TY - JOUR AB - We prove that in an undirected graph there are at most O(n²) cuts of size strictly less than of the size of the minimum cut. AU - Henzinger, Monika H AU - Williamson, David P. ID - 11761 IS - 1 JF - Information Processing Letters SN - 0020-0190 TI - On the number of small cuts in a graph VL - 59 ER - TY - CONF AB - This paper shows how a general technique, called lock-step search, used in dynamic graph algorithms, can be used to improve the running time of two problems arising in program verification and communication protocol design. (1)We consider the nonemptiness problem for Streett automata: We are given a directed graph G = (V, E) with n = ¦V¦ and m = ¦E¦, and a collection of pairs of subsets of vertices, called Streett pairs,〈L i , U i 〉, i = 1.k. The question is whether G has a cycle (not necessarily simple) which, for each 1 ≤ i ≤ k, if it contains a vertex from L i then it also contains a vertex of U i . Let b=Σ i=1..k |L i |+|U i |. The previously best algorithm takes time O((m + b) min{n, k}). We present an algorithm that takes time 𝑂(𝑚min{𝑚𝑙𝑜𝑔𝑛,‾‾‾‾‾‾√𝑘,𝑛}+𝑏𝑚𝑖𝑛{𝑙𝑜𝑔𝑛,𝑘}). (2)In communication protocol pruning we are given a directed graph G = (V, E) with l special vertices. The problem is to efficiently maintain the strongly-connected components of the special vertices on a restricted set of edge deletions. Let m i be the number of edges in the strongly connected component of the ith special vertex. The previously best algorithm repeatedly recomputes the strongly-connected components which leads to a running time of O(Σ i m 2i). We present an algorithm with time 𝑂(𝑙√∑𝑖𝑚1.5𝑖). AU - Henzinger, Monika H AU - Telle, Jan Arne ID - 11804 SN - 0302-9743 T2 - 5th Scandinavian Workshop on Algorithm Theory TI - Faster algorithms for the nonemptiness of streett automata and for communication protocol pruning VL - 1097 ER - TY - CONF AB - We state a new sampling lemma and use it to improve the running time of dynamic graph algorithms. For the dynamic connectivity problem the previously best randomized algorithm takes expected time O(log3 n) per update, amortized over Ω(m) updates. Using the new sampling lemma, we improve its running time to O(log2 n). There exists a lower bound in the cell probe model for the time per operation of Ω(log n/ log log n) for this problem. Similarly improved running times are achieved for 2-edge connectivity, k-weight minimum spanning tree, and bipartiteness. AU - Henzinger, Monika H AU - Thorup, Mikkel ID - 11910 SN - 0302-9743 T2 - 23rd International Colloquium on Automata, Languages, and Programming TI - Improved sampling with applications to dynamic graph algorithms VL - 1099 ER - TY - CONF AB - We are given a set 7 = {Tl , Tz, . . . , Tk} of rooted binary trees, each Ti leaf-labeled by a subset L(x) c {1,2 )...) n}. IfT is a tree on {1,2, . . , n}, we let T]L denote the subtree of T induced by the nodes of L and all their ancestors. The consensus tree problem asks whether there exists a tree T* such that for every I, T’ IC(Ti) is homeomorphic to Ti. We present algorithms which test if a given set of trees has a consensus tree and if so, construct one. The deterministic algorithm takes time min{O(mn’/‘), O(m + n2 logn)}, where m = Ci IZl and uses linear space. The randomized algorithm takes time O(m log3 n) and uses linear space. The previous best for this problem was an 1981 O(mn) algorithm by Aho et al. Our faster deterministic algorithm uses a new efficient algorithm for the following interesting dynamic graph problem: Given a graph G with n nodes and m edges and a sequence of b batches of one or more edge deletions, then after each batch, either find a new component that has just been created or determine that there is no such component. For this problem, we have a simple algorithm with running time O(n2 log n + be min{ n2, m log n}), where be is the number of batches which do not result in a new component. For our particular application, bc 5 1. If all edges are deleted, then the best previously known deterministic algorithm requires time O(mJ;ii) to solve this problem. computational evolutionary biology. The first application is in the problem of inferring consensus of trees when there can be disagreement[l6]. There have, been several models suggested for this problem[2, 3, 4, 8, ?, 11, 17, 181, of which one is called the Local Consensus Tree[l5]. The local consensus tree model presumes that the user provides a local consensus rule which determines the form of the output tree on (perhaps) each triple of leaves, and the objective is to determine whether a tree exists which is consistent with each of the constraints. We will show that we can construct the local consensus tree of k trees on n species in O(kn3) time, improving on the O(lcn3 + n”) running time if we use the Aho et al algorithm. The second application is a heuristic for constructing the maximum likelihood tree based upon combining solutions to small subproblems. This is a simple and yet potentially significantly interesting approach to the evolutionary tree construction problem. AU - Henzinger, Monika H AU - King, Valerie AU - Warnow, Tandy ID - 11927 SN - 0898713668 T2 - 7th Annual ACM-SIAM Symposium on Discrete Algorithms TI - Constructing a tree from homeomorphic subtrees, with applications to computational evolutionary biology ER - TY - CONF AU - Leonid Sazanov AU - Burrows, P AU - Nixon, P J ID - 1942 TI - Presence of a large protein complex containing the ndhK gene product and possessing NADH-specific dehydrogenase activity in thylakoid membranes of higher plant chloroplasts VL - 2 ER - TY - JOUR AB - Two strains of Rhodospirillum rubrum were constructed in which, by a gene dosage effect, the transhydrogenase activity of isolated chromatophores was increased 7-10-fold and 15-20-fold, respectively. The H+/H- ratio (the ratio of protons translocated per hydride ion equivalent transferred from NADPH to an NAD+ analogue, acetyl pyridine adenine dinucleotide), determined by a spectroscopic technique, was approximately 1.0 for chromatophores from the over-expressing strains, but was only approximately 0.6 for wild-type chromatophores. Highly-coupled proteoliposomes were prepared containing purified transhydrogenase from beef-heart mitochondria. Using the same technique, the H+/H- ratio was close to 1.0 for these proteoliposomes. It is suggested that the mechanistic H+/H- ratio is indeed unity, but that a low ratio is obtained in wild-type chromatophores because of inhomogeneity in the vesicle population. AU - Bizouarn, Tania AU - Sazanov, Leonid A AU - Aubourg, Sébastien AU - Jackson, Julie ID - 1952 IS - 1 JF - Biochimica et Biophysica Acta - Bioenergetics SN - 0005-2728 TI - Estimation of the H+/H- ratio of the reaction catalysed by the nicotinamide nucleotide transhydrogenase in chromatophores from over-expressing strains of Rhodospirillum rubrum and in liposomes inlaid with the purified bovine enzyme VL - 1273 ER - TY - JOUR AU - Sazanov, Leonid A AU - Burrows, Paul AU - Nixon, Peter ID - 1951 IS - 3 JF - Biochemical Society Transactions SN - 0300-5127 TI - Detection and characterization of a complex I-like NADH-specific dehydrogenase from pea thylakoids VL - 24 ER - TY - JOUR AB - The metabotropic glutamate receptor subtypes mGluR2 and mGluR5, which are thought to be coupled respectively to the inhibitory cyclic adenosine monophosphate (cAMP) cascade and the phosphatidylinositol hydrolysis/Ca2+ cascade, are known to be expressed on Golgi cells in the granular layer of the rat cerebellar cortex. In the present immunohistochemical study with a monoclonal antibody against mGluR2 and a polyclonal antibody for mGluR5, we examined whether or not mGluR2- and mGluR5-like immunoreactivities were both present in single Golgi cells in the rat cerebellar cortex. In double immunofluorescence histochemistry, no Golgi cells showed mGluR2- and mGluR5-like immunoreactivities simultaneously. Of the total number of Golgi cells immunoreactive for mGluR2 or mGluR5, about 90% were mGluR2-like immunoreactive, and about 10% were mGluR5-like immunoreactive. Golgi cells with mGluR2-like immunoreactivity were distributed evenly in the granular layer of all the cerebellar regions, while those with mGluR5-like immunoreactivity were distributed more frequently in the I, II, VII-X lobules of the vermis and the copula pyramidis of the hemisphere than in other cerebellar regions. The results indicate that Golgi cells containing mGluR2 are segregated from those possessing mGluR5. These two populations of Golgi cells, each equipped with a different metabolic glutamate receptor coupled to a different intracellular signal transduction system, may play different roles in the glutamatergic neuronal circuits in the cerebellar cortex. AU - Neki, Akio AU - Ohishi, Hitoshi AU - Kaneko, Takeshi AU - Shigemoto, Ryuichi AU - Nakanishi, Shigetada AU - Mizuno, Noboru ID - 2492 IS - 3 JF - Neuroscience SN - 0306-4522 TI - Metabotropic glutamate receptors mGluR2 and mGluR5 are expressed in two non-overlapping populations of Golgi cells in the rat cerebellum VL - 75 ER - TY - JOUR AB - The distribution of the neuromedin K receptor (NK3; NKR) in the central nervous system was investigated in the adult rat by using in situ hybridization and immunohistochemical techniques. The rabbit anti-NKR antibody was raised against a bacterial fusion protein containing a C- terminal portion of NKR and affinity purified with a Sepharose 4B column conjugated to the fusion protein. Immunoblot analysis was performed to test the reactivity and specificity of the antibody. Crude membrane was prepared from cDNA-transfected Chinese hamster ovary (CHO) cells expressing each of the rat NKR, substance P receptor (NK1; SPR), and substance K receptor (NK2; SKR) and from the hypothalamus, cerebral cortex, and cerebellum. Immunoreactive bands were observed specifically in the NKR-CHO cells, hypothalamus, and cerebral cortex but not in the SPR- or SKR-CHO cells, nor in the cerebellum. Molecular weights of the immunoreactive bands ranged from 73 to 89 kDa and from 59 to 83 kDa in the NKR-CHO cells and tissues, respectively. The distribution of NKR-like immunoreactivity coincided with that of NKR mRNA. The expression of NKR was indicated on neuronal cell bodies and dendrites. NKR was found to be expressed intensely or moderately in neurons in the glomerular and granule cell layers of the main olfactory bulb; glomerular and mitral cell layers of the accessory olfactory bulb; layers IV and V of the cerebral neocortex; medial septal nucleus; nucleus of the diagonal band; bed nucleus of the stria terminalis; globus pallidus; ventral pallidum; paraventricular nucleus; supraoptic nucleus; zona incerta; dorsal, lateral, and posterior hypothalamic areas; amygdaloid nuclei; medial habenular nucleus; ventral tegmental area; midbrain periaqueductal gray; interpeduncular nuclei; substantia nigra pars compacta; linear, median, dorsal, and pontine raphe nuclei; posteromedial tegmental nucleus; sphenoid nucleus; nucleus of the solitary tract; intermediate and rostroventrolateral reticular nuclei; and lamina II of the caudal spinal trigeminal nucleus and spinal dorsal horn. These findings are discussed in relation to the physiological functions associated with neuromedin K. AU - Ding, Yu AU - Shigemoto, Ryuichi AU - Takada, Masahiko AU - Ohishi, Hitoshi AU - Nakanishi, Shigetada AU - Mizuno, Noboru ID - 2564 IS - 2 JF - Journal of Comparative Neurology SN - 0021-9967 TI - Localization of the neuromedin K receptor (NK3) in the central nervous system of the rat VL - 364 ER - TY - JOUR AB - The present study indicated presynaptic localization of a metabotropic glutamate receptor, mGluR8, in projection neurons of the main olfactory bulb of rat. An antibody was produced by using a peptide corresponding to C-terminal 23 amino acids of mouse mGluR8. It was confirmed that the C-terminal 23 amino acids of rat mGluR8 were the same as those of mouse mGluR8 except for one, and that the antibody specifically recognized mGluR8 in the rat rhinencephalon. In layer Ia of the piriform cortex (a target area of projection fibers from the main olfactory bulb), mGluR8-like immunoreactivity (mGluR8-LI) was reduced after transection of the lateral olfactory tract, and mGluR8-LI was observed in axon terminals which were filled with round synaptic vesicles and made asymmetric synapses with dendritic spines. AU - Kinoshita, Ayae AU - Ohishi, Hitoshi AU - Neki, Akio AU - Nomura, Sakashi AU - Shigemoto, Ryuichi AU - Takada, Masahiko AU - Nakanishi, Shigetada AU - Mizuno, Noboru ID - 2566 IS - 1 JF - Neuroscience Letters SN - 0304-3940 TI - Presynaptic localization of a metabotropic glutamate receptor, mGluR8, in the rhinencephalic areas: A light and electron microscope study in the rat VL - 207 ER - TY - JOUR AB - Immunoreactivity for the metabotropic glutamate receptor 7 (mGluR7) and that for phosphate-activated glutaminase (PAG) were examined in the trigeminal (TG), dorsal root (DRG), nodose (NG), superior cervical, celiac, and pelvic ganglia of the rat. Virtually all neuronal cell bodies showed mGluR7-like immunoreactivity (mGluR7-LI) in these ganglia. On the other hand, PAG-like immunoreactivity (PAG) was seen in almost all neuronal cell bodies in the TG, DRG and NG, but not in the other ganglia. Co-existence of mGluR7- and PAG-LI in the TG, DRG and NG was confirmed by a double-immunofluorescence immunohistochemical method. The results indicate that virtually all sensory ganglion neurons are glutamatergic and equipped with mGluR7. AU - Li, Jin AU - Ohishi, Hitoshi AU - Kaneko, Takeshi AU - Shigemoto, Ryuichi AU - Neki, Akio AU - Nakanishi, Shigetada AU - Mizuno, Noboru ID - 2565 IS - 1-2 JF - Neuroscience Letters SN - 0304-3940 TI - Immunohistochemical localization of a metabotropic glutamate receptor, mGluR7, in ganglion neurons of the rat; with special reference to the presence in glutamatergic ganglion neurons VL - 204 ER - TY - JOUR AB - A monoclonal antibody against a metabotropic glutamate receptor, mGluR2, was produced by using a glutathione S-transferase (GST) fusion protein containing an N-terminal sequence of rat mGluR2. Intense mGluR2-like immunoreactivity (mGluR2-LI) was seen mainly in neuropil of the cerebral cortical regions, hippocampus, olfactory bulb, some diencephalic nuclei, dorsal cochlear nucleus and cerebellar cortex. In the cerebellar cortex, mGluR2-LI was seen only in Golgi cells. In Ammon's hem, mGluR2-LI was marked in the stratum lucidum of CA3 and the stratum lacunosum-moleculare of CA1-CA3, but not detected in the stratum pyramidale. The results indicate that mGluR2 is located not only presynaptically but also postsynaptically. AU - Neki, Akio AU - Ohishi, Hitoshi AU - Kaneko, Takeshi AU - Shigemoto, Ryuichi AU - Nakanishi, Shigetada AU - Mizuno, Noboru ID - 2562 IS - 3 JF - Neuroscience Letters SN - 0304-3940 TI - Pre- and postsynaptic localization of a metabotropic glutamate receptor, mGluR2, in the rat brain: An immunohistochemical study with a monoclonal antibody VL - 202 ER - TY - JOUR AB - Localization of a metabotropic glutamate receptor, mGluR4a, was immunohistochemically examined in the rat cerebellum with an antibody, which was produced by using a synthetic peptide corresponding to a C-terminal sequence of rat mGluR4a. Marked mGluR4a-like immunoreactivity (mGluRLta-LI) was seen in neuropil of the molecular layer of the cerebellar cortex. Electron microscopically, mGluR4a-LI was observed in many axon terminals in the molecular layer. These axon terminals showing mGluR4a-LI were filled with round synaptic vesicles and were in asymmetric synaptic contacts most frequently with dendritic spines. The results indicate that mGluR4a are located presynaptically in the parallel fibers arising from the granule cells in the cerebellar cortex. AU - Kinoshita, Ayae AU - Ohishi, Hitoshi AU - Nomura, Sakashi AU - Shigemoto, Ryuichi AU - Nakanishi, Shigetada AU - Mizuno, Noboru ID - 2568 IS - 3 JF - Neuroscience Letters SN - 0304-3940 TI - Presynaptic localization of a metabotropic glutamate receptor, mGluR4a, in the cerebellar cortex: A light and electron microscope study in the rat VL - 207 ER - TY - JOUR AB - Morphological substrates for interactions between γ-aminobutyric acid (GABA) and substance P upon neurons expressing substance Preceptor (SPR) in the nucleus of the solitary tract (NST) were investigated by immunocytochemical electron microscopy. In the NST of the rat, many GABA-like immunoreactive axon terminals were in symmetric synaptic contacts with dendritic profiles; they were observed on nearly a half of the SPR-like immunoreactive dendritic profiles in the medial part of the caudal half of the NST. AU - Jia, Hong AU - Wang, Bai AU - Rao, Zhi AU - Shi, Ji AU - Shigemoto, Ryuichi AU - Kaneko, Takeshi AU - Mizuno, Noboru ID - 2569 IS - 1 JF - Neuroscience Letters SN - 0304-3940 TI - GABAergic synapses upon neurons expressing substance P receptors in the nucleus of the solitary tract: An immunocytochemical electron microscope study in the rat VL - 210 ER - TY - JOUR AB - Trigeminothalamic and spinothalamic-tact neurons provided with substance P receptor (SPR) were examined in the rat by SPR immunofluorescence histochemistry combined with Fluoro-Gold (FG) fluorescent retrograde labeling. After FG injection in the thalamic regions, FG-labeled cells with SPR-like immunoreactivity were seen mainly in laminae I and m of the medullary and spinal dorsal horns and lateral spinal nucleus. In these regions, about one-fourth to one-third of FG-labeled cells showed SPR-like immunoreactivity. AU - Li, Jin AU - Ding, Yu AU - Shigemoto, Ryuichi AU - Mizuno, Noboru ID - 2567 IS - 1-2 JF - Brain Research SN - 0006-8993 TI - Distribution of trigeminothalamic and spinothalamic-tract neurons showing substance P receptor-like immunoreactivity in the rat VL - 719 ER - TY - JOUR AB - The distribution of the mRNA for a pituitary adenylate cyclase- activating polypeptide (PACAP) receptor (PACAP-R) was examined in the rat brain, and also in the hypophysis and pineal gland, by in situ hybridization with a specific 35S-labeled riboprobe which was generated from a rat PACAP-R cDNA clone. In the brain, expression of PACAP-R mRNA was most prominent in the periglomerular and granule cells of the olfactory bulb, granule cells of the dentate gyrus, supraoptic nucleus, and area postrema. The expression was also intense in the piriform, cingulate, and retrosplenial cortices, pyramidal cells in CA2, non-pyramidal cells in CA1- CA3, neuronal cells in the hilus of the dentate gyrus, lateral septal nucleus, intercalated amygdaloid nucleus, anterodorsal thalamic nucleus, most of the midline and intralaminar thalamic nuclei, many regions of the hypothalamus, dorsal motor nucleus of the vagus nerve, hypoglossal nucleus, and lateral reticular nucleus. No significant expression was detected in the mitral and tufted cells in the olfactory bulb, pyramidal cells in CA1 and CA3, posterior nuclear group of the thalamus, dorsal lateral geniculate nucleus, and Purkinje, Golgi, and granule cells in the cerebellar cortex. Moderate-to-weak expression was further observed in many other regions of the brain. In the cerebellar cortex, presumed Bergmann gila cells showed moderate expression. In the hypophysis, the expression was moderate in the anterior lobe, and weak to moderate in the posterior lobe; no significant expression was observed in the intermediate lobe. In the pineal gland, the expression was very weak, if any. Thus, the expression of PACAP-R was detected not only on neuronal cells but also on some particular glial cells. The present study has shown, for the first time, the exact site of PACAP-R expression in the brain and hypophysis. Although the functional significance of PACAP and PACAP-R in the brain still remains to be clarified, the present results are considered to provide some direction for future functional studies. AU - Hashimoto, Hitoshi AU - Nogi, Hiroyuki AU - Mori, Kensaku AU - Ohishi, Hitoshi AU - Shigemoto, Ryuichi AU - Yamamoto, Kyohei AU - Matsuda, Toshio AU - Mizuno, Noboru AU - Nagata, Shigekazu AU - Baba, Akemichi ID - 2572 IS - 4 JF - Journal of Comparative Neurology SN - 0021-9967 TI - Distribution of the mRNA for a pituitary adenylate cyclase-activating polypeptide receptor in the rat brain: An in situ hybridization study VL - 371 ER - TY - JOUR AB - lonotropic and metabotropic (mGluR1a) glutamate receptors were reported to be segregated from each other within the postsynaptic membrane at individual synapses. In order to establish whether this pattern of distribution applies to the hippocampal principal cells and to other postsynaptic metabotropic glutamate receptors, the mGluR1a/b/c and mGluR5 subtypes were localized by immunocytochemistry. Principal cells in all hippocampal fields were reactive for mGluR5, the strata oriens and radiatum of the CA1 area being most strongly immunolabelled. Labelling for mGluR1b/c was strongest on some pyramids in the CA3 area, weaker on granule cells and absent on CA1 pyramids. Subpopulations of non-principal cells showed strong mGluR1 or mGluR5 immunoreactivity. Electron microscopic pre-embedding immunoperoxidase and both pre- and postembedding immunogold methods consistently revealed the extrasynaptic location of both mGluRs in the somatic and dendritic membrane of pyramidal and granule cells. The density of immunolabelling was highest on dendritic spines. At synapses, immunoparticles for both mGluR1 and mGluR5 were found always outside the postsynaptic membrane specializations. Receptors were particularly concentrated in a perisynaptic annulus around type 1 synaptic junctions, including the invaginations at 'perforated' synapses. Measurements of immunolabelling on dendritic spines showed decreasing levels of receptor as a function of distance from the edge of the synaptic specialization. We propose that glutamatergic synapses with an irregular edge develop in order to increase the circumference of synaptic junctions leading to an increase in the metabotropic to ionotropic glutamate receptor ratio at glutamate release sites. The perisynaptic position of postsynaptic metabotropic glutamate receptors appears to be a general feature of glutamatergic synaptic organization and may apply to other G-protein-coupled receptors. © European Neuroscience Association. AU - Luján, Rafael AU - Nusser, Zoltán AU - Roberts, John AU - Shigemoto, Ryuichi AU - Somogyi, Péter ID - 2574 IS - 7 JF - European Journal of Neuroscience SN - 0953-816X TI - Perisynaptic location of metabotropic glutamate receptors mGluR1 and mGluR5 on dendrites and dendritic spines in the rat hippocampus VL - 8 ER - TY - JOUR AB - Developmental changes of the distribution pattern of substance P receptor (SPR) were investigated immunohistochemically in the rat striatum. The SPR immunoreactivity in the striatum first emerged at postnatal day 1 and transiently showed a patchy pattern of distribution until it displayed the adult pattern of homogeneous distribution by the end of the third postnatal week. The SPR-immunoreactive patches were most marked in the medial and dorsolateral parts of the striatum, as well as in the subcallosal streak. They matched tyrosine hydroxylase-enriched areas and, conversely, avoided calbindin-enriched zones. No neurons within the SPR-immunoreactive patches contained either choline acetyltransferase or somatostatin, which is known to be contained in intrinsic neurons in the striatum. The vast majority of SPR-immunoreactive patch neurons also contained DARPP-32, a phosphoprotein that is expressed in striatal projection neurons with D1 dopamine receptor. The results indicate that SPR-immunoreactive patches which appear transiently in the developing striatum are in register with the striatal patch compartment, and that SPR immunoreactivity within these patches may be expressed on projection neurons rather than intrinsic neurons. Such SPR immunoreactivity in projection neurons in striatal patches may fade out in adulthood. AU - Tokuno, Hironobu AU - Takada, Masahiko AU - Kaneko, Takeshi AU - Shigemoto, Ryuichi AU - Mizuno, Noboru ID - 2573 IS - 1 JF - Developmental Brain Research SN - 0165-3806 TI - Patchy distribution of substance P receptor immunoreactivity in the developing rat striatum VL - 95 ER - TY - JOUR AB - The probability of synaptic neurotransmitter release from nerve terminals is regulated by presynaptic receptors responding to transmitters released from the same nerve terminal or from terminals of other neurons. The release of glutamate, the major excitatory neurotransmitter, is suppressed by presynaptic auto receptors. Here we show that a metabotropic glutamate receptor (mGluR7) in the rat hippocampus is restricted to the presynaptic grid, the site of synaptic vesicle fusion. Pyramidal cell terminals presynaptic to mGluR1α-expressing interneurons have at least a ten-fold higher level of presynaptic mGluR7 than terminals making synapses with pyramidal cells and other types of interneuron. Distinct levels of mGluR7 are found at different synapses made by individual pyramidal axons or even single boutons. These results raise the possibility that presynaptic neurons could regulate the probability of transmitter release at individual synapses according to the postsynaptic target AU - Shigemoto, Ryuichi AU - Kulik, Ákos AU - Roberts, John AU - Ohishi, Hitoshi AU - Nusser, Zoltán AU - Kaneko, Takeshi AU - Somogyi, Péter ID - 2570 IS - 6582 JF - Nature SN - 0028-0836 TI - Target-cell-specific concentration of a metabotropic glutamate receptor in the presynaptic active zone VL - 381 ER - TY - JOUR AB - Subtype 2 of the metabotropic glutamate receptor (mGluR2) is expressed in the presynaptic elements of hippocampal mossy fiber-CA3 synapses. Knockout mice deficient in mGluR2 showed no histological changes and no alterations in basal synaptic transmission, paired-pulse facilitation, or tetanus-induced long-term potentiation (LTP) at the mossy fiber-CA3 synapses. Long-term depression (LTD) induced by low-frequency stimulation, however, was almost fully abolished. The mutant mice performed normally in water maze learning tasks. Thus, the presynaptic mGluR2 is essential for inducing LTD at the mossy fiber-CA3 synapses, but this hippocampal LTD does not seem to be required for spatial learning. AU - Yokoi, Mineto AU - Kobayashi, Kazuto AU - Manabe, Toshiya AU - Takahashi, Tomoyuki AU - Sakaguchi, Isako AU - Katsuura, Goro AU - Shigemoto, Ryuichi AU - Ohishi, Hitoshi AU - Nomura, Sakashi AU - Nakamura, Kenji AU - Nakao, Kazuki AU - Katsuki, Motoya AU - Nakanishi, Shigetada ID - 2571 JF - Science SN - 0036-8075 TI - Impairment of hippocampal mossy fiber LTD in mice lacking mGluR2 VL - 273 ER - TY - JOUR AB - We investigate whether the eigenfunctions of the two-dimensional magnetic Schrödinger operator have a Gaussian decay of type exp(-Cx2) at infinity (the magnetic field is rotationally symmetric). We establish this decay if the energy (E) of the eigenfunction is below the bottom of the essential spectrum (B), and if the angular Fourier components of the external potential decay exponentially (real analyticity in the angle variable). We also demonstrate that almost the same decay is necessary. The behavior of C in the strong field limit and in the small (B - E) limit is also studied. AU - Erdös, László ID - 2726 IS - 2 JF - Geometric and Functional Analysis SN - 1016-443X TI - Gaussian decay of the magnetic eigenfunctions VL - 6 ER - TY - JOUR AB - We prove that the two dimensional free magnetic Schrödinger operator, with a fixed constant magnetic field and Dirichlet boundary conditions on a planar domain with a given area, attains its smallest possible eigenvalue if the domain is a disk. We also give some rough bounds on the lowest magnetic eigenvalue of the disk. AU - László Erdös ID - 2725 IS - 3 JF - Calculus of Variations and Partial Differential Equations TI - Rayleigh-type isoperimetric inequality with a homogeneous magnetic field VL - 4 ER - TY - CONF AB - Virtual environments open up new opportunities and challenges for geometric modeling systems. A general approach to geometric modeling suitable for the Cave Automatic Virtual Environment is described. The approach is based on alpha complexes, and some of its capabilities are demonstrated by applying it to the study of biomolecules. AU - Edelsbrunner, Herbert AU - Fu, Ping AU - Quian, Jiang ID - 3553 SN - 9780897918251 T2 - Proceedings of the ACM Symposium on Virtual Reality Software and Technology TI - Geometric modeling in CAVE ER - TY - JOUR AB - Experiments on Drosophila suggest that genetic recombination may result in lowered fitness of progeny (a 'recombination load'). This has been interpreted as evidence either for a direct effect of recombination on fitness, or for the maintenance of linkage disequilibria by epistatic selection. Here we show that such a recombination load is to be expected even if selection favours increased genetic recombination. This is because of the fact that, although a modifier may suffer an immediate loss of fitness if it increases recombination, it eventually becomes associated with a higher additive genetic variance in fitness, which allows a faster response to direction selection. This argument applies to mutation-selection balance with synergistic epistasis, directional selection on quantitative traits, and ectopic exchange among transposable elements. Further experiments are needed to determine whether the selection against recombination due to the immediate load is outweighed by the increased additive variance in fitness produced by recombination. AU - Charlesworth, Brian AU - Barton, Nicholas H ID - 3635 IS - 1 JF - Genetical Research SN - 0016-6723 TI - Recombination load associated with selection for increased recombination VL - 67 ER - TY - JOUR AB - The evolutionary processes responsible for adaptation and speciation on islands differ in several ways from those on the mainland. Most attention has been given to the random genetic drift that arises when a population is founded from just a few colonizing genomes. Theoretical obstacles to 'founder effect speciation' are discussed, together with recent proposals for avoiding them. It is argued that although certain kinds of epistasis can facilitate the evolution of strong reproductive isolation, this favours divergence by selection as much as by random drift. AU - Barton, Nicholas H AU - Mallet, James ID - 3634 IS - 1341 JF - Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences SN - 0962-8436 TI - Natural selection and random genetic drift as causes of evolution on islands VL - 351 ER - TY - JOUR AB - We have developed general modeling software for a Cave Automatic Virtual Environment (CAVE); one of its applications is modeling 3D protein structures, generating both outside-in and inside-out views of geometric models. An advantage of the CAVE over other virtual environments is that multiple viewers can observe the same scene at the same time and place. Our software is scalable-from high-end virtual environments such as the CAVE, to mid-range immersive desktop systems, down to low-end graphics workstations. In the current configuration, a parallel Silicon Graphics Power Challenge supercomputer architecture performs the computationally intensive construction of surface patches remotely, and sends the results through the I-WAY (Information Wide Area Year) using VBNS (Very-high-Bandwidth Network Systems) to the graphics machines that drive the CAVE and our graphics visualization software, Valvis (Virtual ALpha shapes VISualizer). AU - Akkiraju, Nataraj AU - Edelsbrunner, Herbert AU - Fu, Ping AU - Qian, Jiang ID - 4024 IS - 4 JF - IEEE Computer Graphics and Applications SN - 0018-9162 TI - Viewing geometric protein structures from inside a CAVE VL - 16 ER - TY - JOUR AB - Questions of chemical reactivity can often be cast as questions of molecular geometry. Common geometric models for proteins and other molecules are the space-filling diagram, the solvent accessible surface and the molecular surface. In this paper we present a new approach to triangulating the surface of a molecule under the three models, which is fast, robust, and results in topologically correct triangulations. Our computations are based on a simplicial complex dual to the molecule models. All proposed algorithms are parallelizable. AU - Akkiraju, Nataraj AU - Edelsbrunner, Herbert ID - 4025 IS - 1-3 JF - Discrete Applied Mathematics SN - 0166-218X TI - Triangulating the surface of a molecule VL - 71 ER - TY - JOUR AB - Jaws and branchial arches together are a basic, segmented feature of the vertebrate head, Seven arches develop in the zebrafish embryo (Danio rerio), derived largely from neural crest cells that form the cartilaginous skeleton, In this and the following paper we describe the phenotypes of 109 arch mutants, focusing here on three classes that affect the posterior pharyngeal arches, including the hyoid and five gill-bearing arches, In lockjaw, the hyoid arch is strongly reduced and subsets of branchial arches do not develop, Mutants of a large second class, designated the flathead group, lack several adjacent branchial arches and their associated cartilages. Five alleles at the flathead locus all lead to larvae that lack arches 4-6, Among 34 other flathead group members complementation tests are incomplete, but at least six unique phenotypes can be distinguished, These all delete continuous stretches of adjacent branchial arches and unpaired cartilages in the ventral midline, Many show cell death in the midbrain, from which some neural crest precursors of the arches originate, lockjaw and a few mutants in the flathead group, including pistachio, affect both jaw cartilage and pigmentation, reflecting essential functions of these genes in at least two neural crest lineages, Mutants of a third class, including boxer, dackel and pincher, affect pectoral fins and axonal trajectories in the brain, as well as the arches. Their skeletal phenotypes suggest that they disrupt cartilage morphogenesis in all arches, Our results suggest that there are sets of genes that: (1) specify neural crest cells in groups of adjacent head segments, and (2) function in common genetic pathways in a variety of tissues including the brain, pectoral fins and pigment cells as well as pharyngeal arches. AU - Schilling, Thomas AU - Piotrowski, Tatjana AU - Grandel, Heiner AU - Brand, Michael AU - Heisenberg, Carl-Philipp J AU - Jiang, Yunjin AU - Beuchle, Dirk AU - Hammerschmidt, Matthias AU - Kane, Donald AU - Mullins, Mary AU - Van Eeden, Fredericus AU - Kelsh, Robert AU - Furutani Seiki, Makoto AU - Granato, Michael AU - Haffter, Pascal AU - Odenthal, Jörg AU - Warga, Rachel AU - Trowe, Torsten AU - Nüsslein Volhard, Christiane ID - 4151 IS - 1 JF - Development SN - 0950-1991 TI - Jaw and branchial arch mutants in zebrafish I: Branchial arches VL - 123 ER - TY - JOUR AB - In a large scale screen for mutants with defects in the embryonic development of the zebrafish we identified mutations in four genes, floating head (flh), memo (mom), no tail (ntl), and dec, that are required for early notochord formation. Mutations in flh and ntl have been described previously, while mom and doe are newly identified genes. Mutant mom embryos lack a notochord in the trunk, and trunk somites from the right and left side of the embryo fuse underneath the neural tube. In this respect morn appears similar to flh. In contrast, notochord precursor cells are present in both ntl and doc embryos. In order to gain a greater understanding of the phenotypes, we have analysed the expression of several axial mesoderm markers in mutant embryos of all four genes. In flh and mom, Ntl expression is normal in the germ ring and tailbud, while the expression of Nd and other notochord markers in the axial mesodermal region is disrupted. Nd expression is normal in doc embryos until early semitic stages, when there is a reduction in expression which is first seen in anterior regions of the embryo. This suggests a function for doc in the maintenance of ntl expression. Other notochord markers such as twist, sonic hedgehog and axial are not expressed in the axial mesoderm of ntl embryos, their expression parallels the expression of ntl in the axial mesoderm of mutant doc,flh and mom embryos, indicating that ntl is required for the expression of these markers. The role of doc in the expression of the notochord markers appears indirect via ntl. Floor plate formation is disrupted in most regions in flh and mom mutant embryos but is present in mutant ntl and doc embryos. In mutant embryos with strong ntl alleles the band of cells expressing floor plate markers is broadened. A similar broadening is also observed in the axial mesoderm underlying the floor plate of ntl embryos, suggesting a direct involvement of the notochord precursor cells in floor plate induction. Mutations in al of these four genes result in embryos lacking a horizontal myoseptum and muscle pioneer cells, both of which are thought to be induced by the notochord. These somite defects can be traced back to an impairment of the specification of the adaxial cells during early stages of development. Transplantation of wild-type cells into mutant doc embryos reveals that wild-type notochord cells are sufficient to induce horizontal myoseptum formation in the flanking mutant tissue. Thus dec, like flh and ntl, acts cell autonomously in the notochord. In addition to the four mutants with defects in early notochord formation, we have isolated 84 mutants, defining at least 15 genes, with defects in later stages of notochord development. These are listed in an appendix to this study. AU - Odenthal, Jörg AU - Haffter, Pascal AU - Vogelsang, Elisabeth AU - Brand, Michael AU - Van Eeden, Fredericus AU - Furutani Seiki, Makoto AU - Granato, Michael AU - Hammerschmidt, Matthias AU - Heisenberg, Carl-Philipp J AU - Jiang, Yunjin AU - Kane, Donald AU - Kelsh, Robert AU - Mullins, Mary AU - Warga, Rachel AU - Allende, Miguel AU - Weinberg, Eric AU - Nüsslein Volhard, Christiane ID - 4166 IS - 1 JF - Development SN - 0950-1991 TI - Mutations affecting the formation of the notochord in the zebrafish, Danio rerio VL - 123 ER - TY - JOUR AB - We identified 6 genes that are essential for specifying ventral regions of the early zebrafish embryo, Mutations in these genes cause an expansion of structures normally derived from dorsal-lateral regions of the blastula at the expense of ventrally derived structures, A series of phenotypes of varied strengths is observed with different alleles of these mutants, The weakest phenotype is a reduction in the ventral tail fin, observed as a dominant phenotype of swirl, piggytail, and somitabun and a recessive phenotype of min fin, lost-a-fin and some piggytail alleles, With increasing phenotypic strength, the blood and pronephric anlagen are also reduced or absent, while the paraxial mesoderm and anterior neuroectoderm is progressively expanded, In the strong phenotypes, displayed by homozygous embryos of snailhouse, swirl and somitabun, the somites circle around the embryo and the midbrain region is expanded laterally, Several mutations in this group of genes are semidominant as well as recessive indicating a strong dosage sensitivity of the processes involved, Mutations in the piggytail gene display an unusual dominance that depends on both a maternal and zygotic heterozygous genotype, while somitabun is a fully penetrant dominant maternal-effect mutation, The similar and overlapping phenotypes of mutants of the 6 genes identified suggest that they function in a common pathway, which begins in oogenesis, but also depends on factors provided after the onset of zygotic transcription, presumably during blastula stages, This pathway provides ventral positional information, counteracting the dorsalizing instructions of the organizer, which is localized in the dorsal shield. AU - Mullins, Mary AU - Hammerschmidt, Matthias AU - Kane, Donald AU - Odenthal, Jörg AU - Brand, Michael AU - Van Eeden, Fredericus AU - Furutani Seiki, Makoto AU - Granato, Michael AU - Haffter, Pascal AU - Heisenberg, Carl-Philipp J AU - Jiang, Yunjin AU - Kelsh, Robert AU - Nüsslein Volhard, Christiane ID - 4170 IS - 1 JF - Development SN - 0950-1991 TI - Genes establishing dorsoventral pattern formation in the zebrafish embryo: The ventral specifying genes VL - 123 ER - TY - JOUR AB - In a large-scale screen for mutants with defects in embryonic development we identified 17 genes (65 mutants) specifically required for the development of xanthophores, We provide evidence that these genes are required for three different aspects of xanthophore development, (1) Pigment cell formation and migration (pfeffer and salt); (2) pigment synthesis (edison, yobo, yocca and brie) and (3) pigment translocation (esrom, tilsit and tofu). The number of xanthophore cells that appear in the body is reduced in embryos with mutations in the two genes, salt and pfeffer. In heterozygous and homozygous salt and pfeffer adults, the melanophore stripes are interrupted, indicating that xanthophore cells have an important function in adult melanophore pattern formation, Most other genes affect only larval pigmentation, In embryos mutant for edison, yobo, yocca and brie, differences in pteridine synthesis can be observed under UV light and by thin-layer chromatography. Homozygous mutant females of yobo show a recessive maternal effect, Embryonic development is slowed down and embryos display head and tail truncations, Xanthophores in larvae mutant in the three genes esrom, tilsit and tofu appear less spread out, In addition, these mutants display a defect in retinotectal axon pathfinding, These mutations may affect xanthophore pigment distribution within the cells or xanthophore cell shape, Mutations in seven genes affecting xanthophore pigmentation remain unclassified. AU - Odenthal, Jörg AU - Rossnagel, Karin AU - Haffter, Pascal AU - Kelsh, Robert AU - Vogelsang, Elisabeth AU - Brand, Michael AU - Van Eeden, Fredericus AU - Furutani Seiki, Makoto AU - Granato, Michael AU - Hammerschmidt, Matthias AU - Heisenberg, Carl-Philipp J AU - Jiang, Yunjin AU - Kane, Donald AU - Mullins, Mary AU - Nüsslein Volhard, Christiane ID - 4164 IS - 1 JF - Development SN - 0950-1991 TI - Mutations affecting xanthophore pigmentation in the zebrafish, Danio rerio VL - 123 ER - TY - JOUR AB - In a large-scale screen, we isolated mutants displaying a specific visible phenotype in embryos or early larvae of the zebrafish, Danio rerio. Males were mutagenized with ethylnitrosourea (ENU) and F-2 families of single pair matings between sibling F-l fish, heterozygous for a mutagenized genome, were raised. Egg lays were obtained from several crosses between F-2 siblings, resulting in scoring of 3857 mutagenized genomes. F-3 progeny were scored at the second, third and sixth day of development, using a stereomicroscope. In a subsequent screen, fixed embryos were analyzed for correct retinotectal projection. A total of 4264 mutants were identified. Two thirds of the mutants displaying rather general abnormalities were eventually discarded. We kept and characterized 1163 mutants. In complementation crosses performed between mutants with similar phenotypes, 894 mutants have been assigned to 372 genes. The average allele frequency is 2.4. We identified genes involved in early development, notochord, brain, spinal cord, somites, muscles, heart, circulation, blood, skin, fin, eye, otic vesicle, jaw and branchial arches, pigment pattern, pigment formation, gut, liver, motility and touch response. Our collection contains alleles of almost all previously described zebrafish mutants. From the allele frequencies and other considerations we estimate that the 372 genes defined by the mutants probably represent more than half of all genes that could have been discovered using the criteria of our screen. Here we give an overview of the spectrum of mutant phenotypes obtained, and discuss the limits and the potentials of a genetic saturation screen in the zebrafish. AU - Haffter, Pascal AU - Granato, Michael AU - Brand, Michael AU - Mullins, Mary AU - Hammerschmidt, Matthias AU - Kane, Donald AU - Odenthal, Jörg AU - Van Eeden, Fredericus AU - Jiang, Yunjin AU - Heisenberg, Carl-Philipp J AU - Kelsh, Robert AU - Furutani Seiki, Makoto AU - Vogelsang, Elisabeth AU - Beuchle, Dirk AU - Schach, Ursula AU - Fabian, Cosima AU - Nüsslein Volhard, Christiane ID - 4212 IS - 1 JF - Development SN - 0950-1991 TI - The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio VL - 123 ER - TY - JOUR AB - Zebrafish embryos and larvae have stage-specific patterns of motility or locomotion, Two embryonic structures accomplish this behavior: the central nervous system (CNS) and skeletal muscles. To identify genes that are functionally involved in mediating and controlling different patterns of embryonic and larval motility, we included a simple touch response test in our zebrafish large-scale genetic screen, In total we identified 166 mutants with specific defects in embryonic motility. These mutants fall into 14 phenotypically distinct groups comprising at least 48 genes, Here we describe the various phenotypic groups including mutants with no or reduced motility, mechanosensory defective mutants, 'spastic' mutants, circling mutants and motor circuit defective mutants, In 63 mutants, defining 18 genes, striation of semitic muscles is reduced, Phenotypic analysis provides evidence that these 18 genes have distinct and consecutive functions during semitic muscle development. The genes sloth (slo) and frozen (fro) already act during myoblast differentiation, while 13 genes appear to function later, in the formation of myofibers and the organization of sarcomeres, Mutations in four other genes result in muscle-specific degeneration, 103 mutations, defining at least 30 genes, cause no obvious defects in muscle formation and may instead affect neuronal development. Analysis of the behavioral defects suggests that these genes participate in the diverse locomotion patterns observed, such as touch response, rhythmic tail movements, equilibrium control, or that they simply confer general motility to the animal, In some of these mutants specific defects in the developing nervous system are detected, Mutations in two genes, nevermind (nev) and macho (mao), affect axonal projection in the optic tectum, whereas axon formation and elongation of motorneurons are disrupted by mutations in the diwanka (diw) and the unplugged (unp) genes. AU - Granato, Michael AU - Van Eeden, Fredericus AU - Schach, Ursula AU - Trowe, Torsten AU - Brand, Michael AU - Furutani Seiki, Makoto AU - Haffter, Pascal AU - Hammerschmidt, Matthias AU - Heisenberg, Carl-Philipp J AU - Jiang, Yunjin AU - Kane, Donald AU - Kelsh, Robert AU - Mullins, Mary AU - Odenthal, Jörg AU - Nüsslein Volhard, Christiane ID - 4214 JF - Development SN - 0950-1991 TI - Genes controlling and mediating locomotion behavior of the zebrafish embryo and larva VL - 123 ER - TY - JOUR AB - In a screen for early developmental mutants of the zebrafish, we have identified mutations specifically affecting the internal organs, We identified 53 mutations affecting the cardiovascular system, Nine of them affect specific landmarks of heart morphogenesis. Mutations in four genes cause a failure in the fusion of the bilateral heart primordia, resulting in cardia bifida. In lonely atrium, no heart venticle is visible and the atrium is directly fused to the outflow tract. In the overlooped mutant, the relative position of the two heart chambers is distorted, The heart is enormously enlarged in the santa mutant, In two mutants, scotch tape and superglue, the cardiac jelly between the two layers of the heart is significantly reduced, We also identified a number of mutations affecting the function of the heart, The mutations affecting heart function can be subdivided into two groups, one affecting heart contraction and another affecting the rhythm of the heart beat. Among the contractility group of mutants are 5 with no heart beat at all and 15 with a reduced heart beat of one or both chambers, 6 mutations are in the rhythmicity group and specifically affect the beating pattern of the heart, Mutations in two genes, bypass and kurzschluss, cause specific defects in the circulatory system, In addition to the heart mutants, we identified 23 mutations affecting the integrity of the liver, the intestine or the kidney, In this report, we demonstrate that it is feasible to screen for genes specific for the patterning or function of certain internal organs in the zebrafish, The mutations presented here could serve as an entrypoint to the establishment of a genetic hierarchy underlying organogenesis. AU - Chen, Jaunian AU - Haffter, Pascal AU - Odenthal, Jörg AU - Vogelsang, Elisabeth AU - Brand, Michael AU - Van Eeden, Fredericus AU - Furutani Seiki, Makoto AU - Granato, Michael AU - Hammerschmidt, Matthias AU - Heisenberg, Carl-Philipp J AU - Jiang, Yunjin AU - Kane, Donald AU - Kelsh, Robert AU - Mullins, Mary AU - Nüsslein Volhard, Christiane ID - 4215 JF - Development SN - 0950-1991 TI - Mutations affecting the cardiovascular system and other internal organs in zebrafish VL - 123 ER - TY - JOUR AB - Forty zebrafish mutants with localized or general neural degeneration are described. The onset and duration of degeneration and the distribution of ectopically dying cells are specific characteristics of each mutant, Mutants are classified into four groups by these parameters. Class I: late focal neural degeneration mutants, These 18 mutants have restricted cell death mainly in the tectum and the dorsal hindbrain after 36 hours, The degeneration does not spread and disappears at later stages of development. Class LI: early focal neural degeneration mutants. Ten mutants in this class exhibit transient restricted degeneration affecting mainly the diencephalon, the hindbrain and the spinal cord at 20 hours, The midbrain is less affected. The degeneration shifts to the dorsal diencephalon and the tectum at 36 hours. Class III: late spreading neural degeneration mutants. The 8 mutants in this class display a degeneration that is first seen in the tectum and subsequently spreads throughout the nervous system from 36 hours on. Class IV: early general neural degeneration mutants, This class of four mutants already shows overall cell degeneration in the nervous system at the 15-somite stage. Three of the class I mutants show a change in the pattern of gene expression in the anlage of a brain structure prior to the onset of degeneration. These results suggest that focal cell death may be a useful clue for the detection of early patterning defects of the vertebrate nervous system in regions devoid of visible landmarks. AU - Furutani Seiki, Makoto AU - Jiang, Yunjin AU - Brand, Michael AU - Heisenberg, Carl-Philipp J AU - Houart, Corinne AU - Beuchle, Dirk AU - Van Eeden, Fredericus AU - Granato, Michael AU - Haffter, Pascal AU - Hammerschmidt, Matthias AU - Kane, Donald AU - Kelsh, Robert AU - Mullins, Mary AU - Odenthal, Jörg AU - Nüsslein Volhard, Christiane ID - 4213 IS - 1 JF - Development SN - 0950-1991 TI - Neural degeneration mutants in the zebrafish, Danio rerio VL - 123 ER - TY - JOUR AB - We have identified several genes that are required for various morphogenetic processes during gastrulation and tail formation, Two genes are required in the anterior region of the body axis: one eyed pinhead (oep) and dir ty nose (dns). oep mutant embryos are defective in prechordal plate formation and the specification of anterior and ventral structures of the central nervous system, In dns mutants, cells of the prechordal plate, such as the prospective hatching gland cells, fail to specify. Two genes are required for convergence and extension movements. In mutant trilobite embryos, extension movements on the dorsal side of the embryo are affected, whereas in the formerly described spadetail mutants, for which two new alleles have been isolated, convergent movements of ventrolateral cells to the dorsal side are blocked. Two genes are required for the development of the posterior end of the body axis, In pipetail mutants, the tailbud fails to move ventrally on the yolk sac after germ ring closure, and the tip of the tail fails to detach from the yolk tube. Mutants in kugelig (kgg) do not form the yolk tube at the posterior side of the yolk sac. AU - Hammerschmidt, Matthias AU - Pelegri, Francisco AU - Mullins, Mary AU - Kane, Donald AU - Brand, Michael AU - Van Eeden, Fredericus AU - Furutani Seiki, Makoto AU - Granato, Michael AU - Haffter, Pascal AU - Heisenberg, Carl-Philipp J AU - Jiang, Yunjin AU - Kelsh, Robert AU - Odenthal, Jörg AU - Warga, Rachel AU - Nüsslein Volhard, Christiane ID - 4208 IS - 1 JF - Development SN - 0950-1991 TI - Mutations affecting morphogenesis during gastrulation and tail formation in the zebrafish, Danio rerio VL - 123 ER - TY - JOUR AB - Mutations causing a visible phenotype in the adult serve as valuable visible genetic markers in multicellular genetic model organisms such as Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana. In a large scale screen for mutations affecting early development of the zebrafish, we identified a number of mutations that are homozygous viable or semiviable. Here we describe viable mutations which produce visible phenotypes in the adult fish. These predominantly affect the fins and pigmentation, but also the eyes and body length of the adult. A number of dominant mutations caused visible phenotypes in the adult fish, Mutations in three genes, long fin, another long fin and wanda affected fin formation in the adult. Four mutations were found to cause a dominant reduction of the overall body length in the adult. The adult pigment pattern was found to be changed by dominant mutations in wanda, asterix, obelix, leopard, salz and pfeffer. Among the recessive mutations producing visible phenotypes in the homozygous adult, a group of mutations that failed to produce melanin was assayed for tyrosinase activity. Mutations in sandy produced embryos that failed to express tyrosinase activity. These are potentially useful for using tyrosinase as a marker for the generation of transgenic lines of zebrafish. AU - Haffter, Pascal AU - Odenthal, Jörg AU - Mullins, Mary AU - Lin, Shuo AU - Farrell, Michael AU - Vogelsang, Elisabeth AU - Haas, Fabian AU - Brand, Michael AU - Van Eeden, Fredericus AU - Furutani Seiki, Makoto AU - Granato, Michael AU - Hammerschmidt, Matthias AU - Heisenberg, Carl-Philipp J AU - Jiang, Yunjin AU - Kane, Donald AU - Kelsh, Robert AU - Hopkins, Nancy AU - Nüsslein Volhard, Christiane ID - 4210 IS - 4 JF - Development Genes and Evolution SN - 0043-5546 TI - Mutations affecting pigmentation and shape of the adult zebrafish VL - 206 ER - TY - JOUR AB - We describe two genes, dino and mercedes, which are required for the organization of the zebrafish body plan, In dine mutant embryos, the tail is enlarged at the expense of the head and the anterior region of the trunk, The altered expression patterns of various marker genes reveal that, with the exception of the dorsal most marginal zone, all regions of the early dine mutant embryo acquire more ventral fates, These alterations are already apparent before the onset of gastrulation, mercedes mutant embryos show a similar but weaker phenotype, suggesting a role in the same patterning processes. The phenotypes suggests that dine and mercedes are required for the establishment of dorsal fates in both the marginal and the animal zone of the early gastrula embryo, Their function in the patterning of the ventrolateral mesoderm and the induction of the neuroectoderm is similar to the function of the Spemann organizer in the amphibian embryo. AU - Hammerschmidt, Matthias AU - Pelegri, Francisco AU - Mullins, Mary AU - Kane, Donald AU - Van Eeden, Fredericus AU - Granato, Michael AU - Brand, Michael AU - Furutani Seiki, Makoto AU - Haffter, Pascal AU - Heisenberg, Carl-Philipp J AU - Jiang, Yunjin AU - Kelsh, Robert AU - Odenthal, Jörg AU - Warga, Rachel AU - Nüsslein Volhard, Christiane ID - 4211 IS - 1 JF - Development SN - 0950-1991 TI - Dino and Mercedes, two genes regulating dorsal development in the zebrafish embryo VL - 123 ER - TY - JOUR AB - Ageing, or senescence, is a decline in state at later ages that is manifested through a reduction in survival and fecundity. Ageing means that reproductive prospects and hence the life history options (trade-offs) open to the organism decline. Evolutionary theories of ageing suggest that it evolves in response to the level of externally imposed mortality and insults to fertility, either as part of life history optimization or as a result of mutation pressure. Several recent empirical and theoretical studies have produced apparently anomalous results. Some have suggested that the rate of ageing can decline at later ages, others that demographic evidence for ageing can appear in parallel with an improvement in state. All of these studies used measures of ageing that would not be expected to give an accurate reflection of changes in the state of the organism with age. We propose that Fisher's `reproductive value' is a natural measure of state at each age, which includes prospects for both survival and reproduction. If this measure is used, the apparently anomalous findings are not at variance with evolutionary theories of ageing. AU - Partridge, Linda AU - Barton, Nicholas H ID - 4292 IS - 1375 JF - Proceedings of the Royal Society of London Series B Biological Sciences SN - 0950-1193 TI - On measuring the rate of ageing VL - 263 ER - TY - JOUR AU - Melcher, Thorsten AU - Geiger, Jörg AU - Jonas, Peter M AU - Monyer, Hannah ID - 3462 IS - 2 JF - Neurochemistry International SN - 0197-0186 TI - Analysis of molecular determinants in native AMPA receptors VL - 28 ER - TY - JOUR AB - In many eukaryotic cells going through M-phase, a bipolar spindle is formed by microtubules nucleated from centrosomes. These microtubules, in addition to being `'captured” by kinetochores, may be stabilized by chromatin in two different ways: short-range stabilization effects may affect microtubules in close contact with the chromatin, while long-range stabilization effects may `'guide” microtubule growth towards the chromatin (e.g., by introducing a diffusive gradient of an enzymatic activity that affects microtubule assembly). Here, we use both meiotic and mitotic extracts from Xenopus laevis eggs to study microtubule aster formation and microtubule dynamics in the presence of chromatin. In `'low-speed” meiotic extracts, in the presence of salmon sperm chromatin, we find that short-range stabilization effects lead to a strong anisotropy of the microtubule asters. Analysis of the dynamic parameters of microtubule growth shows that this anisotropy arises from a decrease in the catastrophe frequency, an increase in the rescue frequency and a decrease in the growth velocity. In this system we also find evidence for long-range `'guidance” effects, which lead to a weak anisotropy of the asters. Statistically relevant results on these long-range effects are obtained in `'high-speed” mitotic extracts in the presence of artificially constructed chromatin stripes. We find that aster anisotropy is biased in the direction of the chromatin and that the catastrophe frequency is reduced in its vicinity. In this system we also find a surprising dependence of the catastrophe and the rescue frequencies on the length of microtubules nucleated from centrosomes: the catastrophe frequency increases and the rescue frequency decreases with microtubule length. AU - Dogterom, Marileen AU - Felix, M. AU - Guet, Calin C AU - Leibler, Stanislas ID - 3756 IS - 1 JF - Journal of Cell Biology SN - 0021-9525 TI - Influence of M-phase chromatin on the anisotropy of microtubule asters VL - 133 ER - TY - JOUR AB - Questions about lines in space arise frequently as subproblems in three-dimensional computational geometry. In this paper we study a number of fundamental combinatorial and algorithmic problems involving arrangements of n lines in three-dimensional space. Our main results include: 1. A tight Θ(n2) bound on the maximum combinatorial description complexity of the set of all oriented lines that have specified orientations relative to the n given lines. 2. A similar bound of Θ(n3) for the complexity of the set of all lines passing above the n given lines. 3. A preprocessing procedure using O(n2+ε) time and storage, for any ε > 0, that builds a structure supporting O(logn)-time queries for testing if a line lies above all the given lines. 4. An algorithm that tests the "towering property" in O(n4/3+ε) time, for any ε > 0: do n given red lines lie all above n given blue lines? The tools used to obtain these and other results include Plücker coordinates for lines in space and ε-nets for various geometric range spaces. AU - Chazelle, Bernard AU - Edelsbrunner, Herbert AU - Guibas, Leonidas AU - Sharir, Micha AU - Stolfi, Jorge ID - 4027 IS - 5 JF - Algorithmica SN - 0178-4617 TI - Lines in space: Combinatorics and algorithms VL - 15 ER - TY - JOUR AB - A set of n weighted points in general position in R(d) defines a unique regular triangulation. This paper proves that if the points are added one by one, then flipping in a topological order will succeed in constructing this triangulation. If, in addition, the points are added in a random sequence and the history of the flips is used for locating the next point, then the algorithm takes expected time at most O(n log n + n(inverted left perpendicular d/2 inverted right perpendicular)). Under the assumption that the points and weights are independently and identically distributed, the expected running time is between proportional to and a factor log n more than the expected size of the regular triangulation. The expectation is over choosing the points and over independent coin-flips performed by the algorithm. AU - Edelsbrunner, Herbert AU - Shah, Nimish ID - 4026 IS - 3 JF - Algorithmica SN - 0178-4617 TI - Incremental topological flipping works for regular triangulations VL - 15 ER - TY - GEN AU - Liang, Jie AU - Edelsbrunner, Herbert AU - Subramaniam, Shankar ID - 4030 IS - 2, Part 2 T2 - Fortieth Annual Meeting TI - Effects of molecular shape representations on boundary element method for protein electrostatics computations VL - 70 ER - TY - GEN AU - Liang, Jie AU - Edelsbrunner, Herbert AU - Pamidghantam, Sudhakar AU - Subramaniam, Shankar ID - 4031 IS - 2, Part 2 T2 - Fortieth Annual Meeting TI - Analytical method for molecular shapes: Area, volume, cavities, interface and pockets VL - 70 ER - TY - JOUR AB - Mutations giving rise to anatomical defects in the inner ear have been isolated in a large scale screen for mutations causing visible abnormalities in the zebrafish embryo (Haffter, P., Granato, M., Brand, M. et al. (1996) Development 123, 1-36). 58 mutants have been classified as having a primary ear phenotype; these fall into several phenotypic classes, affecting presence or size of the otoliths, size and shape of the otic vesicle and formation of the semicircular canals, and define at least 20 complementation groups. Mutations in seven genes cause loss of one or both otoliths, but do not appear to affect development of other structures within the ear. Mutations in seven genes affect morphology and patterning of the inner ear epithelium, including formation of the semicircular canals and, in some, development of sensory patches (maculae and cristae). Within this class, dog-eared mutants show abnormal development of semicircular canals and lack cristae within the ear, while in van gogh, semicircular canals fail to form altogether, resulting in a tiny otic vesicle containing a single sensory patch. Both these mutants show defects in the expression of homeobox genes within the otic vesicle. In a further class of mutants, ear size is affected while patterning appears to be relatively normal; mutations in three genes cause expansion of the otic vesicle, while in little ears and microtic, the ear is abnormally small, but still contains all five sensory patches, as in the wild type. Many of the ear and otolith mutants show an expected behavioural phenotype: embryos fail to balance correctly, and may swim on their sides, upside down, or in circles. Several mutants with similar balance defects have also been isolated that have no obvious structural ear defect, but that may include mutants with vestibular dysfunction of the inner ear (Granato, M., van Eeden, F. J. M., Schach, U. et al. (1996) Development, 123, 399-413,). Mutations in 19 genes causing primary defects in other structures also show an ear defect. In particular, ear phenotypes are often found in conjunction with defects of neural crest derivatives (pigment cells and/or cartilaginous elements of the jaw). At least one mutant, dog-eared, shows defects in both the ear and another placodally derived sensory system, the lateral line, while hypersensitive mutants have additional trunk lateral line organs. AU - Whitfield, Tanya AU - Granato, Michael AU - Van Eeden, Fredericus AU - Schach, Ursula AU - Brand, Michael AU - Furutani Seiki, Makoto AU - Haffter, Pascal AU - Hammerschmidt, Matthias AU - Heisenberg, Carl-Philipp J AU - Jiang, Yunjin AU - Kane, Donald AU - Kelsh, Robert AU - Mullins, Mary AU - Odenthal, Jörg AU - Nüsslein Volhard, Christiane ID - 4142 JF - Development SN - 0950-1991 TI - Mutations affecting development of the zebrafish inner ear and lateral line VL - 123 ER - TY - JOUR AB - As part of a large scale chemical mutagenesis screen of the zebrafish (Danio rerio) genome, we have identified 33 mutants with defects in hematopoiesis, Complementation analysis placed 32 of these mutants into 17 complementation groups, The allelism of the remaining 1 blood mutant is currently unresolved, We have categorized these blood mutants into four phenotypic classes based on analyses of whole embryos and isolated blood cells, as well as by in situ hybridization using the hematopoietic transcription factors GATA-1 and GATA-2, Embryos mutant for the gene moonshine have few if any proerythroblasts visible on the day circulation begins and normal erythroid cell differentiation is blocked as determined by staining for hemoglobin and GATA-1 expression, Mutations in five genes, chablis, frascati, merlot, retsina, thunderbird and two possibly unique mutations cause a progressive decrease in the number of blood cells during the first 5 days of development, Mutations in another seven genes, chardonnay, chianti, grenache, sauternes, weibherbst and zinfandel, and two additional mutations result in hypochromic blood cells which also decrease in number as development proceeds, Several of these mutants have immature cells in the circulation, indicating a block in normal erythroid development. The mutation in zinfandel is dominant, and 2-day old heterozygous carriers fail to express detectable levels of hemoglobin and have decreasing numbers of circulating cells during the first 5 days of development, Mutations in two genes, freixenet and yquem, result in the animals that are photosensitive with autofluorescent blood, similar to that found in the human congenital porphyrias, The collection of mutants presented here represent several steps required for normal erythropoiesis, The analysis of these mutants provides a powerful approach towards defining the molecular mechanisms involved in vertebrate hematopoietic development. AU - Ransom, David AU - Haffter, Pascal AU - Odenthal, Jörg AU - Brownlie, Alison AU - Vogelsang, Elisabeth AU - Kelsh, Robert AU - Brand, Michael AU - Van Eeden, Fredericus AU - Furutani Seiki, Makoto AU - Granato, Michael AU - Hammerschmidt, Matthias AU - Heisenberg, Carl-Philipp J AU - Jiang, Yunjin AU - Kane, Donald AU - Mullins, Mary AU - Nüsslein Volhard, Christiane ID - 4154 IS - 1 JF - Development SN - 0950-1991 TI - Characterization of zebrafish mutants with defects in embryonic hematopoiesis VL - 123 ER - TY - JOUR AB - In a large scale screen for mutants that affect the early development of the zebrafish, 109 mutants were found that cause defects in the formation of the jaw and the more posterior pharyngeal arches, Here we present the phenotypic description and results of the complementation analysis of mutants belonging to two major classes: (1) mutants with defects in the mandibular and hyoid arches and (2) mutants with defects in cartilage differentiation and growth in all arches, Mutations in four of the genes identified during the screen show specific defects in the first two arches and leave the more posterior pharyngeal arches largely unaffected (schmerle, sucker, hoover and sturgeon). In these mutants ventral components of the mandibular and hyoid arches are reduced (Meckel's cartilage and ceratohyal cartilage) whereas dorsal structures (palato-quadrate and hyosymplectic cartilages) are of normal size or enlarged, Thus, mutations in single genes cause defects in the formation of first and second arch structures but also differentially affect development of the dorsal and ventral structures within one arch. In 27 mutants that define at least 8 genes, the differentiation of cartilage and growth is affected. In hammerhead mutants particularly the mesodermally derived cartilages are reduced, whereas jellyfish mutant larvae are characterized by a severe reduction of all cartilaginous elements, leaving only two pieces in the position of the ceratohyal cartilages. In all other mutant larvae all skeletal elements are present, but consist of smaller and disorganized chondrocytes. These mutants also exhibit shortened heads and reduced pectoral fins. In homozygous knorrig embryos, tumor-like outgrowths of chondrocytes occur along the edges of all cartilaginous elements. The mutants presented here may be valuable tools for elucidating the genetic mechanisms that underlie the development of the mandibular and the hyoid arches, as well as the process of cartilage differentiation. AU - Piotrowski, Tatjana AU - Schilling, Thomas AU - Brand, Michael AU - Jiang, Yunjin AU - Heisenberg, Carl-Philipp J AU - Beuchle, Dirk AU - Grandel, Heiner AU - Van Eeden, Fredericus AU - Furutani Seiki, Makoto AU - Granato, Michael AU - Haffter, Pascal AU - Hammerschmidt, Matthias AU - Kane, Donald AU - Kelsh, Robert AU - Mullins, Mary AU - Odenthal, Jörg AU - Warga, Rachel AU - Nüsslein Volhard, Christiane ID - 4156 IS - 1 JF - Development SN - 0950-1991 TI - Jaw and branchial arch mutants in zebrafish II: Anterior arches and cartilage differentiation VL - 123 ER - TY - JOUR AB - In a screen for embryonic mutants in the zebrafish a large number of mutants were isolated with abnormal brain morphology, We describe here 26 mutants in 13 complementation groups that show abnormal development of large regions of the brain, Early neurogenesis is affected in white tail (wit), During segmentation stages, homozygous wit embryos display an irregularly formed neural keel, particularly in the hindbrain, Using a variety of molecular markers, a severe increase in the number of various early differentiating neurons can be demonstrated, In contrast, late differentiating neurons, radial glial cells and some nonneural cell types, such as the neural crest-derived melanoblasts, are much reduced, Somitogenesis appears delayed, In addition, very reduced numbers of melanophores are present posterior to the mid-trunk, The wit phenotype is reminiscent of neurogenic mutants in Drosophila, such as Notch or Delta, In mutant parachute (pac) embryos the general organization of the hindbrain is disturbed and many rounded cells accumulate loosely in the hindbrain and midbrain ventricles, Mutants in a group of 6 genes, snakehead(snk), natter (nat), otter (ott) fullbrain (ful) viper (vip) and white snake (wis) develop collapsed brain ventricles, before showing signs of general degeneration, atlantis (atl), big head (bid), wicked brain (win), scabland (sbd) and eisspalte (ele) mutants have different malformation of the brain folds, Some of them have transient phenotypes, and mutant individuals may grow up to adults. AU - Jiang, Yunjin AU - Brand, Michael AU - Heisenberg, Carl-Philipp J AU - Beuchle, Dirk AU - Furutani Seiki, Makoto AU - Kelsh, Robert AU - Warga, Rachel AU - Granato, Michael AU - Haffter, Pascal AU - Hammerschmidt, Matthias AU - Kane, Donald AU - Mullins, Mary AU - Odenthal, Jörg AU - Van Eeden, Fredericus AU - Nüsslein Volhard, Christiane ID - 4191 IS - 1 JF - Development SN - 0950-1991 TI - Mutations affecting neurogenesis and brain morphology in the zebrafish, Danio rerio VL - 123 ER - TY - JOUR AB - Neural crest development involves cell-fate specification, proliferation, patterned cell migration, survival and differentiation, Zebrafish neural crest derivatives include three distinct chromatophores, which are well-suited to genetic analysis of their development, As part of a large-scale mutagenesis screen for embryonic/early larval mutations, we have isolated 285 mutations affecting all aspects of zebrafish larval pigmentation, By complementation analysis, we define 94 genes, We show here that comparison of their phenotypes permits classification of these mutations according to the types of defects they cause, and these suggest which process of neural crest development is probably affected, Mutations in eight genes affect the number of chromatophores: these include strong candidates for genes necessary for the processes of pigment cell specification and proliferation, Mutations in five genes remove part of the wild-type pigment pattern, and suggest a role in larval pigment pattern formation, Mutations in five genes show ectopic chromatophores in distinct sites, and may have implications for chromatophore patterning and proliferation, 76 genes affect pigment or morphology of one or more chromatophore types: these mutations include strong candidates for genes important in various aspects of chromatophore differentiation and survival, In combination with the embryological advantages of zebrafish, these mutations should permit cellular and molecular dissection of many aspects of neural crest development. AU - Kelsh, Robert AU - Brand, Michael AU - Jiang, Yunjin AU - Heisenberg, Carl-Philipp J AU - Lin, Shuo AU - Haffter, Pascal AU - Odenthal, Jörg AU - Mullins, Mary AU - Van Eeden, Fredericus AU - Furutani Seiki, Makoto AU - Granato, Michael AU - Hammerschmidt, Matthias AU - Kane, Donald AU - Warga, Rachel AU - Beuchle, Dirk AU - Vogelsang, Lisa AU - Nüsslein Volhard, Christiane ID - 4186 IS - 1 JF - Development SN - 0950-1991 TI - Zebrafish pigmentation mutations and the processes of neural crest development VL - 123 ER - TY - JOUR AB - This report describes mutants of the zebrafish having phenotypes causing a general arrest in early morphogenesis. These mutants identify a group of loci making up about 20% of the loci identified by mutants with visible morphological phenotypes within the first day of development. There are 12 Class I mutants, which fall into 5 complementation groups and have cells that lyse before morphological defects are observed. Mutants at three loci, speed bump, ogre and zombie, display abnormal nuclei. The 8 Class II mutants, which fall into 6 complementation groups, arrest development before cell lysis is observed. These mutants seemingly stop development in the late segmentation stages, and maintain a body shape similar to a 20 hour embryo. Mutations in speed bump, ogre, zombie, specter, poltergeist and troll were tested for cell lethality by transplanting mutant cells into wild-type hosts. With poltergeist, transplanted mutant cells all survive. The remainder of the mutants tested were autonomously but conditionally lethal: mutant cells, most of which lyse, sometimes survive to become notochord, muscles, or, in rare cases, large neurons, all cell types which become postmitotic in the gastrula. Some of the genes of the early arrest group may be necessary for progression though the cell cycle; if so, the survival of early differentiating cells may be based on having their terminal mitosis before the zygotic requirement for these genes. AU - Kane, Donald AU - Maischein, Hans AU - Brand, Michael AU - Van Eeden, Fredericus AU - Furutani Seiki, Makoto AU - Granato, Michael AU - Haffter, Pascal AU - Hammerschmidt, Matthias AU - Heisenberg, Carl-Philipp J AU - Jiang, Yunjin AU - Kelsh, Robert AU - Mullins, Mary AU - Odenthal, Jörg AU - Warga, Rachel AU - Nüsslein Volhard, Christiane ID - 4189 IS - 1 JF - Development SN - 0950-1991 TI - The zebrafish early arrest mutants VL - 123 ER - TY - JOUR AB - Epiboly, the enveloping of the yolk cell by the blastoderm, is the first zebrafish morphogenetic movement, We isolated four mutations that affect epiboly: half baked, avalanche, lawine and weg, Homozygous mutant embryos arrest the vegetal progress of the deep cells of the blastoderm; only the yolk syncytial layer of the yolk cell and the enveloping layer of the blastoderm reach the vegetal pole of the embryo, The mutations half baked, avalanche and lawine produce a novel dominant effect, termed a zygotic-maternal dominant effect: heterozygous embryos produced from heterozygous females slow down epiboly and accumulate detached cells over the neural tube; a small fraction of these mutant individuals are viable, Heterozygous embryos produced from heterozygous males crossed to homozygous wild-type females complete epiboly normally and are completely viable. Additionally, embryos heterozygous for half baked have an enlarged hatching gland, a partial dominant phenotype, The phenotypes of these mutants demonstrate that, for the spreading of cells during epiboly, the movement of the deep cells of the blastoderm require the function of genes that are not necessary for the movement of the enveloping layer or the yolk cell, Furthermore, the dominant zygotic-maternal effect phenotypes illustrate the maternal and zygotic interplay of genes that orchestrate the early cell movements of the zebrafish. AU - Kane, Donald AU - Hammerschmidt, Matthias AU - Mullins, Mary AU - Maischein, Hans AU - Brand, Michael AU - Van Eeden, Fredericus AU - Furutani Seiki, Makoto AU - Granato, Michael AU - Haffter, Pascal AU - Heisenberg, Carl-Philipp J AU - Jiang, Yunjin AU - Kelsh, Robert AU - Odenthal, Jörg AU - Warga, Rachel AU - Nüsslein Volhard, Christiane ID - 4188 IS - 1 JF - Development SN - 0950-1991 TI - The zebrafish epiboly mutants VL - 123 ER - TY - JOUR AB - We identified four zebrafish mutants with defects in forebrain induction and patterning during embryogenesis. The four mutants define three genes: masterblind (mbl), silverblick (slb), and knollnase (kas), In mbl embryos, the anterior forebrain acquires posterior forebrain characteristics: anterior structures such as the eyes, olfactory placodes and the telencephalon are missing, whereas the epiphysis located in the posterior forebrain is expanded, In slb embryos, the extension of the embryonic axis is initially delayed and eventually followed by a partial fusion of the eyes, Finally, in kas embryos, separation of the telencephalic primordia is incomplete and dorsal midline cells fail to form a differentiated roof plate, Analysis of the mutant phenotypes indicates that we have identified genes essential for the specification of the anterior forebrain (mbl), positioning of the eyes (slb) and differentiation of the roof plate (kas). In an appendix to this study we list mutants showing alterations in the size of the eyes and abnormal differentiation of the lenses. AU - Heisenberg, Carl-Philipp J AU - Brand, Michael AU - Jiang, Yunjin AU - Warga, Rachel AU - Beuchle, Dirk AU - Van Eeden, Fredericus AU - Furutani Seiki, Makoto AU - Granato, Michael AU - Haffter, Pascal AU - Hammerschmidt, Matthias AU - Kane, Donald AU - Kelsh, Robert AU - Mullins, Mary AU - Odenthal, Jörg AU - Nüsslein Volhard, Christiane ID - 4203 JF - Development SN - 0950-1991 TI - Genes involved in forebrain development in the zebrafish, Danio rerio VL - 123 ER - TY - JOUR AB - Tissues of the dorsal midline of vertebrate embryos, such as notochord and floor plate, have been implicated in inductive interactions that pattern the neural tube and somites. In our screen for embryonic visible mutations in the zebrafish we found 113 mutations in more than 27 genes with altered body shape, often with additional defects in CNS development. We concentrated on a subgroup of mutations in ten genes (the midline-group) that cause defective development of the floor plate. By using floor plate markers, such as the signaling molecule sonic hedgehog, we show that the schmalspur (sur) gene is needed for early floor plate development, similar to one-eyed-pinhead (oep) and the previously described cyclops (eye) gene. In contrast to oep and cyc, sur embryos show deletions of ventral CNS tissue restricted to the mid- and hindbrain, whereas the forebrain appears largely unaffected. In the underlying mesendodermal tissue of the head, sur is needed only for development of the posterior prechordal plate, whereas oep and eye are required for both anterior and posterior prechordal plate development. Our analysis of sur mutants suggests that defects within the posterior prechordal plate may cause aberrant development of ventral CNS structures in the mid- and hindbrain. Later development of the floor plate is affected in mutant chameleon, you-too, sonic-you, iguana, detour, schmalkars and monorail embryos; these mutants often show additional defects in tissues that are known to depend on signals from notochord and floor plate, For example, sur, con, and yot mutants show reduction of motor neurons; median deletions of brain tissue are seen in sur, con and yot embryos; and eye, con, yet, igu and dtr mutants often show no or abnormal formation of the optic chiasm. We also find fusions of the ventral neurocranium for all midline mutants tested, which may reveal a hitherto unrecognized function of the midline in influencing differentiation of neural crest cells at their destination. As a working hypothesis, we propose that midline-group genes may act to maintain proper structure and inductive function of zebrafish midline tissues. AU - Brand, Michael AU - Heisenberg, Carl-Philipp J AU - Warga, Rachel AU - Pelegri, Francisco AU - Karlstrom, Rolf AU - Beuchle, Dirk AU - Picker, Alexander AU - Jiang, Yunjin AU - Furutani Seiki, Makoto AU - Van Eeden, Fredericus AU - Granato, Michael AU - Haffter, Pascal AU - Hammerschmidt, Matthias AU - Kane, Donald AU - Kelsh, Robert AU - Mullins, Mary AU - Odenthal, Jörg AU - Nüsslein Volhard, Christiane ID - 4216 IS - 1 JF - Development SN - 0950-1991 TI - Mutations affecting development of the midline and general body shape during zebrafish embryogenesis VL - 123 ER - TY - JOUR AB - Mutations in two genes affect the formation of the boundary between midbrain and hindbrain (MHB): no isthmus (noi) and acerebellar (ace), noi mutant embryos lack the MHB constriction, the cerebellum and optic tectum, as well as the pronephric duct. Analysis of noi mutant embryos with neuron-specific antibodies shows that the MHB region and the dorsal and ventral midbrain are absent or abnormal, but that the rostral hindbrain is unaffected with the exception of the cerebellum, Using markers that are expressed during its formation (eng, wnt1 and pax-b), we find that the MHB region is already misspecified in noi mutant embryos during late gastrulation. The tectum is initially present and later degenerates, The defect in ace mutant embryos is more restricted: MHB and cerebellum are absent, but a tectum is formed, Molecular organisation of the tectum and tegmentum is disturbed, however, since eng, wntl and pax-b marker gene expression is not maintained, We propose that noi and ace are required for development of the MHB region and of the adjacent mid- and hindbrain, which are thought to be patterned by the MHB region, Presence of pax-b RNA, and absence of pax-b protein, together with the observation of genetic linkage and the occurrence of a point mutation, show that noi mutations are located in the pax-b gene, pax-b is a vertebrate orthologue of the Drosophila gene paired, which is involved in a pathway of cellular interactions at the posterior compartment boundary in Drosophila, Our results confirm and extend a previous report, and show that at least one member of this conserved signalling pathway is required for formation of the boundary between midbrain and hindbrain in the zebrafish. AU - Brand, Michael AU - Heisenberg, Carl-Philipp J AU - Jiang, Yunjin AU - Beuchle, Dirk AU - Lun, Klaus AU - Furutani Seiki, Makoto AU - Granato, Michael AU - Haffter, Pascal AU - Hammerschmidt, Matthias AU - Kane, Donald AU - Kelsh, Robert AU - Mullins, Mary AU - Odenthal, Jörg AU - Van Eeden, Fredericus AU - Nüsslein Volhard, Christiane ID - 4219 IS - 1 JF - Development SN - 0950-1991 TI - Mutations in zebrafish genes affecting the formation of the boundary between midbrain and hindbrain VL - 123 ER - TY - JOUR AB - Somitogenesis is the basis of segmentation of the mesoderm in the trunk and tail of vertebrate embryos, Two groups of mutants with defects in this patterning process have been isolated in our screen for zygotic mutations affecting the embryonic development of the zebrafish (Danio rerio), In mutants of the first group, boundaries between individual somites are invisible early on, although the paraxial mesoderm is present, Later, irregular boundaries between somites are present, Mutations infused somites (fss) and beamter (bea) affect all somites, whereas mutations in deadly seven (des), after eight (aei) and white tail (wit) only affect the more posterior somites, Mutants of all genes but wit are homozygous viable and fertile, Skeletal stainings and the expression pattern of myoD and snail1 suggest that anteroposterior patterning within individual somites is abnormal, In the second group of mutants, formation of the horizontal myoseptum, which separates the dorsal and ventral part of the myotome, is reduced, Six genes have been defined in this group (you-type genes), yea-too mutants show the most severe phenotype; in these the adaxial cells, muscle pioneers and the primary motoneurons are affected, in addition to the horizontal myoseptum. The horizontal myoseptum is also missing in mutants that lack a notochord. The similarity of the somite phenotype in mutants lacking the notochord and in the you-type mutants suggests that the genes mutated in these two groups are involved in a signaling pathway from the notochord, important for patterning of the somites. AU - Van Eeden, Fredericus AU - Granato, Michael AU - Schach, Ursula AU - Brand, Michael AU - Furutani Seiki, Makoto AU - Haffter, Pascal AU - Hammerschmidt, Matthias AU - Heisenberg, Carl-Philipp J AU - Jiang, Yunjin AU - Kane, Donald AU - Kelsh, Robert AU - Mullins, Mary AU - Odenthal, Jörg AU - Warga, Rachel AU - Allende, Miguel AU - Weinberg, Eric AU - Nüsslein Volhard, Christiane ID - 4222 IS - 1 JF - Development SN - 0950-1991 TI - Mutations affecting somite formation and patterning in the zebrafish, Danio rerio VL - 123 ER - TY - JOUR AB - In the zebrafish, Danio rerio, a caudal and pectoral fin fold develop during embryogenesis. At larval stages the caudal fin fold is replaced by four different fins, the unpaired anal, dorsal and tail fins. In addition the paired pelvic fins are formed, We have identified a total of 118 mutations affecting larval fin formation, Mutations in 11 genes lead to abnormal morphology or degeneration of both caudal and pectoral fin folds, Most mutants survive to adulthood and form a surprisingly normal complement of adult fins, Mutations in nine genes result in an increased or reduced size of the pectoral fins, Interestingly, in mutants of one of these genes, dackel (dak), pectoral fin buds form initially, but later the fin epithelium fails to expand, Expression of sonic hedgehog mRNA in the posterior mesenchyme of the pectoral fin bud is initiated in dak embryos, but not maintained, Mutations in five other genes affect adult fin but not larval fin development, Two mutants, longfin (lof) and another longfin (alf) have generally longer fins. Stein und bein (sub) has reduced dorsal and pelvic fins, whereas finless (fls) and wanda (wan) mutants affect all adult fins, Finally, mutations in four genes causing defects in embryonic skin formation will be briefly reported. AU - Van Eeden, Fredericus AU - Granato, Michael AU - Schach, Ursula AU - Brand, Michael AU - Furutani Seiki, Makoto AU - Haffter, Pascal AU - Hammerschmidt, Matthias AU - Heisenberg, Carl-Philipp J AU - Jiang, Yunjin AU - Kane, Donald AU - Kelsh, Robert AU - Mullins, Mary AU - Odenthal, Jörg AU - Warga, Rachel AU - Nüsslein Volhard, Christiane ID - 4220 IS - 1 JF - Development SN - 0950-1991 TI - Genetic analysis of fin formation in the zebrafish, Danio rerio VL - 123 ER - TY - CHAP AB - Any sample of genes traces back to a single common ancestor. Each gene also has other properties: its sequence, its geographic location and the phenotype and fitness of the organism that carries it. With sexual reproduction, different genes have different genealogies, which gives us much more information, but also greatly complicates population genetic analysis. We review the close relation between the distribution of genealogies and the classic theory of identity by descent in spatially structured populations, and develop a simple diffusion approximation to the distribution of coalescence times in a homogeneous two-dimensional habitat. This shows that when neighbourhood size is large (as in most populations) only a small fraction of pairs of genes are closely related, and only this fraction gives information about current rates of gene flow. The increase of spatial dispersion with lineage age is thus a poor estimator of gene flow. The bulk of the genealogy depends on the long-term history of the population; we discuss ways of inferring this history from the concordance between genealogies across loci. AU - Barton, Nicholas H AU - Wilson, Ian ID - 4294 SN - 978-0198549840 T2 - New uses for new phylogenies TI - Genealogies and geography ER - TY - CHAP AB - Genetic studies are beginning to provide insights into the evolutionary processes that reduce the fitness of hybrids between recently diverged species. However, the deleterious gene interactions responsible for this fitness reduction are still poorly understood. AU - Barton, Nicholas H ID - 4295 SN - 0960-9822 T2 - Current Biology TI - Speciation: more than the sum of its parts VL - 6 ER - TY - THES AB - A {\em hybrid automaton\/} consists of a finite automaton interacting with a dynamical system. Hybrid automata are used to model embedded controllers and other systems that consist of interacting discrete and continuous components. A hybrid automaton is {\em rectangular\/} if each of its continuous variables~x satisfies a nondeterministic differential equation of the form a≤dxdt≤b, where a and~b are rational constants. Rectangular hybrid automata are particularly useful for the analysis of communication protocols in which local clocks have bounded drift, and for the conservative approximation of systems with more complex continuous behavior. We examine several verification problems on the class of rectangular hybrid automata, including reachability, temporal logic model checking, and controller synthesis. Both dense-time and discrete-time models are considered. We identify subclasses of rectangular hybrid automata for which these problems are decidable and give complexity analyses. An investigation of the structural properties of rectangular hybrid automata is undertaken. One method for proving the decidability of verification problems on infinite-state systems is to find finite quotient systems on which analysis can proceed. Three state-space equivalence relations with strong connections to temporal logic are bisimilarity, similarity, and language equivalence. We characterize the quotient spaces of rectangular hybrid automata with respect to these equivalence relations. AU - Kopke, Peter ID - 4419 TI - The Theory of Rectangular Hybrid Automata ER - TY - CONF AB - We use linear hybrid automata to define linear approximations of the phase portraits of nonlinear hybrid systems. The approximating automata can be analyzed automatically using the symbolic model checker HyTech. We demonstrate the technique through the study of predator-prey systems, where we compute population bounds for both species. We also identify a class of nonlinear hybrid automata for which linear phase-portrait approximations can be generated automatically. AU - Henzinger, Thomas A AU - Wong Toi, Howard ED - Alur, Rajeev ED - Henzinger, Thomas A ED - Sontag, Eduardo ID - 4426 SN - 9783540611554 T2 - Hybrid Systems III: Verification and Control TI - Linear phase-portrait approximations for nonlinear hybrid systems VL - 1066 ER - TY - CHAP AB - We model a steam-boiler control system using hybrid automata. We provide two abstracted linear models of the nonlinear behavior of the boiler. For each model, we define and verify a controller that maintains safe operation of the boiler. The less abstract model permits the design of a more efficient controller. We also demonstrate how the tool HyTech can be used to automatically synthesize control parameter constraints that guarantee safety of the boiler. AU - Henzinger, Thomas A AU - Wong Toi, Howard ID - 4427 SN - 9783540495666 T2 - Formal Methods for Industrial Applications: Specifying and Programming the Steam Boiler Control TI - Using HyTech to synthesize control parameters for a steam boiler VL - 1165 ER - TY - CONF AB - Three natural equivalence relations on the infinite state space of a hybrid automaton are language equivalence, simulation equivalence, and bisimulation equivalence. When one of these equivalence relations has a finite quotient, certain model checking and controller synthesis problems are decidable. When bounds on the number of equivalence classes are obtained, bounds on the running times of model checking and synthesis algorithms follow as corollaries. We characterize the time-abstract versions of these equivalence relations on the state spaces of rectangular hybrid automata (RHA), in which each continuous variable is a clock with bounded drift. These automata are useful for modeling communications protocols with drifting local clocks, and for the conservative approximation of more complex hybrid systems. Of our two main results, one has positive implications for automatic verification, and the other has negative implications. On the positive side, we find that the (finite) language equivalence quotient for RHA is coarser than was previously known by a multiplicative exponential factor. On the negative side, we show that simulation equivalence for RHA is equality (which obviously has an infinite quotient). Our main positive result is established by analyzing a subclass of timed automata, called one-sided timed automata (OTA), for which the language equivalence quotient is coarser than for the class of all timed automata. An exact characterization of language equivalence for OTA requires a distinction between synchronous and asynchronous definitions of (bi)simulation: if time actions are silent, then the induced quotient for OTA is coarser than if time actions (but not their durations) are visible. AU - Henzinger, Thomas A AU - Kopke, Peter ID - 4443 SN - 9783540616047 T2 - 7th International Conference on Concurrency Theory TI - State equivalences for rectangular hybrid automata VL - 1119 ER - TY - CONF AB - In temporal-logic model checking, we verify the correctness of a program with respect to a desired behavior by checking whether a structure that models the program satisfies a temporal-logic formula that specifies the behavior. The main practical limitation of model checking is caused by the size of the state space of the program, which grows exponentially with the number of concurrent components. This problem, known as the state-explosion problem, becomes more difficult when we consider real-time model checking, where the program and the specification involve quantitative references to time. In particular, when use timed automata to describe real-time programs and we specify timed behaviors in the logic TCTL, a real-time extension of the temporal logic CTL with clock variables, then the state space under consideration grows exponentially not only with the number of concurrent components, but also with the number of clocks and the length of the clock constraints used in the program and the specification. Two powerful methods for coping with the state-explosion problem are on-the-fly and space-efficient model checking. In on-the-fly model checking, we explore only the portion of the state space of the program whose exploration is essential for determining the satisfaction of the specification. In space-efficient model checking, we store in memory the minimal information required, preferring to spend time on reconstructing information rather than spend space on storing it. In this work we develop an automata-theoretic approach to TCTL model checking that combines both methods. We suggest, for the first time, a PSPACE on-the-fly model-checking algorithm for TCTL. AU - Henzinger, Thomas A AU - Kupferman, Orna AU - Vardi, Moshe ID - 4495 SN - 978-3-540-70625-0 T2 - 7th International Conference on Concurrency Theory TI - A space-efficient on-the-fly algorithm for real-time model checking VL - 1119 ER - TY - CONF AB - We summarize several recent results about hybrid automata. Our goal is to demonstrate that concepts from the theory of discrete concurrent systems can give insights into partly continuous systems, and that methods for the verification of finite-state systems can be used to analyze certain systems with uncountable state spaces AU - Henzinger, Thomas A ID - 4519 SN - 1043-6871 T2 - Proceedings 11th Annual IEEE Symposium on Logic in Computer Science TI - The theory of hybrid automata ER - TY - GEN ED - Henzinger, Thomas A ED - Alur, Rajeev ID - 4585 TI - 8th International Conference on Computer Aided Verification VL - 1102 ER - TY - CONF AB - We present a formal model for concurrent systems. The model represents synchronous and asynchronous components in a uniform framework that supports compositional (assume-guarantee) and hierarchical (stepwise refinement) reasoning. While synchronous models are based on a notion of atomic computation step, and asynchronous models remove that notion by introducing stuttering, our model is based on a flexible notion of what constitutes a computation step: by applying an abstraction operator to a system, arbitrarily many consecutive steps can be collapsed into a single step. The abstraction operator, which may turn an asynchronous system into a synchronous one, allows us to describe systems at various levels of temporal detail. For describing systems at various levels of spatial detail, we use a hiding operator that may turn a synchronous system into an asynchronous one. We illustrate the model with diverse examples from synchronous circuits, asynchronous shared-memory programs, and synchronous message passing AU - Alur, Rajeev AU - Henzinger, Thomas A ID - 4588 SN - 0018-9162 T2 - Proceedings 11th Annual IEEE Symposium on Logic in Computer Science TI - Reactive modules ER - TY - JOUR AB - Presents a model-checking procedure and its implementation for the automatic verification of embedded systems. The system components are described as hybrid automata-communicating machines with finite control and real-valued variables that represent continuous environment parameters such as time, pressure and temperature. The system requirements are specified in a temporal logic with stop-watches, and verified by symbolic fixpoint computation. The verification procedure-implemented in the Cornell Hybrid Technology tool, HyTech-applies to hybrid automata whose continuous dynamics is governed by linear constraints on the variables and their derivatives. We illustrate the method and the tool by checking safety, liveness, time-bounded and duration requirements of digital controllers, schedulers and distributed algorithms AU - Alur, Rajeev AU - Henzinger, Thomas A AU - Ho, Pei ID - 4611 IS - 3 JF - IEEE Transactions on Software Engineering SN - 0018-9162 TI - Automatic symbolic verification of embedded systems VL - 22 ER - TY - JOUR AB - The most natural, compositional, way of modeling real-time systems uses a dense domain for time. The satisfiability of timing constraints that are capable of expressing punctuality in this model, however, is known to be undecidable. We introduce a temporal language that can constrain the time difference between events only with finite, yet arbitrary, precision and show the resulting logic to be EXPSPACE-complete. This result allows us to develop an algorithm for the verification of timing properties of real-time systems with a dense semantics. AU - Alur, Rajeev AU - Feder, Tomás AU - Henzinger, Thomas A ID - 4610 IS - 1 JF - Journal of the ACM SN - 0004-5411 TI - The benefits of relaxing punctuality VL - 43 ER - TY - BOOK ED - Alur, Rajeev ED - Henzinger, Thomas A ED - Sontag, Eduardo D ID - 4612 SN - 0302-9743 TI - Hybrid Systems III: Verification and Control VL - 1066 ER - TY - JOUR AB - The tra-1 gene is a terminal regulator of somatic sex in Caenorhabditis elegans: high tra-1 activity elicits female development, low tra-1 activity elicits male development. To investigate the function and evolution of tra- 1, we examined the tra-1 gene from the closely related nematode C. briggsae. Ce-tra-1 and Cb-tra-1 are unusually divergent. Each gene generates two transcripts, but only one of these is present in both species. This common transcript encodes TRA-1A, which shows only 44% amino acid identity between the species, a figure much lower than that for previously compared genes. A Cb-tra-1 transgene rescues many tissues of tra-1(null) mutants of C. elegans but not the somatic gonad or germ line. This transgene also causes nongonadal feminization of XO animals, indicating incorrect sexual regulation. Alignment of Ce-TRA-1A and Cb-TRA-1A defined several conserved regions likely to be important for tra-1 function. The phenotype differences between Ce-tra- 1(null) mutants rescued by Cb-tra-1 transgenes and wild-type C. elegans indicate significant divergence of regulatory regions. These molecular and functional studies suggest that evolution of sex determination in nematodes is rapid and genetically complex. AU - de Bono, Mario AU - Hodgkin, J. ID - 6161 IS - 2 JF - Genetics KW - amino acid sequence KW - article KW - caenorhabditis elegans KW - evolution KW - genetic variability KW - nonhuman KW - priority journal KW - sex determination KW - Amino Acid Sequence KW - Animals KW - Animals KW - Genetically Modified KW - Base Sequence KW - Caenorhabditis KW - Caenorhabditis elegans KW - Caenorhabditis elegans Proteins KW - DNA KW - Helminth KW - DNA-Binding Proteins KW - Evolution KW - Molecular KW - Female KW - Helminth Proteins KW - Membrane Proteins KW - Molecular Sequence Data KW - Mutagenesis KW - RNA KW - Messenger KW - Sequence Homology KW - Amino Acid KW - Sex Determination (Analysis) KW - Transcription Factors KW - Transgenes KW - Turner Syndrome KW - Animalia KW - Caenorhabditis KW - Caenorhabditis briggsae KW - Caenorhabditis elegans KW - Nematoda SN - 00166731 TI - Evolution of sex determination in Caenorhabditis: Unusually high divergence of tra-1 and its functional consequences VL - 144 ER -