Miracle-dz/UniFAR-FTUs huggingface dataset:
PII: S0042-6989(96)00254-4

Motion integration occurs over a restricted range of visual space. However, there have been studies suggesting interactions among motion detectors operating on widely separated spatial regions. To understand these lateral spatial interactions beyond motion pooling regions, we examined the effect of surrounding motion on the direction of the center stimulus under several stimulus conditions. We have found that there is a motion direction shift of the center stimulus caused by surrounding motion depending on its motion direction, spatial pro~imity to the center stimulus, contrast, speed, and the extent of motion area. This effect was ohserved both for monocular and dichoptic presentations of the pattern. However, the perceived direction shift decreased when the spatial frequency ratio of the center and surround stimuli viwied, or a non-Fourier motion pattern was used for both center and surround stimuli. We present a model consisting of lateral inhibitory interactions between pattern motion unit networks tb explain the direction shift observed in the experiments. @ 1997 Elsevier Science Ltd. All rights reserved.
PII: S0925-4773(99)00219-1

The Drosophila gap gene KruÈppel (Kr) encodes a zinc ®nger-type transcription factor required for controlling the spatial expression of other segmentation genes during early blastoderm stage. Here we show that two independent and transferable repressor domains of KruÈppel act to control expression of the pair-rule gene hairy, and that the minimal cis-acting element of hairy stripe7 (h7) mediates either KruÈppeldependent activation or repression in different regions of the blastoderm embryo. The C-terminal region of KruÈppel which encompasses the predominant repressor domain is not essential for activation, but is required to fully suppress h7-mediated transcription in response to high levels of KruÈppel activity. This domain contains an interaction motif for dCtBP, a homologue of the human co-repressor CtBP. dCtBP activity is, however, dispensable for KruÈppel-mediated repression in the embryo since KruÈppel-mediated repression functions in the absence of dCtBP. Possible modes of h7-mediated gene regulation in response to the different domains and levels of KruÈppel are discussed. q 1999 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(00)00282-3

In developing Drosophila notum, wingless expression is regulated by Decapentaplegic signaling positively and negatively so that only notal cells receiving optimal levels of Decapentaplegic signals express wingless (Sato et al., 1999b. Development 126, 1457±1466). Here, we show evidence that this Decapentaplegic-dependent regulation of notal wingless expression includes plural mechanisms, involving pannier and u-shaped. In the medial notum, Pannier and U-shaped form a complex (Haenlin et al., 1997. Genes Dev. 11, 3096±3108). The expression of pannier and u-shaped is positively regulated by Decapentaplegic signals emanating from the dorsal-most region. The Pannier/U-shaped complex serves as a repressor and a transcriptional activator, respectively, for wingless and u-shaped expression. In the more lateral region, wingless expression is up-regulated by U-shaped-unbound Pannier. wingless expression is also weakly regulated by its own signaling. q 2000 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(01)00585-8

The paired-like homeodomain (HD) protein Chx10 is distinguished by the presence of the CVC domain, a conserved 56 amino acid sequence C-terminal to the HD. In mammals, Chx10 is essential both for the proliferation of retinal progenitor cells and for the formation or survival of retinal bipolar interneurons. We describe the cloning and characterization of a mouse Chx10 homologue, Vsx1; phylogenetic analysis suggests that Vsx1 and its putative vertebrate orthologues have evolved rapidly. Vsx1 expression in the adult is predominantly retinal. Whereas Chx10 is expressed both in retinal progenitors in the developing eye and apparently in all bipolar cells of the mature retina, Vsx1 expression is first detected in the eye at postnatal day 5, where it is restricted to cone bipolar cells. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
Dynamic Visualization of a-C

Tae-Jin Kim,1 Shuai Zheng,2 Jie Sun,3 Ismaeel Muhamed,4 JunWu,5LeiLei,6XinyuKong,4DeborahE.Leckband,2,4,5,6,7,8,* and Yingxiao Wang1,2,3,6,8,9,* 1Neuroscience Program 2Department of Bioengineering and Beckman Institute for Advanced Science and Technology 3Department of Integrative and Molecular Physiology 4Department of Biochemistry 5Department of Chemical and Biomolecular Engineering 6Center for Biophysics and Computational Biology 7Department of Chemistry 8Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA 9Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
PII: S0925-4773(02)00296-4

The iroquois (iro) homeobox genes participate in many developmental processes both in vertebrates and invertebrates, among them are neural plate formation and neural patterning. In this work, we study in detail Xenopus Iro (Xiro) function in primary neurogenesis. We show that misexpression of Xiro genes promotes the activation of the proneural gene Xngnr1 but suppresses neuronal differentiation. This is probably due to upregulation of at least two neuronal-fate repressors: XHairy2A and XZic2. Accordingly, primary neurons arise at the border of the Xiro expression domains. In addition, we identify XGadd45-g as a new gene repressed by Xiro. XGadd45-g encodes a cell-cycle inhibitor and is expressed in territories where cells will exit mitosis, such as those where primary neurons arise. Indeed, XGadd45-g misexpression causes cell cycle arrest. We conclude that, during Xenopus primary neuron formation, in Xiro expressing territories neuronal differentiation is impaired, while in adjacent cells, XGadd45-g may help cells stop dividing and differentiate as neurons. q 2002 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(01)00326-4

The LAMB1 gene encodes the laminin b1 subunit of laminin, an extracellular matrix protein. Using several transgenic mouse lines containing various lengths of the LAMB1 promoter driving lacZ reporter gene expression, regions of LAMB1 promoter that contain cis-acting DNA regulatory element(s) have been identi®ed. The 3.9LAMB1bgal transgene is expressed in various tissues during development. LAMB1 transgene expression is observed in a selective set of nephrons of the neonatal and adult kidneys. The cis-acting DNA regulatory elements responsible for LAMB1 transgene expression in ovaries and in juvenile kidneys are present between 2'1.4 and 20.7 kb relative to the transcription start site, while those of adult kidneys are located between 22.5 and 21.4 kb. The LAMB1 transgene is also expressed in the epididymis of 1 week old transgenic mice. Mutation of the retinoic acid response element (RARE) in the context of the 3.9LAMB1bgal transgene results in loss of LAMB1 transgene expression in all tissues. Thus, sequences between 22.5 and 20.7 kb plus the RARE are required for appropriate expression of the LAMB1 transgene in mice. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(00)00407-X

Secreted frizzled related proteins (Sfrps) are thought to bind and regulate Wnt activity through a cysteine rich domain that is highly similar to that of Frizzled receptors. To investigate possible roles for Sfrps in chick development, we have isolated partial cDNAs encoding Sfrp-1 and Sfrp-2 and have thoroughly characterized the expression patterns of both genes. Both sfrp-1 and sfrp-2 are expressed at all stages of development analyzed, ranging from Hamburger and Hamilton stage 4 through stage 32. Expression of both sfrp-1 and sfrp-2 is observed in mesodermal and ectodermal derivatives, while sfrp-1 is also found in endodermal lineages. q 2000 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(99)00045-3

The vertebrate Six genes are homologues of the Drosophila homeobox gene sine oculis (so), which is essential for development of the entire visual system. Here we describe two new Six genes in Drosophila, D-Six3 and D-Six4, which encode proteins with strongest similarity to vertebrate Six3 and Six4, respectively. In addition, we report the partial sequences of 12 Six gene homologues from several lower vertebrates and show that the class of Six proteins can be subdivided into three major families, each including one Drosophila member. Similar to so, both D-Six3 and D-Six4 are initially expressed at the blastoderm stage in narrow regions of the prospective head and during later stages in speci®c groups of head midline neurectodermal cells. D-Six3 may also be essential for development of the clypeolabrum and several head sensory organs. Thus, the major function of the ancestral Six gene probably involved speci®cation of neural structures in the cephalic region. q 1999 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(01)00395-1

Avian neural crest cells migrate on precise pathways to their target areas where they form a wide variety of cellular derivatives, including neurons, glia, pigment cells and skeletal components. In one portion of their pathway, trunk neural crest cells navigate in the somitic mesoderm in a segmental fashion, invading the rostral, while avoiding the caudal, half-sclerotome. This pattern of cell migration, imposed by the somitic mesoderm, contributes to the metameric organization of the peripheral nervous system, including the sensory and sympathetic ganglia. At hindbrain levels, neural crest cells also travel from the neural tube in a segmental manner via three migratory streams of cells that lie adjacent to even-numbered rhombomeres. In this case, the adjacent mesoderm does not possess an obvious segmental organization, compared to the somitic mesoderm at trunk levels. Thus, the mechanisms by which the embryo controls segmentally-organized cell migrations have been a fascinating topic over the past several years. Here, I discuss ®ndings from classical and recent studies that have delineated several of the tissue, cellular and molecular elements that contribute to the segmental organization of neural crest migration, primarily in the avian embryo. One common theme is that neural crest cells are prohibited from entering particular territories in the embryo due to the expression of inhibitory factors. However, permissive, migration-promoting factors may also play a key role in coordinating neural crest migration. q 2001 Published by Elsevier Science Ireland Ltd.
PII: S0042-6989(96)00246-5

Several studies have examined various.aspectsof ocular blood flow in attempts to elaborate the pathophysiology of various retino-vascular diseases (Sinclair et 1982; Rimmer 1988; Sebag 1989; Langham & Kramer, 1990; Langham et 1991). Non-invasive procedures such as body inversion (Lovasik 1988; Kergoat & Lovasik, 1990; Lovasik & Kergoat, 1994), suctionophthaImodynamometry(Grunwald 1984b; Kergoat & Lovasik, 1992), vigorous exercise (Brinchmann-Hansen 1989; Kergoat & Forcier, 1994; Kergoat & Lovasik, 1995), and inhalation of various gases (Riva 1983;Grunwald 1984a;Fallen 19.85;Linsenmeier 1987; Davies 1990) have been used to produce short-termchanges in normal retinal physiology for measuring the responsivity of retinal neurons or their vascular supply during the induced physiological stress. All of these approaches provided useful information about the speed and efficiency with which the retinal vascular regulatory mechanism can compensate for experimentally induced vascular stress. However, there have been no studies that have examined in systematic fashion the effects of experimentally induced vascular stress on retino-neural function in one eye and the consequential effects on physiology in the contralateral eye.
PII: S0925-4773(00)00450-0

In the developing retina, a retinoic acid (RA) gradient along the dorso-ventral axis is believed to be a prerequisite for the establishment of dorso-ventral asymmetry. This RA gradient is thought to result from the asymmetrical distribution of RA-generating aldehyde dehydrogenases along the dorso-ventral axis. Here, we identi®ed a novel aldehyde dehydrogenase speci®cally expressed in the chick ventral retina, using restriction landmark cDNA scanning (RLCS). Since this molecule showed enzymatic activity to produce RA from retinaldehyde, we designated it retinaldehyde dehydrogenase 3 (RALDH-3). Structural similarity suggested that RALDH-3 is the orthologue of human aldehyde dehydrogenase 6. We also isolated RALDH-1 which is expressed in the chick dorsal retina and implicated in RA formation. Raldh-3 was preferentially expressed ®rst in the surface ectoderm overlying the ventral portion of the prospective eye region and then in the ventral retina, earlier than Raldh-1 in chick and mouse embryos. High level expression of Raldh-3 was also observed in the nasal region. In addition, we found that Pax6 mutants are devoid of Raldh-3 expression. These results suggested that Raldh-3 is the key enzyme in the formation of an RA gradient along the dorso-ventral axis during the early eye development, and also in the development of the olfactory system. q 2000 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(02)00054-0

The Bar homeobox genes play an essential role during nervous system and eye development in Drosophila. We isolated a medaka Bar gene closely related to the Drosophila and mammalian Bar genes. In the medaka embryo, OlBar is expressed from gastrula stages onwards, in a region demarcating the presumptive prosencephalic-mesencephalic boundary. Later in development, OlBar transcripts are found in populations of differentiating neuronal cells of the brain and the retina. q 2002 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(99)00304-4

In Drosophila lateral glial cell development is initiated by the transcription factor encoded by glial cells missing. glial cells missing activates downstream transcription factors such as repo and pointed which subsequently control terminal glial differentiation. The gene loco has been identi®ed as a potential target gene of pointed and is involved in terminal glial differentiation. It encodes an RGS domain protein expressed speci®cally by the lateral glial cells in the developing embryonic CNS. Here we analyzed the loco promoter and the control of the glial-speci®c transcription pattern. Using promoter±reporter gene fusions we identi®ed a 1.9 kb promoter element capable of directing the almost complete loco gene expression pattern. Sequence analysis suggested the presence of gcm and pointed DNA binding sites. Following in vitro mutagenesis of these sites we demonstrated their relevance in vivo. The expression of loco is initially dependent on gcm. During subsequent stages of embryonic development gcm and pointed appear to activate loco transcription synergistically. In addition, at least two other factors appear to repress loco expression in the ectoderm and in the CNS midline cells. q 2000 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(02)00197-1

Amphioxus Bblhx3 was identified as a LIM-homeobox gene expressed in gastrulae. Structural analysis suggested that it is a member of lhx3 but not of lhx1 gene group. Whole mount in situ hybridization revealed that expression of Bblhx3 was initiated at the early gastrula stage and continued at least until 10-day larvae. Expression of Bblhx3 first appeared in the vegetal and future dorsal area in initial gastrulae and became restricted to the endoderm during gastrulation. In neurulae and early larvae, Bblhx3 was expressed in the developing neural tube, the notochord and preoral pit lineage. In 10-day larvae, Bblhx3 was expressed only in the preoral pit. This expression pattern is apparently distinct from that of vertebrate lhx3 genes that are not expressed during gastrulation. q 2002 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(02)00327-1

Recent studies in zebrafish have contributed to our understanding of early endoderm formation in vertebrates. Specifically, they have illustrated the importance of Nodal signaling as well as three transcription factors, Faust/Gata5, Bonnie and Clyde, and Casanova, in this process. Ongoing genetic and embryological studies in zebrafish are also contributing to our understanding of later aspects of endoderm development, including the formation of the gut and its associated organs, the liver and pancreas. The generation of transgenic lines expressing GFP in these organs promises to be particularly helpful in such studies. q 2002 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0042-6989(96)00088-0

If the spatial-frequency of sinusoidal signals in a contrast-detection experiment varies randomly from trial to trial, then performance is decreased compared with that in a situation where it remains constant. This spatial-frequency uncertainty effect can more or less be compensated by presenting informative cues shortly before each trial. Single-band, as well as multiple-band models, have been proposed to explain the uncertainty and cuing effects. While the latter assume that under uncertainty multiple channels are monitored simultaneously, the former propose that in each trial a single, but sometimes inappropriate, channel is selected for monitoring. Until now it is open which of these models is valid. Therefore, psychometric functions were collected under different conditions of spatial-frequency uncertainty. It appears that the size of the uncertainty effect varies with spatial-frequency. This result can be ,explained by a multiple-band model, as computational analysis reveals. Copyright 01996 Elsevief/3cience Ltd.
PII: S0925-4773(02)00019-9

To better understand the relationship between the endocrine and exocrine cell types in the Xenopus pancreas, we have cloned the Xenopus amylase cDNA and compared its expression profile with that of four other pancreatic markers: insulin, glucagon, elastase and trypsinogen. Our results demonstrate that the first pancreatic marker to be expressed is insulin, exclusively in the dorsal pancreas. These insulin-expressing cells form small groups which resemble islets, but no insulin is detected in the ventral pancreas until stage 47. In contrast, the exocrine markers, amylase, elastase and trypsinogen are first expressed only in the ventral pancreas beginning at stage 41; by stage 45 their expression extends into the dorsal pancreas. Glucagon, on the other hand, is not expressed in the pancreas until stage 45. In the endocrine cell clusters we do not find glucagon-expressing cells surrounding insulin-expressing cells, either in the tadpole or in the mature frog pancreas. q 2002 Elsevier Science Ireland Ltd. All rights reserved.
SUMOylation of the a-Kleisin

Background: Cohesion between sister chromatids is fundamental to ensure faithful chromosome segregation during mitosis and accurate repair of DNA damage postreplication. At the molecular level, cohesion establishment involves two defined events, a chromatin binding step and a chromatid entrapment event driven by posttranslational modifications on cohesin subunits. Results: Here, we show that modification by the small ubiquitin-like protein (SUMO) is required for sister chromatid tethering after DNA damage. We find that all subunits of cohesin becomeSUMOylated upon exposure toDNAdamaging agents or presence of a DNA double-strand break. We have mapped all lysine residues on cohesin’s a-kleisin subunit Mcd1 (Scc1) where SUMO can conjugate. We demonstrate that Mcd1 SUMOylation-deficient alleles are still recruited to DSBproximal regions but are defective in tethering sister chromatids and consequently fail to establish damage-induced cohesion both at DSBs and undamaged chromosomes. Moreover, we demonstrate that the bulk of Mcd1 SUMOylation in response to damage is carried out by the SUMO E3 ligase Nse2, a subunit of the related Smc5-Smc6 complex. SUMOylation occurs in cells with compromised Chk1 kinase activity, necessary for known posttranslational modifications on Mcd1, required for damage-induced cohesion. Conclusions: These findings demonstrate that SUMOylation of Mcd1 is a novel prerequisite for the establishment of DNA damage-induced cohesion at DSB-proximal regions and cohesion-associating regions (CARs) genome-wide.
PII: S0925-4773(02)00032-1

Recent studies have shown that aberrantly expressed gastrin-releasing peptide (GRP) and its receptor (GRP-R) critically regulate tumor cell differentiation in colon cancers developing in humans and mice. This finding suggested that the ability of GRP/GRP-R to promote a welldifferentiated phenotype in colon cancer might reflect a re-capitulation of a normal role in regulating intestinal organogenesis. To determine if this was the case, we compared and contrasted intestinal development in GRPR mice with their wild type littermates. GRP/GRP-R coexpression in wild type mice was only observed in villous enterocytes between N-1 and N-12. During this time frame villous growth was completely attenuated in GRPR mice. The contribution of GRP/GRP-R to villous growth was due to their act in increasing enterocyte proliferation prior to N-8 but increasing enterocyte size thereafter. From N-12 onwards, small intestinal villous growth in GRPR mice resumed such that no difference in this structure could be detected at adulthood between mice of either genotype. We next studied GRP/GRPR expression in human abortuses. These proteins were co-expressed by villous enterocytes only between weeks 14 and 20 post-conception, a time frame analogous to when they are expressed in the murine intestine. Thus, this study shows for the first time that GRP/GRP-R play a transient and non-critical role in intestinal development, yet provides a rationale for their re-appearance in colon cancer. q 2002 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(99)00290-7

Signaling triggered by polypeptide growth factors leads to the activation of their target genes. Several homeobox genes are known to be induced in response to polypeptide growth factors in early Xenopus development. In particular, Xmsx-1, an amphibian homologue of vertebrate Msx-1, is well characterized as a target gene of bone morphogenetic protein (BMP). Here, using a dominant-negative form of Xmsx-1 (VP-Xmsx-1), which is a fusion protein made with the virus-derived VP16 activation domain, we have examined whether Xmsx-1 activity is required in the endogenous ventralizing pathway. VP-Xmsx-1 induced a secondary body axis, complete with muscle and neural tissues, when overexpressed in ventral blastomeres, suggesting that Xmsx-1 activity is necessary for both mesoderm and ectoderm to be ventralized. We have also examined the epistatic relationship between Xmsx-1 and another ventralizing homeobox protein, Xvent-1, and show that Xmsx-1 is likely to be acting upstream of Xvent-1. We propose that Xmsx-1 is required in the BMP-stimulated ventralization pathway that involves the downstream activation of Xvent-1. q 2000 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(01)00502-0

Hoxa2 is required for a variety of developmental processes in the branchial arches and in the hindbrain. We have created a Hoxa2 allele that is about 45% as active in transcription as its wild-type counterpart. This allele, together with the Hoxa2 null and wild-type alleles, allowed the generation of embryos developing in the presence of different levels of Hoxa2 activity. Analysis of these embryos indicates that in general the hindbrain is more resistant to Hoxa2 deficiencies than the second branchial arch. Also, within the second arch, proximo-caudal areas are more sensitive than the rostro-distal. In the hindbrain, basic segmentation and patterning processes seem to occur normally at Hoxa2 levels as low as 20% of the normal. In addition, specific neuronal markers along the dorso-ventral axis of the hindbrain seem differentially affected by reduced Hoxa2 levels. These results provide new clues to understand the role of Hoxa2 in the different embryonic areas where it is required. q 2001 Elsevier Science Ireland Ltd. All rights reserved.