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author:("Liu, tubing")
1.  The lysosomal cathepsin protease CPL-1 plays a leading role in phagosomal degradation of apoptotic cells in Caenorhabditis elegans 
Molecular Biology of the Cell  2014;25(13):2071-2083.
In Caenorhabditis elegans, the lysosomal cathepsin protease CPL-1 is indispensable for clearance of apoptotic cells by playing a leading role in destruction of cell corpses in phagolysosomes.
During programmed cell death, the clearance of apoptotic cells is achieved by their phagocytosis and delivery to lysosomes for destruction in engulfing cells. However, the role of lysosomal proteases in cell corpse destruction is not understood. Here we report the identification of the lysosomal cathepsin CPL-1 as an indispensable protease for apoptotic cell removal in Caenorhabditis elegans. We find that loss of cpl-1 function leads to strong accumulation of germ cell corpses, which results from a failure in degradation rather than engulfment. CPL-1 is expressed in a variety of cell types, including engulfment cells, and its mutation does not affect the maturation of cell corpse–containing phagosomes, including phagosomal recruitment of maturation effectors and phagosome acidification. Of importance, we find that phagosomal recruitment and incorporation of CPL-1 occurs before digestion of cell corpses, which depends on factors required for phagolysosome formation. Using RNA interference, we further examine the role of other candidate lysosomal proteases in cell corpse clearance but find that they do not obviously affect this process. Collectively, these findings establish CPL-1 as the leading lysosomal protease required for elimination of apoptotic cells in C. elegans.
doi:10.1091/mbc.E14-01-0015
PMCID: PMC4072580  PMID: 24829385
2.  Identification of Differentially Expressed Genes in Leaf of Reaumuria soongorica under PEG-Induced Drought Stress by Digital Gene Expression Profiling 
PLoS ONE  2014;9(4):e94277.
Reaumuria soongorica (Pall.) Maxim., a resurrection semi-shrub, is a typical constructive and dominant species in desert ecosystems in northwestern China. However, the gene expression characteristics of R. soongorica under drought stress have not been elucidated. Digital gene expression analysis was performed using Illumina technique to investigate differentially expressed genes (DEGs) between control and PEG-treated samples of R. soongorica. A total of 212,338 and 211,052 distinct tags were detected in the control and PEG-treated libraries, respectively. A total of 1,325 genes were identified as DEGs, 379 (28.6%) of which were up-regulated and 946 (71.4%) were down-regulated in response to drought stress. Functional annotation analysis identified numerous drought-inducible genes with various functions in response to drought stress. A number of regulatory proteins, functional proteins, and proteins induced by other stress factors in R. soongorica were identified. Alteration in the regulatory proteins (transcription factors and protein kinase) may be involved in signal transduction. Functional proteins, including flavonoid biosynthetic proteins, late embryogenesis abundant (LEA) proteins, small heat shock proteins (sHSP), and aquaporin and proline transporter may play protective roles in response to drought stress. Flavonoids, LEA proteins and sHSP function as reactive oxygen species scavenger or molecular chaperone. Aquaporin and proline transporters regulate the distribution of water and proline throughout the whole plant. The tolerance ability of R. soongorica may be gained through effective signal transduction and enhanced protection of functional proteins to reestablish cellular homeostasis. DEGs obtained in this study may provide useful insights to help further understand the drought-tolerant mechanism of R. soongorica.
doi:10.1371/journal.pone.0094277
PMCID: PMC3988058  PMID: 24736242
3.  Six1 Regulates MyoD Expression in Adult Muscle Progenitor Cells 
PLoS ONE  2013;8(6):e67762.
Quiescent satellite cells are myogenic progenitors that enable regeneration of skeletal muscle. One of the early events of satellite cell activation following myotrauma is the induction of the myogenic regulatory factor MyoD, which eventually induces terminal differentiation and muscle function gene expression. The purpose of this study was to elucidate the mechanism by which MyoD is induced during activation of satellite cells in mouse muscle undergoing regeneration. We show that Six1, a transcription factor essential for embryonic myogenesis, also regulates MyoD expression in muscle progenitor cells. Six1 knock-down by RNA interference leads to decreased expression of MyoD in myoblasts. Chromatin immunoprecipitation assays reveal that Six1 binds the Core Enhancer Region of MyoD. Further, transcriptional reporter assays demonstrate that Core Enhancer Region reporter gene activity in myoblasts and in regenerating muscle depends on the expression of Six1 and on Six1 binding sites. Finally, we provide evidence indicating that Six1 is required for the proper chromatin structure at the Core Enhancer Region, as well as for MyoD binding at its own enhancer. Together, our results reveal that MyoD expression in satellite cells depends on Six1, supporting the idea that Six1 plays an important role in adult myogenesis, in addition to its role in embryonic muscle formation.
doi:10.1371/journal.pone.0067762
PMCID: PMC3695946  PMID: 23840772
4.  Visual Scanning Patterns during the Dimensional Change Card Sorting Task in Children with Autism Spectrum Disorder 
Autism Research and Treatment  2012;2012:123053.
Impaired cognitive flexibility in children with autism spectrum disorder (ASD) has been reported in previous literature. The present study explored ASD children's visual scanning patterns during the Dimensional Change Card Sorting (DCCS) task using eye-tracking technique. ASD and typical developing (TD) children completed the standardized DCCS procedure on the computer while their eye movements were tracked. Behavioral results confirmed previous findings on ASD children's deficits in executive function. ASD children's visual scanning patterns also showed some specific underlying processes in the DCCS task compared to TD children. For example, ASD children looked shorter at the correct card in the postswitch phase and spent longer time at blank areas than TD children did. ASD children did not show a bias to the color dimension as TD children did. The correlations between the behavioral performance and eye moments were also discussed.
doi:10.1155/2012/123053
PMCID: PMC3459256  PMID: 23050145
5.  Discovery, optimization and validation of an optimal DNA-binding sequence for the Six1 homeodomain transcription factor 
Nucleic Acids Research  2012;40(17):8227-8239.
The Six1 transcription factor is a homeodomain protein involved in controlling gene expression during embryonic development. Six1 establishes gene expression profiles that enable skeletal myogenesis and nephrogenesis, among others. While several homeodomain factors have been extensively characterized with regards to their DNA-binding properties, relatively little is known of the properties of Six1. We have used the genomic binding profile of Six1 during the myogenic differentiation of myoblasts to obtain a better understanding of its preferences for recognizing certain DNA sequences. DNA sequence analyses on our genomic binding dataset, combined with biochemical characterization using binding assays, reveal that Six1 has a much broader DNA-binding sequence spectrum than had been previously determined. Moreover, using a position weight matrix optimization algorithm, we generated a highly sensitive and specific matrix that can be used to predict novel Six1-binding sites with highest accuracy. Furthermore, our results support the idea of a mode of DNA recognition by this factor where Six1 itself is sufficient for sequence discrimination, and where Six1 domains outside of its homeodomain contribute to binding site selection. Together, our results provide new light on the properties of this important transcription factor, and will enable more accurate modeling of Six1 function in bioinformatic studies.
doi:10.1093/nar/gks587
PMCID: PMC3458543  PMID: 22730291
6.  Cooperation between myogenic regulatory factors and SIX family transcription factors is important for myoblast differentiation 
Nucleic Acids Research  2010;38(20):6857-6871.
Precise regulation of gene expression is crucial to myogenesis and is thought to require the cooperation of various transcription factors. On the basis of a bioinformatic analysis of gene regulatory sequences, we hypothesized that myogenic regulatory factors (MRFs), key regulators of skeletal myogenesis, cooperate with members of the SIX family of transcription factors, known to play important roles during embryonic skeletal myogenesis. To this day little is known regarding the exact molecular mechanism by which SIX factors regulate muscle development. We have conducted a functional genomic study of the role played by SIX1 and SIX4 during the differentiation of skeletal myoblasts, a model of adult muscle regeneration. We report that SIX factors cooperate with the members of the MRF family to activate gene expression during myogenic differentiation, and that their function is essential to this process. Our findings also support a model where SIX factors function not only ‘upstream’ of the MRFs during embryogenesis, but also ‘in parallel’ to them during myoblast differentiation. We have identified new essential nodes that depend on SIX factor function, in the myogenesis regulatory network, and have uncovered a novel way by which MRF function is modulated during differentiation.
doi:10.1093/nar/gkq585
PMCID: PMC2978361  PMID: 20601407

Results 1-6 (6)