Structure of viral connectors and their function in bacteriophage assembly and DNA packaging
Authors: Valpuesta Jose M. , Carrascosa Jose L.
Published: March 2009

The viruses have been an attractive model for the study of basic mechanisms of protein/protein and protein/nucleic acid interactions involved in the assembly of macromolecular aggregates. This has been due primarily to their relative genetic simplicity as compared to their structural and functional complexity. Although most of the initial studies were carried out on bacterial and plant viruses, increasing data has also been accumulated from animal viruses, which has led to an understanding of some basic principles, as well as to many specific strategies in every system. The study of virus assembly has been a source of ideas that underlie our present knowledge of the organization of biological systems. It has also provided, since the production of bacteriophage mutants which have allowed the study of assembly intermediates, the first system in which the genetic studies played a dominant role. The increasing volume of data over the last years has revealed how the structural components can interact sequentially through an ordered pathway to yield macromolecular assemblies that satisfy the demands of stability required for a successful transfer of genetic information from host to host.
Specificity and promiscuity in membrane helix interactions
Authors: Lemmon Mark A. , Engelman Donald M.
Published: March 2009

The membrane-spanning portions of many integral membrane proteins consist of one or a number of transmembrane α-helices, which are expected to be independently stable on thermodynamic grounds. Side-by-side interactions between these transmembrane α-helices are important in the folding and assembly of such integral membrane proteins and their complexes. In considering the contribution of these helix–helix interactions to membrane protein folding and oligomerization, a distinction between the energetics and specificity should be recognized. A number of contributions to the energetics of transmembrane helix association within the lipid bilayer will be relatively non-specific, including those resulting from charge–charge interactions and lipid–packing effects. Specificity (and part of the energy) in transmembrane α-helix association, however, appears to rely mainly upon a detailed stereochemical fit between sets of dynamically accessible states of particular helices. In some cases, these interactions are mediated in part by prosthetic groups.
Electrical activity of vertebrate photoreceptors
Authors: Tomita Tsuneo
Published: March 2009

It has been known since the time of Schultze (1866) that in the vertebrate retina there are two types of photoreceptors, rods and cones, and that they serve different visual functions; rods for scotopic vision, and cones for photopic. The terminology originates from the shape of the outer segments in which the photosensitive pigment molecules are contained. The cone outer segments are conic and taper towards the tips, while the rod outer segments are typically cylindrical. Fig. 1 is a schematic diagram from Brown, Gibbons & Wald (1963) of the ultrastructure of the rod and cone outer segments of the mudpuppy, Necturus, as studied by electron microscopy. Both appear to be made up of a pile of transverse paired membranes. In cones these arise by infolding of the plasma membrane, and in rods they have probably arisen in a similar way, but each pair of membranes is sealed around the edge so as to form a closed double-membrane disc (Sjöstrand, 1961). Because of the universal lamellation within the rod and cone outer segments, it looks as if there were no appreciable intracellular space, but yet Toyoda, Nosaki & Tomita (1969), and Toyoda et al. (1970) were successful in intracellular recording from the outer segments of single rods of the nocturnal gecko and frog.
The technique of thermal measurements in excitable tissues
Authors: Howarth J. V.
Published: March 2009

The first recorded measurements of temperature changes in a muscle during contraction were made more than 120 years ago by means of a series of thermocouples connected to a galvanometer. The technique is the same today. In principle it is that of the adiabatic isoperibol calorimeter (Wadsö, 1970); heat generated by the system under study is shared with a thermal transducer, the electrical output of which is a measure of the consequent change of temperature and may be displayed by one of several devices. Most exponents in this field have to rely on home-produced assemblies and it is the intention of this article to consider the practical details of the separate components and, where possible, to discuss some of the various innovations which different workers have brought to the technique.
Magnetic resonance studies of the pathophysiology of murine malaria
Authors: Deslauriers Roxanne , Geoffrion Yves , Butler Keith W. , Smith Ian C. P.
Published: March 2009

The non-invasive and non-destructive aspects of NMR and ESR spectroscopy have prompted a variety of research on the pathophysiological impact of murine malaria. NMR is unique in its ability to monitor intracellular pH non-invasively in a heterogeneous sample, a compartmentalized cell and in a whole organism. It has also been shown to be sensitive to unusual structures and metabolic products in free-living protozoa such asAcanthamoeba(Deslaurierset al.1982a) andTetrahymena(Deslaurierset al.1982b; Jarrellet al.1981). Using the appropriate spin probe, ESR can give valuable information on membrane structure (Schreier, Polnaszek & Smith; 1978). It is particularly useful when quantities of material are limited.
Volterra representation and Wiener-like identification of nonlinear systems: scope and limitations
Authors: Palm Günther , Pöpel Bertram
Published: March 2009

After the work of Marmarelis & Naka (1972, 1973) in the catfish retina, systems analysis using stochastic stimuli has had a boom in the seventies (e.g. McCann & Marmarelis, 1975; Eckert & Bishop, 1975; French & Wong, 1977; Lipson, 1975; McCann, 1974; Naka, Marmarelis & Chan, 1975; Spekreijse & Reits, 1982; Trimble & Phillips, 1978; Terzuolo et al. 1982). White-noise analysis was considered to be a general tool for investigating nonlinear systems gaining a maximum of information with a minimum of assumptions about the system. The modification of the original Wiener theory (Wiener, 1958; Cameron & Martin, 1947; McKean, 1972) by Lee & Schetzen (1965) made the theory fairly easy to implement into widely available computers and thus accessible to a larger number of experimenters.
Biomolecular dynamics: A report from a workshop in Gysinge, Sweden, October 4–7, 1982
Authors: Edholm Olle , Nilsson Lennart , Berg Otto , Ehrenberg Måns , Claesens Flora , Gräslund Astrid , Jönsson Bo , Teleman Olle
Published: March 2009

From the results of X-ray crystallography a wealth of information is now available concerning the detailed molecular structure of proteins, nucleic acids, and membrane components. This has made it possible to apply successfully various spectroscopie techniques for time resolved studies as well as theoretical simulations of internal molecular dynamics in the biological macromolecules and molecular aggregates. We were particularly pleased to see professor Ivar Waller among the participants of the workshop since new use of the wellknown Debye–Waller factor has greatly contributed to this development. A molecular picture is presently emerging including the dimension of time which ultimately will give us a detailed understanding of the functional interactions between biomolecules in general, and in particular enzyme catalysis, nucleic acid functions, and transport of matter and information through membranes.
The production and absorption of heat associated with electrical activity in nerve and electric organ
Authors: Ritchie J. M. , Keynes R. D.
Published: March 2009

All living cells require a supply of energy from appropriate metabolic pathways in order in fulfill their physiological functions. A special function common to peripheral nerve fibres and the electroplates of the electric organ is the generation of electrical potentials and a consequent flow of current. A large fraction of their metabolism is therefore devoted basically to maintenance of the unequal distribution of sodium and potassium ions across the cell membranes on which their electrical excitability depends, and involves a consumption of ATP by the membrane-bound Na, K—ATPase system known as the sodium pump.
Use of deuterium labelling in NMR studies of antibody combining site structure
Authors: Anglister Jacob
Published: March 2009

Antibody molecules secreted by B-lymphocytes play a central role in the immune defense systems of higher organisms. The major function of the antibody molecule is to bind specifically to foreign molecules (antigens) and to effect their inactivation and/or removal. Antibody molecules exist in millions of different forms, each with a unique amino acid sequence and combining site structure. Collectively called immunoglobulins (abbreviated as Ig), they form one of the major classes of proteins present in the blood, constituting 20% of the total plasma protein by weight.
Structural features of cytochrome oxidase
Authors: Saraste Matti
Published: March 2009

This article tries to be a compact summary of some recent research on cytochromecoxidase (EC 1.9.3.1), an important enzyme in membrane bioenergetics. Cytochrome oxidase is the terminal catalyst of the mitochondrial respiratory chain. It uses the electrons flowing through the chain to reduce oxygen molecules to water. Four electrons and four protons are consumed in the reduction of O2to two molecules of water (Fig. 1). Cytochrome oxidase contains four redoxactive metal centres. Two of these are copper atoms, two haem A groups. These four centres are employed in the dioxygen-binding site and in the electron-transferring pathways from cytochromec. The enzyme is also called cytochromeaa3, because the protein-bound haems are functionally and spectroscopically different.
Enzymic modification of environmental intoxicants: the role of cytochrome P–450
Authors: Blumberg W. E.
Published: March 2009

As of November 1977, the American Chemical Society's Chemical Abstracts Service computer registry of chemicals contained 4039907 distinct entities, and has been growing at an average rate of about 6000 per week. How many of these chemicals are in everyday use? Current estimates from the Environmental Protection Agency indicate that there may be as many as 50000 commonly used chemicals, not including pesticides, pharmaceuticals, and food additives. The EPA estimates that there may be as many as 1500 different active ingredients in pesticides. The Food and Drug Administration estimates that there are about 4000 active ingredients in drugs and about 2000 other ancillary compounds used in the drug industry. The FDA also estimates that there are about 2500 additives used for nutritional value and flavouring and 3000 chemicals used to preserve processed food. Thus there seem to be about 63000 chemicals in common use.
Genes, pollutants and human diseases
Authors: Trosko James E. , Chang Chia-Cheng
Published: March 2009

The use of traditional Western concepts of disease (i.e. the ‘germ’ theory) has guided the use of scientific knowledge and technologies in the Control of acute infectious diseases (Gori & Peters, 1975; Trosko & Chang, 1978c). The intervention of all sorts of technologies has prolonged the life expectancy, allowing more people to reach the limit of what appears to be a rather fixed life-span (Hayflick, 1976). At the same time, human beings have used technologies to alter out dependence on the natural enviroment We intervene on many levels to minimize threats to our dependence on natural forces for food (e.g. agricultural technology, food additives), for water (e.g. wells or dams), for health (e.g. instituting sanitary measures or using drugs), for protection against the elements (e.g. wearing clothes, building homes with heaters and air conditioners) and for pleasure (e.g. snowmobiles, etc.). It is now extremely clear that much of the ‘effluents of our technological affluence’ can be harmful to living systems.
Roles of electrostatic interaction in proteins
Authors: Nakamura Haruki
Published: March 2009

Electrostatic effects play an essential role in specific molecular recognition and molecular assembly in many biologically important molecules. The specific electric field at the active site also regulates the catalytic reaction of a protein. Moreover, intramolecular or inter-subunit electrostatic interactions, such as saltbridges, hydrogen bonds, and charge-dipole interactions, are considered to work to stabilize protein molecules. Those electrostatic roles recently observed in proteins are reviewed with a description of the origins and principles of electrostatic forces, and analyses will be made using simple models to illuminate the physical basis.
Trends and Challenges in Experimental Macromolecular Crystallography
Authors: Chayen N. E. , Boggon T. J. , Cassetta A. , Deacon A. , Gleichmann T. , Habash J. , Harrop S. J. , Helliwell J. R. , Nieh Y. P. , Peterson M. R. , Raftery J. , Snell E. H. , Hädener A. , Niemann A. C. , Siddons D. P. , Stojanoff V. , Thompson A. W. , Ursby T. , Wulff M.
Published: March 2009

Macromolecular X-ray crystallography underpins the vigorous field of structural molecular biology having yielded many protein, nucleic acid and virus structures in fine detail. The understanding of the recognition by these macromolecules, as receptors, of their cognate ligands involves the detailed study of the structural chemistry of their molecular interactions. Also these structural details underpin the rational design of novel inhibitors in modern drug discovery in the pharmaceutical industry. Moreover, from such structures the functional details can be inferred, such as the biological chemistry of enzyme reactivity. There is then a vast number and range of types of biological macromolecules that potentially could be studied. The completion of the protein primary sequencing of the yeast genome, and the human genome sequencing project comprising some 105proteins that is underway, raises expectations for equivalent three dimensional structural databases.
PNA-nucleic acid complexes. Structure, stability and dynamics
Authors: Eriksson Magdalena , Nielsen Peter E.
Published: March 2009

Growing interest in gene targeting drugs has inspired the development of a multitude of nucleic acid analogues, many of which feature substitutions in the phosphodiester moiety of the backbone (reviewed by Mesmaeker et al. 1995 and Nielsen, 1995). Peptide nucleic acid (PNA) is an example of a more radical redesign of DNA. The entire sugar-phosphate backbone is substituted by a chain of peptide-like N-(2-aminoethyl)glycine units so that an achiral and uncharged DNA-mimic is obtained (Fig. 1; Nielsen et al. 1991). The synthesis is based on standard peptide chemistry (Christensen et al. 1995) and has been automated. PNA can relatively easily be modified to include modifications of the backbone as well as of the bases (Hyrup & Nielsen, 1996). PNA is chemically stable and, in contrast to natural nucleic acids and peptides, PNA is expected to remain intact in living cells since it is not a substrate for natural hydrolytic enzymes and is not degraded by cell extracts (Demidov et al. 1994).
The solar Julia sets of basic quadratic Cremer polynomials
Authors: BLOKH A. , BUFF X. , CHÉRITAT A. , OVERSTEEGEN L.
Published: March 2009

In general, little is known about the exact topological structure of Julia sets containing a Cremer point. In this paper we show that there exist quadratic Cremer Julia sets of positive area such that for a full Lebesgue measure set of angles the impressions are degenerate, the Julia set is connected im kleinen at the landing points of these rays, and these points are contained in no other impression.
A quantitative mean ergodic theorem for uniformly convex Banach spaces
Authors: KOHLENBACH U. , LEUŞTEAN L.
Published: March 2009

We provide an explicit uniform bound on the local stability of ergodic averages in uniformly convex Banach spaces. Our result can also be viewed as a finitary version in the sense of Tao of the mean ergodic theorem for such spaces and so generalizes similar results obtained for Hilbert spaces by Avigad et al [Local stability of ergodic averages. Trans. Amer. Math. Soc. to appear] and Tao [Norm convergence of multiple ergodic averages for commuting transformations. Ergod. Th. & Dynam. Sys.28(2) (2008), 657–688].
Control scheme including prediction and augmented reality for teleoperation of mobile robots
Authors: Slawiñski Emanuel , Mut Vicente
Published: March 2009

This paper proposes a control scheme for the teleoperation of a mobile robot in presence of time delay. Our proposal uses a compensation of the time delay based on a human operator's model and a simple 3D augmented reality scheme; both are related through a prediction system. Unlike other strategies, the proposed scheme has a model of the human operator inside it, including his decision so that human and robot “push in the same direction.” The stability of the teleoperation system adding the proposed control scheme is proven concluding how the time delay changes the convergence rate and the convergence ball size. Finally, to illustrate the performance and stability of the proposed control structure, several teleoperation experiments in presence of various delays are shown.
Survey and case-control study during epidemics of Puumala virus infection
Authors: WINTER C. H. , BROCKMANN S. O. , PIECHOTOWSKI I. , ALPERS K. , AN DER HEIDEN M. , KOCH J. , STARK K. , PFAFF G.
Published: March 2009

In Baden-Wuerttemberg, a federal state in south-west Germany, a large outbreak of 1089 laboratory-confirmed human Puumala virus (PUUV) infections occurred in 2007. We conducted a survey to describe the disease burden and a case-control study to identify risk factors for acquiring PUUV. Case-patients were interviewed about clinical outcome and both case-patients and randomly recruited controls were interviewed about exposure. We calculated matched odds ratios (mOR) using a conditional logistic regression model. Multivariable analysis of 191 matched case-control pairs showed that case-patients were more likely than controls to have seen small rodents/their droppings (mOR 1·9, 95% CI 1·2–3·0), cleaned utility rooms (mOR 1·8, 95% CI 1·0–3·4) and visited forest shelters (mOR 3·9, 95% CI 1·1–14·3). Two thirds of case-patients required hospitalization. During PUUV epidemics rodent control measures and use of protective equipment should be considered in utility rooms and shelters.
Assessment and simulation of the implementation of brucellosis control programme in an endemic area of the Middle East
Authors: HEGAZY Y. M. , RIDLER A. L. , GUITIAN F. J.
Published: March 2009

Brucellosis is an important zoonosis in Middle Eastern countries. In this study we assessed the extent of the application of planned official brucellosis control programmes in Kafr El Sheikh governorate, Egypt and we used a stochastic simulation model to assess the probable impact of changes to the official control strategy on the dynamics of small-ruminant brucellosis. Our results show that <7% of female livestock were tested in any given year in the study area and that quarantine was not consistently applied to infected herds. Simulation results revealed the inability of the applied control measures to reduce the prevalence of small-ruminant brucellosis. Given our assumptions, the intensity with which infected animals are removed under the actual levels of implementation of test-and-slaughter programmes would permit brucellosis to remain endemic at a level >8% of the sheep and goat population.
New reports of Australian cutaneous leishmaniasis in Northern Australian macropods
Authors: DOUGALL A. , SHILTON C. , LOW CHOY J. , ALEXANDER B. , WALTON S.
Published: March 2009

Cutaneous leishmaniasis caused by various species of Leishmania is a significant zoonotic disease in many parts of the world. We describe the first cases of Australian cutaneous leishmaniasis in eight northern wallaroos, one black wallaroo and two agile wallabies from the Northern Territory of Australia. Diagnosis was made through a combination of gross appearance of lesions, cytology, histology, direct culture, serology and a species-specific real-time PCR. The causative organism was found to be the same unique species of Leishmania previously identified in red kangaroos. These clinical findings provide further evidence for the continuous transmission of the Australian Leishmania species and its presence highlights the importance of continued monitoring and research into the life-cycle of this parasite.
Predicate transformers for extended probability and non-determinism
Authors: KEIMEL KLAUS , PLOTKIN GORDON D.
Published: March 2009

We investigate laws for predicate transformers for the combination of non-deterministic choice and (extended) probabilistic choice, where predicates are taken to be functions to the extended non-negative reals, or to closed intervals of such reals. These predicate transformers correspond to state transformers, which are functions to conical powerdomains, which are the appropriate powerdomains for the combined forms of non-determinism. As with standard powerdomains for non-deterministic choice, these come in three flavours – lower, upper and (order-)convex – so there are also three kinds of predicate transformers. In order to make the connection, the powerdomains are first characterised in terms of relevant classes of functionals.

Much of the development is carried out at an abstract level, a kind of domain-theoretic functional analysis: one considers d-cones, which are dcpos equipped with a module structure over the non-negative extended reals, in place of topological vector spaces. Such a development still needs to be carried out for probabilistic choice per se; it would presumably be necessary to work with a notion of convex space rather than a cone.
Using oceanic‐atmospheric oscillations for long lead time streamflow forecasting
Authors: Kalra Ajay , Ahmad Sajjad
Published: March 2009

We present a data‐driven model, Support Vector Machine (SVM), for long lead time streamflow forecasting using oceanic‐atmospheric oscillations. The SVM is based on statistical learning theory that uses a hypothesis space of linear functions based on Kernel approach and has been used to predict a quantity forward in time on the basis of training from past data. The strength of SVM lies in minimizing the empirical classification error and maximizing the geometric margin by solving inverse problem. The SVM model is applied to three gages, i.e., Cisco, Green River, and Lees Ferry in the Upper Colorado River Basin in the western United States. Annual oceanic‐atmospheric indices, comprising Pacific Decadal Oscillation (PDO), North Atlantic Oscillation (NAO), Atlantic Multidecadal Oscillation (AMO), and El Nino–Southern Oscillations (ENSO) for a period of 1906–2001 are used to generate annual streamflow volumes with 3 years lead time. The SVM model is trained with 86 years of data (1906–1991) and tested with 10 years of data (1992–2001). On the basis of correlation coefficient, root means square error, and Nash Sutcliffe Efficiency Coefficient the model shows satisfactory results, and the predictions are in good agreement with measured streamflow volumes. Sensitivity analysis, performed to evaluate the effect of individual and coupled oscillations, reveals a strong signal for ENSO and NAO indices as compared to PDO and AMO indices for the long lead time streamflow forecast. Streamflow predictions from the SVM model are found to be better when compared with the predictions obtained from feedforward back propagation artificial neural network model and linear regression.
Cross‐talk between the VEGF‐A and HGF signalling pathways in endothelial cells
Authors: Sulpice Eric , Ding Shunli , Muscatelli‐Groux Béatrice , Bergé Mathieu , Han Zhong Chao , Plouet Jean , Tobelem Gérard , Merkulova‐Rainon Tatyana
Published: March 2009

Background information. Endothelial cells play a major role in angiogenesis, the process by which new blood vessels arise from a pre‐existing vascular bed. VEGF‐A (vascular endothelial growth factor‐A) is a key regulator of angiogenesis during both development and in adults. HGF (hepatocyte growth factor) is a pleiotropic cytokine that may promote VEGF‐A‐driven angiogenesis, although the signalling mechanisms underlying this co‐operation are not completely understood.

Results. We analysed the effects of the combination of VEGF‐A and HGF on the activation of VEGFR‐2 (VEGF receptor‐2) and c‐met receptors, and on the stimulation of downstream signalling pathways in endothelial cells. We found that VEGFR‐2 and c‐met do not physically associate and do not transphosphorylate each other, suggesting that co‐operation involves signalling events more distal from receptor activation. We demonstrate that the VEGF isoform VEGF‐A165and HGF stimulate a similar set of MAPKs (mitogen‐activated protein kinases), although the kinetics and strengths of the activation differ depending on the growth factor and pathway. An enhanced activation of the signalling was observed when endothelial cells were stimulated by the combination of VEGF‐A165and HGF. Moreover, the combination of VEGF‐A and HGF results in a statistically significant synergistic activation of ERK1/2 (extracellular‐signal‐regulated kinase 1/2) and p38 kinases. We demonstrated that VEGF‐A165and HGF activate FAK (focal adhesion kinase) with different kinetics and stimulate the recruitment of phosphorylated FAK to different subsets of focal adhesions. VEGF‐A165and HGF regulate distinct morphogenic aspects of the cytoskeletal remodelling that are associated with the preferential activation of Rho or Rac respectively, and induce structurally distinct vascular‐like patternsin vitroin a Rho‐ or Rac‐dependent manner.

Conclusions. Under angiogenic conditions, combining VEGF‐A with HGF can promote neovascularization by enhancing intracellular signalling and allowing more finely regulated control of the signalling molecules involved in the regulation of the cytoskeleton and cellular migration and morphogenesis.
Gene expression modulation of liver energy metabolism by oleoyl-oestrone in overweight rats
Authors: Del Mar Romero María , Fernández-López José Antonio , Alemany Marià , Esteve Montserrat
Published: March 2009

We intended to determine how the liver copes with the massive handling of lipids induced by OE (oleoyl-oestrone), as well as to characterize and differentiate the actual OE effects from those that may be only the consequence of decreased food intake. Thus we used male rats treated with oral OE (10 nmol/g per day) compared with a vehicle only PF (pair-fed) group and controls fed ad libitum (vehicle only). Plasma parameters, and total liver lipids, glycogen, DNA and total mRNA were measured. RNA was extracted and used for real-time PCR analysis of the gene expression of enzymes and regulatory factors of liver energy metabolism. Most hepatic proteins showed similar gene expressions in OE and controls, but the differences widened between OE and PF rats, showing that OE effects could not be merely attributed to a lower energy intake. The liver of OE-treated rats largely maintained its ability to mobilize glucose for the synthesis of fats; this was achieved in part by a peculiar combination of regulative modifications that facilitate both fatty acid disposal and restrained glucose utilization under conditions of limited food supply but ample availability of internal energy stores. In conclusion, the results presented suggest that the effect of OE on liver metabolism may be (at least in part) mediated through an insulin-sensitivity-dependent modulation of the expression of SREBP-1c (sterol-regulatory-element-binding protein-1c), resulting in the unique combined effect of mildly increased (or maintained) glucose disposal but also limited enhancement of lipogenesis.
Electrospray ionization mass spectrometry as a method for studying the high-pressure denaturation of proteins
Authors: Stefanowicz Piotr , Petry-Podgorska Inga , Kowalewska Karolina , Jaremko Lukasz , Jaremko Mariusz , Szewczuk Zbigniew
Published: March 2009

High-pressure denaturation of proteins can provide important information concerning their folding and function. These studies require expensive and complicated equipment. In this paper, we present a new convenient method for studying high-pressure denaturation of proteins combining DHX (deuterium–hydrogen exchange) and electrospray ionization MS. Application of various values of pressure causes different degrees of protein unfolding resulting in molecules with a different number of protons available for exchange with deuterons. After decompression a protein refolds and a certain number of deuterons are trapped within the hydrophobic core of a refolded protein. Redissolving the deuterated protein in an aqueous buffer initiates the DHX of amides located on the protein surface only, which can be monitored under atmospheric pressure by MS. Depending on the degree of deuteration after high-pressure treatment, the DHX kinetics are different and indicate how many deuterons were trapped in the protein after refolding. The dependence of this number on pressure gives information on the denaturation state of a protein. The distribution of deuterium along the sequence of a high-pressure-denatured protein was studied the ECD (electron-capture-induced dissociation) on a Fourier-transform mass spectrometer, enabling the monitoring of high-pressure denaturation with single amino acid resolution.
Belonging through Land/Scape
Authors: Schein Richard H
Published: March 2009

This paper addresses racialized practices of belonging through two examples which span the period after the Civil War in central Kentucky, and which might stand for questions of race, belonging, land, and landscape in the United States more broadly. It is focused empirically upon people who often have been written out of ‘belonging’, precisely through land and landscape. The examples presented are not intended simply to unmask the ideological undergirdings of land and landscape but, rather, to raise the possibilities for an oppositional politics of belonging in which land and landscape figure as the practical stage upon and through which citizenship and community can be practiced. The conclusions are directed toward grounding concerns for belonging-as-social-justice, which, in these cases, is an incremental achievement, eked out of daily existence, and largely-but not always-in response to dominant social, political, economic, and cultural practice.
Selective and direct inhibition of TRPC3 channels underlies biological activities of a pyrazole compound
Authors: Kiyonaka Shigeki , Kato Kenta , Nishida Motohiro , Mio Kazuhiro , Numaga Takuro , Sawaguchi Yuichi , Yoshida Takashi , Wakamori Minoru , Mori Emiko , Numata Tomohiro , Ishii Masakazu , Takemoto Hiroki , Ojida Akio , Watanabe Kenta , Uemura Aya , Kurose Hitoshi , Morii Takashi , Kobayashi Tsutomu , Sato Yoji , Sato Chikara , Hamachi Itaru , Mori Yasuo
Published: March 2009

Canonical transient receptor potential (TRPC) channels control influxes of Ca
2+
and other cations that induce diverse cellular processes upon stimulation of plasma membrane receptors coupled to phospholipase C (PLC). Invention of subtype-specific inhibitors for TRPCs is crucial for distinction of respective TRPC channels that play particular physiological roles in native systems. Here, we identify a pyrazole compound (Pyr3), which selectively inhibits TRPC3 channels. Structure-function relationship studies of pyrazole compounds showed that the trichloroacrylic amide group is important for the TRPC3 selectivity of Pyr3. Electrophysiological and photoaffinity labeling experiments reveal a direct action of Pyr3 on the TRPC3 protein. In DT40 B lymphocytes, Pyr3 potently eliminated the Ca
2+
influx-dependent PLC translocation to the plasma membrane and late oscillatory phase of B cell receptor-induced Ca
2+
response. Moreover, Pyr3 attenuated activation of nuclear factor of activated T cells, a Ca
2+
-dependent transcription factor, and hypertrophic growth in rat neonatal cardiomyocytes, and in vivo pressure overload-induced cardiac hypertrophy in mice. These findings on important roles of native TRPC3 channels are strikingly consistent with previous genetic studies. Thus, the TRPC3-selective inhibitor Pyr3 is a powerful tool to study in vivo function of TRPC3, suggesting a pharmaceutical potential of Pyr3 in treatments of TRPC3-related diseases such as cardiac hypertrophy.
Supramolecular polymer formed by reversible self-assembly of tetrakisporphyrin
Authors: Haino Takeharu , Fujii Takashi , Watanabe Akihide , Takayanagi Urara
Published: March 2009

S-shaped tetrakisporphyrin 2 forms supramolecular polymeric assemblies via a complementary affinity of its bisporphyrin units in solution. The self-association constant determined by applying the isodesmic model is >10
6
L mol
−1
, which suggests that a sizable polymer forms at millimolar concentrations at room temperature. The electron deficient aromatic guest (TNF) binds within the molecular clefts provided by the bisporphyrin units via a charge-transfer interaction. This guest complexation completely disrupts supramolecular polymeric assembly. The long, fibrous fragments of the polymeric assemblies were characterized by atomic-force microscopy imaging of a film cast on a mica surface. The polymeric assemblies have lengths of >1μm and show a coiled structure with a higher level of organization. The approach discussed in this report concerning the quick preparation of supramolecular polymeric assemblies driven by noncovalent forces sets the stage for the preparation of a previously undescribed class of macromolecular porphyrin architectures.
MetJ repressor interactions with DNA probed by in-cell NMR
Authors: Augustus Anne M. , Reardon Patrick N. , Spicer Leonard D.
Published: March 2009

Atomic level characterization of proteins and other macromolecules in the living cell is challenging. Recent advances in NMR instrumentation and methods, however, have enabled in-cell studies with prospects for multidimensional spectral characterization of individual macromolecular components. We present NMR data on the in-cell behavior of the MetJ repressor from
Escherichia coli
, a protein that regulates the expression of genes involved in methionine biosynthesis. NMR studies of whole cells along with corresponding studies in cell lysates and in vitro preparations of the pure protein give clear evidence for extensive nonspecific interactions with genomic DNA. These interactions can provide an efficient mechanism for searching out target sequences by reducing the dependence on 3-dimensional diffusion through the crowded cellular environment. DNA provides the track for MetJ to negotiate the obstacles inherent in cells and facilitates locating and binding specific repression sites, allowing for timely control of methionine biosynthesis.
The two-component system QseEF and the membrane protein QseG link adrenergic and stress sensing to bacterial pathogenesis
Authors: Reading Nicola C. , Rasko David A. , Torres Alfredo G. , Sperandio Vanessa
Published: March 2009

Bacterial pathogens sense host cues to activate expression of virulence genes. Most of these signals are sensed through histidine kinases (HKs), which comprise the main sensory mechanism in bacteria. The host stress hormones epinephrine (Epi) and norepinephrine are sensed through the QseC HK, which initiates a complex signaling cascade to regulate virulence gene expression in enterohemorrhagic
Escherichia coli
(EHEC). Epi signaling through QseC activates expression of the genes encoding the QseEF 2-component system. QseE is an HK, and QseF is a response regulator. Here, we show that QseE is a second bacterial adrenergic receptor that gauges the stress signals Epi, sulfate, and phosphate. The
qseEF
genes are organized within an unusual operonic structure, in that a gene is encoded between
qseE
and
qseF
. This gene was renamed
qseG
, and it was shown to encode an outer membrane (OM) protein. EHEC uses a type III secretion system (TTSS) to translocate effector proteins to the epithelial cells that rearrange the host cytoskeleton to form pedestal-like structures that cup the bacterium. QseE, QseG, and QseF are necessary for pedestal formation. Although QseE and QseF are involved in the transcriptional control of genes necessary for pedestal formation, QseG is necessary for translocation of effectors into epithelial cells. QseG is an OM protein necessary for translocation of TTSS effectors that also works in conjunction with a 2-component signaling system that senses host stress signals.
Cyclophilin 40 is required for microRNA activity in
Arabidopsis
Authors: Smith Michael R. , Willmann Matthew R. , Wu Gang , Berardini Tanya Z. , Möller Barbara , Weijers Dolf , Poethig R. Scott
Published: March 2009

Loss-of-function mutations of
SQUINT
(
SQN
)—which encodes the
Arabidopsis
orthologue of cyclophilin 40 (CyP40)—cause the precocious expression of adult vegetative traits, an increase in carpel number, and produce abnormal spacing of flowers in the inflorescence. Here we show that the vegetative phenotype of
sqn
is attributable to the elevated expression of miR156-regulated members of the SPL family of transcription factors and provide evidence that this defect is a consequence of a reduction in the activity of ARGONAUTE1 (AGO1). Support for this latter conclusion was provided by the phenotypic similarity between hypomorphic alleles of
AGO1
and null alleles of
SQN
and by the genetic interaction between
sqn
and these alleles. Our results suggest that AGO1, or an AGO1-interacting protein, is a major client of CyP40 and that miR156 and its targets play a central role in the regulation of vegetative phase change in
Arabidopsis
.
MicroRNA expression profiles predictive of human renal allograft status
Authors: Anglicheau Dany , Sharma Vijay K. , Ding Ruchuang , Hummel Aurélie , Snopkowski Catherine , Dadhania Darshana , Seshan Surya V. , Suthanthiran Manikkam
Published: March 2009

Immune rejection of organ transplants is a life-threatening complication and is exemplified by alterations in the expression of protein-encoding genes. Because microRNAs (miRNAs) regulate the expression of genes implicated in adaptive immunity, we investigated whether acute rejection (AR) is associated with alterations in miRNA expression within allografts and whether expression profiles are diagnostic of AR and predict allograft function. Seven of 33 renal allograft biopsies (12 AR and 21 normal) were profiled using microfluidic cards containing 365 mature human miRNAs (training set), and a subset of differentially expressed miRNAs were quantified in the remaining 26 allograft biopsies (validation set). We found a strong association between intragraft expression of miRNAs and messenger RNAs (mRNAs), and that AR, and renal allograft function, could be predicted with a high level of precision using intragraft levels of miRNAs. Our investigation of miRNA expression in normal human peripheral blood mononuclear cells (PBMCs) showed that miRNAs (miR-142–5p, -155, and -223) overexpressed in AR biopsies are highly expressed in PBMCs, and that stimulation with the mitogen phytohaemagglutinin results in an increase in the abundance of miR-155 and a decrease in miR-223 and let-7c. Quantification of miRNAs in primary cultures of human renal epithelial cells (HRECs) showed that miR-30a-3p, -10b, and let-7c are highly expressed in HRECs, and that stimulation results in a decreased expression of miR-30a-3p. Our studies, in addition to suggesting a cellular basis for the altered intragraft expression of miRNAs, propose that miRNA expression patterns may serve as biomarkers of human renal allograft status.
Medial temporal theta state before an event predicts episodic encoding success in humans
Authors: Guderian Sebastian , Schott Björn H. , Richardson-Klavehn Alan , Düzel Emrah
Published: March 2009

We report a human electrophysiological brain state that predicts successful memory for events before they occur. Using magnetoencephalographic recordings of brain activity during episodic memory encoding, we show that amplitudes of theta oscillations shortly preceding the onsets of words were higher for later-recalled than for later-forgotten words. Furthermore, single-trial analyses revealed that recall rate in all 24 participants tested increased as a function of increasing prestimulus theta amplitude. This positive correlation was independent of whether participants were preparing for semantic or phonemic stimulus processing, thus likely signifying a memory-related theta state rather than a preparatory task set. Source analysis located this theta state to the medial temporal lobe, a region known to be critical for encoding and recall. These findings provide insight into state-related aspects of memory formation in humans, and open a perspective for improving memory through theta-related brain states.
Reconstructing web evolution and spider diversification in the molecular era
Authors: Blackledge Todd A. , Scharff Nikolaj , Coddington Jonathan A. , Szüts Tamas , Wenzel John W. , Hayashi Cheryl Y. , Agnarsson Ingi
Published: March 2009

The evolutionary diversification of spiders is attributed to spectacular innovations in silk. Spiders are unique in synthesizing many different kinds of silk, and using silk for a variety of ecological functions throughout their lives, particularly to make prey-catching webs. Here, we construct a broad higher-level phylogeny of spiders combining molecular data with traditional morphological and behavioral characters. We use this phylogeny to test the hypothesis that the spider orb web evolved only once. We then examine spider diversification in relation to different web architectures and silk use. We find strong support for a single origin of orb webs, implying a major shift in the spinning of capture silk and repeated loss or transformation of orb webs. We show that abandonment of costly cribellate capture silk correlates with the 2 major diversification events in spiders (1). Replacement of cribellate silk by aqueous silk glue may explain the greater diversity of modern orb-weaving spiders (Araneoidea) compared with cribellate orb-weaving spiders (Deinopoidea) (2). Within the “RTA clade,” which is the sister group to orb-weaving spiders and contains half of all spider diversity, >90% of species richness is associated with repeated loss of cribellate silk and abandonment of prey capture webs. Accompanying cribellum loss in both groups is a release from substrate-constrained webs, whether by aerially suspended webs, or by abandoning webs altogether. These behavioral shifts in silk and web production by spiders thus likely played a key role in the dramatic evolutionary success and ecological dominance of spiders as predators of insects.