长江源区同域分布兔狲、藏狐和赤狐的时空重叠度

兔狲(Otocolobus manul)、藏狐(Vulpes ferrilata)和赤狐(V. vulpes)是青藏高原三江源区域分布的重要小型食肉兽。本研究于2014年6月至2019年9月在青海省长江源区沱沱河和通天河沿岸选取208个位点布设红外相机, 通过所获取的时空分布数据比较了上述3种同域分布小型食肉兽的时空利用情况。通过空间重叠度系数的比较分析, 兔狲和藏狐、兔狲和赤狐以及藏狐和赤狐之间的空间重叠度系数分别为0.25、0.48和0.17, 这表明兔狲、藏狐和赤狐三者在空间利用上存在一定的差异。通过核密度估计方法分析, 兔狲和藏狐属典型的昼行性动物, 而赤狐以夜行性活动为主。兔狲、藏狐和赤狐每个物种在冷暖两季的日活动节律重叠指数分别为0.83、0.78和0.88。两两比较分析表明, 兔狲和藏狐二者的日活动节律重叠指数最高(0.84), 兔狲和赤狐在夜间活动时段存在一定重叠(0.63), 而藏狐和赤狐的时间生态位分化最明显, 重叠指数最低(0.48)。此外, 在暖季, 两两物种之间的日活动节律重叠指数均小于其冷季的重叠指数。综上所述, 长江源区兔狲、藏狐和赤狐3种小型食肉兽可通过空间和时间资源的利用差异来降低物种间的干扰和竞争, 从而达到同域物种共存的目的。     

Establishing a dual knock-out cell line by lentivirus based combined CRISPR/Cas9 and Loxp/Cre system

The clustered regulatory interspersed short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) system has been widely used for gene knock-out. Lentiviral vectors have been commonly used as a delivery method for this system, however, prolonged Cas9/sgRNA expression due to lentiviral integration can lead to accumulating off-target mutations. To solve this issue in engineering a gene knock-out cell line, this study established a novel system, which was composed of two lentiviral vectors. One lentiviral vector carried simultaneously sgRNAs and CRISPR/Cas9 expression cassettes targeting single or multiple gene(s); the other lentiviral vector carried Cre that could remove excess sgRNAs and Cas9 expression cassettes in the genome after gene targeting was achieved. To prove the principle, two candidate genes, extracellular matrix protein 1 (ECM1) and progranulin (PGRN), both highly expressed in MDA-MB-231 cells, were selected for testing the novel system. A dual knock-out of ECM1 and PGRN was successfully achieved in MDA-MB-231 cell line, with the sgRNAs and Cas9 expression cassettes being removed by Cre. This system should have great potential in applications for multiple genes knock-out in vitro.     

胸腺肽α1-Spl DnaX内含肽融合蛋白的切割动力学研究

目的:研究胸腺肽α1(Tα1)与Spl DnaX内含肽融合蛋白AS的体外切割动力学。方法:构建Tα1和SplDnaX内含肽的融合表达载体pET-AS,转化大肠杆菌BL21(DE3),经乳糖诱导获得可溶性表达的融合蛋白AS,用镍亲和层析纯化该蛋白;综合评价温度、β-巯基乙醇(β-ME)浓度和诱导切割时间对Spl DnaX内含肽介导融合蛋白AS自切割释放Tα1的影响。结果:在大肠杆菌中诱导表达了融合蛋白AS,经镍柱纯化获得该蛋白;随着温度升高和β-ME浓度增加,诱导切割时间延长,Spl DnaX内含肽介导的切割率逐渐增大;最终采用300 mmol/Lβ-ME切割24 h,融合蛋白的硫解切割率大于90%。结论:通过对Spl DnaX内含肽的诱导切割条件进行摸索,确定了最适宜的切割条件,为利用该方法制备Tα1和其他小分子多肽提供了技术基础。     

Red重组系统及在微生物基因敲除中的应用

在完成了对各种微生物基因组的测序以后,功能基因学的研究变得尤为重要。研究基因功能最直接的方法便是将待研究的基因失活。最初构建基因突变体是采用大肠杆菌的RecA系统,但是RecA重组系统操作复杂,重组效率低。最近建立了Red重组系统,该系统由3个蛋白组成：α蛋白(即λ核酸外切酶),β蛋白,Gam蛋白。应用Red系统进行基因敲除,可以直接利用线性打靶DNA,两侧同源臂长度在35~60 bp即可发生同源重组,且重组效率高。 Abstract:Since many DNA-sequencing projects of varied microorganisms have been completed,studies on their functional genomics become more important.Inactivation of an interesting gene is a direct method to characterize its function.Though the Esherichia coli RecA recombination system can be used to produce gene mutants,it needs a complex manipulation process.Furthermore,its efficiency is very low.Recently a Red recombination system was developed.This recombination system consists of three proteins:α protein（λ exonuclease）,β protein and Gam protein.In this system,the linear targeting DNA which contains a selectable marker flanked with a homologous region as short as only 35~60 bp can be directly targeted for gene knock-out with a higher efficiency.     

Configuration of PKCα-C2 Domain Bound to Mixed SOPC/SOPS Lipid Monolayers

X-ray reflectivity measurements are used to determine the configuration of the C2 domain of protein kinase Cα (PKCα-C2) bound to a lipid monolayer of a 7:3 mixture of 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine and 1-stearoyl-2-oleoyl-sn-glycero-3-phosphoserine supported on a buffered aqueous solution. The reflectivity is analyzed in terms of the known crystallographic structure of PKCα-C2 and a slab model representation of the lipid layer. The configuration of lipid-bound PKCα-C2 is described by two angles that define its orientation, θ = 35° ± 10° and φ =210° ± 30°, and a penetration depth (=7.5 ± 2 Å) into the lipid layer. In this structure, the β-sheets of PKCα-C2 are nearly perpendicular to the lipid layer and the domain penetrates into the headgroup region of the lipid layer, but not into the tailgroup region. This configuration of PKCα-C2 determined by our x-ray reflectivity is consistent with many previous findings, particularly mutational studies, and also provides what we believe is new molecular insight into the mechanism of PKCα enzyme activation. Our analysis method, which allows us to test all possible protein orientations, shows that our data cannot be explained by a protein that is orientated parallel to the membrane, as suggested by earlier work.     

Life history and population dynamics of the Japanese Yam,Dioscorea japonica Thunb.

The adaptive significance of the emergence mode ofDioscorea japonica was studied with respect to initial plant size (seed, bulbil and tuber) and light intensity, using mathematical simulation based on Yokoi's (1976) model. Under 1.5% full sunlight conditions, plants emerging with only one leaf did not develop a shoot system throughout the growing period (Hori and Oshima, 1986). Simulation indicated that, for this species of plant under poor productive conditions, the optimal time for switch-over from the vegetative to reproductive growth phase to maximize the tuber weight at the end of the growing period, occurred immediately following the start of autotrophic growth. By means of shoot growth patterns, small and large size plants acquired the ability of shade tolerance and shade avoidance, respectively. Further, the life history ofD. japonica could be expressed as a flow chart based on plant size and light intensity data.     

Integrative structure and function of the yeast exocyst complex

Exocyst is an evolutionarily conserved hetero‐octameric tethering complex that plays a variety of roles in membrane trafficking, including exocytosis, endocytosis, autophagy, cell polarization, cytokinesis, pathogen invasion, and metastasis. Exocyst serves as a platform for interactions between the Rab, Rho, and Ral small GTPases, SNARE proteins, and Sec1/Munc18 regulators that coordinate spatial and temporal fidelity of membrane fusion. However, its mechanism is poorly described at the molecular level. Here, we determine the molecular architecture of the yeast exocyst complex by an integrative approach, based on a 3D density map from negative‐stain electron microscopy (EM) at ~16 Å resolution, 434 disuccinimidyl suberate and 1‐ethyl‐3‐(3‐dimethylaminopropyl)carbodiimide hydrochloride cross‐links from chemical‐crosslinking mass spectrometry, and partial atomic models of the eight subunits. The integrative structure is validated by a previously determined cryo‐EM structure, cross‐links, and distances from in vivo fluorescence microscopy. Our subunit configuration is consistent with the cryo‐EM structure, except for Sec5. While not observed in the cryo‐EM map, the integrative model localizes the N‐terminal half of Sec3 near the Sec6 subunit. Limited proteolysis experiments suggest that the conformation of Exo70 is dynamic, which may have functional implications for SNARE and membrane interactions. This study illustrates how integrative modeling based on varied low‐resolution structural data can inform biologically relevant hypotheses, even in the absence of high‐resolution data.     

Multivariate data analysis of growth medium trends affecting antibody glycosylation

Use of multivariate data analysis for the manufacturing of biologics has been increasing due to more widespread use of data-generating process analytical technologies (PAT) promoted by the US FDA. To generate a large dataset on which to apply these principles, we used an in-house model CHO DG44 cell line cultured in automated micro bioreactors alongside PAT with four commercial growth media focusing on antibody quality through N-glycosylation profiles. Using univariate analyses, we determined that different media resulted in diverse amounts of terminal galactosylation, high mannose glycoforms, and aglycosylation. Due to the amount of in-process data generated by PAT instrumentation, multivariate data analysis was necessary to ascertain which variables best modeled our glycan profile findings. Our principal component analysis revealed components that represent the development of glycoforms into terminally galacotosylated forms (G1F and G2F), and another that encompasses maturation out of high mannose glycoforms. The partial least squares model additionally incorporated metabolic values to link these processes to glycan outcomes, especially involving the consumption of glutamine. Overall, these approaches indicated a tradeoff between cellular productivity and product quality in terms of the glycosylation. This work illustrates the use of multivariate analytical approaches that can be applied to complex bioprocessing problems for identifying potential solutions.