Patterns of Adaptive and Neutral Diversity Identify the Xiaoxiangling Mountains as a Refuge for the Giant Panda

Genetic variation plays a significant role in maintaining the evolutionary potential of a species. Comparing the patterns of adaptive and neutral diversity in extant populations is useful for understanding the local adaptations of a species. In this study, we determined the fine-scale genetic structure of 6 extant populations of the giant panda (Ailuropoda melanoleuca) using mtDNA and DNA fingerprints, and then overlaid adaptive variations in 6 functional Aime-MHC class II genes (DRA, DRB3, DQA1, DQA2, DQB1, and DQB2) on this framework. We found that: (1) analysis of the mtDNA and DNA fingerprint-based networks of the 6 populations identified the independent evolutionary histories of the 2 panda subspecies; (2) the basal (ancestral) branches of the fingerprint-based Sichuan-derived network all originated from the smallest Xiaoxiangling (XXL) population, suggesting the status of a glacial refuge in XXL; (3) the MHC variations among the tested populations showed that the XXL population exhibited extraordinary high levels of MHC diversity in allelic richness, which is consistent with the diversity characteristics of a glacial refuge; (4) the phylogenetic tree showed that the basal clades of giant panda DQB sequences were all occupied by XXL-specific sequences, providing evidence for the ancestor-resembling traits of XXL. Finally, we found that the giant panda had many more DQ alleles than DR alleles (33∶13), contrary to other mammals, and that the XXL refuge showed special characteristics in the DQB loci, with 7 DQB members of 9 XXL-unique alleles. Thus, this study identified XXL as a glacial refuge, specifically harboring the most number of primitive DQB alleles.     

Development of a novel recombinant strain Zygosacharomyces rouxii JL2011 for 1,3-propanediol production from glucose

1,3-propanediol (1,3-PDO) is one of the most important industrial chemicals due to its highly desired properties and its wide applications as a key component of the emerging polymer industry. Biotechnology route has been one of the most interesting methods for 1,3-PDO production, whereas, the dha genes were essential to 1,3-PDO biosynthesis. In this study, we cloned and placed the dha cassettes under the control of a glyceraldehyde 3-phosphate dehydrogenase gene promoter pGAP and homologous ZrFPS1 gene promoter pZrfps1; these two promoters were further integrated into the chromosome of Z. rouxii JL2011 to generate recombinant strain JL2011-GZ and JL2011-ZZ, respectively. The results showed that the two strains could produce 1,3-PDO from glucose with a final yield of 6.9 and 10.3 g/l, respectively. The engineered strain JL2011-ZZ showed a 2.3- and 1.5-fold increase in the specific activities and final concentration of 1,3-PDO, respectively, with respect to JL2011-GZ. Batch fermentation with aerobic/micro-aerobic combined strategy of JL2011-ZZ resulted a titer of 17.1 g/l and a yield from glucose of 8.6 %. These results demonstrated that JL2011-ZZ would be a potential strain for 1,3-PDO production from glucose.     

Coaxial Microincision Cataract Surgery versus Standard Coaxial Small-Incision Cataract Surgery: A Meta-Analysis of Randomized Controlled Trials

Background

We conducted this meta-analysis to compare the outcomes of coaxial microincision cataract surgery (C-MICS) and standard coaxial small incision cataract surgery (C-SICS).

Methods

The outcomes of randomized controlled trials (RCTs) reporting C-MICS and C-SICS were collected from PubMed, Web of Science, and The Cochrane Library in May 2015. The final meta-analysis was conducted on the following intraoperative and postoperative outcomes: ultrasound time (UST), effective phacoemulsification time (EPT), balanced salt solution use (BSS use), cumulative dissipated energy (CDE), mean surgery time, endothelial cell loss percentage (ECL%), best corrected visual acuity (BCVA), increased central corneal thickness (CCT), laser flare photometry values and surgically induced astigmatism (SIA).

Results

A total of 15 RCTs, involving 1136 eyes, were included in the final meta-analysis. No significant between-group differences were detected in EPT, BSS use, CDE, BCVA, laser flare photometry values or increased CCT. However, the C-MICS group showed less SIA (at postoperative day 7: p<0.01; at postoperative day 30 or more: p<0.01) and greater ECL% (at postoperative day 60 or more: p<0.01), whereas the C-SICS group required a shorter UST (p<0.01).

Conclusions

The present meta-analysis suggested that the C-MICS technique was more advantageous than C-SICS in terms of SIA, but C-MICS required a longer UST and induced a higher ECL%. Further studies should be done to confirm our results.     

Formation,regeneration, and transformation of protoplasts of Streptomyces diastatochromogenes 1628

Toyocamycin exhibits effective biological activities for use against plant pathogenic fungi thanks to its structural similarity to nucleoside. It has been recognized as a promising agricultural antibiotic utilized in controlling the occurrence of plant diseases. In our previous study, a strain that was isolated was identified and designated as Streptomyces diastatochromogenes whose major secondary metabolite was toyocamycin, but the production was largely limited. Protoplast transformation is a useful technique in the improvement of streptomycete. In this study, we optimized some key factors necessary for protoplast formation, regeneration, and transformation of S. diastatochromogenes. When mycelium was cultivated in CP medium with 1 % glycine, harvested at 48 h old, and then treated with 3 mg lysozyme/mL in P buffer for 1 h, the greatest regeneration frequency (42.5 %) of protoplasts was obtained. By using 1?×?10⁹/mL protoplasts with polyethylene glycol 1000 at a concentration of 30 % (w/v), the best performance of protoplast transformation efficiency was 4.8?×?10³/μg DNA transformants.     

A comparative study of one- and two-photon absorption properties of pyrene and perylene diimide derivatives

Two important classes of organic molecules, perylene diimide (PDI) and pyrene derivatives have been found to possess relatively excellent photophysical and photochemical properties and especially high two-photon absorption cross sections (δ ^T _max). Herein, one-photon absorption (OPA) and two-photon absorption (TPA) properties of some novel PDI and pyrene derivatives were comparatively investigated by the density functional theory (DFT) and Zerner’s intermediate neglect of differential overlap (ZINDO) methods. The calculated results indicate that with respect to PDI derivatives, the maximum TPA cross-sections for pyrene compounds increase obviously, the maximum peaks of OPA and TPA spectra are blue-shifted, the ΔE _H-L (energy gaps between the highest occupied orbital and the lowest unoccupied orbital) increase. The different π-conjugated bridges (fluorene and pyrene) and terminal groups have slight effect on the OPA properties. Nevertheless, the molecules bearing 1,6-disubstituted pyrene as the π-conjugated bridge display the largest δ ^T _max in both series of compounds 3 and 4. Moreover, the δ ^T _max values of molecules with benzothiazole-substituted terminal groups are larger than those of the molecules with diphenylamine, which is attributed to benzothiazole groups stabilizing the planarity of the branch parts, extending the conjugated length and increasing the π-electron delocalized extent. Furthermore, the molecular size has marked effect on OPA and TPA properties. It is worthy to mention that cruciform 8 displays the largest δ ^T _max among all the studied molecules in the range of 600–1100 nm. This research could provide a better understanding for the origin of the linear and nonlinear optical properties, and it would be helpful to gain more information about designing two-photon absorption materials with large δ ^T _max.     

Auto-adaptive Alpha Allocation: A Strategy to Mitigate Risk on Study Assumptions

In some clinical development programs, there are potential biomarkers with promising but uncertain predictive effect, while the probability of success in the overall population cannot be readily dismissed. It is risky to focus only on the overall population, or just the biomarker subpopulation. In 2009, Chen and Beckman proposed a Bayesian decision framework to optimize the type I error rate (alpha) allocation in a Phase III clinical study with possible predictive subset effect. The utilization of internal data in this framework is of particular interest because it provides an opportunity to mitigate the potential risk of misspecified study assumptions using an auto-adaptive strategy. In this paper, we examine this auto-adaptive strategy in detail through extensive numerical case studies and provide guidance on the appropriate use of partial current trial (internal) data in this data-driven optimization framework. We show that internal data can be used to inform the alpha allocation to hypothesis testing in the overall population and the subgroup. The resulting adaptive testing strategy is robust with respect to the uncertainty in the predictive subgroup effect and biomarker prevalence.     

双低菜粕高水平替代饲料鱼粉对大黄鱼潜在风险的评估:生长、健康和营养价值

研究从生长、健康和营养价值方面评估了高水平的双低菜粕替代饲料鱼粉对大黄鱼潜在的危害。在鱼粉含量60%的基础饲料（FM）上按照质量分数用双低菜粕分别替代15%（CM15）、30%（CM30）、60%（CM60）和100%（CM100）的鱼粉,配制成5种实验饲料。每种饲料投喂5个网箱的大黄鱼[初重（135.38±1.02）g],即每个处理5个重复,进行12周的养殖实验。结果表明,当双低菜粕替代水平在15%和30%时,大黄鱼的生长及饲料系数并没有受到显著性的影响。然而,当替代水平高于30%时,大黄鱼的末重和特定生长率均显著降低,而饲料系数显著升高（P < 0.05）。当替代水平达到100%时,大黄鱼摄食率达到最高值而肥满度达到最低值（P < 0.05）。在组织形态方面,大黄鱼摄食双低菜粕替代的饲料后肠道绒毛的弯曲程度减少并且排列更加不规则,而肝细胞则呈现出圆形空泡状并伴随着细胞核的偏移。对大黄鱼骨骼进行X-射线扫描发现,摄食双低菜粕的大黄鱼椎体和头部出现了畸形。在营养价值方面,双低菜粕替代鱼粉并未显著影响大黄鱼背肌的脂肪含量、蛋白含量和氨基酸组成,然而脂肪酸组成受到了显著影响,即N-6系列脂肪酸含量显著升高,而DHA与EPA含量显著降低（P < 0.05）。根据欧洲食品安全局（EFSA）的相关标准,这些营养价值的变化并没有影响大黄鱼作为健康食品的功能。由此可见,高水平（60%和100%）的双低菜粕替代鱼粉对大黄鱼的负面影响主要表现为降低大黄鱼的生长性能、改变肠道和肝脏组织形态,以及影响大黄鱼的骨骼健康。然而,双低菜粕替代鱼粉养殖大黄鱼的肌肉仍然符合人类的膳食要求。因此,双低菜粕替代鱼粉并没有影响大黄鱼作为食用鱼的营养价值。     

Bimodal protein targeting through activation of cryptic mitochondrial targeting signals by an inducible cytosolic endoprotease

Bimodal targeting of the endoplasmic reticular protein, cytochrome P4501A1 (CYP1A1), to mitochondria involves activation of a cryptic mitochondrial targeting signal through endoprotease processing of the protein. Here, we characterized the endoprotease that regulates mitochondrial targeting of CYP1A1. The endoprotease, which was induced by beta-naphthoflavone, was a dimer of 90 kDa and 40 kDa subunits, each containing Ser protease domains. The purified protease processed CYP1A1 in a sequence-specific manner, leading to its mitochondrial import. The glucocorticoid receptor, retinoid X receptor, and p53 underwent similar processing-coupled mitochondrial transport. The inducible 90 kDa subunit was a limiting factor in many cells and some tissues and, thus, regulates the mitochondrial levels of these proteins. A number of other mitochondria-associated proteins with noncanonical targeting signals may also be substrates of this endoprotease. Our results describe a new mechanism of mitochondrial protein import that requires an inducible cytoplasmic endoprotease for activation of cryptic mitochondrial targeting signals.     

饲料中添加外源酶对大黄鱼和鲈氮磷排泄的影响

本研究以大黄鱼和鲈为实验对象,探讨饲料中添加植酸酶(PY)和非淀粉性多糖酶(WX和VP)对其氨氮和可溶性磷(PO3-4-P)排泄的影响.以含植物蛋白的饲料为基础饲料,分别向每千克饲料中添加200mg植酸酶(酶的活性为2500IU/g)、 800mg WX(主要包括葡聚糖酶、戊聚糖酶和纤维素酶,各种酶的活性皆为50IU/g)、 400mg VP(主要为木聚糖酶,酶的活性为1000IU/g)以及800mg WX 400mg VP配制出5种实验饲料.实验鱼在海水网箱中经过8周的摄食驯养后,转入室内水族箱中进行氮磷排泄测定实验.在水族箱中经2天的适应后,测定饥饿状态下氨氮及可溶性磷的排泄率.然后饱食投喂,并连续测定摄食后48h内鱼体氨氮和可溶性磷的排泄率.实验期间水温为26.5-32.5℃,盐度为32.5‰-36‰,溶氧在7 mg/L以上.实验结果表明,饥饿状态下实验鱼的氨氮和可溶性磷排泄不受实验饲料影响(p>0.05).而在饱食条件下,实验饲料中添加非淀粉性多糖酶(WX、VP及WX VP)显著降低了实验鱼的氨氮排泄率(p<0.05),而添加植酸酶组实验鱼的氨氮排泄率与对照组差异不显著.饲料处理对实验鱼可溶性磷的排泄率的影响不显著(p>0.05),但添加植酸酶组实验鱼的可溶性磷排泄率有增加的趋势.     

Context shapes: Efficient complementary shape matching for protein-protein docking

We describe an efficient method for partial complementary shape matching for use in rigid protein-protein docking. The local shape features of a protein are represented using boolean data structures called Context Shapes. The relative orientations of the receptor and ligand surfaces are searched using precalculated lookup tables. Energetic quantities are derived from shape complementarity and buried surface area computations, using efficient boolean operations. Preliminary results indicate that our context shapes approach outperforms state-of-the-art geometric shape-based rigid-docking algorithms.