@article{ShumyantsevaIvanovBistolasetal.2004,
  author    = {Shumyantseva, V. V. and Ivanov, Y. D. and Bistolas, Nikitas and Scheller, Frieder W. and Archakov, Alexander I. and Wollenberger, Ursula},
  title     = {Direct electron transfer of cytochrome P450 2B4 at electrodes modified with non-ionic detergent and colloidal clay nanoparticles},
  year      = {2004},
  abstract  = {A method for construction of biosensors with membranous cytochrome P450 isoenzymes was developed based on clay/ detergent/protein mixed films. Thin films of sodium montmorillonite colloid with incorporated cytochrome P450 2134 (CYP2B4) with nonionic detergent were prepared on glassy carbon electrodes. The modified electrodes were electrochemically characterized, and bio-electrocatalytic reactions were followed. CYP2B4 can be reduced fast on clay- modified glassy carbon electrodes in the presence of the nonionic detergent Tween 80. In anaerobic solutions, reversible oxidation and reduction is obtained with a formal potential between -0.292 and - 0.305 V vs Ag/AgCl 1 M KCl depending on the preparation of the biosensor. In air-saturated solution, bio-electrocatalytic reduction currents can be obtained with the CYP2B4-modified electrode on addition of typical substrates such as aminopyrine and benzphetamine. This reaction was suppressed when methyrapone, an inhibitor of P450 reactions, was present. Measurement of product formation also indicates the bioelectrocatialysis by CYP2B4},
  language  = {en}
}
@article{ZbilutGiulianiColosimoetal.2004,
  author    = {Zbilut, J. P. and Giuliani, A. and Colosimo, A. and Mitchell, J. C. and Colafranceschi, M. and Marwan, Norbert and Webber, C. L. and Uversky, V. N.},
  title     = {Charge and hydrophobicity patterning along the sequence predicts the folding mechanism and aggregation of proteins : a computational approach},
  issn      = {1535-3893},
  year      = {2004},
  abstract  = {The presence of partially folded intermediates along the folding funnel of proteins has been suggested to be a signature of potentially aggregating systems. Many studies have concluded that metastable, highly flexible intermediates are the basic elements of the aggregation process. In a previous paper, we demonstrated how the choice between aggregation and folding behavior was influenced by hydrophobicity distribution patterning along the sequence, as quantified by recurrence quantification analysis (RQA) of the Myiazawa-Jernigan coded primary structures. In the present paper, we tried to unify the "partially folded intermediate" and "hydrophobicity/charge" models of protein aggregation verifying the ability of an empirical relation, developed for rationalizing the effect of different mutations on aggregation propensity of acyl-phosphatase and based on the combination of hydrophobicity RQA and charge descriptors, to discriminate in a statistically significant way two different protein populations: (a) proteins that fold by a process passing by partially folded intermediates and (b) proteins that do not present partially folded intermediates},
  language  = {en}
}
@article{PacholskyVakeelHimmeletal.2004,
  author    = {Pacholsky, Dirk and Vakeel, Padmanabhan and Himmel, Mirko and Lowe, T. and Stradal, T. and Rottner, K. and F{\"u}rst, Dieter Oswald and vanderVen, Peter F. M.},
  title     = {Xin repeats define a novel actin-binding motif},
  issn      = {0021-9533},
  year      = {2004},
  abstract  = {Xin is a protein that is expressed during early developmental stages of cardiac and skeletal muscles. Immunolocalization studies indicated a peripheral localization in embryonic mouse heart, where Xin localizes with beta- catenin and N-cadherin. In adult tissues, Xin is found primarily in the intercalated discs of cardiomyocytes and the myotendinous junctions of skeletal muscle cells, both specialized attachment sites of the myofibrillar ends to the sarcolemma. A large part of the Xin protein consists of unique 16 amino acid repeats with unknown function. We have investigated the characteristics of the Xin repeats by transfection experiments and actin-binding assays and ascertained that, upon expression in cultured cells, these repeats bind to and stabilize the actin-based cytoskeleton. In vitro co- sedimentation assays with skeletal muscle actin indicated that they not only directly bind actin filaments, but also have the capability of arranging microfilaments into networks that sediment upon low-speed centrifugation. Very similar repeats were also found in Xin-repeat protein 2' (XIRP2), a novel protein that seems to be expressed mainly in striated muscles. Human XIRP2 contains 28 Xin repeats with properties identical to those of Xin. We conclude that the Xin repeats define a novel, repetitive actin-binding motif present in at least two different muscle proteins. These Xin- repeat proteins therefore constitute the first two members of a novel family of actin-binding proteins},
  language  = {en}
}
@article{WiegandJeltschWard2004,
  author    = {Wiegand, K. and Jeltsch, Florian and Ward, D.},
  title     = {Minimum recruitment frequency in plants with episodic recruitment},
  year      = {2004},
  abstract  = {There is concern about the lack of recruitment of Acacia trees in the Negev desert of Israel. We have developed three models to estimate the frequency of recruitment necessary for long-term population survival (i.e. positive average population growth for 1,000 years and <10\% probability of extinction). Two models assume purely episodic recruitment based on the general notion that recruitment in and environments is highly episodic. They differ in that the deterministic model investigates average dynamics while the stochastic model does not. Studies indicating that recruitment episodes in and environments have been overemphasized motivated the development of the third model. This semi-stochastic model simulates a mixture of continuous and episodic recruitment. Model analysis was done analytically for the deterministic model and via running model simulations for the stochastic and semi-stochastic models. The deterministic and stochastic models predict that, on average, 2.2 and 3.7 recruitment events per century, respectively, are necessary to sustain the population. According to the semi-stochastic model, 1.6 large recruitment events per century and an annual probability of 50\% that a small recruitment event occurs are needed. A consequence of purely episodic recruitment is that all recruitment episodes produce extremely large numbers of recruits (i.e. at odds with field observations), an evaluation that holds even when considering that rare events must be large. Thus, the semi- stochastic model appears to be the most realistic model. Comparing the prediction of the semi-stochastic model to field observations in the Negev desert shows that the absence of observations of extremely large recruitment events is no reason for concern. However, the almost complete absence of small recruitment events is a serious reason for concern. The lack of recruitment may be due to decreased densities of large mammalian herbivores and might be further exacerbated by possible changes in climate, both in terms of average precipitation and the temporal distribution of rain},
  language  = {en}
}
@article{WeberOesterheltGrossetal.2004,
  author    = {Weber, Andreas P. M. and Oesterhelt, Christine and Gross, Wolfgang and Br{\"a}utigam, Andrea and Imboden, Lori and Krassovskaya, Inga and Linka, Nicole and Truchina, Julia and Schneidereit, J{\"o}rg and Voll, Lars and Zimmermann, Marc and Jamai, Aziz and Riekhof, Wayne and Yu, Bin and Garavito, Michael R. and Benning, Christoph},
  title     = {EST-analysis of the thermo-acidophilic red microalga Galdieria sulphuraria reveals potential for lipid A biosynthesis and unveils the pathway of carbon export from rhodoplasts},
  year      = {2004},
  abstract  = {When we think of extremophiles, organisms adapted to extreme environments, prokaryotes come to mind first. However, the unicellular red micro-alga Galdieria sulphuraria (Cyanidiales) is a eukaryote that can represent up to 90\% of the biomass in extreme habitats such as hot sulfur springs with pH values of 0-4 and temperatures of up to 56 degreesC. This red alga thrives autotrophically as well as heterotrophically on more than 50 different carbon sources, including a number of rare sugars and sugar alcohols. This biochemical versatility suggests a large repertoire of metabolic enzymes, rivaled by few organisms and a potentially rich source of thermo-stable enzymes for biotechnology. The temperatures under which this organism carries out photosynthesis are at the high end of the range for this process, making G. sulphuraria a valuable model for physical studies on the photosynthetic apparatus. In addition, the gene sequences of this living fossil reveal much about the evolution of modern eukaryotes. Finally, the alga tolerates high concentrations of toxic metal ions such as cadmium, mercury, aluminum, and nickel, suggesting potential application in bioremediation. To begin to explore the unique biology of G. sulphuraria, 5270 expressed sequence tags from two different cDNA libraries have been sequenced and annotated. Particular emphasis has been placed on the reconstruction of metabolic pathways present in this organism. For example, we provide evidence for (i) a complete pathway for lipid A biosynthesis; (ii) export of triose-phosphates from rhodoplasts; (iii) and absence of eukaryotic hexokinases. Sequence data and additional information are available at http://genomics.msu.edu/galdieria},
  language  = {en}
}
@article{vanKleunenRitland2004,
  author    = {van Kleunen, Mark and Ritland, K.},
  title     = {Predicting evolution of floral traits associated with mating system in a natural plant population},
  issn      = {1010- 061x},
  year      = {2004},
  abstract  = {Evolution of floral traits requires that they are heritable, that they affect fitness, and that they are not constrained by genetic correlations. These prerequisites have only rarely been examined in natural populations. For Mimulus guttatus, we found by using the Riska-method that corolla width, anther length, ovary length and number of red dots on the corolla were heritable in a natural population. Seed production (maternal fitness) was directly positively affected by corolla width and anther size, and indirectly so by ovary length and number of red dots on the corolla. The siring success (paternal fitness), as estimated from allozyme data, was directly negatively affected by anther-stigma separation, and indirectly so by the corolla length-width ratio. Genetic correlations, estimated with the Lynch-method, were positive between floral size measures. We predict that larger flowers with larger reproductive organs, which generally favour outcrossing, will evolve in this natural population of M. guttatus},
  language  = {en}
}
@article{UsadelKuschinskyRossoetal.2004,
  author    = {Usadel, Bj{\"o}rn and Kuschinsky, Anja M. and Rosso, Mario G. and Eckermann, Nora and Pauly, Markus},
  title     = {RHM2 is involved in mucilage pectin synthesis and is required for the development of the seed coat in Arabidopsis},
  year      = {2004},
  abstract  = {Pectins are major components of primary plant cell walls and the seed mucilage of Arabidopsis. Despite progress in the structural elucidation of pectins, only very few enzymes participating in or regulating their synthesis have been identified. A first candidate gene involved-in the synthesis of pectinaceous rhamnogalacturonan I is RHM2, a putative plant ortholog to NDP-rhamnose biosynthetic enzymes in bacteria. Expression studies with a promoter beta-glucuronidase construct and reverse transcription PCR data show that RHM2 is expressed ubiquitously. Rhm2 T-DNA insertion mutant lines were identified using a reverse genetics approach. Analysis of the rhm2 seeds by various staining methods and chemical analysis of the mucilage revealed a strong reduction of rhamnogalacturonan I in the mucilage and a decrease of its molecular weight. In addition, scanning electron microscopy of the seed surface indicated a distorted testa morphology, illustrating not only a structural but also a developmental role for RGI or rhamnose metabolism in proper testa formation},
  language  = {en}
}
@article{JeltschTewsSchurr2004,
  author    = {Jeltsch, Florian and Tews, J{\"o}rg and Schurr, Frank Martin},
  title     = {Seed dispersal by cattle may cause shrub encroachment of Grewia flava on southern Kalahari rangelands},
  year      = {2004},
  abstract  = {Shrub encroachment, i.e. the increase in woody plant cover, is a major concern for livestock farming in southern Kalahari savannas. We developed a grid-based computer model simulating the population dynamics of Grewia flava, a common, fleshy-fruited encroaching shrub. In the absence of large herbivores, seeds of Grewia are largely deposited in the sub-canopy of Acacia erioloba. Cattle negate this dispersal limitation by browsing on the foliage of Grewia and dispersing seeds into the grassland matrix. In this study we first show that model predictions of Grewia cover dynamics are realistic by comparing model output with shrub cover estimates obtained from a time series of aerial photographs. Subsequently, we apply a realistic range of intensity of cattle-induced seed dispersal combined with potential precipitation and fire scenarios. Based on the simulation results we suggest that cattle may facilitate shrub encroachment of Grewia. The results show that the severity of shrub encroachment is governed by the intensity of seed dispersal. For a high seed dispersal intensity without fire (equivalent to a high stocking rate) the model predicts 56\% shrub cover and 85\% cell cover after 100 yr. With fire both recruitment and shrub cover are reduced, which may, under moderate intensities, prevent shrub encroachment. Climate change scenarios with two-fold higher frequencies of drought and wet years intensified shrub encroachment rates, although long-term mean of precipitation remained constant. As a management recommendation we suggest that shrub encroachment on rangelands may be counteracted by frequent fires and controlling cattle movements to areas with a high proportion of fruiting Grewia shrubs},
  language  = {en}
}
@article{VaajeKolstadHoustonRaoetal.2004,
  author    = {Vaaje-Kolstad, G. and Houston, Douglas R. and Rao, F. V. and Peter, Martin G. and Synstad, Bjoenar and van Aalten, Daan M. F. and Eijsink, Vincent G. H.},
  title     = {Structure of the D142N mutant of the family 18 chitinase ChiB from Serratia marcescens and its complex with allosamidin},
  issn      = {1570-9639},
  year      = {2004},
  abstract  = {Catalysis by ChiB, a family 18 chitinase from Serratia marcescens, involves a conformational change of Asp142 which is part of a characteristic D140XD142XE144 sequence motif In the free enzyme Asp142 points towards Asp140, whereas it rotates towards the catalytic acid, Glu144, upon ligand binding. Mutation of Asp142 to Asn reduced k(cat) and affinity for allosamidin, a competitive inhibitor. The X-ray structure of the D142N mutant showed that Asn142 points towards Glu144 in the absence of a ligand. The active site also showed other structural adjustments (Tyr10, Ser93) that had previously been observed in the wild-type enzyme upon substrate binding. The X-ray structure of a complex of D142N with allosamidin, a pseudotrisaccharide competitive inhibitor, was essentially identical to that of the wild-type enzyme in complex with the same compound. Thus, the reduced allosamidin affinity in the mutant is not caused by structural changes but solely by the loss of electrostatic interactions with Asp142. The importance of electrostatics was further confirmed by the pH dependence of catalysis and allosamidin inhibition. The pH-dependent apparent affinities for allosamidin were not correlated with k(cat), indicating that it is probably better to view the inhibitor as a mimic of the oxazolinium ion reaction intermediate than as a transition state analogue. (C) 2003 Elsevier B.V. All rights reserved},
  language  = {en}
}
@article{JeltschTewsMoloney2004,
  author    = {Jeltsch, Florian and Tews, J{\"o}rg and Moloney, Kirk A.},
  title     = {Modelling seed dispersal in a variable environment : a case study of the fleshy-fruited savanna shrub Grewia flava},
  year      = {2004},
  abstract  = {In ecology much attention has been paid towards seed dispersal of fleshy-fruited plants, however, knowledge is lacking about the Iona-term demographic consequences of variation in dispersal distance and fruit removal rate, particularly given the natural variability of the environment the organism lives in. In this study we used a spatially explicit, two-level stochastic computer model to simulate population dynamics of a fleshy-fruited shrub living in the sub-canopy of solitary savanna trees. On the landscape level we implemented three realistic scenarios of savanna landscape dynamics for a period of 500 years with equal inter-annual mean of environmental variables. The first scenario is representative of a relatively constant environment with normal variability in precipitation, constant tree density and random tree recruitment pattern. The second and third scenarios represent positive auto-correlated, cyclic patterns with alternating phases of tree cover increase and decrease corresponding with favorable and unfavorable rain phases. Our simulation experiments show that when fruit removal rate is extremely low, population persistence is enhanced under relatively constant rain conditions, while alternating rain phases of the cyclic scenarios lead to a significant population decrease. This result confirms previous findings that periodically fluctuating environments may increase local extinction risk. However, when dispersal distance is a limiting factor (whilst removal rate was sufficiently high), tree clumps typically forming in wet phases of both cyclic scenarios compensated for the negative effect of low dispersal distances, while the constant scenario with random tree pattern and larger inter-tree distances resulted in a significant population decline. (C) 2003 Elsevier B.V. All rights reserved},
  language  = {en}
}