Genome shuffling: Progress and applications for phenotype improvement

Although rational method and global technique have been successfully applied in strain improvement respectively, the demand for engineering complex phenotypes required combinatorial approach. The technology of genome shuffling has been presented as a novel whole genome engineering approach for the rapid improvement of cellular phenotypes. This approach using recursive protoplast fusion with multi-parental strains offers the advantage of recombination throughout the entire genome without the necessity for genome sequence data or network information. Genome shuffling has been demonstrated as an effective method, which is not only for producing improved strain but also for providing information on complex phenotype. In this review we attempt to present the advantage of genome shuffling, introduce the procedure of this technology, summarize the applications of this approach for phenotype improvement and then give perspective on the development of this method in the future.     

ROC曲线形状在生态位模型评价中的重要性——以美国白蛾为例

【目的】生态位模型在生物地理学、入侵生物学和保护生物学中具有广泛的应用,被越来越多地用于预测物种潜在分布和现实分布的研究中。本文以美国白蛾为例介绍pROC方案在生态位模型评价中的应用及其注意事项,以期对物种潜在分布预测进行合理的评价,促进生态位模型在我国的合理运用和发展。【方法】介绍ROC曲线和AUC值基本原理,总结其在生态位模型评价中的应用,从物种存在分布点和不存在分布点的可信度出发,分析AUC值用于模型评价的优点和不足,最后介绍局部受试者工作特征曲线的线下面积方案(pROC方案)来弥补传统AUC值的不足。【结果】AUC值虽独立于阈值,但因其综合灵敏度和特异度,而屏蔽这2个指标各自的特征,不能分别评估预测结果的灵敏度和特异度,同时对遗漏率和记账错率不能进行权衡,会误导使用者对模型的评价。与AUC值相比,ROC曲线的形状更具有价值,蕴含丰富的模型评价信息。【结论】模型评价需要将灵敏度和特异度区别对待,ROC曲线形状比AUC值在生态位模型评价中更为重要,pROC方案相对于传统AUC值具有优势,但容易对过度模拟做出不当判断。模型评价与作者研究目的密切相关:当以预测物种潜在分布为目的时(如入侵物种潜在分布、气候变化对物种分布的影响和谱系生物地理学),模型评价应当给予灵敏度(或者遗漏率)更多的权重;当以预测物种现实分布为目的时(如保护区界定和濒危物种引入),模型评价应当给予灵敏度和特异度同等的权重。     

空气和土壤湿度对美洲斑潜蝇发育与存活的影响

美洲斑潜蝇 L iriomyza sativae在相对含水量 0 %～ 10 0 % (W/W)的土壤中均可化蛹 ,但以含水量为 40 %的土壤化蛹量最高 ,占总蛹数的 3 0 .0 %。以相对含水量为 10 0 %的土壤化蛹量最低 ,占总蛹数的 4.2 %。不同土壤含水量对该蝇的羽化具有明显的影响 ,在 3 0℃时 ,以相对含水量为 60 %的土壤最适于蛹的发育 ,其蛹期最短 (7.50 d) ,羽化率最高 (93 .3 % )。反之 ,淫湿 (相对含水量为 10 0 % )和干涸 (相对含水量为 0 % )的土壤均不利于蛹的发育 ,其蛹期延长 (依次为 8.17d和 8.0 d) ,羽化率明显降低(依次为 13 .3 %和 10 .0 % )。在空气相对湿度 (RH )为 0 %、52 %、76%和 10 0 % ,室温为 3 0℃的处理中 ,蛹的失水率随其日龄的增高而增加。在蛹羽化的前 1d,高湿 (RH10 0 % )处理的失水率为 10 .1% ,低湿处理 (RH0 % )为 41.6% ,对照 (RH76% )为 18.2 %。在各 RH 下 ,蛹 1日龄后的逐日累计失水率都与它们的日龄呈明显的线性关系。在 3 0℃ ,蛹在 8h内测定的表皮渗透力最大为2 .59μg/(cm2 · h· mm Hg)     

Error thresholds for quasispecies on single peak Gaussian-distributed fitness landscapes

Based on the Eigen and Crow-Kimura models with a single peak fitness landscape, we propose that the fitness values of all molecules be Gaussian distributed random variables to incorporate the fluctuation effects of the fitness landscapes (noise of environments). And we investigate the quasispecies distribution and error threshold using ensemble average method within this theoretical framework. Numerical results show that a small fluctuation of the fitness landscape causes only a slight change in the concentration distribution and error threshold, which implies that the error threshold is stable against small perturbations. However, for a sizable fluctuation, quite different from the previous deterministic models, our statistical results reveal that the transition from quasi-species to error catastrophe is no longer so sharp, indicating the error threshold is located within a certain range and shifts toward a larger value.     

混合盐碱胁迫对地被菊寒露红生长的影响

该研究以地被菊寒露红(Chrysanthemum morifolium ‘Hanluhong’)为材料,一方面研究混合盐碱胁迫对其生长的影响,另一方面通过模拟青铜峡盐碱胁迫程度,探讨其在青铜峡地区的适生性。设置3个pH梯度(7.0、8.0、9.0),在每个pH梯度下用NaCl、Na_2CO_3、NaHCO_3、Na_2SO_4配置不同浓度(0、0.2%、0.4%、0.6%、0.8%、1.0%)的混合液对地被菊植株进行胁迫处理,观察并测定不同胁迫条件下植株株高、根长、光合特性及叶绿素荧光参数的变化。结果表明:(1)长时间生长在高盐碱环境会使地被菊寒露红生长缓慢,光合作用参数和叶绿素荧光参数下降。(2)青铜峡实验模拟组(pH=8.0,盐浓度为0.4%)的植株株高、根长的伸长速度随胁迫时间的延长均呈先降低后升高的趋势;同时植株的光合作用参数、叶绿素荧光参数有降低趋势,但荧光参数下降变化未达到显著水平。综合分析可得,高盐、高碱环境均不利于地被菊寒露红植株的生长发育。在青铜峡地区的盐碱胁迫强度下,地被菊寒露红具有一定的抗盐碱性,基本能够正常生长,可用于当地植被及生态环境修复和园林造景。     

Left Ventricular Function during Acute High-Altitude Exposure in a Large Group of Healthy Young Chinese Men

Objective

The purpose of this study was to observe left ventricular function during acute high-altitude exposure in a large group of healthy young males.

Methods

A prospective trial was conducted in Szechwan and Tibet from June to August, 2012. By Doppler echocardiography, left ventricular function was examined in 139 healthy young Chinese men at sea level; within 24 hours after arrival in Lhasa, Tibet, at 3700 m; and on day 7 following an ascent to Yangbajing at 4400 m after 7 days of acclimatization at 3700 m. The resting oxygen saturation (SaO2), heart rate (HR) and blood pressure (BP) were also measured at the above mentioned three time points.

Results

Within 24 hours of arrival at 3700 m, the HR, ejection fraction (EF), fractional shortening (FS), stroke volume (SV), cardiac output (CO), and left ventricular (LV) Tei index were significantly increased, but the LV end-systolic dimension (ESD), end-systolic volume (ESV), SaO2, E/A ratio, and ejection time (ET) were significantly decreased compared to the baseline levels in all subjects. On day 7 at 4400 m, the SV and CO were significantly decreased; the EF and FS Tei were not decreased compared with the values at 3700 m; the HR was further elevated; and the SaO2, ESV, ESD, and ET were further reduced. Additionally, the E/A ratio was significantly increased on day 7 but was still lower than it was at low altitude.

Conclusion

Upon acute high-altitude exposure, left ventricular systolic function was elevated with increased stroke volume, but diastolic function was decreased in healthy young males. With higher altitude exposure and prolonged acclimatization, the left ventricular systolic function was preserved with reduced stroke volume and improved diastolic function.     

Noise Induces Oscillation and Synchronization of the Circadian Neurons

The principle clock of mammals, named suprachiasmatic nucleus (SCN), coordinates the circadian rhythms of behavioral and physiological activity to the external 24 h light-dark cycle. In the absence of the daily cycle, the SCN acts as an endogenous clock that regulates the ~24h rhythm of activity. Experimental and theoretical studies usually take the light-dark cycle as a main external influence, and often ignore light pollution as an external influence. However, in modern society, the light pollution such as induced by electrical lighting influences the circadian clock. In the present study, we examined the effect of external noise (light pollution) on the collective behavior of coupled circadian oscillators under constant darkness using a Goodwin model. We found that the external noise plays distinct roles in the network behavior of neurons for weak or strong coupling between the neurons. In the case of strong coupling, the noise reduces the synchronization and the period of the SCN network. Interestingly, in the case of weak coupling, the noise induces a circadian rhythm in the SCN network which is absent in noise-free condition. In addition, the noise increases the synchronization and decreases the period of the SCN network. Our findings may shed new light on the impact of the external noise on the collective behavior of SCN neurons.     

Pur alpha binds to rCGG repeats and modulates repeat-mediated neurodegeneration in a Drosophila model of fragile X tremor/ataxia syndrome

Fragile X-associated tremor/ataxia syndrome (FXTAS) is a recently recognized neurodegenerative disorder in fragile X premutation carriers with FMR1 alleles containing 55-200 CGG repeats. Previously, we developed a Drosophila model of FXTAS and demonstrated that transcribed premutation repeats alone are sufficient to cause neurodegeneration, suggesting that rCGG-repeat-binding proteins (RBPs) may be sequestered from their normal function by rCGG binding. Here, we identify Pur alpha and hnRNP A2/B1 as RBPs. We show that Pur alpha and rCGG repeats interact in a sequence-specific fashion that is conserved between mammals and Drosophila. Overexpression of Pur alpha in Drosophila could suppress rCGG-mediated neurodegeneration in a dose-dependent manner. Furthermore, Pur alpha is also present in the inclusions of FXTAS patient brains. These findings support the disease mechanism of FXTAS of rCGG repeat sequestration of specific RBPs, leading to neuronal cell death, and implicate that Pur alpha plays an important role in the pathogenesis of FXTAS.     

CYLD deficiency promotes pancreatic cancer development by causing mitotic defects

Successful treatment of pancreatic cancer, which has the highest mortality rate among all types of malignancies, has challenged oncologists for decades, and early detection would undoubtedly increase favorable patient outcomes. The identification of proteins involved in pancreatic cancer progression could lead to biomarkers for early detection of this disease. This study identifies one potential candidate, cylindromatosis (CYLD), a deubiquitinase and microtubule-binding protein that plays a suppressive role in pancreatic cancer development. In pancreatic cancer samples, downregulation of CYLD expression resulted from a loss in the copy number of the CYLD gene; additionally, reduced expression of CYLD negatively correlated with the clinicopathological parameters. Further study demonstrated that CYLD deficiency promoted colony formation in vitro and pancreatic cancer growth in vivo. Mechanistic studies revealed that CYLD is essential for spindle orientation and properly oriented cell division; CYLD deficiency resulted in a substantial increase in chromosome missegregation. Taken together, these data indicate a critical role for CYLD in suppressing pancreatic tumorigenesis, implicating its potential as a biomarker for early detection of pancreatic cancer and a prognostic indicator of patient outcomes.