@article{2984, abstract = {Auxins represent an important class of plant hormone that regulate plant development. Plants use specialized carrier proteins to transport the auxin indole-3-acetic acid (IAA) to target tissues. To date, efflux carrier-mediated polar auxin transport has been assumed to represent the sole mode of long distance IAA movement. Localization of the auxin permease AUX1 in the Arabidopsis root apex has revealed a novel phloem-based IAA transport pathway. AUX1, asymmetrically localized to the plasma membrane of root protophloem cells, is proposed to promote the acropetal, post-phloem movement of auxin to the root apex. MS analysis shows that IAA accumulation in aux1 mutant root apices is impaired, consistent with an AUX1 phloem unloading function. AUX1 localization to columella and lateral root cap tissues of the Arabidopsis root apex reveals that the auxin permease regulates a second IAA transport pathway. Expression studies using an auxin-regulated reporter suggest that AUX1 is necessary for root gravitropism by facilitating basipetal auxin transport to distal elongation zone tissues.}, author = {Swarup, Ranjan and Friml, Jirí and Marchant, Alan and Ljung, Karin and Sandberg, Göran and Palme, Klaus and Bennett, Malcolm}, issn = {Genes and Development}, journal = {Genes and Development}, number = {20}, pages = {2648 -- 2653}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{Localization of the auxin permease AUX1 suggests two functionally distinct hormone transport pathways operate in the Arabidopsis root apex}}, doi = {10.1101/gad.210501}, volume = {15}, year = {2001}, } @article{2985, abstract = {The elimination voltammetry with linear scan (EVLS) was used to study adenine and cytosine reduction signals at the mercury electrode. In comparison with the linear scan voltammetry (which provides only one unresolved peak), two elimination functions provide good resolution of individual peaks and significant increase of sensitivity. The first elimination function eliminates the kinetic current (Ik) and conserves the diffusion current (Id). The second elimination function eliminates kinetic and charging currents (Ik and Ic) simultaneously and conserves the diffusion current (Id). Both functions give two well-resolved peaks of adenine and cytosine in a wide concentration range, while the linear sweep voltammetry gives badly resolved peaks due to hydrogen evolution. The best resolution of peaks is observed in acetate buffer at pH 3.8 and the detection limit for both substances is 500 nM. The concentration dependence of EVLS peak heights for one substance at the constant concentration of the other substance is linear. The peak potentials differ in these elimination functions. The difference in EVLS peak potentials gives the possibility to evaluate αna. Elimination voltammetry with linear scan contributes to the resolution of cathodic signals of purine and pyrimidine bases at very negative potentials near supporting electrolyte discharge. Copyright © 2001 Elsevier Science B.V.}, author = {Trnková, Libuše and Friml, Jirí and Dračka, Oldřich}, isbn = {1567-5394}, journal = {Bioelectrochemistry}, number = {2}, pages = {131 -- 136}, publisher = {Elsevier}, title = {{Elimination voltammetry of adenine and cytosine mixtures}}, doi = {10.1016/S1567-5394(01)00119-0}, volume = {54}, year = {2001}, } @inproceedings{3169, abstract = {Several new algorithms for visual correspondence based on graph cuts [7, 14, 17] have recently been developed. While these methods give very strong results in practice, they do not handle occlusions properly. Specifically, they treat the two input images asymmetrically, and they do not ensure that a pixel corresponds to at most one pixel in the other image. In this paper, we present a new method which properly addresses occlusions, while preserving the advantages of graph cut algorithms. We give experimental results for stereo as well as motion, which demonstrate that our method performs well both at detecting occlusions and computing disparities.}, author = {Kolmogorov, Vladimir and Zabih, Ramin}, booktitle = {Proceedings of the 8th IEEE International Conference on Computer Vision}, isbn = {0769511430}, location = {Vancouver, Canada}, pages = {508 -- 515}, publisher = {IEEE}, title = {{Computing visual correspondence with occlusions using graph cuts}}, doi = {10.1109/ICCV.2001.937668}, volume = {2}, year = {2001}, } @inbook{3434, abstract = {This chapter contains sections titled: Introduction - History - Developing an Intuition of Likelihood - Method of Maximum Likelihood - Bayesian Inference - Markov Chain Monte Carlo - Assessing Uncertainty of Phylogenies - Hypothesis Testing and Model Choice - Comparative Analysis - Conclusions - References}, author = {Huelsenbeck, John and Bollback, Jonathan P}, booktitle = {Handbook of Statistical Genetics}, editor = {Balding, David and Bishop, Martin and Cannings, Chriss}, isbn = {9781119429142 }, pages = {415 -- 439}, publisher = {Wiley-Blackwell}, title = {{Application of the likelihood function in phylogenetic analysis}}, doi = {10.1002/9780470061619.ch15}, year = {2001}, } @article{3438, abstract = {As a discipline, phylogenetics is becoming transformed by a flood of molecular data. These data allow broad questions to be asked about the history of life, but also present difficult statistical and computational problems. Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences.}, author = {Huelsenbeck, John and Ronquist, Fredrik and Nielsen, Rasmus and Bollback, Jonathan P}, issn = {0036-8075}, journal = {Science}, number = {5550}, pages = {2310 -- 2314}, publisher = {American Association for the Advancement of Science}, title = {{Bayesian inference of phylogeny and its impact on evolutionary biology}}, doi = {10.1126/science.1065889}, volume = {294}, year = {2001}, } @article{3439, abstract = {High molecular weight DNA was extracted from the primary Neotropical malaria vector, Anopheles darlingi from Capanema, Pará, Brazil, to create a small insert genomic library, and then a phagemid library. Enriched sublibraries were constructed from the phagemid library using a microsatellite oligo primed second strand synthesis protocol. The resulting 242 760 individual clones were screened. The mean clone size of the positive clones was 302 bp. Flanking primers were designed for each suitable microsatellite sequence. Eight polymorphic loci were optimized and characterized. The allele size ranges are based on 253 samples of A. darlingi from eastern Amazonian and central Brazil.}, author = {Conn, Jan and Bollback, Jonathan P and Onyabe, David and Robinson, Tessa and Wilkerson, Richard and Povoa, Marinete}, issn = {1471-8278}, journal = {Molecular Ecology Notes}, number = {4}, pages = {223 -- 225}, publisher = {Wiley-Blackwell}, title = {{Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi}}, doi = { 10.1046/j.1471-8278.2001.00078.x}, volume = {1}, year = {2001}, } @article{3440, abstract = {Several methods have been proposed to infer the states at the ancestral nodes on a phylogeny. These methods assume a specific tree and set of branch lengths when estimating the ancestral character state. Inferences of the ancestral states, then, are conditioned on the tree and branch lengths being true. We develop a hierarchical Bayes method for inferring the ancestral states on a tree. The method integrates over uncertainty in the tree, branch lengths, and substitution model parameters by using Markov chain Monte Carlo. We compare the hierarchical Bayes inferences of ancestral states with inferences of ancestral states made under the assumption that a specific tree is correct. We find that the methods are correlated, but that accommodating uncertainty in parameters of the phylogenetic model can make inferences of ancestral states even more uncertain than they would be in an empirical Bayes analysis. }, author = {Huelsenbeck, John and Bollback, Jonathan P}, issn = {0039-7989}, journal = {Systematic Biology}, number = {3}, pages = {351 -- 366}, publisher = {Oxford University Press}, title = {{Empirical and hierarchical Bayesian estimation of ancestral states}}, doi = {10.1080/10635150119871}, volume = {50}, year = {2001}, } @inproceedings{3447, author = {Krishnendu Chatterjee and Dasgupta, Pallab and Chakrabarti, Partha P}, publisher = {Elsevier}, title = {{Weighted quantified computation tree logic}}, year = {2001}, } @article{3493, abstract = {Although agonists and competitive antagonists presumably occupy overlapping binding sites on ligand-gated channels, these interactions cannot be identical because agonists cause channel opening whereas antagonists do not. One explanation is that only agonist binding performs enough work on the receptor to cause the conformational changes that lead to gating. This idea is supported by agonist binding rates at GABAA and nicotinic acetylcholine receptors that are slower than expected for a diffusion-limited process, suggesting that agonist binding involves an energy-requiring event. This hypothesis predicts that competitive antagonist binding should require less activation energy than agonist binding. To test this idea, we developed a novel deconvolution-based method to compare binding and unbinding kinetics of GABAA receptor agonists and antagonists in outside-out patches from rat hippocampal neurons. Agonist and antagonist unbinding rates were steeply correlated with affinity. Unlike the agonists, three of the four antagonists tested had binding rates that were fast, independent of affinity, and could be accounted for by diffusion- and dehydration-limited processes. In contrast, agonist binding involved additional energy-requiring steps, consistent with the idea that channel gating is initiated by agonist-triggered movements within the ligand binding site. Antagonist binding does not appear to produce such movements, and may in fact prevent them.}, author = {Jones, M.V and Jonas, Peter M and Sahara, Y. and Westbrook, G.}, issn = {0006-3495}, journal = {Biophysical Journal}, number = {5}, pages = {2660 -- 2670}, publisher = {Biophysical Society}, title = {{Microscopic kinetics and energetics distinguish GABAA receptor agonists from antagonists}}, doi = {10.1016/S0006-3495(01)75909-7 }, volume = {81}, year = {2001}, } @article{3494, abstract = {Mutual synaptic interactions between GABAergic interneurons are thought to be of critical importance for the generation of network oscillations and for temporal encoding of information in the hippocampus. However, the functional properties of synaptic transmission between hippocampal interneurons are largely unknown. We have made paired recordings from basket cells (BCs) in the dentate gyrus of rat hippocampal slices, followed by correlated light and electron microscopical analysis. Unitary GABAAreceptor-mediated IPSCs at BC–BC synapses recorded at the soma showed a fast rise and decay, with a mean decay time constant of 2.5 ± 0.2 msec (32°C). Synaptic transmission at BC–BC synapses showed paired-pulse depression (PPD) (32 ± 5% for 10 msec interpulse intervals) and multiple-pulse depression during repetitive stimulation. Detailed passive cable model simulations based on somatodendritic morphology and localization of synaptic contacts further indicated that the conductance change at the postsynaptic site was even faster, decaying with a mean time constant of 1.8 ± 0.6 msec. Sequential triple recordings revealed that the decay time course of IPSCs at BC–BC synapses was approximately twofold faster than that at BC–granule cell synapses, whereas the extent of PPD was comparable. To examine the consequences of the fast postsynaptic conductance change for the generation of oscillatory activity, we developed a computational model of an interneuron network. The model showed robust oscillations at frequencies >60 Hz if the excitatory drive was sufficiently large. Thus the fast conductance change at interneuron–interneuron synapses may promote the generation of high-frequency oscillations observed in the dentate gyrusin vivo. }, author = {Bartos, Marlene and Vida, Imre and Frotscher, Michael and Geiger, Jörg and Jonas, Peter M}, issn = {0270-6474}, journal = {Journal of Neuroscience}, number = {8}, pages = {2687 -- 2698}, publisher = {Society for Neuroscience}, title = {{Rapid signaling at inhibitory synapses in a dentate gyrus interneuron network.}}, doi = {10.1523/JNEUROSCI.21-08-02687.2001}, volume = {21}, year = {2001}, } @article{3495, abstract = {High Ca2+ permeability and its control by voltage-dependent Mg2+ block are defining features of NMDA receptors. These features are lost if the principal NR1 subunit carries an asparagine (N) to arginine (R) substitution in a critical channel site at NR1 position 598. NR1(R) expression from a single allele in gene-targeted NR1+/R mice is lethal soon after birth, precluding analysis of altered synaptic functions later in life. We therefore employed the forebrain specific αCaMKII promoter to drive tTA-mediated tetracyclin sensitive transcription of transgenes for NR1(R) and for lacZ as reporter. Transgene expression was observed in cortex, striatum, hippocampus, amygdala and olfactory bulb and was mosaic in all these forebrain regions. It was highest in olfactory bulb granule cells, in most of which Ca2+ permeability and voltage-dependent Mg2+ block of NMDA receptors were reduced to different extents. This indicates significant impairment of NMDA receptor function by NR1(R) in presence of the wild-type NR1 complement. Indeed, even though NR1(R) mRNA constituted only 18% of the entire NR1 mRNA population in forebrain, the transgenic mice died during adolescence unless transgene expression was suppressed by doxycycline. Thus, glutamate receptor function can be altered in the mouse by regulated NR1(R) transgene expression.}, author = {Jerecic, Jasna and Schulze, Christian and Jonas, Peter M and Sprengel, Rolf and Seeburg, Peter and Bischofberger, Joseph}, issn = {0169-328X}, journal = {Molecular Brain Research}, number = {1-2}, pages = {96 -- 104}, publisher = {Elsevier}, title = {{Impaired NMDA receptor function in mouse olfactory bulb neurons by tetracycline-sensitive NR1 (N598R) expression}}, doi = {10.1016/S0169-328X(01)00221-2}, volume = {94}, year = {2001}, } @article{3496, abstract = {The mossy fiber-CA3 pyramidal neuron synapse is a main component of the hippocampal trisynaptic circuitry. Recent studies, however, suggested that inhibitory interneurons are the major targets of the mossy fiber system. To study the regulation of mossy fiber-interneuron excitation, we examined unitary and compound excitatory postsynaptic currents in dentate gyrus basket cells, evoked by paired recording between granule and basket cells or extracellular stimulation of mossy fiber collaterals. The application of an associative high-frequency stimulation paradigm induced posttetanic potentiation (PTP) followed by homosynaptic long-term potentiation (LTP). Analysis of numbers of failures, coefficient of variation, and paired-pulse modulation indicated that both PTP and LTP were expressed presynaptically. The Ca2+ chelator 1,2-bis(2-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid (BAPTA) did not affect PTP or LTP at a concentration of 10 mM but attenuated LTP at a concentration of 30 mM. Both forskolin, an adenylyl cyclase activator, and phorbolester diacetate, a protein kinase C stimulator, lead to a long-lasting increase in excitatory postsynaptic current amplitude. H-89, a protein kinase A inhibitor, and bisindolylmaleimide, a protein kinase C antagonist, reduced PTP, whereas only bisindolylmaleimide reduced LTP. These results may suggest a differential contribution of protein kinase A and C pathways to mossy fiber-interneuron plasticity. Interneuron PTP and LTP may provide mechanisms to maintain the balance between synaptic excitation of interneurons and that of principal neurons in the dentate gyrus-CA3 network. }, author = {Alle, Henrik and Jonas, Peter M and Geiger, Jörg}, issn = {0027-8424}, journal = {PNAS}, number = {25}, pages = {14708 -- 14713}, publisher = {National Academy of Sciences}, title = {{PTP and LTP at a hippocampal mossy fiber-interneuron synapse}}, doi = {10.1073/pnas.251610898 }, volume = {98}, year = {2001}, } @misc{3507, abstract = {A molecular classification method is based on a space filling description of a molecule. The three dimensional body corresponding to the space filling molecular structure is divided into Voronoi regions to provide a basis for efficiently processing local structural information. A Delaunay triangulation provides a basis for systematically processing information relating to the Voronoi regions into shape descriptors in the form of topological elements. Preferably, additional shape and/or property descriptors are included in the classification method. The classification methods generally are used to identify similarities between molecules that can be used as property predictors for a variety of applications. Generally, the property predictions are the basis for selection of compounds for incorporation into efficacy evaluations.}, author = {Liang, Jie and Edelsbrunner, Herbert}, title = {{Molecular classification for property prediction}}, year = {2001}, } @article{3517, abstract = {A modular multichannel microdrive ('hyperdrive') is described. The microdrive uses printed circuit board technology and flexible fused silica capillaries. The modular design allows for the fabrication of 4-32 independently movable electrodes or `tetrodes'. The drives are re-usable and re-loading the drive with electrodes is simple. }, author = {Szabo, Imre and Czurkó, András and Csicsvari, Jozsef L and Hirase, Hajima and Leinekugel, Xavier and Buzsáki, György}, issn = {0165-0270}, journal = {Journal of Neuroscience Methods}, number = {1}, pages = {105 -- 110}, publisher = {Elsevier}, title = {{The application of printed circuit board technology for fabrication of multi-channel micro-drives}}, doi = {10.1016/S0165-0270(00)00362-9}, volume = {105}, year = {2001}, } @article{3540, abstract = {What determines the firing rate of cortical neurons in the absence of external sensory input or motor behavior, such as during sleep? Hero we report that, in a familiar environment, the discharge frequency of simultaneously recorded individual CA1 pyramidal neurons and the coactivation of cell pairs remain highly correlated across sleep-wake-steep sequences. However, both measures were affected when new sets of neurons were activated in a novel environment. Nevertheless, the grand mean firing rate of the whole pyramidal cell population remained constant across behavioral states and testing conditions. The findings suggest that long-term firing patterns of single cells can be modified by experience. We hypothesize that increased firing rates of recently used neurons are associated with a concomitant decrease in the discharge activity of the remaining population, leaving the mean excitability of the hippocampal network unaltered.}, author = {Hirase, Hajima and Leinekugel, Xavier and Czurkó, András and Csicsvari, Jozsef L and Buzsáki, György}, issn = {0027-8424}, journal = {PNAS}, number = {16}, pages = {9386 -- 9390}, publisher = {National Academy of Sciences}, title = {{Firing rates of hippocampal neurons are preserved during subsequent sleep episodes and modified by novel awake experience}}, doi = {10.1073/pnas.161274398}, volume = {98}, year = {2001}, } @article{3546, abstract = {Local versus distant coherence of hippocampal CA1 pyramidal cells was investigated in the behaving rat. Temporal cross-correlation of pyramidal cells revealed a significantly stronger relationship among local (<140 <mu>m) pyramidal neurons compared with distant (>300 mum) neurons during non-theta-associated immobility and sleep but not during theta-associated running and walking. In contrast, cross-correlation between local pyramidal cell-interneuron pairs was significantly stronger than between distant pairs during theta oscillations but were similar during non-theta-associated behaviors. We suggest that network state-dependent functional clustering of neuronal activity emerges because of the differential contribution of the main excitatory inputs, the perforant path, and Schaffer collaterals during theta and non-theta behaviors.}, author = {Hirase, Hajima and Leinekugel, Xavier and Csicsvari, Jozsef L and Czurkó, András and Buzsáki, György}, issn = {0270-6474}, journal = {Journal of Neuroscience}, number = {10}, publisher = {Society for Neuroscience}, title = {{Behavior-dependent states of the hippocampal network affect functional clustering of neurons}}, doi = {10.1523/JNEUROSCI.21-10-j0003.2001}, volume = {21}, year = {2001}, } @book{3586, abstract = {The book combines topics in mathematics (geometry and topology), computer science (algorithms), and engineering (mesh generation). The original motivation for these topics was the difficulty faced (both conceptually and in the technical execution) in any attempt to combine elements of combinatorial and of numerical algorithms. Mesh generation is a topic where a meaningful combination of these different approaches to problem solving is inevitable. The book develops methods from both areas that are amenable to combination, and explains recent breakthrough solutions to meshing that fit into this category.The book should be an ideal graduate text for courses on mesh generation. The specific material is selected giving preference to topics that are elementary, attractive, lend themselves to teaching, useful, and interesting.}, author = {Edelsbrunner, Herbert}, isbn = {0-521-79309-2}, pages = {190}, publisher = {Cambridge University Press}, title = {{Geometry and Topology for Mesh Generation}}, doi = {10.1017/CBO9780511530067}, volume = {7}, year = {2001}, } @misc{3596, author = {Barton, Nicholas H}, booktitle = {Trends in Genetics}, issn = {0168-9479}, pages = {420 -- 420}, publisher = {Elsevier}, title = {{Mendel and mathematics}}, doi = {10.1016/S0168-9525(01)02315-0}, volume = {17}, year = {2001}, } @article{3622, abstract = {The extent of genetic variation in fitness and its components and genetic variation's dependence on environmental conditions remain key issues in evolutionary biology. We present measurements of genetic variation in preadult viability in a laboratory-adapted population of Drosophila melanogaster, made at four different densities. By crossing flies heterozygous for a wild-type chromosome and one of two different balancers (TM1, TM2), we measure both heterozygous (TM1/+, TM2/+) and homozygous (+/+) viability relative to a standard genotype (TM1/TM2). Forty wild-type chromosomes were tested, of which 10 were chosen to be homozygous viable. The mean numbers produced varied significantly between chromosome lines, with an estimated between-line variance in loge numbers of 0.013. Relative viabilities also varied significantly across chromosome lines, with a variance in loge homozygous viability of 1.76 and of loge heterozygous viability of 0.165. The between-line variance for numbers emerging increased with density, from 0.009 at lowest density to 0.079 at highest. The genetic variance in relative viability increases with density, but not significantly. Overall, the effects of different chromosomes on relative viability were remarkably consistent across densities and across the two heterozygous genotypes (TM1, TM2). The 10 lines that carried homozygous viable wild-type chromosomes produced significantly more adults than the 30 lethal lines at low density and significantly fewer adults at the highest density. Similarly, there was a positive correlation between heterozygous viability and mean numbers at low density, but a negative correlation at high density.}, author = {Gardner, Michael and Fowler, Kevin and Patridge, Linda and Barton, Nicholas H}, issn = {0014-3820}, journal = {Evolution}, number = {8}, pages = {1609 -- 1620}, publisher = {Wiley-Blackwell}, title = {{Genetic variation for preadult viability in Drosophila melanogaster}}, doi = {10.1111/j.0014-3820.2001.tb00680.x}, volume = {55}, year = {2001}, } @article{3927, abstract = {TNF-alpha has been clearly identified as central mediator of T cell activation-induced acute hepatic injury in mice, e.g., Con A hepatitis. In this model, liver injury depends on both TNFRs, i.e., the 55-kDa TNFR1 as well as the 75-kDa TNFR2. We show in this report that the hepatic TNFRs are not transcriptionally regulated, but are regulated by receptor shedding. TNF directly mediates hepatocellular death by activation of TNFR1 but also induces the expression of inflammatory proteins, such as cytokines and adhesion molecules. Here we provide evidence that resistance of TNFR1(-/-) and TNFR2(-/-) mice against Con A hepatitis is not due to an impaired production of the central mediators TNF and IFN-gamma. Con A injection results in a massive induction of ICAM-1, VCAM-1, and E-selectin in the liver. Lack of either one of both TNFRs did not change adhesion molecule expression in the livers of Con A-treated mice, presumably reflecting the fact that other endothelial cell-activating cytokines up-regulated adhesion molecule expression. However, treatment of TNFR1(-/-) and TNFR2(-/-) mice with murine rTNF revealed a predominant role for TNFR1 for the induction of hepatic adhesion molecule expression. Pretreatment with blocking Abs against E- and P-selectin or of ICAM(-/-) mice with anti-VCAM-1 Abs failed to prevent Con A hepatitis, although accumulation of the critical cell population, i.e., CD4(+) T cells was significantly inhibited. Hence, up-regulation of adhesion molecules during acute hepatitis unlikely contributes to organ injury but rather represents a defense mechanism.}, author = {Wolf, Dominik and Hallmann, Rupert and Sass, Gabriele and Sixt, Michael K and Küsters, Sabine and Fregien, Bastian and Trautwein, Christian and Tiegs, Gisa}, issn = {0022-1767}, journal = {Journal of Immunology}, number = {2}, pages = {1300 -- 1307}, publisher = {American Association of Immunologists}, title = {{TNF-α-induced expression of adhesion molecules in the liver is under the control of TNFR1--relevance for concanavalin A-induced hepatitis}}, doi = {10.4049/jimmunol.166.2.1300}, volume = {166}, year = {2001}, }