Nef of HIV-1 interacts directly with calcium-bound calmodulin

It was recently found that the myristoyl group of CAP-23/NAP-22, a neuron-specific protein kinase C substrate, is essential for the interaction between the protein and Ca(2+)-bound calmodulin (Ca(2+)/CaM). Based on the N-terminal amino acid sequence alignment of CAP-23/NAP-22 and other myristoylated proteins, including the Nef protein from human immunodeficiency virus (HIV), we proposed a new hypothesis that the protein myristoylation plays important roles in protein-calmodulin interactions. To investigate the possibility of direct interaction between Nef and calmodulin, we performed structural studies of Ca(2+)/CaM in the presence of a myristoylated peptide corresponding to the N-terminal region of Nef. The dissociation constant between Ca(2+)/CaM and the myristoylated Nef peptide was determined to be 13.7 nM by fluorescence spectroscopy analyses. The NMR experiments indicated that the chemical shifts of some residues on and around the hydrophobic clefts of Ca(2+)/CaM changed markedly in the Ca(2+)/CaM-Nef peptide complex with the molar ratio of 1:2. Correspondingly, the radius of gyration determined by the small angle X-ray scattering measurements is 2-3 A smaller that of Ca(2+)/CaM alone. These results demonstrate clearly that Nef interacts directly with Ca(2+)/CaM.     

Effects of anthropogenic nitrogen discharge on dissolved inorganic nitrogen transport in global rivers

Excess nutrients from fertilizer application, pollution discharge, and water regulations outflow through rivers from lands to oceans, seriously impacting coastal ecosystems. A reasonable representation of these processes in land surface models and River Transport Models (RTMs) is very important for understanding human–environment interactions. In this study, the schemes of riverine dissolved inorganic nitrogen (DIN) transport and human activities including nitrogen discharge and water regulation, were synchronously incorporated into a land surface model coupled with a RTM. The effects of anthropogenic nitrogen discharge on the DIN transport in rivers were studied based on simulations of the period 1991–2010 throughout the entire world, conducted using the developed model, which had a spatial resolution of about 1° for land processes and 0.5° for river transport, and data on fertilizer application, point source pollution, and water use. Our results showed that rivers in western Europe and eastern China were seriously polluted, on average, at a rate of 5,000–15,000 tons per year. In the Yangtze River Basin, the amount of point source pollution in 2010 was about four times more than that in 1991, while the amount of fertilizer used in 2010 doubled, which resulted in the increased riverine DIN levels. Further comparisons suggested that the riverine DIN in the USA was affected primarily by nitrogen fertilizer use, the changes in DIN flow rate in European rivers was dominated by point source pollution, and rivers in China were seriously polluted by both the two pollution sources. The total anthropogenic impact on the DIN exported to the Pacific Ocean has increased from 10% to 30%, more significantly than other oceans. In general, our results indicated that incorporating the schemes of nitrogen transport and human activities into land surface models could be an effective way to monitor global river water quality and diagnose the performance of the land surface modeling.     

Harmonic Scalpel versus Electrocautery Dissection in Modified Radical Mastectomy for Breast Cancer: A Meta-Analysis

Background

Despite the common use of conventional electrocautery in modified radical mastectomy for breast cancer, the harmonic scalpel is recently emerging as a dominant surgical instrument for dissection and haemostasis, which is thought to reduce the morbidity, such as seroma and blood loss. But the results of published trials are inconsistent. So we made the meta-analysis to assess the intraoperative and postoperative endpoints among women undergoing modified radical mastectomy with harmonic scalpel or electrocautery.

Methods

A comprehensive literature search of case-control studies from PubMed, MEDLINE, EMBASE and Cochrane Library databases involving modified radical mastectomy with harmonic scalpel or electrocautery was performed. We carried out a meta-analysis of primary endpoints including postoperative drainage, seroma development, intraoperative blood loss and secondly endpoints including operative time and wound complications. We used odds ratios (ORs) with 95% confidence intervals (CIs) to evaluate the effect size for categorical outcomes and standardised mean differences (SMDs) for continuous outcomes.

Results

A total of 11 studies with 702 patients were included for this meta-analysis. There was significant difference in total postoperative drainage (SMD: -0.74 [95%CI: -1.31, -0.16]; P< 0.01), seroma development[OR: 0.49 (0.34, 0.70); P < 0.01], intraoperative blood loss(SMD: -1.14 [95%CI: -1.81,-0.47]; P < 0.01) and wound complications [OR: 0.38 (0.24, 0.59); P < 0.01] between harmonic scalpel dissection and standard electrocautery in modified radical mastectomy for breast cancer. No difference was found as for operative time between harmonic scalpel dissection and standard electrocautery (SMD: 0.04 [95%CI: -0.41, 0.50]; P = 0.85).

Conclusion

Compared to standard electrocautery, harmonic scalpel dissection presents significant advantages in decreasing postoperative drainage, seroma development, intraoperative blood loss and wound complications in modified radical mastectomy for breast cancer, without increasing operative time. Harmonic scalpel can be recommended as a preferential surgical instrument in modified radical mastectomy.     

Probing acid replacements of thiophene PTP1B inhibitors

The following account describes our systematic effort to replace one of the carboxylate groups of our diacid thiophene PTP1B inhibitors. Active hits were validated using enzymatic assays before pursuing efforts to improve the potency. Only when the C2 carboxylic acid was replaced with another ionizable functional group was reversible and competitive inhibition retained. Use of a tetrazole ring or 1,2,5-thiadiazolidine-3-one-1,1-dioxide as a carboxylate mimetic led to the discovery of two unique starting series that showed improved permeability (PAMPA) and potency of the order of 300nM. The SAR from these efforts underscores some of the major challenges in developing small molecule inhibitors for PTP1B.     

Specific overexpression of SIRT1 in mesenchymal stem cells rescues hematopoiesis niche in BMI1 knockout mice through promoting CXCL12 expression

Osteoblastic lineage cells (OBCs) are bone-building cells and essential component of hematopoietic niche, but mechanisms whereby bone-building and hematopoiesis-supportive activities of OBCs could be regulated simultaneously remain largely unknown. Here we found that B cell-specific Moloney murine leukemia virus integration site 1 (Bmi1) was involved in such a co-regulatory mechanism. In this study, we first found that, accompanied with marked decline of osteogenic activity, the hematopoietic niche in Bmi1 knockout (KO) mice was severely impaired and manifested as CXCL12 expression falls and LSK homing failure; however, intratibial injection with CXCL12 effectively facilitated LSK accumulation in bone marrow of Bmi1 KO mice. To try to rescue these defects in Bmi1 KO mice, we generated Bmi1^KO/Sirt1^Tg (KO-TG) double mutant mice with Sirt1 specific overexpression in mesenchymal progenitor cells (MPCs) in Bmi1 KO mice, and our data showed that KO-TG mice had significantly increased bone-building activity, elevated Cxcl12 expression by MPCs, increased LSK homing and expanded LSK pool in bone marrow compared to Bmi1 KO mice. Of note, similar improvements in KO-TG mice were observed in Bmi1 KO mice fed with dietary resveratrol, an established Sirt1 activator, comparing with KO control mice. Therefore, pharmacologic activation of Bmi1/Sirt1 signaling pathway could simultaneously promote bone-building and hematopoiesis-supportive activities of OBCs.     

酒精促PC12细胞凋亡及对神经鞘磷脂合酶表达和活性的影响

目的 观察酒精诱导PCI2细胞凋亡及其凋亡过程中神经鞘磷脂合酶活性和mRNA表达量的变化.方法 MTr法测定酒精对PCI2细胞增殖的抑制作用.Hoeelmt33258染色荧光显微镜观察PCI2细胞凋亡形态学变化.DNA琼脂糖凝胶电泳检测细胞凋亡梯状DNA条带.RT-PCR法检测酒精对PCI2细胞SMSI和SMS2 mRNA表达的影响.薄层层析法测定SMS的活性.结果 PCI2细胞去血清培养24 h,酒精浓度在100、200、400和800 mmoL/L时,细胞存活率分别是单纯去血清的87.54%、70.73%、57.89%和51.70%,表现出较强的细胞增殖抑制作用（P〈0.05）;细胞核形态学变化显示酒精处理组凋亡细胞增多,表现染色质凝集,细胞核变小、核碎裂成碎片等典型细胞凋亡特征性变化,凋亡率随着酒精浓度的增大而升高,去血清组的酒精浓度为100、200和300 mmol/L时,细胞凋亡率呈剂量依赖关系;琼脂糖凝胶电泳可见酒精处理组有不同程度的DNA断裂,显示凋亡细胞典型的梯状DNA.RT-PCR检测酒精对PCI2细胞SMS转录水平结果显示,不同浓度酒精作用于PCI2细胞0.5 h,SMSI表达量无显著变化,当作用时间达1h和2 h,SMSl表达量显著增加,并呈剂量依赖性,而SMS2的mRNA表达则不受酒精作用的影响;薄层层析法检测细胞总SMS活性显示,不同浓度酒精作用2 h,细胞SMS活性随酒精浓度增加而升高.结论 酒精可导致PCI2细胞凋亡并与酒精浓度呈正相关.酒精致PCI2细胞凋亡过程中SMSl的mRNA表达量增高,酶活性增强,提示酒精致PCI2细胞凋亡作用与鞘磷脂循环有关.     

基于小流域尺度的土壤重金属分布与土地利用相关性研究——以厦门市坂头水库流域为例

人类活动改变流域集水区土地利用方式同时提高了土壤重金属水平,并影响地表水重金属负荷。以具有明确地理边界的流域作为研究单元可能实现计量区别不同人类活动或因其引起的土地利用方式对土壤重金属空间分布及其环境风险的贡献。但不同人类活动及其改变的土地利用方式对土壤和地表水重金属负荷的相对贡献研究缺乏可操作性方法论。以我国典型的山塘水库小流域—福建省厦门市坂头水库流域为例,结合遥感影像解译、野外土壤重金属水平调查和GIS地统计方法,针对小流域尺度土壤重金属空间分布及其环境风险与土地利用方式相关性研究进行方法论的探索。坂头水库流域覆盖205km2,土地利用类型有林地、农业用地、城镇用地、绿地和水面等5大类。按照不同土地利用类型覆盖面积为权重,以统计最小样本数为准则,在该流域内共采集150个表层土壤样品,针对6种具有人为源特征重金属(Cu、Zn、Pb、Cr、Ni、Cd)土壤总量及富集水平进行分析,以潜在生态风险指数评价流域土壤重金属风险,并结合土地利用类型分析了其空间特征。结果表明:与林地和绿地相比,城镇用地和农业用地表层土壤重重金属水平显著较高;土壤重金属富集水平及其潜在生态风险依次为:城镇用地农业用地绿地林地;城镇化加重了流域土壤重金属Cu、Zn和Cd的污染风险;土壤Pb富集水平与土地利用方式无关,可能为大气沉降来源;所有土地利用方式土壤Cr和Ni总量低于区域土壤背景值,但城镇用地的富集指数显著高于林地。基于土地利用方式的反距离加权空间插值(LU-IDW)也清晰地揭示了土壤重金属富集及其潜在生态风险与人类活动密切相关,尤其是城镇化。以野外调查结合遥感卫星图像解译和基于土地利用方式的空间插值的研究方法有效地揭示了研究流域土壤重金属的空间分布特征及其潜在风险评价空间模式,为小流域尺度的环境质量演变研究提供了方法论和案例。     

大鼠肠癌中Ⅳ型胶原酶及ras P21表达的研究

用二甲肼诱发Ｗｉｓｔａｒ大鼠肠癌,并应用免疫组化双标记方法对肠道良、恶性病变中Ⅳ型胶原酶的表达及基底膜的改变作了研究,同时观察Ｐ２１的表达情况。结果显示,肠道良性病变及良性肿瘤中Ⅳ型胶原酶反应阳性率为２１．７４％,在肠癌中阳性率为７９．４１％,两者差异极显著（Ｐ＜０．０１）。Ⅳ型胶原染色显示,良性病变及良性肿瘤基底膜完整,而肠癌中基底膜出现断裂或缺失。表明Ⅳ型胶原酶对基底膜的破坏及肠癌浸润转移起重要作用。Ｐ２１在肠良性病变及良性肿瘤中阳性率为３０．４３％,而在肠癌中为６７．６５％,两者差异也有极显著意义（Ｐ＜０．０１）。肠癌中Ⅳ型胶原酶的表达与Ｐ２１的表达之间呈正相关（ｒ＝０．８１３,Ｐ＜０．０５）。     

Annotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning

Genomewide association studies (GWAS) have identified a large number of loci associated with neuropsychiatric traits, however, understanding the molecular mechanisms underlying these loci remains difficult. To help prioritize causal variants and interpret their functions, computational methods have been developed to predict regulatory effects of non-coding variants. An emerging approach to variant annotation is deep learning models that predict regulatory functions from DNA sequences alone. While such models have been trained on large publicly available dataset such as ENCODE, neuropsychiatric trait-related cell types are under-represented in these datasets, thus there is an urgent need of better tools and resources to annotate variant functions in such cellular contexts. To fill this gap, we collected a large collection of neurodevelopment-related cell/tissue types, and trained deep Convolutional Neural Networks (ResNet) using such data. Furthermore, our model, called MetaChrom, borrows information from public epigenomic consortium to improve the accuracy via transfer learning. We show that MetaChrom is substantially better in predicting experimentally determined chromatin accessibility variants than popular variant annotation tools such as CADD and delta-SVM. By combining GWAS data with MetaChrom predictions, we prioritized 31 SNPs for Schizophrenia, suggesting potential risk genes and the biological contexts where they act. In summary, MetaChrom provides functional annotations of any DNA variants in the neuro-development context and the general method of MetaChrom can also be extended to other disease-related cell or tissue types.     

象山港电厂温排水增温对浮游细菌群落空间分布的影响

沿海电厂产生的温排水已造成了较严重的环境问题,如生物病害和赤潮暴发频率增加。现有研究多关注温排水增温对浮游动、植物多样性的影响,而缺乏在物质能量循环过程起核心纽带作用的微生物对增温的响应和反馈。考虑到生态系统对增温的反馈取决于浮游植物的初级生产力和微生物异养呼吸之间的平衡,利用Illumina测序技术结合水体理化性质研究了象山港电厂温排水增温梯度下浮游细菌的空间分布特征。温排水预期的海水增温显著地增加了水体中硝氮(P=0.041,单因素方差分析)、化学需氧量(P0.001)、油污(P=0.004)和余氯(P=0.003)的浓度;但降低了溶解氧(P=0.034)和叶绿素a(P=0.045)的含量。此外,相似性分析发现温排水增温显著地(r=0.338;P=0.042)改变了浮游细菌群落结构,空间分布遵循空间距离-群落相似性衰减(r=-0.582;P=0.026)模型,周转速率为0.0013。细菌多样性主要受水体溶解氧、化学需要量和叶绿素a的影响,分别控制了34.6%、20.1%和10.0%的多样性变异。冗余分析(RDA)群落变异主要受环境因子(包括温度、油污、溶解氧和叶绿素a)的影响,一共解释了55.6%的群落变异;增温仅解释了4.8%的群落变异。因此,浮游细菌群落结构主要受环境因子的影响,这种各因子对群落变异相对贡献比例的特征与增温主要通过改变水质和浮游植物特征,以间接作用影响细菌群落组成的观念一致。此外,细菌多样性和群落组成受不同环境因子的驱动。相比而言,空间距离只控制了较小比例的群落变异(7.1%)。此外,筛选到11个细菌科,这些科的相对丰度与增温幅度显著相关,变化特征与各科已知的生态功能相吻合,如海洋螺菌科(Oceanospirillaceae)中有些菌株能够降解石油污染物,其相对丰度在高油污浓度站点增加(油污浓度与增温幅度正相关,r=0.558;P=0.030);嗜温的弧菌科相对丰度与增温幅度正相关。综上,研究结果初步明确了浮游细菌群落对电厂温排水增温的响应特征,并筛选到敏感的细菌科来指示和预测增温对生态功能的潜在影响。