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Schoups A, Vogels R, Qian N, Orban G. Practising orientation identification improves orientation coding in V1 neurons. Nature 2001; 412:549-53. [PMID: 11484056 DOI: 10.1038/35087601] [Citation(s) in RCA: 619] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The adult brain shows remarkable plasticity, as demonstrated by the improvement in fine sensorial discriminations after intensive practice. The behavioural aspects of such perceptual learning are well documented, especially in the visual system. Specificity for stimulus attributes clearly implicates an early cortical site, where receptive fields retain fine selectivity for these attributes; however, the neuronal correlates of a simple visual discrimination task remained unidentified. Here we report electrophysiological correlates in the primary visual cortex (V1) of monkeys for learning orientation identification. We link the behavioural improvement in this type of learning to an improved neuronal performance of trained compared to naive neurons. Improved long-term neuronal performance resulted from changes in the characteristics of orientation tuning of individual neurons. More particularly, the slope of the orientation tuning curve that was measured at the trained orientation increased only for the subgroup of trained neurons most likely to code the orientation identified by the monkey. No modifications of the tuning curve were observed for orientations for which the monkey had not been trained. Thus training induces a specific and efficient increase in neuronal sensitivity in V1.
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Qian N, Sejnowski TJ. Predicting the secondary structure of globular proteins using neural network models. J Mol Biol 1988; 202:865-84. [PMID: 3172241 DOI: 10.1016/0022-2836(88)90564-5] [Citation(s) in RCA: 570] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We present a new method for predicting the secondary structure of globular proteins based on non-linear neural network models. Network models learn from existing protein structures how to predict the secondary structure of local sequences of amino acids. The average success rate of our method on a testing set of proteins non-homologous with the corresponding training set was 64.3% on three types of secondary structure (alpha-helix, beta-sheet, and coil), with correlation coefficients of C alpha = 0.41, C beta = 0.31 and Ccoil = 0.41. These quality indices are all higher than those of previous methods. The prediction accuracy for the first 25 residues of the N-terminal sequence was significantly better. We conclude from computational experiments on real and artificial structures that no method based solely on local information in the protein sequence is likely to produce significantly better results for non-homologous proteins. The performance of our method of homologous proteins is much better than for non-homologous proteins, but is not as good as simply assuming that homologous sequences have identical structures.
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Bradley DC, Qian N, Andersen RA. Integration of motion and stereopsis in middle temporal cortical area of macaques. Nature 1995; 373:609-11. [PMID: 7854417 DOI: 10.1038/373609a0] [Citation(s) in RCA: 173] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The primate visual system incorporates a highly specialized subsystem for the analysis of motion in the visual field. A key element of this subsystem is the middle temporal (MT) cortical area, which contains a majority of direction-selective neurons. MT neurons are also selective for binocular disparity (depth), which is perplexing given that they are not sensitive to motion through depth. What is the role of disparity in MT? Our data suggest an important link between disparity and transparent motion detection. Motion signals in different directions tend to inhibit each other within a given MT receptive field. This inhibition has an averaging effect which minimizes MT responses to random motion signals created by light intensity changes and other non-motion stimuli (motion noise). But, in the absence of disparity cues, inhibition may also occur between surfaces moving in different directions through the same part of the visual field (transparent motion), thus impairing the detection of either surface. Here we show that inhibition in MT occurs mainly between motion signals with similar disparities. Transparent surface movements at different depths are thus represented independently in MT (that is, without inhibiting each other) whereas spurious motion signals from a given surface tend to cancel out. To our knowledge, these results provide the first evidence for a functional integration of motion and disparity in MT.
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Rådström P, Bäckman A, Qian N, Kragsbjerg P, Påhlson C, Olcén P. Detection of bacterial DNA in cerebrospinal fluid by an assay for simultaneous detection of Neisseria meningitidis, Haemophilus influenzae, and streptococci using a seminested PCR strategy. J Clin Microbiol 1994; 32:2738-44. [PMID: 7852565 PMCID: PMC264152 DOI: 10.1128/jcm.32.11.2738-2744.1994] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Primers specific to conserved and variable regions in the 16S rRNA sequence were selected from the partially sequenced 16S rRNA genes of Neisseria meningitidis, Haemophilus influenzae, Streptococcus pneumoniae, S. agalactiae, and Staphylococcus epidermidis. The PCR assay was divided into two DNA amplifications. The first resulted in a general bacterial amplicon, and the second resulted in a species-specific amplicon. The high specificity of the PCR assay was documented after testing bacteria of 28 different species (133 strains). A total of 304 clinical cerebrospinal fluid samples, including 125 samples from patients with bacterial meningitis, were assayed to investigate the diagnostic sensitivity and specificity for bacterial meningitis. The assay showed high sensitivity (0.94) and specificity (0.96) with the clinical samples, although some false results were obtained, the reasons for which are discussed. With agarose gel electrophoresis for detection of the PCR products, the detection limit for meningococci in cerebrospinal fluid was 3 x 10(2) CFU/ml.
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Qian N, Frank D, O'Keefe D, Dao D, Zhao L, Yuan L, Wang Q, Keating M, Walsh C, Tycko B. The IPL gene on chromosome 11p15.5 is imprinted in humans and mice and is similar to TDAG51, implicated in Fas expression and apoptosis. Hum Mol Genet 1997; 6:2021-9. [PMID: 9328465 DOI: 10.1093/hmg/6.12.2021] [Citation(s) in RCA: 119] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We searched for novel imprinted genes in a region of human chromosome 11p15.5, which contains several known imprinted genes. Here we describe the cloning and characterization of the IPL ( I mprinted in P lacenta and L iver) gene, which shows tissue-specific expression and functional imprinting, with the maternal allele active and the paternal allele relatively inactive, in many human and mouse tissues. Human IPL is highly expressed in placenta and shows low but detectable expression in fetal and adult liver and lung. Mouse Ipl maps to the region of chromosome 7 which is syntenic with human 11p15.5 and this gene is expressed in placenta and at higher levels in extraembryonic membranes (yolk sac), fetal liver and adult kidney. Mouse and human IPL show sequence similarity to TDAG51 , a gene which was shown to be essential for Fas expression and susceptibility to apoptosis in a T lymphocyte cell line. Like several other imprinted genes, mouse and human IPL genes are small and contain small introns. These data expand the repertoire of known imprinted genes and will be helpful in testing the mechanism of genomic imprinting and the role of imprinted genes in growth regulation.
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Abstract
We previously proposed a physiologically realistic model for stereo vision based on the quantitative binocular receptive field profiles mapped by Freeman and coworkers. Here we present several new results about the model that shed light on the physiological processes involved in disparity computation. First, we show that our model can be extended to a much more general class of receptive field profiles than the commonly used Gabor functions. Second, we demonstrate that there is, however, an advantage of using the Gabor filters: similar to our perception, the stereo algorithm with the Gabor filters has a small bias towards zero disparity. Third, we prove that the complex cells as described by Freeman et al. compute disparity by effectively summing up two related cross products between the band-pass filtered left and right retinal image patches. This operation is related to cross-correlation but it overcomes some major problems with the standard correlator. Fourth, we demonstrate that as few as two complex cells at each spatial location are sufficient for a reasonable estimation of binocular disparity. Fifth, we find that our model can be significantly improved by considering the fact that complex cell receptive field are, on average, larger than those of simple cells. This fact is incorporated into the model by averaging over several quadrature pairs of simple cells with nearby and overlapping receptive fields to construct a model complex cell. The disparity tuning curve of the resulting complex cell is much more reliable than the constructed from a single quadrature pair of simple cells used previously, and the computed disparity maps for random dot stereograms with the new algorithm are very similar to human perception, with sharp transitions at disparity boundaries. Finally, we show that under most circumstances our algorithm works equally well with either of the two well-known receptive field models in the literature.
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Song W, Treich I, Qian N, Kuchin S, Carlson M. SSN genes that affect transcriptional repression in Saccharomyces cerevisiae encode SIN4, ROX3, and SRB proteins associated with RNA polymerase II. Mol Cell Biol 1996; 16:115-20. [PMID: 8524287 PMCID: PMC230984 DOI: 10.1128/mcb.16.1.115] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The RNA polymerase II of Saccharomyces cerevisiae exists in holoenzyme forms containing a complex, known as the mediator, associated with the carboxyl-terminal domain. The mediator includes several SRB proteins and is required for transcriptional activation. Previous work showed that a cyclin-dependent kinase-cyclin pair encoded by SSN3 and SSN8, two members of the SSN suppressor family, are identical to two SRB proteins in the mediator. Here we have identified the remaining SSN genes by cloning and genetic analysis. SSN2 and SSN5 are identical to SRB9 and SRB8, respectively, which encode additional components of the mediator. Genetic evidence implicates the SSN genes in transcriptional repression. Thus, these identities provide genetic insight into mediator and carboxyl-terminal domain function, strongly suggesting a role in mediating transcriptional repression as well as activation. We also show that SSN4 and SSN7 are the same as SIN4 and ROX3, respectively, raising the possibility that these genes also encode mediator proteins.
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King TP, Lu G, Gonzalez M, Qian N, Soldatova L. Yellow jacket venom allergens, hyaluronidase and phospholipase: sequence similarity and antigenic cross-reactivity with their hornet and wasp homologs and possible implications for clinical allergy. J Allergy Clin Immunol 1996; 98:588-600. [PMID: 8828537 DOI: 10.1016/s0091-6749(96)70093-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Three known allergens of yellow jacket (Vespula vulgaris) venom are antigen 5, hyaluronidase, and phospholipase. Yellow jacket antigen 5 has been previously cloned and expressed in bacteria; it contains 204 amino acid residues, and it has 69% and 60% sequence identities with the homologous proteins of white-faced hornet (Dolichovespula maculata) and wasp (Polistes annularis), respectively. These studies are now extended to yellow jacket hyaluronidase and phospholipase; they contain 331 and 300 amino acid residues, respectively, and they show 92% and 67% sequence identity with their homologs of white-faced hornet. Tests with the natural and the recombinant vespid allergens in mice indicate partial antigenic cross-reactivity of their homologous proteins at both B- and T-cell levels. There is greater cross-reactivity among hornet and yellow jacket allergens than that among hornet or yellow jacket and wasp allergens. The order of cross-reaction of the three vespid allergens is hyaluronidase > antigen 5 > phospholipase. The continuous (linear) B-cell epitopes of vespid allergens show greater cross-reactivity than their discontinuous epitopes do. The discontinuous B-cell epitopes are immunodominant for all vespid allergens. The low degree of cross-reactivity of the immunodominant discontinuous B-cell epitopes of vespid allergens should be taken into consideration in selection of venoms for immunotherapy of patients with sensitivity to multiple vespids.
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Dao D, Frank D, Qian N, O'Keefe D, Vosatka RJ, Walsh CP, Tycko B. IMPT1, an imprinted gene similar to polyspecific transporter and multi-drug resistance genes. Hum Mol Genet 1998; 7:597-608. [PMID: 9499412 DOI: 10.1093/hmg/7.4.597] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Human chromosome 11p15.5 and distal mouse chromosome 7 include a megabase-scale chromosomal domain with multiple genes subject to parental imprinting. Here we describe mouse and human versions of a novel imprinted gene, IMPT1 , which lies between IPL and p57 KIP2 and which encodes a predicted multi-membrane-spanning protein similar to bacterial and eukaryotic polyspecific metabolite transporter and multi-drug resistance pumps. Mouse Impt1 and human IMPT1 mRNAs are highly expressed in tissues with metabolite transport functions, including liver, kidney, intestine, extra-embryonic membranes and placenta, and there is strongly preferential expression of the maternal allele in various mouse tissues at fetal stages. In post-natal tissues there is persistent expression, but the allelic bias attenuates. An allelic expression bias is also observed in human fetal and post-natal tissues, but there is significant interindividual variation and rare somatic allele switching. The fact that Impt1 is relatively repressed on the paternal allele, together with data from other imprinted genes, allows a statistical conclusion that the primary effect of human chromosome 11p15.5/mouse distal chromosome 7 imprinting is domain-wide relative repression of genes on the paternal homolog. Dosage regulation of the metabolite transporter gene(s) by imprinting might regulate placental and fetal growth.
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Qian N, Andersen RA. A physiological model for motion-stereo integration and a unified explanation of Pulfrich-like phenomena. Vision Res 1997; 37:1683-98. [PMID: 9231233 DOI: 10.1016/s0042-6989(96)00164-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Many psychophysical and physiological experiments indicate that visual motion analysis and stereoscopic depth perception are processed together in the brain. However, little computational effort has been devoted to combining these two visual modalities into a common framework based on physiological mechanisms. We present such an integrated model in this paper. We have previously developed a physiologically realistic model for binocular disparity computation (Qian, 1994). Here we demonstrate that under some general and physiological assumptions, our stereo vision model can be combined naturally with motion energy models to achieve motion-stereo integration. The integrated model may be used to explain a wide range of experimental observations regarding motion-stereo interaction. As an example, we show that the model can provide a unified account of the classical Pulfrich effect (Morgan & Thompson, 1975) and the generalized Pulfrich phenomena to dynamic noise patterns (Tyler, 1974; Falk, 1980) and stroboscopic stimuli (Burr & Ross, 1979).
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Abstract
Interactions between excitatory and inhibitory synaptic inputs on dendrites determine the level of activity in neurons. Models based on the cable equation predict that silent shunting inhibition can strongly veto the effect of an excitatory input. The cable model assumes that ionic concentrations do not change during the electrical activity, which may not be a valid assumption, especially for small structures such as dendritic spines. We present here an analysis and computer simulations to show that for large Cl- conductance changes, the more general Nernst-Planck electrodiffusion model predicts that shunting inhibition on spines should be much less effective than that predicted by the cable model. This is a consequence of the large changes in the intracellular ionic concentration of Cl- that can occur in small structures, which would alter the reversal potential and reduce the driving force for Cl-. Shunting inhibition should therefore not be effective on spines, but it could be significantly more effective on the dendritic shaft at the base of the spine. In contrast to shunting inhibition, hyperpolarizing synaptic inhibition mediated by K+ currents can be very effective in reducing the excitatory synaptic potentials on the same spine if the excitatory conductance change is less than 10 nS. We predict that if the inhibitory synapses found on cortical spines are to be effective, then they should be mediated by K+ through GABAB receptors.
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Qian N, Stanley GA, Hahn-Hägerdal B, Rådström P. Purification and characterization of two phosphoglucomutases from Lactococcus lactis subsp. lactis and their regulation in maltose- and glucose-utilizing cells. J Bacteriol 1994; 176:5304-11. [PMID: 8071206 PMCID: PMC196715 DOI: 10.1128/jb.176.17.5304-5311.1994] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Two distinct forms of phosphoglucomutase were found in Lactococcus lactis subsp. lactis, strains 19435 and 65.1, growing on maltose: beta-phosphoglucomutase (beta-PGM), which catalyzes the reversible conversion of beta-glucose 1-phosphate to glucose 6-phosphate in the maltose catabolism, and alpha-phosphoglucomutase (alpha-PGM). beta-PGM was purified to more than 90% homogeneity in crude cell extract from maltose-grown lactococci, and polyclonal antisera to the enzyme were prepared. The molecular mass of beta-PGM was estimated by gel filtration to be 28 kDa; its isoelectric point was 4.8. The corresponding values for alpha-PGM were 65 kDa and 4.4, respectively. The expression of both PGM enzymes was investigated under different growth conditions. The specific activity and amount of beta-PGM per milliliter of cell extract increased with time in lactococci grown on maltose, but the enzyme was absent in lactococci grown on glucose, indicating enzyme synthesis to be induced by maltose in the growth medium. When glucose was added to maltose-grown lactococci, both the specific activity and amount of beta-PGM per milliliter of cell extract decreased rapidly. This suggests that synthesis of beta-PGM is repressed by glucose in the medium. Although the specific activity of alpha-PGM did not change during growth on maltose or glucose, lactococcal strain 19435 showed a much higher specific activity of both alpha- and beta-PGM than strain 65.1 when grown on maltose.
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Matthews N, Luber B, Qian N, Lisanby SH. Transcranial magnetic stimulation differentially affects speed and direction judgments. Exp Brain Res 2001; 140:397-406. [PMID: 11685392 DOI: 10.1007/s002210100837] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2001] [Accepted: 06/18/2001] [Indexed: 10/27/2022]
Abstract
This study was conducted to determine whether humans' judgments about the speed and direction of moving stimuli was differentially affected by transcranial magnetic stimulation (TMS). Subjects viewed two successively presented moving stimuli that differed from each other both in speed and direction of motion. Single-pulse TMS was applied either medially (approximately 2 cm above the inion) or laterally (approximately 5 cm lateral to and 4 cm above the inion), while subjects judged the speed and direction differences. The physical stimulation (visual and TMS) was identical on the two tasks, as was discriminability (d') when TMS was not applied. We found significant criterion (beta) shifts on the speed discrimination task at both stimulation sites. Specifically, on TMS trials the proportion of "slower" judgments increased significantly, consistent with subjective reports that stimuli often appeared to slow when TMS was applied. The subjective reports indicated no corresponding change in perceived direction. We also found that speed discriminability was impaired significantly more than direction discriminability, but only when TMS was applied medially. Indeed, after controlling for TMS-related changes in reaction time, speed discriminability was impaired significantly, while direction discriminability remained largely intact. This dissociation suggests that the sensory response constraining speed discrimination is at least partially independent from the sensory response constraining direction discrimination. Combined with previous psychophysical data, the present data suggest a double dissociation between speed and direction discrimination in humans.
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Abstract
Disparity tuning of visual cells in the brain depends on the structure of their binocular receptive fields (RFs). Freeman and coworkers have found that binocular RFs of a typical simple cell can be quantitatively described by two Gabor functions with the same gaussian envelope but different phase parameters in the sinusoidal modulations (Freeman and Ohzawa 1990). This phase-parameter-based RF description has recently been questioned by Wagner and Frost (1993) based on their identification of a so-called characteristic disparity (CD) in some cells' disparity tuning curves. They concluded that their data favor the traditional binocular RF model, which assumes on overall positional shift between a cell's left and right RFs. Here we set to resolve this issue by studying the dependence of cells' disparity tuning on their underlying RF structures through mathematical analyses and computer simulations. We model the disparity tuning curves in Wagner and Frost's experiments and demonstrate that the mere existence of approximate CDs in real cells cannot be used to distinguish the phase-parameter-based RF description from the traditional position-shift-based RF description. Specifically, we found that model simple cells with either type RF description do not have a CD. Model complex cells with the position-shift-based RF description have a precise CD, and those with the phase-parameter-based RF description have an approximate CD. We also suggest methods for correctly distinguishing the two types of RF descriptions. A hybrid of the two RF models may be required to fit the behavior of some real cells, and we show how to determine the relative contributions of the two RF models.
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Xie Y, Chen D, Jiang K, Song L, Qian N, Du Y, Yang Y, Wang F, Chen T. Hair shaft miniaturization causes stem cell depletion through mechanosensory signals mediated by a Piezo1-calcium-TNF-α axis. Cell Stem Cell 2021; 29:70-85.e6. [PMID: 34624205 DOI: 10.1016/j.stem.2021.09.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 07/19/2021] [Accepted: 09/13/2021] [Indexed: 12/17/2022]
Abstract
In aging, androgenic alopecia, and genetic hypotrichosis disorders, hair shaft miniaturization is often associated with hair follicle stem cell (HFSC) loss. However, the mechanism causing this stem cell depletion in vivo remains elusive. Here we show that hair shaft loss or a reduction in diameter shrinks the physical niche size, which results in mechanical compression of HFSCs and their apoptotic loss. Mechanistically, cell compression activates the mechanosensitive channel Piezo1, which triggers calcium influx. This confers tumor necrosis factor alpha (TNF-α) sensitivity in a hair-cycle-dependent manner in otherwise resistant HFSCs and induces ectopic apoptosis. Persistent hair shaft miniaturization during aging and genetic hypotrichosis disorders causes long-term HFSC loss by inducing continuous ectopic apoptosis through Piezo1. Our results identify an unconventional role of the inert hair shaft structure as a functional niche component governing HFSC survival and reveal a mechanosensory axis that regulates physical-niche-atrophy-induced stem cell depletion in vivo.
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Abstract
Two experiments were conducted to determine the extent to which perceptual learning transfers between orientation and direction discrimination. Naive observers were trained to discriminate orientation differences between two single-line stimuli, and direction differences between two single-moving-dot stimuli. In the first experiment, observers practiced the orientation and direction tasks along orthogonal axes in the fronto-parallel plane. In the second experiment, a different group of observers practiced both tasks along a single axis. Perceptual learning was observed on both tasks in both experiments. Under the same-axis condition, the observers' orientation sensitivity was found to be significantly elevated after the direction training, indicating a transfer of learning from direction to orientation. There was no evidence of transfer in any other cases tested. In addition, the rate of learning on the orientation task was much higher than the rate on the direction task. The implications of these findings on the neural mechanisms subserving orientation and direction discrimination are discussed.
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Yu Z, Jiang K, Xu Z, Huang H, Qian N, Lu Z, Chen D, Di R, Yuan T, Du Z, Xie W, Lu X, Li H, Chai R, Yang Y, Zhu B, Kunieda T, Wang F, Chen T. Hoxc-Dependent Mesenchymal Niche Heterogeneity Drives Regional Hair Follicle Regeneration. Cell Stem Cell 2018; 23:487-500.e6. [PMID: 30122476 DOI: 10.1016/j.stem.2018.07.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 05/09/2018] [Accepted: 07/24/2018] [Indexed: 11/17/2022]
Abstract
Mesenchymal niche cells instruct activity of tissue-resident stem and progenitor cell populations. Epithelial stem cells in hair follicles (HFs) have region-specific activity, which may arise from intrinsic cellular heterogeneity within mesenchymal dermal papilla (DP) cells. Here we show that expression of Hoxc genes is sufficient to reprogram mesenchymal DP cells and alter the regenerative potential of epithelial stem cells. Hoxc gene expression in adult skin dermis closely correlates with regional HF regeneration patterns. Disrupting the region-specific expression patterns of Hoxc genes, by either decreasing their epigenetic repression via Bmi1 loss or inducing ectopic interactions of the Hoxc locus with an active epigenetic region, leads to precocious HF regeneration. We further show that a single Hoxc gene is sufficient to activate dormant DP niches and promote regional HF regeneration through canonical Wnt signaling. Altogether, these results reveal that Hoxc genes bestow mesenchymal niches with tissue-level heterogeneity and plasticity.
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Research Support, Non-U.S. Gov't |
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Liu Y, Zhang QY, Qian N, Zhou RL. Relationship between LAPTM4B gene polymorphism and susceptibility of gastric cancer. Ann Oncol 2006; 18:311-6. [PMID: 17074969 DOI: 10.1093/annonc/mdl394] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND A novel gene called LAPTM4B (lysosome-associated protein transmembrane 4beta) was mapped to 8q22, and contains seven exons. The 2.25-kb messenger RNA of the gene encodes a putative lysosome-associated protein with four transmembrane regions. There are two alleles of the gene, named as LAPTM4B*1 and LAPTM4B*2. Allele *1 differs from allele *2 in that it contains only one copy of a 19-bp sequence in the 5' untranslated region (UTR), whereas this sequence is duplicated and tandemly arranged in allele *2. Studies showed that the allelic variation of LAPTM4B was associated with the genetic susceptibility of hepatocellular carcinoma but not with that of esophageal squamous cell carcinoma. This study was designed to investigate the possible association between the allelic variation of LAPTM4B and the genetic susceptibility of gastric cancer. MATERIALS AND METHODS The genotype of LAPTM4B was analyzed in 350 unrelated healthy adult individuals and 214 patients with gastric cancer by utilizing polymerase chain reaction based on specific primers. The genotypic distribution of LAPTM4B was analyzed by chi(2) test. RESULTS The allelic frequencies of the *2 were 33.88% and 24.14% in the gastric cancer group and the healthy control group, respectively, which was significantly different between the two groups (P < 0.001). There was a significant difference in the overall genotypic distribution between the patients and the controls (P = 0.023). The risk of suffering from gastric cancer was increased 1.819 times in the individuals of the *1/2 genotype [95% confidence interval (CI) 1.273-2.601] and 2.387 times in the individuals of the *2/2 genotype of LAPTM4B (95% CI 1.195-4.767) compared with the *1/1 genotype. No association between the genotypic distribution of LAPTM4B and the clinical information on patients of gastric cancer such as age, pathological type, differentiation classification of TNM, and infection of hepatitis B virus was shown. CONCLUSION This study indicated that allele *2 of LAPTM4B might be the risk factor of gastric cancer, which could be associated with genetic susceptibility of gastric cancer.
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Research Support, Non-U.S. Gov't |
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Saxena A, Qian N, Kovach IM, Kozikowski AP, Pang YP, Vellom DC, Radić Z, Quinn D, Taylor P, Doctor BP. Identification of amino acid residues involved in the binding of Huperzine A to cholinesterases. Protein Sci 1994; 3:1770-8. [PMID: 7849595 PMCID: PMC2142623 DOI: 10.1002/pro.5560031017] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Huperzine A, a potential agent for therapy in Alzheimer's disease and for prophylaxis of organophosphate toxicity, has recently been characterized as a reversible inhibitor of cholinesterases. To examine the specificity of this novel compound in more detail, we have examined the interaction of the 2 stereoisomers of Huperzine A with cholinesterases and site-specific mutants that detail the involvement of specific amino acid residues. Inhibition of fetal bovine serum acetylcholinesterase by (-)-Huperzine A was 35-fold more potent than (+)-Huperzine A, with KI values of 6.2 nM and 210 nM, respectively. In addition, (-)-Huperzine A was 88-fold more potent in inhibiting Torpedo acetylcholinesterase than (+)-Huperzine A, with KI values of 0.25 microM and 22 microM, respectively. Far larger KI values that did not differ between the 2 stereoisomers were observed with horse and human serum butyrylcholinesterases. Mammalian acetylcholinesterase, Torpedo acetylcholinesterase, and mammalian butyrylcholinesterase can be distinguished by the amino acid Tyr, Phe, or Ala in the 330 position, respectively. Studies with mouse acetylcholinesterase mutants, Tyr 337 (330) Phe and Tyr 337 (330) Ala yielded a difference in reactivity that closely mimicked the native enzymes. In contrast, mutation of the conserved Glu 199 residue to Gln in Torpedo acetylcholinesterase produced only a 3-fold increase in KI value for the binding of Huperzine A.(ABSTRACT TRUNCATED AT 250 WORDS)
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Abstract
The motion of an object can be described by a single velocity vector, or equivalently, by direction and speed separately. Similarly, our ability to see subtle differences in the motion of two objects could be constrained by either a velocity-based sensory response, or separate sensory responses to direction and speed. To distinguish between these possibilities we investigated whether direction discrimination and speed discrimination were differentially affected by changes in the axis-of-motion. Psychophysical data from 12 naive observers indicated that direction discrimination depended on axis-of-motion, but speed discrimination did not. The difference suggests that a velocity-based sensory response is not the limiting factor on the two tasks. Instead, the results imply that the sensory response which constrains speed discrimination is at least partially independent from the sensory response which constrains direction discrimination.
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Molecular modeling (GEMM 7.3) and molecular mechanics calculations (YETI V 5.3) using the X-ray coordinates for acetylcholinesterase (AChE) from Torpedo californica indicate electrostatic stabilization by the active site, Glu-199, of the developing positive charge on the incipient carbonium ion in the dealkylation in the adducts of AChE with PSCR and PSCS diastereomers of 2-(3,3-dimethylbutyl) methylphosphonofluoridate (soman). His-440 is indispensable as a general acid catalyst of C-O bond breaking in the dealkylation reaction and that of bond breaking to the Ser gamma-O in reactivation. This demand for catalysis seems to be satisfied for the reactivation of enzyme from the PSCS diastereomer of soman, but not from the P(S)C(R) diastereomer.
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Kang H, Chen H, Huang P, Qi J, Qian N, Deng L, Guo L. Glucocorticoids impair bone formation of bone marrow stromal stem cells by reciprocally regulating microRNA-34a-5p. Osteoporos Int 2016; 27:1493-1505. [PMID: 26556739 DOI: 10.1007/s00198-015-3381-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/20/2015] [Indexed: 12/11/2022]
Abstract
UNLABELLED The inhibitory effects of glucocorticoids (GCs) on bone marrow stromal stem cell (BMSC) proliferation and osteoblastic differentiation are an important pathway through which GCs decrease bone formation. We found that microRNA-34a-5p was a critical player in dexamethasone (Dex)-inhibited BMSC proliferation and osteogenic differentiation. MicroRNA-34a-5p might be used as a therapeutic target for GC-impaired bone formation. INTRODUCTION The inhibitory effects of glucocorticoids (GCs) on bone marrow stromal stem cell (BMSC) proliferation and osteoblastic differentiation are an important pathway through which GCs decrease bone formation. The mechanisms of this process are still not completely understood. Recent studies implicated an important role of microRNAs in GC-mediated responses in various cellular processes, including cell proliferation and differentiation. Therefore, we hypothesized that these regulatory molecules might be implicated in the process of GC-decreased BMSC proliferation and osteoblastic differentiation. METHODS Western blot, quantitative real-time PCR, and cell proliferation and osteoblastic differentiation assays were employed to investigate the role of microRNAs in GC-inhibited BMSC proliferation and osteoblastic differentiation. RESULTS We found that microRNA-34a-5p was reciprocally regulated by Dex during the process of BMSC proliferation and osteoblastic differentiation. Furthermore, we confirmed that microRNA-34a-5p was a critical player in Dex-inhibited BMSC proliferation and osteogenic differentiation. Mechanistic studies showed that Dex inhibited BMSC proliferation by microRNA-34a-5p targeting cell cycle factors, including CDK4, CDK6, and Cyclin D1. Furthermore, downregulation of microRNA-34a-5p by Dex leads to Notch signaling activation, resulting in inhibition of BMSC osteogenic differentiation. CONCLUSIONS These results showed that microRNA-34a-5p, a crucial regulator for BMSC proliferation and osteogenic differentiation, might be used as a therapeutic target for GC-impaired bone formation.
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The phase and energy methods for computing binocular disparity maps from stereograms are motivated differently, have different physiological relevances, and involve different computational steps. Nevertheless, we demonstrate that at the final stages where disparity values are made explicit, the simplest versions of the two methods are exactly equivalent. The equivalence also holds when the quadrature-pair construction in the energy method is replaced with a more physiologically plausible phase-averaging step. The equivalence fails, however, when the phase-difference receptive field model is replaced by the position-shift model. Additionally, intermediate results from the two methods are always quite distinct. In particular, the energy method generates a distributed disparity representation similar to that found in the visual cortex, while the phase method does not. Finally, more elaborate versions of the two methods are in general not equivalent. We also briefly compare these two methods with some other stereo models in the literature.
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Using random dot stimuli well controlled for dot speed, we found that the moving features in expanding patterns appear to move faster than those in rotating patterns. The illusion is well correlated with the strength of the global motion signal. For example, in displays where the number of motion directions defining the patterns is reduced, the magnitude of the illusion decreases. Similarly, the strength of the effect diminishes as dot density is reduced. In patterns where only wedge-shaped segments of the stimuli are left exposed, the difference in perceived speed increases with the angular size of the wedge. Stimulus placement relative to the fixation point has little effect on the persistence of this phenomenon-expansion patterns appear to contain elements of greater speed, independent of stimulus eccentricity. These results argue against a local explanation for this perceptual illusion, suggesting that the global motion pattern of the stimulus, per se, is responsible.
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