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author:("Zhang, yard")
1.  Changes in Forest Soil Properties in Different Successional Stages in Lower Tropical China 
PLoS ONE  2013;8(11):e81359.
Natural forest succession often affects soil physical and chemical properties. Selected physical and chemical soil properties were studied in an old-growth forest across a forest successional series in Dinghushan Nature Reserve, Southern China.
Methodology/Principal Findings
The aim was to assess the effects of forest succession change on soil properties. Soil samples (0–20 cm depth) were collected from three forest types at different succession stages, namely pine (Pinus massoniana) forest (PMF), mixed pine and broadleaf forest (PBMF) and monsoon evergreen broadleaf forest (MEBF), representing early, middle and advanced successional stages respectively. The soil samples were analyzed for soil water storage (SWS), soil organic matter (SOM), soil microbial biomass carbon (SMBC), pH, NH4+-N, available potassium (K), available phosphorus (P) and microelements (available copper (Cu), available zinc (Zn), available iron (Fe) and available boron (B)) between 1999 and 2009. The results showed that SWS, SOM, SMBC, Cu, Zn, Fe and B concentrations were higher in the advanced successional stage (MEBF stage). Conversely, P and pH were lower in the MEBF but higher in the PMF (early successional stage). pH, NH4+-N, P and K declined while SOM, Zn, Cu, Fe and B increased with increasing forest age. Soil pH was lower than 4.5 in the three forest types, indicating that the surface soil was acidic, a stable trend in Dinghushan.
These findings demonstrated significant impacts of natural succession in an old-growth forest on the surface soil nutrient properties and organic matter. Changes in soil properties along the forest succession gradient may be a useful index for evaluating the successional stages of the subtropical forests. We caution that our inferences are drawn from a pseudo-replicated chronosequence, as true replicates were difficult to find. Further studies are needed to draw rigorous conclusions regarding on nutrient dynamics in different successional stages of forest.
PMCID: PMC3828269  PMID: 24244738
2.  Effects of black yeast-derived β-1,3-1,6-glucan on serum cytokine and microRNA expression in transplanted sarcoma in mice 
Biomedical Reports  2012;1(1):139-143.
β-1,3-1,6-glucans are the most abundant glucose polymers in the cell walls of fungi. Previous studies have shown that β-1,3-1,6-glucans derived from fungi possess immunomodulating activitivies. Antitumor effects of these compounds have also been reported in animal models. Current studies mainly focus on the direct effects of β-1,3-1,6-glucans on immune systems, but no data are available to address the underlying molecular events in tumor cells. β-1,3-1,6-glucan purified from black yeast at 5 mg/100 g body weight (study group) or saline (control group) was intragastrically administered on a daily basis to subcutaneously-injected mice with mouse S180 sarcoma cells. Tumor sizes, tumor weights, serum concentrations of cytokines and levels of microRNAs (miRNAs) in transplanted tumors were compared between the treated and control groups. The volumes and weights of transplanted tumors were significantly lower in the treatment groups compared to the control groups by ∼150% and 70%, respectively. The treated mice demonstrated significantly higher levels of cytokines, including IL-2, IL-4, IL-6, IL-8, IL-10 and IL-12, compared to the control mice. Notably, the expression of several miRNAs in transplanted tumor tissues also markedly changed. These data suggest that black yeast-derived β-1,3-1,6-glucan, not only stimulates cytokine release from immune cells, but also changes the expression profiles of miRNAs in transplanted tumors.
PMCID: PMC3956731  PMID: 24648910
β-1,3-1,6-glucan; S180 sarcoma cell; transplanted tumor; cytokine; microRNA
3.  High Throughput Screen for Escherichia coli Heat Shock Protein 70 (Hsp70/DnaK): ATPase Assay in Low Volume By Exploiting Energy Transfer 
Journal of biomolecular screening  2010;15(10):1211-1219.
Members of the heat shock protein 70 (Hsp70) family of molecular chaperones are emerging as potential therapeutic targets. Their ATPase activity has classically been measured using colorimetric phosphate-detection reagents, such as quinaldine red (QR). While such assays are suitable for 96-well plate formats, they typically lose sensitivity when attempted in lower volume due to path length and meniscus effects. These limitations and Hsp70’s weak enzymatic activity have combined to create significant challenges in high throughput screening. To overcome these difficulties, we have adopted an energy transfer strategy that was originally reported by Zuck et al. (Anal. Biochem. 2005, 342:254–259). Briefly, white 384-well plates emit fluorescence when irradiated at 430 nm. In turn, this intrinsic fluorescence can be quenched by energy transfer with the QR-based chromophore. Using this more sensitive approach, we tested 55,400 compounds against DnaK, a prokaryotic member of the Hsp70 family. The assay performance was good (Z′ ~ 0.6, CV ~8%) and at least one promising new inhibitor was identified. In secondary assays, this compound specifically blocked stimulation of DnaK by its co-chaperone, DnaJ. Thus, this simple and inexpensive adaptation of a colorimetric method might be suitable for screening against Hsp70-family members.
PMCID: PMC3052282  PMID: 20926844
phosphate; malachite green; ATPase; molecular chaperone; fluorescence assay
4.  Purification, crystallization and preliminary X-ray diffraction analysis of glutathionylated Trx1 C33S mutant from yeast 
Cytosolic Trx1 containing a C33S mutant was overexpressed, purified, glutathionylated and crystallized. The crystals diffracted to 1.80 Å resolution.
Thioredoxins (Trxs) are a family of small redox-active proteins that are found in all living organisms. In Saccharomyces cerevisiae, two cytosolic Trxs (Trx1 and Trx2) and one mitochondrial Trx (Trx3) have previously been identified. In this work, cytosolic Trx1 containing a C33S mutant was overexpressed, purified, glutathionylated and crystallized using the hanging-drop vapour-diffusion method. A set of X-ray diffraction data was collected to 1.80 Å resolution. The crystal belonged to space group P1, with unit-cell parameters a = 38.53, b = 38.81, c = 41.70 Å, α = 72.91, β = 87.51, γ = 60.58°.
PMCID: PMC2628853  PMID: 19153453
thioredoxins; Saccharomyces cerevisiae
5.  Expression, purification, crystallization and preliminary X-ray diffraction analysis of thioredoxin Trx1 from Saccharomyces cerevisiae  
In the present work, the cytosolic form of thioredoxin from S. cerevisiae was cloned, expressed, purified and crystallized.
Thioredoxins play key roles in the cellular response to oxidative stress. Three isoforms of thioredoxin have been identified in Saccharomyces cerevisiae: two that are cytosolic (Trx1 and Trx2) and one that is mitochondrial (Trx3). In the present work, the cytosolic form Trx1 was cloned, expressed, purified and crystallized. Crystals were obtained by the hanging-drop vapour-diffusion method. A data set was collected from a single crystal to 1.7 Å resolution. The crystal belongs to space group P212121, with unit-cell parameters a = 32.29, b = 46.59, c = 64.20 Å, α = β = γ = 90°.
PMCID: PMC2374243  PMID: 18391437
thioredoxins; Trx1
6.  Expression, purification, crystallization and preliminary X-ray diffraction analysis of mitochondrial thioredoxin Trx3 from Saccharomyces cerevisiae  
Crystals of mitochondrial thioredoxin Trx3 from S. cerevisiae were obtained and diffraction data were collected to 2.0 Å resolution.
There are three thioredoxin isoforms in the yeast Saccharomyces cerevisiae: two cytosolic/nuclear thioredoxins, Trx1 and Trx2, and one mitochondrial thioredoxin, Trx3. In the present work, S. cerevisiae Trx3 overexpressed in Escherichia coli was purified and crystallized. The Trx3 crystals were obtained by the hanging-drop vapour-diffusion method. A data set diffracting to 2.0 Å resolution was collected from a single crystal. The crystal belongs to space group P31, with unit-cell parameters a = b = 49.57, c = 94.55 Å, α = β = 90, γ = 120°. The asymmetric unit is assumed to contain two subunits of Trx3, with a V M value of 2.62 Å3 Da−1 and a solvent content of 53%.
PMCID: PMC2225218  PMID: 17077505
thioredoxins; Trx3

Results 1-6 (6)