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author:("Hu, xiaoi")
1.  Land Use/Cover Change in the Middle Reaches of the Heihe River Basin over 2000-2011 and Its Implications for Sustainable Water Resource Management 
PLoS ONE  2015;10(6):e0128960.
The Heihe River Basin (HRB) is a typical arid inland river basin in northwestern China. From the 1960s to the 1990s, the downstream flow in the HRB declined as a result of large, artificial changes in the distribution of water and land and a lack of effective water resource management. Consequently, the ecosystems of the lower reaches of the basin substantially deteriorated. To restore these degraded ecosystems, the Ecological Water Diversion Project (EWDP) was initiated by the Chinese government in 2000. The project led to agricultural and ecological changes in the middle reaches of the basin. In this study, we present three datasets of land use/cover in the middle reaches of the HRB derived from Landsat TM/ETM+ images in 2000, 2007 and 2011. We used these data to investigate changes in land use/cover between 2000 and 2011 and the implications for sustainable water resource management. The results show that the most significant land use/cover change in the middle reaches of the HRB was the continuous expansion of farmland for economic interests. From 2000 to 2011, the farmland area increased by 12.01%. The farmland expansion increased the water resource stress; thus, groundwater was over-extracted and the ecosystem was degraded in particular areas. Both consequences are negative and potentially threaten the sustainability of the middle reaches of the HRB and the entire river basin. Local governments should therefore improve the management of water resources, particularly groundwater management, and should strictly control farmland reclamation. Then, water resources could be ecologically and socioeconomically sustained, and the balance between upstream and downstream water demands could be ensured. The results of this study can also serve as a reference for the sustainable management of water resources in other arid inland river basins.
PMCID: PMC4482701  PMID: 26115484
2.  Long-Term Effect on Natural Killer Cells by Interferon-α Therapy on the Outcomes of HCV Infection 
Natural killer (NK) cells act as innate immune cells against hepatitis C virus (HCV) infection. Interferon-α (IFN-α) and ribavirin are the standard treatments for patients with HCV infection. This study is aimed at investigating the dynamic changes in the frequency of different subsets of NK cells following treatment in xx chronic hepatitis C (CHC) patients. CHC patients were treated with peg-IFN or IFN-α, and followed up for 72 weeks. The frequency of different subsets of NK in CHC patients was determined longitudinally by flow cytometry. Treatment with the standard therapy increased the percentages of NKp30+, NKp46+, and CD107a+ NK cells, which were positively correlated with the declining of serum HCV-RNA, but not IFN-γ+ NK cells. NKG2A+ and KIR2DL3+ NK cells were associated with an early virological response in CHC patients. Treatment with IFN-α adjusts the balance of activated receptors and inhibitory receptors and enhances the cytotoxic activity of NK cells. Therefore, measuring NK subsets may be valuable for therapeutic responses in CHC patients.
PMCID: PMC4015508  PMID: 24367931
3.  Toxic Effect of a Marine Bacterium on Aquatic Organisms and Its Algicidal Substances against Phaeocystis globosa 
PLoS ONE  2015;10(2):e0114933.
Harmful algal blooms have caused enormous damage to the marine ecosystem and the coastal economy in China. In this paper, a bacterial strain B1, which had strong algicidal activity against Phaeocystis globosa, was isolated from the coastal waters of Zhuhai in China. The strain B1 was identified as Bacillus sp. on the basis of 16S rDNA gene sequence and morphological characteristics. To evaluate the ecological safety of the algicidal substances produced by strain B1, their toxic effects on marine organisms were tested. Results showed that there were no adverse effects observed in the growth of Chlorella vulgaris, Chaetoceros muelleri, and Isochrystis galbana after exposure to the algicidal substances at a concentration of 1.0% (v/v) for 96 h. The 48h LC50 values for Brachionus plicatilis, Moina mongolica Daday and Paralichthys olivaceus were 5.7, 9.0 and 12.1% (v/v), respectively. Subsequently, the algicidal substances from strain B1 culture were isolated and purified by silica gel column, Sephadex G-15 column and high-performance liquid chromatography. Based on quadrupole time-of-flight mass spectrometry and PeakView Software, the purified substances were identified as prolyl-methionine and hypoxanthine. Algicidal mechanism indicated that prolyl-methionine and hypoxanthine inhibited the growth of P. globosa by disrupting the antioxidant systems. In the acute toxicity assessment using M. mongolica, 24h LC50 values of prolyl-methionine and hypoxanthine were 7.0 and 13.8 g/L, respectively. The active substances produced by strain B1 can be considered as ecologically and environmentally biological agents for controlling harmful algal blooms.
PMCID: PMC4315471  PMID: 25646807
4.  Methylation Patterns of the IFN-γ Gene in Cervical Cancer Tissues 
Scientific Reports  2014;4:6331.
Objective: To explore the relationship between methylation of interferon gamma (IFN-γ) gene and tumorigenesis in cervical cancer tissues, the biopsy specimens of cervical cancer and cervical intraepithelial neoplasia (CIN) (I-III) patients as well as normal controls were collected and analyzed. Methods: The methylation of the IFN-γ gene was verified by using methylation-specific PCR and DNA sequencing analysis, and the expression levels of IFN-γ mRNA were detected using quantitative real-time reverse transcriptase-polymerase chain reaction (qRT-PCR). Results: The methylation rates of the IFN-γ gene were significantly higher in cervical cancer tissues (15/43, 34.9%) than those in CIN (3/23, 13.0% of CIN I; 6/39, 15.4% of CIN II/III) and normal cervical tissues (2/43, 4.7%) (P < 0.01). Furthermore, the mRNA expression of IFN-γ in cervical tumors with methylation (0.71 ± 0.13, n = 8) was lower than that in those without methylation (1.58 ± 0.32, n = 27) (P < 0.05). Likewise, the IFN-γ expression levels in CIN II/III tissues with methylation (0.87 ± 0.16, n = 5) were significantly (P < 0.01) lower compared to those without methylation (2.12 ± 0.27, n = 32). Conclusion: The hypermethylation of IFN-γ gene may be related with tumorigenesis of cervical cancer.
PMCID: PMC4160705  PMID: 25208560
5.  Increased numbers of CD5+CD19+CD1dhighIL-10+ Bregs, CD4+Foxp3+ Tregs, CD4+CXCR5+Foxp3+ follicular regulatory T (TFR) cells in CHB or CHC patients 
IL-10+ regulatory B (Bregs), CD4+Foxp3+ regulatory T (Tregs), and CD4+CXCR5+Foxp3+ follicular regulatory T (TFR) cells regulate the progression of infection disease. This study aimed at examining how those cells associated with the development of chronic hepatitis B (CHB) and chronic hepatitis C (CHC) in a Chinese population.
The numbers of circulating IL-10+ Bregs, Tregs and TFR cells in 31 CHC, 58 CHB patients and 22 healthy controls (HC) were examined by flow cytometry. The potential association of those cells with clinical measures was analyzed.
The numbers of CD5+CD19+CD1dhighIL-10+ Bregs, Tregs and TFR cells and the levels of serum IL-10, IFN-γ and IL-2 in the CHB, and IL-10 and IFN-γ in the CHC patients were significantly higher than that in the HC (p < 0.05). Furthermore, the numbers of circulating IL-10+ Bregs and the levels of serum IL-10, but not other cytokines tested were positively correlated with the levels of serum HBV DNA and ALT in the HBeAg− CHB patients as well as HCV RNA and ALT in CHC patients. Additionally, the numbers of circulating TFR cells were positively correlated with the levels of serum HBV DNA and ALT in the CHB patients as well as HCV RNA and ALT in the CHC patients.
Increased numbers of circulating IL-10+ Bregs and TFR cells are associated with poor virus eradication and liver injury in CHB and CHC patients. Furthermore, the levels of serum IL-10 is associated with the hepatic flares.
PMCID: PMC4173099  PMID: 25199644
Chronic hepatitis C (CHC); Chronic hepatitis B (CHB); Breg; Follicular regulatory T (TFR); T follicular helper (TFH); Forkhead box protein 3 (Foxp3); IL-10; HBsAg
6.  A Scallop IGF Binding Protein Gene: Molecular Characterization and Association of Variants with Growth Traits 
PLoS ONE  2014;9(2):e89039.
Scallops represent economically important aquaculture shellfish. The identification of genes and genetic variants related to scallop growth could benefit high-yielding scallop breeding. The insulin-like growth factor (IGF) system is essential for growth and development, with IGF binding proteins (IGFBPs) serving as the major regulators of IGF actions. Although an effect of IGF on growth was detected in bivalve, IGFBP has not been reported, and members of the IGF system have not been characterized in scallop.
We cloned and characterized an IGFBP (PyIGFBP) gene from the aquaculture bivalve species, Yesso scallop (Patinopecten yessoensis, Jay, 1857). Its full-length cDNA sequence was 1,445 bp, with an open reading frame of 378 bp, encoding 125 amino acids, and its genomic sequence was 10,193 bp, consisting of three exons and two introns. The amino acid sequence exhibited the characteristics of IGFBPs, including multiple cysteine residues and relatively conserved motifs in the N-terminal and C-terminal domains. Expression analysis indicated that PyIGFBP was expressed in all the tissues and developmental stages examined, with a significantly higher level in the mantle than in other tissues and a significantly higher level in gastrulae and trochophore larvae than in other stages. Furthermore, three single nucleotide polymorphisms (SNPs) were identified in this gene. SNP c.1054A>G was significantly associated with both shell and soft body traits in two populations, with the highest trait values in GG type scallops and lowest in AG type ones.
We cloned and characterized an IGFBP gene in a bivalve, and this report also represents the first characterizing an IGF system gene in scallops. A SNP associated with scallop growth for both the shell and soft body was identified in this gene. In addition to providing a candidate marker for scallop breeding, our results also suggest the role of PyIGFBP in scallop growth.
PMCID: PMC3929647  PMID: 24586493
7.  Large-Scale Development of Gene-Associated Single-Nucleotide Polymorphism Markers for Molluscan Population Genomic, Comparative Genomic, and Genome-Wide Association Studies 
Mollusca is the second most diverse group of animals in the world. Despite their perceived importance, omics-level studies have seldom been applied to this group of animals largely due to a paucity of genomic resources. Here, we report the first large-scale gene-associated marker development and evaluation for a bivalve mollusc, Chlamys farreri. More than 21,000 putative single-nucleotide polymorphisms (SNPs) were identified from the C. farreri transcriptome. Primers and probes were designed and synthesized for 4500 SNPs, and 1492 polymorphic markers were successfully developed using a high-resolution melting genotyping platform. These markers are particularly suitable for population genomic analysis due to high polymorphism within and across populations, a low frequency of null alleles, and conformation to neutral expectations. Unexpectedly, high cross-species transferability was observed, suggesting that the transferable SNPs may largely represent ancestral genetic variations that have been preserved differentially among subfamilies of Pectinidae. Gene annotations were available for 73% of the markers, and 65% could be anchored to the recently released Pacific oyster genome. Large-scale association analysis revealed key candidate genes responsible for scallop growth regulation, and provided markers for further genetic improvement of C. farreri in breeding programmes.
PMCID: PMC3989488  PMID: 24277739
mollusca; single-nucleotide polymorphism (SNP); transcriptome; high resolution melting (HRM); genome-wide association (GWAS)
8.  RADtyping: An Integrated Package for Accurate De Novo Codominant and Dominant RAD Genotyping in Mapping Populations 
PLoS ONE  2013;8(11):e79960.
Genetic linkage maps are indispensable tools in genetic, genomic and breeding studies. As one of genotyping-by-sequencing methods, RAD-Seq (restriction-site associated DNA sequencing) has gained particular popularity for construction of high-density linkage maps. Current RAD analytical tools are being predominantly used for typing codominant markers. However, no genotyping algorithm has been developed for dominant markers (resulting from recognition site disruption). Given their abundance in eukaryotic genomes, utilization of dominant markers would greatly diminish the extensive sequencing effort required for large-scale marker development. In this study, we established, for the first time, a novel statistical framework for de novo dominant genotyping in mapping populations. An integrated package called RADtyping was developed by incorporating both de novo codominant and dominant genotyping algorithms. We demonstrated the superb performance of RADtyping in achieving remarkably high genotyping accuracy based on simulated and real mapping datasets. The RADtyping package is freely available at detailen.asp?id=727.
PMCID: PMC3836964  PMID: 24278224
9.  High-Resolution Linkage and Quantitative Trait Locus Mapping Aided by Genome Survey Sequencing: Building Up An Integrative Genomic Framework for a Bivalve Mollusc 
Genetic linkage maps are indispensable tools in genetic and genomic studies. Recent development of genotyping-by-sequencing (GBS) methods holds great promise for constructing high-resolution linkage maps in organisms lacking extensive genomic resources. In the present study, linkage mapping was conducted for a bivalve mollusc (Chlamys farreri) using a newly developed GBS method—2b-restriction site-associated DNA (2b-RAD). Genome survey sequencing was performed to generate a preliminary reference genome that was utilized to facilitate linkage and quantitative trait locus (QTL) mapping in C. farreri. A high-resolution linkage map was constructed with a marker density (3806) that has, to our knowledge, never been achieved in any other molluscs. The linkage map covered nearly the whole genome (99.5%) with a resolution of 0.41 cM. QTL mapping and association analysis congruously revealed two growth-related QTLs and one potential sex-determination region. An important candidate QTL gene named PROP1, which functions in the regulation of growth hormone production in vertebrates, was identified from the growth-related QTL region detected on the linkage group LG3. We demonstrate that this linkage map can serve as an important platform for improving genome assembly and unifying multiple genomic resources. Our study, therefore, exemplifies how to build up an integrative genomic framework in a non-model organism.
PMCID: PMC3925396  PMID: 24107803
bivalve; genome sequencing; 2b-RAD genotyping; linkage mapping; quantitative trait locus mapping
10.  Identification of Reference Genes for qRT-PCR Analysis in Yesso Scallop Patinopecten yessoensis 
PLoS ONE  2013;8(9):e75609.
Bivalves comprise around 30,000 extant species and have received much attention for their importance in ecosystems, aquaculture and evolutionary studies. Despite the increasing application of real-time quantitative reverse transcription PCR (qRT-PCR) in gene expression studies on bivalve species, little research has been conducted on reference gene selection which is critical for reliable and accurate qRT-PCR analysis. For scallops, systematic evaluation of reference genes that can be used among tissues or embryo/larva stages is lacking, and β-actin (ACT) is most frequently used as qRT-PCR reference gene without validation.
In this study, 12 commonly used candidate reference genes were selected from the transcriptome data of Yesso scallop (Patinopecten yessoensis) for suitable qRT-PCR reference genes identification. The expression of these genes in 36 tissue samples and 15 embryo/larva samples under normal physiological conditions was examined by qRT-PCR, and their expression stabilities were evaluated using three statistic algorithms, geNorm, NormFinder, and comparative ∆Ct method. Similar results were obtained by the three approaches for the most and the least stably expressed genes. Final comprehensive ranking for the 12 genes combing the results from the three programs showed that, for different tissues, DEAD-box RNA helicase (HELI), ubiquitin (UBQ), and 60S ribosomal protein L16 (RPL16) were the optimal reference genes combination, while for different embryo/larva stages, gene set containing Cytochrome B (CB), Cytochrome C (CC), Histone H3.3 (His3.3), and Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were recommended for qRT-PCR normalization. ACT was among the least stable genes for both adult tissues and embryos/larvae.
This work constitutes the first systematic analysis on reference genes selection for qRT-PCR normalization in scallop under normal conditions. The suitable reference genes we recommended will be useful for the identification of genes related to biological processes in Yesso scallop, and also in the reference gene selection for other scallop or bivalve species.
PMCID: PMC3777977  PMID: 24069432
11.  The Molecular Mechanism of a Cis-Regulatory Adaptation in Yeast 
PLoS Genetics  2013;9(9):e1003813.
Despite recent advances in our ability to detect adaptive evolution involving the cis-regulation of gene expression, our knowledge of the molecular mechanisms underlying these adaptations has lagged far behind. Across all model organisms, the causal mutations have been discovered for only a handful of gene expression adaptations, and even for these, mechanistic details (e.g. the trans-regulatory factors involved) have not been determined. We previously reported a polygenic gene expression adaptation involving down-regulation of the ergosterol biosynthesis pathway in the budding yeast Saccharomyces cerevisiae. Here we investigate the molecular mechanism of a cis-acting mutation affecting a member of this pathway, ERG28. We show that the causal mutation is a two-base deletion in the promoter of ERG28 that strongly reduces the binding of two transcription factors, Sok2 and Mot3, thus abolishing their regulation of ERG28. This down-regulation increases resistance to a widely used antifungal drug targeting ergosterol, similar to mutations disrupting this pathway in clinical yeast isolates. The identification of the causal genetic variant revealed that the selection likely occurred after the deletion was already present at high frequency in the population, rather than when it was a new mutation. These results provide a detailed view of the molecular mechanism of a cis-regulatory adaptation, and underscore the importance of this view to our understanding of evolution at the molecular level.
Author Summary
Evolutionary adaptation is the process that has given rise to the ubiquitous, yet remarkable, fit between all living organisms and their environments. The molecular mechanisms of these adaptations have been a subject of great interest, but we still know very little about their mechanisms, particularly in the case of regulatory adaptations. In this work, we investigate the molecular mechanism of a regulatory adaptation that we previously identified in ERG28, a component of the ergosterol biosynthesis pathway in budding yeast. Ergosterol is an abundant lipid component of the fungal plasma membrane, and is of major biomedical importance, being targeted by numerous antifungal drugs. We identified the causal mutation underlying the ERG28 adaptation, a two-base deletion in its promoter which leads to lower abundance of its mRNA. This deletion acts via disrupting the binding of at least two transcription factors, Mot3 and Sok2, to the promoter. The deletion increases resistance to a widely used antifungal drug, Amphotericin B, which targets ergosterol. This effect is reminiscent of misregulation of the ergosterol pathway observed in clinical yeast isolates that have evolved resistance to Amphotericin B. Our results may therefore have medical implications, while also advancing our basic understanding of evolutionary mechanisms.
PMCID: PMC3778017  PMID: 24068973
12.  Molecular Characterization of RXR (Retinoid X Receptor) Gene Isoforms from the Bivalve Species Chlamys farreri 
PLoS ONE  2013;8(9):e74290.
Bivalves are among the oldest classes of invertebrates, and they exhibit diverse types of sexual patterning. However, our current understanding of the mechanisms of sex determination and differentiation in bivalves remains very limited. The retinoid X receptors (RXRs), which are members of the nuclear receptor family, are involved in sex differentiation in many organisms.
In the present study, four full-length RXR-encoding cDNAs (CfRXRs) named CfRXRa, CfRXRb, CfRXRc and CfRXRd were retrieved from Zhikong scallop (Chlamys farreri). The four RXRs exhibited the conserved five-domain structure of nuclear receptor superfamily members and differed from each other only in the T-box of the C domain. The three variants, designated T (+4), T (+20) and T (+24), contained insertions of 4, 20 and 24 amino acids, respectively. The entire CfRXR gene is composed of eight exons and seven introns, and the four isoforms are generated via alternative mRNA splicing. Expression analysis showed that all four isoforms were expressed in both the testis and the ovary during the differentiation stage, whereas no expression was detected in the growth, mature or resting stages. This result suggests that CfRXRs are involved in germ cell differentiation in both sexes. The expression of the four isoforms was also detected in other tissues examined, including mantle, gill, digestive gland, and adductor muscle of sexually mature male and female Zhikong scallops, implying the multiple biological functions of CfRXRs.
Our study presents the first report of RXR isoforms in bivalves. Further investigation of the functional roles of different RXR isoforms may provide deep insights into the regulatory mechanism of sex differentiation in C. farreri.
PMCID: PMC3774650  PMID: 24066133
13.  Correction: Molecular Characterization of TGF-β Type I Receptor Gene (Tgfbr1) in Chlamys farreri, and the Association of Allelic Variants with Growth Traits 
PLoS ONE  2013;8(7):10.1371/annotation/75437eff-feb9-4592-baeb-ec7b98d1d212.
PMCID: PMC4102268
14.  Development of a Rapid and Efficient Method for Non-Lethal DNA Sampling and Genotyping in Scallops 
PLoS ONE  2013;8(7):e68096.
Non-lethal DNA sampling has long appealed to researchers studying population and conservation genetics, as it does not necessitate removing individuals permanently from their natural environment or destroying valuable samples. However, such an approach has not yet been well established in bivalves. In this study, we demonstrate that the gill represents a good source of tissue for non-lethal sampling in scallops. Removal of a few gill filaments caused no noticeable behavioral abnormalities or increased mortality rates in Zhikong scallop (Chlamys farreri) during a three-month period of observation. To facilitate rapid gill-based DNA extraction, six methods (MA-MF) were designed and evaluated, each requiring less than one hour of processing time. The optimal method was identified as MF, in terms of maintaining DNA integrity and genotyping accuracy. Further optimization of MF method by orthogonal experimental design suggested that the utilization of gills could be limited to 2 mg of sample, which is sufficient for performing up to 20,000 PCR reactions. We also demonstrate the excellent cross-species utility of MF in two additional scallop species, Yesso scallop (Patinopecten yessoensis) and bay scallop (Argopecten irradians). Taken together, our study provides a rapid and efficient approach for applying non-lethal DNA sampling in bivalve species, which would serve as a valuable tool for maintaining bivalve populations and conservation genetics, as well as in breeding studies.
PMCID: PMC3706602  PMID: 23874509
15.  Transcriptome Sequencing of Zhikong Scallop (Chlamys farreri) and Comparative Transcriptomic Analysis with Yesso Scallop (Patinopecten yessoensis) 
PLoS ONE  2013;8(5):e63927.
Bivalves play an important role in the ecosystems they inhabit and represent an important food source all over the world. So far limited genetic research has focused on this group of animals largely due to the lack of sufficient genetic or genomic resources. Here, we performed de novo transcriptome sequencing to produce the most comprehensive expressed sequence tag resource for Zhikong scallop (Chlamys farreri), and conducted the first transcriptome comparison for scallops.
In a single 454 sequencing run, 1,033,636 reads were produced and then assembled into 26,165 contigs. These contigs were then clustered into 24,437 isotigs and further grouped into 20,056 isogroups. About 47% of the isogroups showed significant matches to known proteins based on sequence similarity. Transcripts putatively involved in growth, reproduction and stress/immune-response were identified through Gene ontology (GO) and KEGG pathway analyses. Transcriptome comparison with Yesso scallop (Patinopecten yessoensis) revealed similar patterns of GO representation. Moreover, 38 putative fast-evolving genes were identified through analyzing the orthologous gene pairs between the two scallop species. More than 46,000 single nucleotide polymorphisms (SNPs) and 350 simple sequence repeats (SSRs) were also detected.
Our study provides the most comprehensive transcriptomic resource currently available for C. farreri. Based on this resource, we performed the first large-scale transcriptome comparison between the two scallop species, C. farreri and P. yessoensis, and identified a number of putative fast-evolving genes, which may play an important role in scallop speciation and/or local adaptation. A large set of single nucleotide polymorphisms and simple sequence repeats were identified, which are ready for downstream marker development. This transcriptomic resource should lay an important foundation for future genetic or genomic studies on C. farreri.
PMCID: PMC3646770  PMID: 23667690
16.  The evolution of machining-induced surface of single-crystal FCC copper via nanoindentation 
Nanoscale Research Letters  2013;8(1):211.
The physical properties of the machining-induced new surface depend on the performance of the initial defect surface and deformed layer in the subsurface of the bulk material. In this paper, three-dimensional molecular dynamics simulations of nanoindentation are preformed on the single-point diamond turning surface of single-crystal copper comparing with that of pristine single-crystal face-centered cubic copper. The simulation results indicate that the nucleation of dislocations in the nanoindentation test on the machining-induced surface and pristine single-crystal copper is different. The dislocation embryos are gradually developed from the sites of homogeneous random nucleation around the indenter in the pristine single-crystal specimen, while the dislocation embryos derived from the vacancy-related defects are distributed in the damage layer of the subsurface beneath the machining-induced surface. The results show that the hardness of the machining-induced surface is softer than that of pristine single-crystal copper. Then, the nanocutting simulations are performed along different crystal orientations on the same crystal surface. It is shown that the crystal orientation directly influences the dislocation formation and distribution of the machining-induced surface. The crystal orientation of nanocutting is further verified to affect both residual defect generations and their propagation directions which are important in assessing the change of mechanical properties, such as hardness and Young's modulus, after nanocutting process.
PMCID: PMC3673828  PMID: 23641932
Machining-induced surface; Nanoindentation; Nucleation of dislocations; Molecular dynamics simulation
17.  Neural stem cell-like cells derived from autologous bone mesenchymal stem cells for the treatment of patients with cerebral palsy 
Stem cell therapy is a promising treatment for cerebral palsy, which refers to a category of brain diseases that are associated with chronic motor disability in children. Autologous MSCs may be a better cell source and have been studied for the treatment of cerebral palsy because of their functions in tissue repair and the regulation of immunological processes.
To assess neural stem cell–like (NSC-like) cells derived from autologous marrow mesenchymal stem cells as a novel treatment for patients with moderate-to-severe cerebral palsy, a total of 60 cerebral palsy patients were enrolled in this open-label, non-randomised, observer-blinded controlled clinical study with a 6-months follow-up. For the transplantation group, a total of 30 cerebral palsy patients received an autologous NSC-like cells transplantation (1-2 × 107 cells into the subarachnoid cavity) and rehabilitation treatments whereas 30 patients in the control group only received rehabilitation treatment.
We recorded the gross motor function measurement scores, language quotients, and adverse events up to 6 months post-treatment. The gross motor function measurement scores in the transplantation group were significantly higher at month 3 (the score increase was 42.6, 95% CI: 9.8–75.3, P=.011) and month 6 (the score increase was 58.6, 95% CI: 25.8–91.4, P=.001) post-treatment compared with the baseline scores. The increase in the Gross Motor Function Measurement scores in the control group was not significant. The increases in the language quotients at months 1, 3, and 6 post-treatment were not statistically significant when compared with the baseline quotients in both groups. All the 60 patients survived, and none of the patients experienced serious adverse events or complications.
Our results indicated that NSC-like cells are safe and effective for the treatment of motor deficits related to cerebral palsy. Further randomised clinical trials are necessary to establish the efficacy of this procedure.
PMCID: PMC3563497  PMID: 23351389
Cerebral palsy; Neural stem cell-like cells; Bone marrow mesenchymal stem cells; Cell therapy; Autologous transplantation
18.  Antiviral Treatment Alters the Frequency of Activating and Inhibitory Receptor-Expressing Natural Killer Cells in Chronic Hepatitis B Virus Infected Patients 
Mediators of Inflammation  2012;2012:804043.
Natural killer (NK) cells play a critical role in innate antiviral immunity, but little is known about the impact of antiviral therapy on the frequency of NK cell subsets. To this aim, we performed this longitudinal study to examine the dynamic changes of the frequency of different subsets of NK cells in CHB patients after initiation of tenofovir or adefovir therapy. We found that NK cell numbers and subset distribution differ between CHB patients and normal subjects; furthermore, the association was found between ALT level and CD158b+ NK cell in HBV patients. In tenofovir group, the frequency of NK cells increased during the treatment accompanied by downregulated expression of NKG2A and KIR2DL3. In adefovir group, NK cell numbers did not differ during the treatment, but also accompanied by downregulated expression of NKG2A and KIR2DL3. Our results demonstrate that treatment with tenofovir leads to viral load reduction, and correlated with NK cell frequencies in peripheral blood of chronic hepatitis B virus infection. In addition, treatments with both tenofovir and adefovir in chronic HBV infected patients induce a decrease of the frequency of inhibitory receptor+ NK cells, which may account for the partial restoration of the function of NK cells in peripheral blood following treatment.
PMCID: PMC3529875  PMID: 23304062
19.  Molecular Characterization of TGF-β Type I Receptor Gene (Tgfbr1) in Chlamys farreri, and the Association of Allelic Variants with Growth Traits 
PLoS ONE  2012;7(11):e51005.
Scallops are an economically important aquaculture species in Asian countries, and growth-rate improvement is one of the main focuses of scallop breeding. Investigating the genetic regulation of scallop growth could benefit scallop breeding, as such research is currently limited. The transforming growth factor beta (TGF-β) signaling through type I and type II receptors, plays critical roles in regulating cell proliferation and growth, and is thus a plausible candidate growth regulator in scallops.
We cloned and characterized the TGF-β type I receptor (Tgfbr1) gene from Zhikong scallops (Chlamys farreri). The deduced amino acid sequence contains characteristic residues and exhibits the conserved structure of Tgfbr1 proteins. A high expression level of scallop Tgfbr1 was detected during early embryonic stages, whereas Tgfbr1 expression was enriched in the gonad and striated muscle in adults. A single nucleotide polymorphism (SNP, c. 1815C>T) in the 3′ UTR was identified. Scallops with genotype TT had higher growth traits values than those with genotype CC or CT in a full-sib family, and significant differences were found between genotypes CC and TT for shell length, shell height, and striated muscle weight. An expression analysis detected significantly more Tgfbr1 transcripts in the striated muscle of scallops with genotype CC compared to those with genotype TT or CT. Further evaluation in a population also revealed higher striated muscle weight in scallops with genotype TT than those with the other two genotypes. The inverse correlation between striated muscle mass and Tgfbr1 expression is consistent with TGF-β signaling having a negative effect on cell growth.
The scallop Tgfbr1 gene was cloned and characterized, and an SNP potentially associated with both scallop growth and Tgfbr1 expression was identified. Our results suggest the negative regulation of Tgfbr1 in scallop growth and provide a candidate marker for Zhikong scallop breeding.
PMCID: PMC3510168  PMID: 23209843
20.  Reference-free SNP calling: improved accuracy by preventing incorrect calls from repetitive genomic regions 
Biology Direct  2012;7:17.
Single nucleotide polymorphisms (SNPs) are the most abundant type of genetic variation in eukaryotic genomes and have recently become the marker of choice in a wide variety of ecological and evolutionary studies. The advent of next-generation sequencing (NGS) technologies has made it possible to efficiently genotype a large number of SNPs in the non-model organisms with no or limited genomic resources. Most NGS-based genotyping methods require a reference genome to perform accurate SNP calling. Little effort, however, has yet been devoted to developing or improving algorithms for accurate SNP calling in the absence of a reference genome.
Here we describe an improved maximum likelihood (ML) algorithm called iML, which can achieve high genotyping accuracy for SNP calling in the non-model organisms without a reference genome. The iML algorithm incorporates the mixed Poisson/normal model to detect composite read clusters and can efficiently prevent incorrect SNP calls resulting from repetitive genomic regions. Through analysis of simulation and real sequencing datasets, we demonstrate that in comparison with ML or a threshold approach, iML can remarkably improve the accuracy of de novo SNP genotyping and is especially powerful for the reference-free genotyping in diploid genomes with high repeat contents.
The iML algorithm can efficiently prevent incorrect SNP calls resulting from repetitive genomic regions, and thus outperforms the original ML algorithm by achieving much higher genotyping accuracy. Our algorithm is therefore very useful for accurate de novo SNP genotyping in the non-model organisms without a reference genome.
This article was reviewed by Dr. Richard Durbin, Dr. Liliana Florea (nominated by Dr. Steven Salzberg) and Dr. Arcady Mushegian.
PMCID: PMC3472322  PMID: 22682067
Next-generation sequencing; single nucleotide polymorphism; genotyping; maximum likelihood; mixed Poisson/normal model
21.  Network Analysis of Oyster Transcriptome Revealed a Cascade of Cellular Responses during Recovery after Heat Shock 
PLoS ONE  2012;7(4):e35484.
Oysters, as a major group of marine bivalves, can tolerate a wide range of natural and anthropogenic stressors including heat stress. Recent studies have shown that oysters pretreated with heat shock can result in induced heat tolerance. A systematic study of cellular recovery from heat shock may provide insights into the mechanism of acquired thermal tolerance. In this study, we performed the first network analysis of oyster transcriptome by reanalyzing microarray data from a previous study. Network analysis revealed a cascade of cellular responses during oyster recovery after heat shock and identified responsive gene modules and key genes. Our study demonstrates the power of network analysis in a non-model organism with poor gene annotations, which can lead to new discoveries that go beyond the focus on individual genes.
PMCID: PMC3329459  PMID: 22530030
22.  Transcriptome Sequencing and Characterization for the Sea Cucumber Apostichopus japonicus (Selenka, 1867) 
PLoS ONE  2012;7(3):e33311.
Sea cucumbers are a special group of marine invertebrates. They occupy a taxonomic position that is believed to be important for understanding the origin and evolution of deuterostomes. Some of them such as Apostichopus japonicus represent commercially important aquaculture species in Asian countries. Many efforts have been devoted to increasing the number of expressed sequence tags (ESTs) for A. japonicus, but a comprehensive characterization of its transcriptome remains lacking. Here, we performed the large-scale transcriptome profiling and characterization by pyrosequencing diverse cDNA libraries from A. japonicus.
In total, 1,061,078 reads were obtained by 454 sequencing of eight cDNA libraries representing different developmental stages and adult tissues in A. japonicus. These reads were assembled into 29,666 isotigs, which were further clustered into 21,071 isogroups. Nearly 40% of the isogroups showed significant matches to known proteins based on sequence similarity. Gene ontology (GO) and KEGG pathway analyses recovered diverse biological functions and processes. Candidate genes that were potentially involved in aestivation were identified. Transcriptome comparison with the sea urchin Strongylocentrotus purpuratus revealed similar patterns of GO term representation. In addition, 4,882 putative orthologous genes were identified, of which 202 were not present in the non-echinoderm organisms. More than 700 simple sequence repeats (SSRs) and 54,000 single nucleotide polymorphisms (SNPs) were detected in the A. japonicus transcriptome.
Pyrosequencing was proven to be efficient in rapidly identifying a large set of genes for the sea cucumber A. japonicus. Through the large-scale transcriptome sequencing as well as public EST data integration, we performed a comprehensive characterization of the A. japonicus transcriptome and identified candidate aestivation-related genes. A large number of potential genetic markers were also identified from the A. japonicus transcriptome. This transcriptome resource would lay an important foundation for future genetic or genomic studies on this species.
PMCID: PMC3299772  PMID: 22428017
23.  Dynamic changes of inflammatory markers in brain after hemorrhagic stroke in humans: a postmortem study 
Brain research  2010;1342C:111-117.
This histopathologic case-control study was designed to characterize the dynamic changes in protein expression of nuclear factor-kappa B (NF-κB)/p65 subunit, macrophage inflammatory protein-2 (MIP-2), and matrix metalloproteinase-9 (MMP-9) in postmortem brains of patients with and without intracerebral hemorrhage (ICH). Thirty-six human brains from patients with ICH and six control brains were included in this study. We found that expression levels of NF-κB/p65, MIP-2, and MMP-9 were each upregulated on the injured side of the hippocampus at times ranging from 2 hr to 5 days post-ICH. Interestingly, the expression of all three markers was also upregulated on the uninjured side of the hippocampus and in the cerebellum, although to a lesser extent. These data suggest that inflammation occurs early and persists for several days after ICH in humans and could be involved in the progression of ICH-induced secondary brain damage.
PMCID: PMC2885522  PMID: 20420814
brain damage; intracerebral hemorrhage; MIP-2; MMP-9; NF-κB/p65
24.  Transcriptome Sequencing and De Novo Analysis for Yesso Scallop (Patinopecten yessoensis) Using 454 GS FLX 
PLoS ONE  2011;6(6):e21560.
Bivalves comprise 30,000 extant species, constituting the second largest group of mollusks. However, limited genetic research has focused on this group of animals so far, which is, in part, due to the lack of genomic resources. The advent of high-throughput sequencing technologies enables generation of genomic resources in a short time and at a minimal cost, and therefore provides a turning point for bivalve research. In the present study, we performed de novo transcriptome sequencing to first produce a comprehensive expressed sequence tag (EST) dataset for the Yesso scallop (Patinopecten yessoensis).
In a single 454 sequencing run, 805,330 reads were produced and then assembled into 32,590 contigs, with about six-fold sequencing coverage. A total of 25,237 unique protein-coding genes were identified from a variety of developmental stages and adult tissues based on sequence similarities with known proteins. As determined by GO annotation and KEGG pathway mapping, functional annotation of the unigenes recovered diverse biological functions and processes. Transcripts putatively involved in growth, reproduction and stress/immune-response were identified. More than 49,000 single nucleotide polymorphisms (SNPs) and 2,700 simple sequence repeats (SSRs) were also detected.
Our data provide the most comprehensive transcriptomic resource currently available for P. yessoensis. Candidate genes potentially involved in growth, reproduction, and stress/immunity-response were identified, and are worthy of further investigation. A large number of SNPs and SSRs were also identified and ready for marker development. This resource should lay an important foundation for future genetic or genomic studies on this species.
PMCID: PMC3123371  PMID: 21720557

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