CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems

CRISPR-Cas systems are a diverse family of RNA-protein complexes in bacteria that target foreign DNA sequences for cleavage. Derivatives of these complexes have been engineered to cleave specific target sequences depending on the sequence of a CRISPR-derived guide RNA (gRNA) and the source of the Cas9 protein. Important considerations for the design of gRNAs are to maximize aimed activity at the desired target site while minimizing off-target cleavage. Because of the rapid advances in the understanding of existing CRISPR-Cas9-derived RNA-guided nucleases and the development of novel RNA-guided nuclease systems, it is critical to have computational tools that can accommodate a wide range of different parameters for the design of target-specific RNA-guided nuclease systems. We have developed CRISPRseek, a highly flexible, open source software package to identify gRNAs that target a given input sequence while minimizing off-target cleavage at other sites within any selected genome. CRISPRseek will identify potential gRNAs that target a sequence of interest for CRISPR-Cas9 systems from different bacterial species and generate a cleavage score for potential off-target sequences utilizing published or user-supplied weight matrices with position-specific mismatch penalty scores. Identified gRNAs may be further filtered to only include those that occur in paired orientations for increased specificity and/or those that overlap restriction enzyme sites. For applications where gRNAs are desired to discriminate between two related sequences, CRISPRseek can rank gRNAs based on the difference between predicted cleavage scores in each input sequence. CRISPRseek is implemented as a Bioconductor package within the R statistical programming environment, allowing it to be incorporated into computational pipelines to automate the design of gRNAs for target sequences identified in a wide variety of genome-wide analyses. CRISPRseek is available under the GNU General Public Licence v3.0 at http://www.bioconductor.org.     

A cytoplasmic RNA vector derived from nontransmissible Sendai virus with efficient gene transfer and expression

We have recovered a virion from defective cDNA of Sendai virus (SeV) that is capable of self-replication but incapable of transmissible-virion production. This virion delivers and expresses foreign genes in infected cells, and this is the first report of a gene expression vector derived from a defective viral genome of the Paramyxoviridae. First, functional ribonucleoprotein complexes (RNPs) were recovered from SeV cloned cDNA defective in the F (envelope fusion protein) gene, in the presence of plasmids expressing nucleocapsid protein and viral RNA polymerase. Then the RNPs were transfected to the cells inducibly expressing F protein. Virion-like particles thus obtained had a titer of 0.5 x 10(8) to 1. 0 x 10(8) cell infectious units/ml and contained F-defective RNA genome. This defective vector amplified specifically in an F-expressing packaging cell line in a trypsin-dependent manner but did not spread to F-nonexpressing cells. This vector infected and expressed an enhanced green fluorescent protein reporter gene in various types of animal and human cells, including nondividing cells, with high efficiency. These results suggest that this vector has great potential for use in human gene therapy and vaccine delivery systems.     

Effects of semen plasma from different fractions of individual ejaculates on IVF in pigs

We applied IVM/IVF techniques to investigate effects of preincubation of sperm with different fractions of semen plasma harvested from fresh ejaculates on in vitro penetration and fertilization of in vitro matured oocytes. Three fractions of semen plasma were separated from the complete ejaculate of three Landrace boars and used to coincubate sperm obtained from the first sperm-rich fraction of the same ejaculates. After 14 to 16 h coincubation at room temperature, sperm were preincubated in capacitation medium and then inseminated into fertilization medium containing porcine oocytes matured in vitro. The semen plasma used for coincubation affected penetration rate (P < 0.001); Sperm coincubated with Fraction 1 semen plasma had a higher penetration rate compared with sperm coincubated with Fraction 2 (P < 0.05), but not with Fraction 3. Boar affected male pronucleus formation rates after insemination (P < 0.05), but no difference among boars was found in monospermy rate, average number of sperm penetrating into each fertilized oocyte, or the average number of sperm attached. No boar by fraction interaction was found for any parameters studied.     

Nonlinear responses of productivity and diversity of alpine meadow communities to degradation北大核心CSCD

Aims The alpine meadow degradation could have profound effects on the grassland productivity. The aim of our study is to clarify the dynamic response of community productivity and species diversity in the process of alpine meadow degradation. Methods In the Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Northern Tibetan Grassland Ecosystem Research Station (Nagqu station), we conducted stages experiments with multiple degradation levels: control, mild degraded meadow, moderate degraded meadow, severe degraded meadow and serious sandy meadow. Important findings The response of aboveground biomass to alpine meadow degradation showed a linear or nonlinear increased response patterns, but the belowground biomass and total biomass decreased nonlinearly. As observed in measurement of aboveground biomass, Margalef index, Simpson index, Shannon-Wiener index and Pielou evenness index also exhibit a nonlinear increased response to degradation. The results of structural equation models showed that belowground biomass has a positive relationship with soil carbon content (p < 0.05) and volume water content (p < 0.1). However, soil nutrient and soil physical properties had no significant impact on aboveground biomass (p < 0.1). Compared with soil physical properties, soil nutrition is an important factor influencing the diversity index. In our study, the nonlinear responses of productivity and diversity of alpine meadow were described by using the multiple levels of degradation in space. The results suggested that aboveground productivity cannot interpret the degree of degradation of alpine meadow, and by contrast, alpine meadow degradation should be measured by the change of plant functional groups, such as edible grasses and poisonous forbs. © 2018 Editorial Office of Chinese Journal of Plant Ecology. All rights reserved.     

Coexpression of EGFR and CXCR4 Predicts Poor Prognosis in Resected Pancreatic Ductal Adenocarcinoma

BackgroundEpidermal growth factor receptor (EGFR) is highly expressed in pancreatic ductal adenocarcinoma (PDAC) and is involved in tumorigenesis and development. However, EGFR expression alone has limited clinical and prognostic significance. Recently, the cross-talk between EGFR and G-protein-coupled chemokine receptor CXCR4 has become increasingly recognized.MethodsIn the present study, immunohistochemical staining of EGFR and CXCR4 was performed on paraffin-embedded specimens from 131 patients with surgically resected PDAC. Subsequently, the associations between EGFR expression, CXCR4 expression, EGFR/CXCR4 coexpression and clinicopathologic factors were assessed, and survival analyses were performed.ResultsIn total, 64 (48.9%) patients expressed EGFR, 68 (51.9%) expressed CXCR4, and 33 (25.2%) coexpressed EGFR and CXCR4. No significant association between EGFR and CXCR4 expression was observed (P = 0.938). EGFR expression significantly correlated with tumor differentiation (P = 0.031), whereas CXCR4 expression significantly correlated with lymph node metastasis (P = 0.001). EGFR/CXCR4 coexpression was significantly associated with lymph node metastasis (P = 0.026), TNM stage (P = 0.048), and poor tumor differentiation (P = 0.004). By univariate survival analysis, both CXCR4 expression and EGFR/CXCR4 coexpression were significant prognostic factors for poor disease-free survival (DFS) and overall survival (OS). Moreover, EGFR/CXCR4 coexpression significantly increased the hazard ratio for both recurrence and death compared with EGFR or CXCR4 protein expression alone. Multivariate survival analysis demonstrated that EGFR/CXCR4 coexpression was an independent prognostic factor for DFS (HR = 2.33, P<0.001) and OS (HR = 2.48, P = 0.001).ConclusionsIn conclusion, our data indicate that although EGFR expression alone has limited clinical and prognostic significance, EGFR/CXCR4 coexpression identified a subset of PDAC patients with more aggressive tumor characteristics and a significantly worse prognosis. Our results suggest a potentially important "cross-talk" between CXCR4 and EGFR intracellular pathways and indicate that the simultaneous inhibition of these pathways might be an attractive therapeutic strategy for PDAC.     

Emotional Noun Processing: An ERP Study with Rapid Serial Visual Presentation

Reading is an important part of our daily life, and rapid responses to emotional words have received a great deal of research interest. Our study employed rapid serial visual presentation to detect the time course of emotional noun processing using event-related potentials. We performed a dual-task experiment, where subjects were required to judge whether a given number was odd or even, and the category into which each emotional noun fit. In terms of P1, we found that there was no negativity bias for emotional nouns. However, emotional nouns elicited larger amplitudes in the N170 component in the left hemisphere than did neutral nouns. This finding indicated that in later processing stages, emotional words can be discriminated from neutral words. Furthermore, positive, negative, and neutral words were different from each other in the late positive complex, indicating that in the third stage, even different emotions can be discerned. Thus, our results indicate that in a three-stage model the latter two stages are more stable and universal.     

Epigenetic regulation of autophagy by the methyltransferase EZH2 through an MTOR-dependent pathway

Macroautophagy is an evolutionarily conserved cellular process involved in the clearance of proteins and organelles. Although the autophagy regulation machinery has been widely studied, the key epigenetic control of autophagy process still remains unknown. Here we report that the methyltransferase EZH2 (enhancer of zeste 2 polycomb repressive complex 2 subunit) epigenetically represses several negative regulators of the MTOR (mechanistic target of rapamycin [serine/threonine kinase]) pathway, such as TSC2, RHOA, DEPTOR, FKBP11, RGS16 and GPI. EZH2 was recruited to these genes promoters via MTA2 (metastasis associated 1 family, member 2), a component of the nucleosome remodeling and histone deacetylase (NuRD) complex. MTA2 was identified as a new chromatin binding protein whose association with chromatin facilitated the subsequent recruitment of EZH2 to silenced targeted genes, especially TSC2. Downregulation of TSC2 (tuberous sclerosis 2) by EZH2 elicited MTOR activation, which in turn modulated subsequent MTOR pathway-related events, including inhibition of autophagy. In human colorectal carcinoma (CRC) tissues, the expression of MTA2 and EZH2 correlated negatively with expression of TSC2, which reveals a novel link among epigenetic regulation, the MTOR pathway, autophagy induction, and tumorigenesis.     

Microbulbifer hainanensis sp. nov., a moderately halopilic bacterium isolated from mangrove sediment

Antonie van Leeuwenhoek - A new bacterium was successfully isolated from a mangrove sediment sample in Haikou City, Hainan Province, China. The organism is a Gram-negative, rod-shaped, non-motile...     

蓝细菌病毒A-4L在鱼腥藻(Anabaena variabilis)藻苔中形成同心圆噬斑的成因

摘要:【目的】分析蓝细菌病毒A-4L在鱼腥藻(Anabaena sp.) PCC 7120藻苔中形成同心圆噬斑的原因,阐明A-4L的一个重要生物学特征,为分离、鉴定和筛选新的水华蓝藻病毒提供借鉴。【方法】用初始滴度为2.8×1010PFU/mL的A-4L悬液感染鱼腥藻,在不同时间点收集裂解液绘制一步生长曲线,获得A-4L对鱼腥藻的潜伏期和释放量。将适量A-4L悬液感染不同培养时间的藻苔,逐日观察和记录藻苔病变情况。培养藻苔并接种适量A-4L悬液,分别置于完全持续光照(Light:Dark=24 h:0 h,L:D=24 h:0 h)条件;完全周期光照(L:D=14 h:10h)条件;或前3 d周期光照转后3 d持续光照的条件下,比较不同光照条件对同心圆噬斑形成的影响。然后挑取单个噬斑进行扩大培养,纯化后,负染电镜观察A-4L的超微形态。【结果】A-4L的潜伏期为0.5－2h,释放量约为247 IU/cell (Infectious Units)。在周期光照条件下,藻苔接种A-4L 3－4 d后,出现同心圆噬斑,且同心圆数量与攻毒后的天数(n)有相关性,为“n－1”;同心圆间距约为3 mm。与周期光照条件相比,在持续光照条件下未形成同心圆噬斑。而在周期光照条件转持续光照条件下,由先周期光照时所形成的同心圆在转持续光照后逐渐消失,证实同心圆噬斑的形成依赖于周期光照。负染电镜观察显示A-4L具有一个近似球形的头部,直径约为50 nm以及长度约为10 nm的尾部,形态与短尾蓝细菌病毒相似。【结论】A-4L是一株能形成同心圆噬斑的蓝细菌病毒,并揭示其同心圆噬斑形成的关键条件是周期光照。     

Photosynthetic refixing of CO2 is responsible for the apparent disparity between mitochondrial respiration in the light and in the dark

The net photosynthetic rate (P _N), the sample room CO₂ concentration (CO₂S) and the intercellular CO₂ concentration (C _i) in response to PAR, of C₃ (wheat and bean) and C₄ (maize and three-colored amaranth) plants were measured. Results showed that photorespiration (R _p) of wheat and bean could not occur at 2 % O₂. At 2 % O₂ and 0 μmol mol^?1 CO₂, P _N can be used to estimate the rate of mitochondrial respiration in the light (R _d). The R _d decreased with increasing PAR, and ranged between 3.20 and 2.09 μmol CO₂ m^?2 s^?1 in wheat. The trend was similar for bean (between 2.95 and 1.70 μmol CO₂ m^?2 s^?1), maize (between 2.27 and 0.62 μmol CO₂ m^?2 s^?1) and three-colored amaranth (between 1.37 and 0.49 μmol CO₂ m^?2 s^?1). The widely observed phenomenon of R _d being lower than R _n can be attributed to refixation, rather than light inhibition. For all plants tested, CO₂ recovery rates increased with increasing light intensity from 32 to 55 % (wheat), 29 to 59 % (bean), 54 to 87 % (maize) and 72 to 90 % (three-colored amaranth) at 50 and 2,000 μmol m^?2 s^?1, respectively.