Quantitative FRET measurement based on spectral unmixing of donor,acceptor and spontaneous excitation‐emission spectra

The spontaneous excitation‐emission (ExEm) spectrum is introduced to the quantitative mExEm‐spFRET methodology we recently developed as a spectral unmixing component for quantitative fluorescence resonance energy transfer measurement, named as SPEES‐FRET method. The spectral fingerprints of both donor and acceptor were measured in HepG2 cells with low autofluorescence separately expressing donor and acceptor, and the spontaneous spectral fingerprint of HEK293 cells with strong autofluoresence was measured from blank cells. SPEES‐FRET was performed on improved spectrometer‐microscope system to measure the FRET efficiency (E) and concentration ratio (R _C) of acceptor to donor vales of FRET tandem plasmids in HEK293 cells, and obtained stable and consistent results with the expected values. Moreover, SPEES‐FRET always obtained stable results for the bright and dim cells coexpressing Cerulean and Venus or Cyan Fluorescent Protein (CFP)‐Bax and Yellow fluorescent protein (YFP)‐Bax, and the E values between CFP‐Bax and YFP‐Bax were 0.02 for healthy cells and 0.14 for the staurosporine (STS)‐treated apoptotic cells. Collectively, SPEES‐FRET has very strong robustness against cellular autofluorescence, and thus is applicable to quantitative evaluation on the protein‐protein interaction in living cells with strong autofluoresence.      

The discovery of anthranilic acid-based MMP inhibitors. Part 3: incorporation of basic amines.

Anthranilic acid derivatives bearing basic amines were prepared and evaluated in vitro and in vivo as inhibitors of MMP-1, MMP-9, MMP-13, and TACE. Piperazine 4u has been identified as a potent, selective, orally active inhibitor of MMP-9 and MMP-13.     

PLZF-RARα融合基因的生物学功能研究

构建了8个PLZF-RARα融合基因突变体.用“滞后”胶实验证实PLZF-RARα与PML-RARα一样,亦能以同二聚体的形式结合到维甲酸反应元件(RARE)上,且PLZF的POZ结构域介导PLZF-RARα同二聚体的形成和稳定.但两者与RARE的结合类型存在差异,在DR5G,PML-RARα的结合强度大于PLZF-RARα;而在DR5T,则是PLZF-RARα强于PML-RARα.进一步工作证实PLZF-RARα能与RXR形成异二聚体,并产生4种复合物.用免疫沉淀法发现PLZF-RARα亦能与PLZF形成异二聚体,而且也是通过POZ结构域介导PLZF-RARα和PLZF异二聚体的形成.同PML-RARα一样,PLZF-RARα对RARE的结合反应亦受维甲酸调控.     

Antiviral flavonoids from the root bark of Morus alba L

A prenylated flavonoid, moralbanone, along with seven known compounds kuwanon S, mulberroside C, cyclomorusin, eudraflavone B hydroperoxide, oxydihydromorusin, leachianone G and alpha-acetyl-amyrin were isolated from the root bark of Morus alba L. Leachianone G showed potent antiviral activity (IC(50) = 1.6 microg/ml), whereas mulberroside C showed weak activity (IC(50) = 75.4 microg/ml) against herpes simplex type 1 virus (HSV-1). Their structures were elucidated by spectroscopic methods.     

涡度相关观测的能量闭合状况及其对农田蒸散测定的影响

涡度相关法被认为是测定农田蒸散量的标准方法。然而,能量不闭合现象在涡度相关测量中普遍存在。分析能量不闭合对涡度相关观测的影响,对于提高涡度相关观测精度具有重要意义。以蒸渗仪法为参照,探讨涡度相关观测的能量闭合状况对农田蒸散测定的影响,在导致涡度相关观测能量不闭合的诸多因素中,寻找对蒸散测定有影响的因素。结果表明:涡度相关观测的白天能量平衡比率(EBR)呈秋冬高、春夏低的变化特征,麦季日均EBR范围在0.26—2.84之间,平均1.15;玉米季日均EBR范围在0.19—2.59之间,平均0.78。无论麦季或玉米季,涡度相关法测定的平均蒸散量(ETec)均明显低于蒸渗仪法观测值(ETL),但两者显著相关(P<0.01),并有相似的季节变化。平均蒸散比(ETec/ETL)麦季约为0.61,玉米季约为0.50。在冬小麦田和夏玉米田,ETec/ETL均与EBR显著相关(P<0.01)。麦田种植密度大,下垫面较均匀,蒸散比与EBR成正比(P<0.01),且不受叶面积指数(LAI)大小影响;反之,玉米田种植密度小,只有当LAI>1,下垫面变得较均匀后,蒸散比与EBR的关系才变得显著(P<0.01)。风速小时ETec/ETL与EBR显著相关,风速增加时二者相关性减弱。尤其在玉米田,当摩擦风速(u*)大于0.3 m/s时,ETec/ETL与EBR的相关性不再显著。风速小时,大气湍流微弱,湍流的涡旋较大。在有限的观测时段(0.5h)内,涡度相关仪的传感器难以捕捉足够的湍涡能量,所测湍流能量偏低,导致能量不闭合。以上结果为应用能量平衡比率校正农田蒸散提供了可能途径。     

PSMD: An extensive database for pan‐species microsatellite investigation and marker development

Microsatellites are widely distributed throughout nearly all genomes which have been extensively exploited as powerful genetic markers for diverse applications due to their high polymorphisms. Their length variations are involved in gene regulation and implicated in numerous genetic diseases even in cancers. Although much effort has been devoted in microsatellite database construction, the existing microsatellite databases still had some drawbacks, such as limited number of species, unfriendly export format, missing marker development, lack of compound microsatellites and absence of gene annotation, which seriously restricted researchers to perform downstream analysis. In order to overcome the above limitations, we developed PSMD (Pan‐Species Microsatellite Database, http://big.cdu.edu.cn/psmd/ ) as a web‐based database to facilitate researchers to easily identify microsatellites, exploit reliable molecular markers and compare microsatellite distribution pattern on genome‐wide scale. In current release, PSMD comprises 678,106,741 perfect microsatellites and 43,848,943 compound microsatellites from 18,408 organisms, which covered almost all species with available genomic data. In addition to interactive browse interface, PSMD also offers a flexible filter function for users to quickly gain desired microsatellites from large data sets. PSMD allows users to export GFF3 formatted file and CSV formatted statistical file for downstream analysis. We also implemented an online tool for analysing occurrence of microsatellites with user‐defined parameters. Furthermore, Primer3 was embedded to help users to design high‐quality primers with customizable settings. To our knowledge, PSMD is the most extensive resource which is likely to be adopted by scientists engaged in biological, medical, environmental and agricultural research.     

An isoform of GTPase regulator DOCK4 localizes to the stereocilia in the inner ear and binds to harmonin (USH1C)

The driving forces for the regulation of cell morphology are the Rho family GTPases that coordinate the assembly of the actin cytoskeleton. This dynamic feature is a result of tight coupling between the cytoskeleton and signal transduction and is facilitated by actin-binding proteins (ABPs). Mutations in the actin bundling and PDZ domain-containing protein harmonin are the causes of Usher syndrome type 1C (USH1C), a syndrome of congenital deafness and progressive blindness, as well as certain forms of non-syndromic deafness. Here, we have used the yeast two-hybrid assay to isolate molecular partners of harmonin and identified DOCK4, an unconventional guanine exchange factor for the Rho family of guanosine triphosphatases (Rho GEF GTPases), as a protein interacting with harmonin. Detailed molecular analysis revealed that a novel DOCK4 isoform (DOCK4-Ex49) is expressed in the brain, eye and inner ear tissues. We have further provided evidence that the DOCK4-Ex49 binds to nucleotide free Rac as effectively as DOCK2 and DOCK4 and it is a potent Rac activator. By immunostaining using a peptide antibody specific to DOCK4-Ex49, we showed its localization in the inner ear within the hair bundles along the stereocilia (SC). Together, our data indicate a possible Rac-DOCK4-ABP harmonin-activated signaling pathway in regulating actin cytoskeleton organization in stereocilia.     

Changes of soil organic and inorganic carbon in relation to grassland degradation in Northern Tibet

The effect of livestock grazing on grassland degradation and the resulting impact on soil carbon concentration is an important factor in carbon estimation. We addressed this issue using field observations and laboratory analysis of samples from Tibetan grassland. Based on the field measurements, we investigated the soil organic carbon (SOC) and soil inorganic carbon (SIC) under two contrasting degradation states: lightly or non-degraded grasslands (LDG) and heavily degraded grasslands (HDG). We assessed their relationships with environmental factors using data collected from 99 sites across Northern Tibet during 2011–2012. Data were analyzed using a linear mixed-effects model and one-way ANOVA. The results showed that: (1) SOC concentration decreased and SIC concentration increased following grassland degradation, especially at soil depths in the range of 0–10 cm (P < 0.05); (2) the major environmental factors affecting SOC and SIC were soil pH and plant biomass; (3) spatially, the SOC density increased with the mean annual temperature and mean annual precipitation, whereas SIC exhibited the opposite trend; (4) the SOC density increased at first and then decreased with increasing grazing intensity, with an opposite trend in SIC; and (5) soil carbon storage in this region was 0.14 Pg smaller in the HDG than in the LDG. This study suggests that grassland degradation can significantly affect the vertical distribution and storage of SOC and SIC. The carbon sequestration capacity of the top 100 cm of soil in Northern Tibet was estimated as 0.14 Pg.