Denan Wang - Academia.edu (original) (raw)

Papers by Denan Wang

Development, 2002

In order to assess the in vivo function of integrins containing the β8 subunit, we have generated... more In order to assess the in vivo function of integrins containing the β8 subunit, we have generated integrin β8-deficient mice. Ablation of β8 results in embryonic or perinatal lethality with profound defects in vascular development. Sixty-five percent of integrin β8-deficient embryos die at midgestation, with evidence of insufficient vascularization of the placenta and yolk sac. The remaining 35% die shortly after birth with extensive intracerebral hemorrhage. Examination of brain tissue from integrin β8-deficient embryos reveals abnormal vascular morphogenesis resulting in distended and leaky capillary vessels, as well as aberrant brain capillary patterning. In addition, endothelial cell hyperplasia is found in these mutant brains. Expression studies show that integrin β8 transcripts are localized in endodermal cells surrounding endothelium in the yolk sac and in periventricular cells of the neuroepithelium in the brain. We propose that integrin β8 is required for vascular morphogen...

The Journal of Neuroscience, 2000

48200). L.F.R. is an investigator of the Howard Hughes Medical Institute. We thank Drs. Michael S... more 48200). L.F.R. is an investigator of the Howard Hughes Medical Institute. We thank Drs. Michael Stryker, Ardem Patapoutian, Eric Huang, and Song Hu for very helpful comments on this manuscript, and Drs. Liliana Minichiello and Rüdiger Klein for communication of results before publication. We also thank Regeneron Pharmaceuticals for providing TrkB-IgG, Drs. Mark Mayford and Eric Kandel for the promoter construct of ␣CaMKII, Juanito Meneses and Dr. Roger Pedersen (University of California San Francisco) for help with ES cell work, Judy Chang, Shan-Mei Xu, and Dr. Yuet Wai Kan for pronuclear injection of the CaMKcre construct, Drs. Klaus Rajewsky and Gail Martin for cre genes, Dr. Nigel Killeen for the pBS-lox-neo-tk-lox vector, and Dr. Chris Callahan for the tau-lacZ construct.

Nature neuroscience, Jan 12, 2017

Nociception is an evolutionarily conserved mechanism to encode and process harmful environmental ... more Nociception is an evolutionarily conserved mechanism to encode and process harmful environmental stimuli. Like most animals, Drosophila melanogaster larvae respond to a variety of nociceptive stimuli, including noxious touch and temperature, with stereotyped escape responses through activation of multimodal nociceptors. How behavioral responses to these different modalities are processed and integrated by the downstream network remains poorly understood. By combining trans-synaptic labeling, ultrastructural analysis, calcium imaging, optogenetics and behavioral analyses, we uncovered a circuit specific for mechanonociception but not thermonociception. Notably, integration of mechanosensory input from innocuous and nociceptive sensory neurons is required for robust mechanonociceptive responses. We further show that neurons integrating mechanosensory input facilitate primary nociceptive output by releasing short neuropeptide F, the Drosophila neuropeptide Y homolog. Our findings unvei...

Bioinformatics, Supercomputing and Complex Genome Analysis, 1993

ABSTRACT

The Journal of Neuroscience, 2005

We showed previously that loss of the integrin β8 subunit, which forms αvβ8 heterodimers, results... more We showed previously that loss of the integrin β8 subunit, which forms αvβ8 heterodimers, results in abnormal vascular development in the yolk sac, placenta, and brain. Animals lacking the integrin β8 (itgβ8) gene die either at midgestation, because of insufficient vascularization of the placenta and yolk sac, or shortly after birth with severe intracerebral hemorrhage. To specifically focus on the role of integrins containing the β8 subunit in the brain, and to avoid early lethalities, we used a targeted deletion strategy to deleteitgβ8only from cell types within the brain. Ablatingitgβ8from vascular endothelial cells or from migrating neurons did not result in cerebral hemorrhage. Targeted deletion ofitgβ8from the neuroepithelium, however, resulted in bilateral hemorrhage at postnatal day 0, although the phenotype was less severe than initgβ8-null animals. Newborn mice lackingitgβ8from the neuroepithelium had hemorrhages in the cortex, ganglionic eminence, and thalamus, as well as...

Proceedings of the National Academy of Sciences, 1992

A contiguous high-resolution NotI restriction map of the distal region of the long arm of human c... more A contiguous high-resolution NotI restriction map of the distal region of the long arm of human chromosome 21 was constructed by three strategies: linking clones to identify adjacent pieces of DNA, partial digestion to identify neighboring fragments, and cell line polymorphisms to prove identity or adjacency of DNA fragments. Twenty-nine single-copy DNA probes and five linking clone probes were used to determine the order of 30 Not I fragments, covering 10 megabases of DNA in band q22.3. Smaller Not I fragments occur preferentially in this region, suggesting that band q22.3 is unusually rich in genes, since Not I sites occur almost exclusively in CpG islands. Comparison of the physical map and genetic maps in this region reveals a 10-fold higher than average recombination frequency.

Proceedings of the National Academy of Sciences, 1992

Human chromosome 21 is the smallest of the 22 autosomes and 2 sex chromosomes. Hybridization of t... more Human chromosome 21 is the smallest of the 22 autosomes and 2 sex chromosomes. Hybridization of the human repetitive sequence Alu to pulsed-field gel-fractionated Not I-digested genomic DNA from a human-mouse hybrid cell line containing chromosome 21 as the sole human component identified chromosome 21 Not I restriction fragments. A Not I restriction map of regions of the chromosome was constructed, by identifying neighboring Alu bands with Not I linking clones. This approach simplifies the task of physical mapping and avoids ambiguities in Not I fragment assignments that arise from gel-to-gel mobility variations. A contiguous map was constructed with six Not I linking clones that covers at least the proximal one-third of the long arm of chromosome 21 and spans 20 megabases. A more detailed restriction map revealed 11 likely CpG islands in this region and localized 11 additional DNA markers.

Neuron, 2012

Dendrites are processes of nerve cells (or called neurons) that receive information from the envi... more Dendrites are processes of nerve cells (or called neurons) that receive information from the environment or other neurons. During the development of nervous system, dendrites from the same neuron usually spread evenly in the receptive field and avoid crossing one other. Dendrites from neighboring similar kind of neurons also avoid overlapping through repulsive interactions between dendrites from neighboring neurons to ensure even but non-redundant coverage of the receptive field. This non-overlapping coverage of receptive field involves competition of dendrites for limited space. In fruit flies, the dendrites of one particular type of peripheral sensory neurons named class IV dendritic arborization (da) neurons cover the larval body wall in a non-overlapping manner. In this study, we discovered that dendrites of class IV da neurons grow mainly in a two-dimensional space on the extracellular matrix (ECM), a network of proteins that functions like glue to hold cells together into tissues, between epidermis and muscle. Depriving class IV da neurons of integrins, the protein that binds to ECM, or preventing epidermal cells from producing laminin, one major component of ECM, causes dendrites of class IV da neurons to grow into the epidermis. These results suggest that interaction between intergrin-laminin ensure attachment of dendrites to the ECM. In addition, we found that in fly larvae mutant for genes that were previously shown to control even coverage of dendrites, class IV da neurons fail to limit the growth of their dendrites in a two-dimensional plane and often their dendrites often cross one another. However, increasing the expression of integrins in these mutants effectively reduces dendritic crossing and restores nonoverlapping coverage of their dendrite fields. Therefore, our study provides novel insights into the mechanisms underlying nonoverlapping dendritic coverage.

Neuron, 2003

into one of the daughter cells during asymmetric division, ensures that the two daughters adopt d... more into one of the daughter cells during asymmetric division, ensures that the two daughters adopt different cell fates (Uemura et al., 1989; Rhyu et al., 1994; Knoblich et al., 1995; Spana et al., 1995). Molecular studies of Numb homologs in vertebrates have identified two

Neuron, 2014

During developmental remodeling, neurites destined for pruning often degenerate on-site. Physical... more During developmental remodeling, neurites destined for pruning often degenerate on-site. Physical injury also induces degeneration of neurites distal to the injury site. Prompt clearance of degenerating neurites is important for maintaining tissue homeostasis and preventing inflammatory responses. Here we show that in both dendrite pruning and dendrite injury of Drosophila sensory neurons, epidermal cells rather than hemocytes are the primary phagocytes in clearing degenerating dendrites. Epidermal cells act via Draper-mediated recognition to facilitate dendrite degeneration and to engulf and degrade degenerating dendrites. Using multiple dendritic membrane markers to trace phagocytosis, we show that two members of the CD36 family, croquemort (crq) and debris buster (dsb), act at distinct stages of phagosome maturation for dendrite clearance. Our finding reveals the physiological importance of coordination between neurons and their surrounding epidermis, for both dendrite fragmentation and clearance. Neuron Epidermal Cells Clear Degenerating Dendrites

Methods, 1996

Conventional genome mapping and sequencing involves the mixtures of samples. Obviously, these app... more Conventional genome mapping and sequencing involves the mixtures of samples. Obviously, these approaches creanalysis and processing of individual samples and pieces of ate an increase in experimental efficiency by increasing experimental data. Although these methods work, it is quite the speed at which data accumulate. Some of the apclear that more efficient and less expensive methods are proaches use comparative information (map or seneeded. Our top down physical mapping experiments have foquence data on mixtures of samples or differences cused on the parallel processing of information from multiple among these samples) to construct the primary inforsamples at one time. This approach has aided the construction mation itself (map or sequence data on individual samof genomic restriction maps and allowed us to assess the degree ples or species). of large-scale conservation across wide regions of the human In recognition of the considerable increase in effigenome. The principles of parallel processing were applied in ciency of parallel processing methods, many funding top down experiments that ordered an overlapping cosmid library and scientific organizations have focused on developing from the 14-Mb Schizosaccharomyces pombe genome. This apgenomic resources that can be utilized by multiple sciproach produced an eight-fold increase in efficiency in clone entists simultaneously. Such resources provide access ordering over similar efforts. Recently, we have developed an not only to primary material but also to primary inforenhanced sequencing by hybridization protocol that allows DNA mation about such material. sequence information to be collected on a large number of sam-This review focuses on describing how parallel proples at once. Our current research focuses on applying parallel cessing methods have been applied in our past genomic processing principles to make genome-wide comparisons bemapping, library ordering, and DNA sequencing expertween pairs of samples for analyzing disease states.

Genomics, 1995

Genomic probes can be efficiently obtained for specific chromosomal regions by PCR amplification ... more Genomic probes can be efficiently obtained for specific chromosomal regions by PCR amplification of gel slices containing fractionated restriction enzymecleaved DNA. Here, single-copy, human-specific DNA sequences were amplified using inter-Alu PCR on gel slices containing a NotI digest of DNA from hybrid cell line WAV17. Rodent cell line WAV17 contains human chromosome 21. About 75% of the 0.15-to 3-kb inter-Alu PCR products could be regionally assigned, en masse, by hybridization experiments using inter-Alu PCR probes generated from cell lines containing portions of chromosome 21. This work produced 10 new chromosome 21 markers that came from regions of 21q containing few useful markers. These markers were needed to finish a NotI restriction map for 21q (Wang and Smith (1994) Genomics 20: 441). This approach provides markers needed to close map gaps and for top-down mapping approaches,

Genomics, 1991

Effective procedures have been developed for constructing Not1 linking libraries starting from ch... more Effective procedures have been developed for constructing Not1 linking libraries starting from chromosome-specific genomic libraries. Fifteen different single copy and two rDNA Not1 linking clones from human chromosome 2 1 were identified in two libraries. Their chromosomal origin was confirmed, and regional location established using hybrid cell panels. Hybridization experiments with these probes revealed pairs of genomic Not1 fragments, each ranging in size from co.05 to 4.0 Mb. Many fragments displayed cell type variation. The total size of the Not1 fragments detected in a human fibroblast cell line (GM6167) and mouse hybrid cell containing chromosome 21 as its only human component (WAV17) were approximately 32 and 34 Mb, respectively. If these fragments were all nonoverlapping, this would correspond to about 70% of the 50-Mb content estimated for the whole chromosome. The linking clones will be enormously useful in the subsequent construction of a Not1 restriction map of this chromosome. Characterization of these clones indicates the presence of numerous additional sites for other enzymes that recognize sequences containing CpG. Thus most Not1 linking clones appear to derive from CpG islands and probably identify the 5' end of genes.

Cell, 2006

Neural stem cells are retained in the postnatal subventricular zone (SVZ), a specialized neurogen... more Neural stem cells are retained in the postnatal subventricular zone (SVZ), a specialized neurogenic niche with unique cytoarchitecture and cell-cell contacts. Although the SVZ stem cells continuously regenerate, how they and the niche respond to local changes is unclear. Here we generated nestin-creER tm transgenic mice with inducible Cre recombinase in the SVZ and removed Numb/Numblike, key regulators of embryonic neurogenesis from postnatal SVZ progenitors and ependymal cells. This resulted in severe damage to brain lateral ventricle integrity and identified roles for Numb/ Numblike in regulating ependymal wall integrity and SVZ neuroblast survival. Surprisingly, the ventricular damage was eventually repaired: SVZ reconstitution and ventricular wall remodeling were mediated by progenitors that escaped Numb deletion. Our results show a selfrepair mechanism in the mammalian brain and may have implications for both niche plasticity in other areas of stem cell biology and the therapeutic use of neural stem cells in neurodegenerative diseases.

Cell, 1997

that ultimately give rise to the epithelia of the tubules and glomeruli of the mature kidney. The... more that ultimately give rise to the epithelia of the tubules and glomeruli of the mature kidney. The many branches *Department of Physiology † Howard Hughes Medical Institute of the ureter form the collecting duct tree of the kidney. Molecular genetic analyses in mice have revealed a ‡ Reproductive Genetics Unit Department of Obstetrics, Gynecology complex network of regulatory proteins that control kidney organogenesis. These include the secreted signal-and Reproductive Sciences University of California, San Francisco ing molecules glial cell line-derived neurotrophic factor (GDNF), wnt-4, bone morphogenetic protein 7 (BMP7),

Proceedings of the National Academy of Sciences, 2004

Development of both dendrites and axons is important for the formation of neuronal circuits, beca... more Development of both dendrites and axons is important for the formation of neuronal circuits, because dendrites receive information and the axon is responsible for sending signals. In the past decade, extensive studies have revealed many molecules underlying axonal outgrowth and pathfinding. In contrast, much less is known about the molecular mechanisms that control dendrite development. Here we report the identification of an evolutionarily conserved Ig superfamily member, dendrite arborization and synapse maturation 1 (Dasm1), which plays a critical role in dendrite development. Dasm1 contains five Ig domains and two fibronectin III domains in the extracellular N terminus, a single transmembrane domain, and an intracellular C-terminal tail with a type I PDZ domain binding motif at the end. It is highly expressed in the brain and localized at the dendrites. Suppression of Dasm1 expression in hippocampal neurons via RNA interference or expression of Dasm1 without its cytoplasmic tail...

Development, 2002

In order to assess the in vivo function of integrins containing the β8 subunit, we have generated... more In order to assess the in vivo function of integrins containing the β8 subunit, we have generated integrin β8-deficient mice. Ablation of β8 results in embryonic or perinatal lethality with profound defects in vascular development. Sixty-five percent of integrin β8-deficient embryos die at midgestation, with evidence of insufficient vascularization of the placenta and yolk sac. The remaining 35% die shortly after birth with extensive intracerebral hemorrhage. Examination of brain tissue from integrin β8-deficient embryos reveals abnormal vascular morphogenesis resulting in distended and leaky capillary vessels, as well as aberrant brain capillary patterning. In addition, endothelial cell hyperplasia is found in these mutant brains. Expression studies show that integrin β8 transcripts are localized in endodermal cells surrounding endothelium in the yolk sac and in periventricular cells of the neuroepithelium in the brain. We propose that integrin β8 is required for vascular morphogen...

The Journal of Neuroscience, 2000

48200). L.F.R. is an investigator of the Howard Hughes Medical Institute. We thank Drs. Michael S... more 48200). L.F.R. is an investigator of the Howard Hughes Medical Institute. We thank Drs. Michael Stryker, Ardem Patapoutian, Eric Huang, and Song Hu for very helpful comments on this manuscript, and Drs. Liliana Minichiello and Rüdiger Klein for communication of results before publication. We also thank Regeneron Pharmaceuticals for providing TrkB-IgG, Drs. Mark Mayford and Eric Kandel for the promoter construct of ␣CaMKII, Juanito Meneses and Dr. Roger Pedersen (University of California San Francisco) for help with ES cell work, Judy Chang, Shan-Mei Xu, and Dr. Yuet Wai Kan for pronuclear injection of the CaMKcre construct, Drs. Klaus Rajewsky and Gail Martin for cre genes, Dr. Nigel Killeen for the pBS-lox-neo-tk-lox vector, and Dr. Chris Callahan for the tau-lacZ construct.

Nature neuroscience, Jan 12, 2017

Nociception is an evolutionarily conserved mechanism to encode and process harmful environmental ... more Nociception is an evolutionarily conserved mechanism to encode and process harmful environmental stimuli. Like most animals, Drosophila melanogaster larvae respond to a variety of nociceptive stimuli, including noxious touch and temperature, with stereotyped escape responses through activation of multimodal nociceptors. How behavioral responses to these different modalities are processed and integrated by the downstream network remains poorly understood. By combining trans-synaptic labeling, ultrastructural analysis, calcium imaging, optogenetics and behavioral analyses, we uncovered a circuit specific for mechanonociception but not thermonociception. Notably, integration of mechanosensory input from innocuous and nociceptive sensory neurons is required for robust mechanonociceptive responses. We further show that neurons integrating mechanosensory input facilitate primary nociceptive output by releasing short neuropeptide F, the Drosophila neuropeptide Y homolog. Our findings unvei...

Bioinformatics, Supercomputing and Complex Genome Analysis, 1993

ABSTRACT

The Journal of Neuroscience, 2005

We showed previously that loss of the integrin β8 subunit, which forms αvβ8 heterodimers, results... more We showed previously that loss of the integrin β8 subunit, which forms αvβ8 heterodimers, results in abnormal vascular development in the yolk sac, placenta, and brain. Animals lacking the integrin β8 (itgβ8) gene die either at midgestation, because of insufficient vascularization of the placenta and yolk sac, or shortly after birth with severe intracerebral hemorrhage. To specifically focus on the role of integrins containing the β8 subunit in the brain, and to avoid early lethalities, we used a targeted deletion strategy to deleteitgβ8only from cell types within the brain. Ablatingitgβ8from vascular endothelial cells or from migrating neurons did not result in cerebral hemorrhage. Targeted deletion ofitgβ8from the neuroepithelium, however, resulted in bilateral hemorrhage at postnatal day 0, although the phenotype was less severe than initgβ8-null animals. Newborn mice lackingitgβ8from the neuroepithelium had hemorrhages in the cortex, ganglionic eminence, and thalamus, as well as...

Proceedings of the National Academy of Sciences, 1992

A contiguous high-resolution NotI restriction map of the distal region of the long arm of human c... more A contiguous high-resolution NotI restriction map of the distal region of the long arm of human chromosome 21 was constructed by three strategies: linking clones to identify adjacent pieces of DNA, partial digestion to identify neighboring fragments, and cell line polymorphisms to prove identity or adjacency of DNA fragments. Twenty-nine single-copy DNA probes and five linking clone probes were used to determine the order of 30 Not I fragments, covering 10 megabases of DNA in band q22.3. Smaller Not I fragments occur preferentially in this region, suggesting that band q22.3 is unusually rich in genes, since Not I sites occur almost exclusively in CpG islands. Comparison of the physical map and genetic maps in this region reveals a 10-fold higher than average recombination frequency.

Proceedings of the National Academy of Sciences, 1992

Human chromosome 21 is the smallest of the 22 autosomes and 2 sex chromosomes. Hybridization of t... more Human chromosome 21 is the smallest of the 22 autosomes and 2 sex chromosomes. Hybridization of the human repetitive sequence Alu to pulsed-field gel-fractionated Not I-digested genomic DNA from a human-mouse hybrid cell line containing chromosome 21 as the sole human component identified chromosome 21 Not I restriction fragments. A Not I restriction map of regions of the chromosome was constructed, by identifying neighboring Alu bands with Not I linking clones. This approach simplifies the task of physical mapping and avoids ambiguities in Not I fragment assignments that arise from gel-to-gel mobility variations. A contiguous map was constructed with six Not I linking clones that covers at least the proximal one-third of the long arm of chromosome 21 and spans 20 megabases. A more detailed restriction map revealed 11 likely CpG islands in this region and localized 11 additional DNA markers.

Neuron, 2012

Dendrites are processes of nerve cells (or called neurons) that receive information from the envi... more Dendrites are processes of nerve cells (or called neurons) that receive information from the environment or other neurons. During the development of nervous system, dendrites from the same neuron usually spread evenly in the receptive field and avoid crossing one other. Dendrites from neighboring similar kind of neurons also avoid overlapping through repulsive interactions between dendrites from neighboring neurons to ensure even but non-redundant coverage of the receptive field. This non-overlapping coverage of receptive field involves competition of dendrites for limited space. In fruit flies, the dendrites of one particular type of peripheral sensory neurons named class IV dendritic arborization (da) neurons cover the larval body wall in a non-overlapping manner. In this study, we discovered that dendrites of class IV da neurons grow mainly in a two-dimensional space on the extracellular matrix (ECM), a network of proteins that functions like glue to hold cells together into tissues, between epidermis and muscle. Depriving class IV da neurons of integrins, the protein that binds to ECM, or preventing epidermal cells from producing laminin, one major component of ECM, causes dendrites of class IV da neurons to grow into the epidermis. These results suggest that interaction between intergrin-laminin ensure attachment of dendrites to the ECM. In addition, we found that in fly larvae mutant for genes that were previously shown to control even coverage of dendrites, class IV da neurons fail to limit the growth of their dendrites in a two-dimensional plane and often their dendrites often cross one another. However, increasing the expression of integrins in these mutants effectively reduces dendritic crossing and restores nonoverlapping coverage of their dendrite fields. Therefore, our study provides novel insights into the mechanisms underlying nonoverlapping dendritic coverage.

Neuron, 2003

into one of the daughter cells during asymmetric division, ensures that the two daughters adopt d... more into one of the daughter cells during asymmetric division, ensures that the two daughters adopt different cell fates (Uemura et al., 1989; Rhyu et al., 1994; Knoblich et al., 1995; Spana et al., 1995). Molecular studies of Numb homologs in vertebrates have identified two

Neuron, 2014

During developmental remodeling, neurites destined for pruning often degenerate on-site. Physical... more During developmental remodeling, neurites destined for pruning often degenerate on-site. Physical injury also induces degeneration of neurites distal to the injury site. Prompt clearance of degenerating neurites is important for maintaining tissue homeostasis and preventing inflammatory responses. Here we show that in both dendrite pruning and dendrite injury of Drosophila sensory neurons, epidermal cells rather than hemocytes are the primary phagocytes in clearing degenerating dendrites. Epidermal cells act via Draper-mediated recognition to facilitate dendrite degeneration and to engulf and degrade degenerating dendrites. Using multiple dendritic membrane markers to trace phagocytosis, we show that two members of the CD36 family, croquemort (crq) and debris buster (dsb), act at distinct stages of phagosome maturation for dendrite clearance. Our finding reveals the physiological importance of coordination between neurons and their surrounding epidermis, for both dendrite fragmentation and clearance. Neuron Epidermal Cells Clear Degenerating Dendrites

Methods, 1996

Conventional genome mapping and sequencing involves the mixtures of samples. Obviously, these app... more Conventional genome mapping and sequencing involves the mixtures of samples. Obviously, these approaches creanalysis and processing of individual samples and pieces of ate an increase in experimental efficiency by increasing experimental data. Although these methods work, it is quite the speed at which data accumulate. Some of the apclear that more efficient and less expensive methods are proaches use comparative information (map or seneeded. Our top down physical mapping experiments have foquence data on mixtures of samples or differences cused on the parallel processing of information from multiple among these samples) to construct the primary inforsamples at one time. This approach has aided the construction mation itself (map or sequence data on individual samof genomic restriction maps and allowed us to assess the degree ples or species). of large-scale conservation across wide regions of the human In recognition of the considerable increase in effigenome. The principles of parallel processing were applied in ciency of parallel processing methods, many funding top down experiments that ordered an overlapping cosmid library and scientific organizations have focused on developing from the 14-Mb Schizosaccharomyces pombe genome. This apgenomic resources that can be utilized by multiple sciproach produced an eight-fold increase in efficiency in clone entists simultaneously. Such resources provide access ordering over similar efforts. Recently, we have developed an not only to primary material but also to primary inforenhanced sequencing by hybridization protocol that allows DNA mation about such material. sequence information to be collected on a large number of sam-This review focuses on describing how parallel proples at once. Our current research focuses on applying parallel cessing methods have been applied in our past genomic processing principles to make genome-wide comparisons bemapping, library ordering, and DNA sequencing expertween pairs of samples for analyzing disease states.

Genomics, 1995

Genomic probes can be efficiently obtained for specific chromosomal regions by PCR amplification ... more Genomic probes can be efficiently obtained for specific chromosomal regions by PCR amplification of gel slices containing fractionated restriction enzymecleaved DNA. Here, single-copy, human-specific DNA sequences were amplified using inter-Alu PCR on gel slices containing a NotI digest of DNA from hybrid cell line WAV17. Rodent cell line WAV17 contains human chromosome 21. About 75% of the 0.15-to 3-kb inter-Alu PCR products could be regionally assigned, en masse, by hybridization experiments using inter-Alu PCR probes generated from cell lines containing portions of chromosome 21. This work produced 10 new chromosome 21 markers that came from regions of 21q containing few useful markers. These markers were needed to finish a NotI restriction map for 21q (Wang and Smith (1994) Genomics 20: 441). This approach provides markers needed to close map gaps and for top-down mapping approaches,

Genomics, 1991

Effective procedures have been developed for constructing Not1 linking libraries starting from ch... more Effective procedures have been developed for constructing Not1 linking libraries starting from chromosome-specific genomic libraries. Fifteen different single copy and two rDNA Not1 linking clones from human chromosome 2 1 were identified in two libraries. Their chromosomal origin was confirmed, and regional location established using hybrid cell panels. Hybridization experiments with these probes revealed pairs of genomic Not1 fragments, each ranging in size from co.05 to 4.0 Mb. Many fragments displayed cell type variation. The total size of the Not1 fragments detected in a human fibroblast cell line (GM6167) and mouse hybrid cell containing chromosome 21 as its only human component (WAV17) were approximately 32 and 34 Mb, respectively. If these fragments were all nonoverlapping, this would correspond to about 70% of the 50-Mb content estimated for the whole chromosome. The linking clones will be enormously useful in the subsequent construction of a Not1 restriction map of this chromosome. Characterization of these clones indicates the presence of numerous additional sites for other enzymes that recognize sequences containing CpG. Thus most Not1 linking clones appear to derive from CpG islands and probably identify the 5' end of genes.

Cell, 2006

Neural stem cells are retained in the postnatal subventricular zone (SVZ), a specialized neurogen... more Neural stem cells are retained in the postnatal subventricular zone (SVZ), a specialized neurogenic niche with unique cytoarchitecture and cell-cell contacts. Although the SVZ stem cells continuously regenerate, how they and the niche respond to local changes is unclear. Here we generated nestin-creER tm transgenic mice with inducible Cre recombinase in the SVZ and removed Numb/Numblike, key regulators of embryonic neurogenesis from postnatal SVZ progenitors and ependymal cells. This resulted in severe damage to brain lateral ventricle integrity and identified roles for Numb/ Numblike in regulating ependymal wall integrity and SVZ neuroblast survival. Surprisingly, the ventricular damage was eventually repaired: SVZ reconstitution and ventricular wall remodeling were mediated by progenitors that escaped Numb deletion. Our results show a selfrepair mechanism in the mammalian brain and may have implications for both niche plasticity in other areas of stem cell biology and the therapeutic use of neural stem cells in neurodegenerative diseases.

Cell, 1997

that ultimately give rise to the epithelia of the tubules and glomeruli of the mature kidney. The... more that ultimately give rise to the epithelia of the tubules and glomeruli of the mature kidney. The many branches *Department of Physiology † Howard Hughes Medical Institute of the ureter form the collecting duct tree of the kidney. Molecular genetic analyses in mice have revealed a ‡ Reproductive Genetics Unit Department of Obstetrics, Gynecology complex network of regulatory proteins that control kidney organogenesis. These include the secreted signal-and Reproductive Sciences University of California, San Francisco ing molecules glial cell line-derived neurotrophic factor (GDNF), wnt-4, bone morphogenetic protein 7 (BMP7),

Proceedings of the National Academy of Sciences, 2004

Development of both dendrites and axons is important for the formation of neuronal circuits, beca... more Development of both dendrites and axons is important for the formation of neuronal circuits, because dendrites receive information and the axon is responsible for sending signals. In the past decade, extensive studies have revealed many molecules underlying axonal outgrowth and pathfinding. In contrast, much less is known about the molecular mechanisms that control dendrite development. Here we report the identification of an evolutionarily conserved Ig superfamily member, dendrite arborization and synapse maturation 1 (Dasm1), which plays a critical role in dendrite development. Dasm1 contains five Ig domains and two fibronectin III domains in the extracellular N terminus, a single transmembrane domain, and an intracellular C-terminal tail with a type I PDZ domain binding motif at the end. It is highly expressed in the brain and localized at the dendrites. Suppression of Dasm1 expression in hippocampal neurons via RNA interference or expression of Dasm1 without its cytoplasmic tail...