UHRF1 is regulated by miR-124-3p and promotes cell proliferation in intrahepatic cholangiocarcinoma

Ubiquitin-like with PHD and ring finger domains 1 (UHRF1) is abnormally overexpressed in multiple cancers and closely correlated with tumor-promoting effects, such as high proliferation. However, how UHRF1 functions in intrahepatic cholangiocarcinoma (ICC) has not yet been determined. Herein, we found that UHRF1 is overexpressed in ICC tissues. Downregulated UHRF1 attenuated the transition of the G1/S cell cycle and then suppressed cell proliferation in vitro and tumor growth in vivo. Moreover, upstream regulators of the UHRF1 expression were predicted, and we found that direct binding of miR-124-3p inhibited the UHRF1 expression. Elevated miR-124-3p suppressed proliferation and led to the arrest of the cell cycle. Furthermore, the expression of UHRF1 was positively correlated with PCNA. Clinically, we showed that elevated UHRF1 was associated with poor prognosis, and served as an independent prognostic factor in ICC patients. Together, these findings demonstrate that UHRF1, regulated by miR-124-3p, acts as a tumor promoter by promoting cell proliferation in ICC.     

绿色糖单孢菌木质素过氧化物酶的分离纯化及鉴定

木质素过氧化物酶是一种重要的具有工业应用前景的木质素降解酶,但已报道真菌来源的木质素过氧化物酶只能在酸性低温条件下发挥作用,限制了其进一步的工业应用.通过培养一株耐热耐碱放线茵——绿色糖单孢茵发酵产酶,采用DEAE-Cellulose,CM-Cellulose和Superdex 75凝胶过滤层析等分离纯化方法,得到一种具有耐热耐碱特性的木质素过氧化物酶.经凝胶电泳检测其为单一蛋白,分子量为41 kD.最终纯化倍数达到20倍,活性回收率为6％.采用LTQ法对纯酶进行蛋白质归类鉴定,得到其部分氨基酸片段,为该酶的进一步分子生物学研究奠定基础.     

基于扩展耗模型的可持续发展水平区域空间差异——以中国31个省市为数据源

将区域作为一个以人类生产和消费为中心的社会-经济-自然复合生态系统,构建了一种基于生物物理视角的生态热力学方法,从整体角度对区域的可持续发展水平进行定量评价。该方法囊括了维持复合生态系统运转过程中的自然资源投入、人力资源投入和环境污染损害成本投入等三种要素,完善了可持续发展评价以及绿色GDP核算中人力资源投入和环境成本的价值体现。然后以我国为例,核算了我国31个省市2006—2015年间可持续发展水平的时间动态,并以各省为边界,计算了2015年的区域可持续发展水平差异。计算结果显示:(1)十年间,我国整体上的可持续发展水平在逐步提高,能反映出我国生产率水平的提高和资源利用效率的提高;(2)从要素投入看,自然资源投入仍然占主要,但比例在逐渐降低。环境成本投入比例呈逐步降低趋势,说明环境保护取得了成效。另外,在2010年后,人力资源投入比例增加很快,反映了我国经济发展中劳动力成本上升明显。(3)各省市的计算结果差异较大,在不考虑区域间进出口的情况下,从GDP产出角度,北京的可持续发展水平最高,西藏最低。通过将本文的评价结果与绿色发展指数的评价结果进行比较,发现具有较好的一致性。建立的方法框架是对能值分析方法的扩展和完善,在今后的研究中,还需要继续对该方法框架中没有考虑全面的因素加以考虑,以便于更全面客观地反映区域的可持续发展水平。     

木素过氧化物酶的研究进展

木素过氧化物酶是一种能降解木素,由微生物分泌的胞外酶,广泛应用于生物制浆、纸浆的酶法漂白、有机污染物的降解和环境的生物修复等方面.介绍了木素过氧化物酶的来源、结构与性质、催化机理以及基因工程方面的研究成果,并对其可能带来的工业应用前景以及今后的研究方向进行了展望.     

绿色糖单孢菌-木素过氧化物酶的发酵工艺研究

本研究以一株中度耐热耐碱放线菌--绿色糖单孢菌(Saccharomonospora viridis)为研究对象,用16 L发酵罐对该菌进行了木素过氧化物酶(lignin peroxidases, LiP)的诱导发酵,确定了最适的产酶工艺条件:接种量为10%,C/N为1∶3,搅拌速度为250 r/min,通气量为5 L/min,通过控制通气量和调整搅拌转速,使溶氧维持在35%以上,此条件下绿色糖单孢菌较摇瓶实验提前将近24 h达到产酶高峰,酶活最高可达0.41 U/ml;同时在发酵罐中测定该菌株的生长曲线和代谢曲线以确定其发酵代谢规律.     

Single-cell RNA sequencing reveals a high-resolution cell atlas of xylem in Populus

High-throughput single-cell RNA sequencing (scRNA-seq) has advantages over traditional RNA-seq to explore spatiotemporal information on gene dynamic expressions in heterogenous tissues. We performed Drop-seq, a method for the dropwise sequestration of single cells for sequencing, on protoplasts from the differentiating xylem of Populus alba × Populus glandulosa. The scRNA-seq profiled 9,798 cells, which were grouped into 12 clusters. Through characterization of differentially expressed genes in each cluster and RNA in situ hybridizations, we identified vessel cells, fiber cells, ray parenchyma cells and xylem precursor cells. Diffusion pseudotime analyses revealed the differentiating trajectory of vessels, fiber cells and ray parenchyma cells and indicated a different differentiation process between vessels and fiber cells, and a similar differentiation process between fiber cells and ray parenchyma cells. We identified marker genes for each cell type (cluster) and key candidate regulators during developmental stages of xylem cell differentiation. Our study generates a high-resolution expression atlas of wood formation at the single cell level and provides valuable information on wood formation.     

香坊肠球菌和罗伊氏乳杆菌在无菌猪肠道中的定殖

【背景】已有研究表明,微生物在宿主肠道中的定殖受宿主、肠道环境、微生物物种特性和菌株来源等多个因素的影响。一般认为,来源于同类宿主的微生物菌株,在该类宿主肠道中具有定殖优势,但缺乏在物种和菌株水平上研究微生物自身特性在宿主肠道中定殖的研究报道。【目的】将不同来源(同类宿主肠道、非同类宿主肠道和非肠道环境)、具有不同生物学特性的3株香坊肠球菌(Enterococcus xiangfangensis)和4株罗伊氏乳杆菌(Lactobacillusreuteri)对无菌猪肠道进行定殖,在物种和菌株2个水平上探究物种特性和菌株来源对宿主肠道定殖的偏好性,揭示影响微生物定殖效率的关键因素。【方法】在本项研究中,将从藏猪(Tibetan pigs)、小鼠(ob/ob mice)、食蟹猴(Macaca fascicularis)和发酵食品中分离得到的多株香坊肠球菌和罗伊氏乳杆菌,制成混合菌剂对无菌巴马香猪(Bama miniature pig)进行为期4周的饲喂,并通过实时荧光定量PCR方法检测这7株菌在无菌猪肠道中的定殖情况。【结果】在物种水平上,香坊肠球菌和罗伊氏乳杆菌在无菌猪体内具有相近的定殖...     

KDiamend: a package for detecting key drivers in a molecular ecological network of disease

Background

Microbial abundance profiles are applied widely to understand diseases from the aspect of microbial communities. By investigating the abundance associations of species or genes, we can construct molecular ecological networks (MENs). The MENs are often constructed by calculating the Pearson correlation coefficient (PCC) between genes. In this work, we also applied multimodal mutual information (MMI) to construct MENs. The members which drive the concerned MENs are referred to as key drivers.

Results

We proposed a novel method to detect the key drivers. First, we partitioned the MEN into subnetworks. Then we identified the most pertinent subnetworks to the disease by measuring the correlation between the abundance pattern and the delegated phenotype—the variable representing the disease phenotypes. Last, for each identified subnetwork, we detected the key driver by PageRank. We developed a package named KDiamend and applied it to the gut and oral microbial data to detect key drivers for Type 2 diabetes (T2D) and Rheumatoid Arthritis (RA). We detected six T2D-relevant subnetworks and three key drivers of them are related to the carbohydrate metabolic process. In addition, we detected nine subnetworks related to RA, a disease caused by compromised immune systems. The extracted subnetworks include InterPro matches (IPRs) concerned with immunoglobulin, Sporulation, biofilm, Flaviviruses, bacteriophage, etc., while the development of biofilms is regarded as one of the drivers of persistent infections.

Conclusion

KDiamend is feasible to detect key drivers and offers insights to uncover the development of diseases. The package is freely available at http://www.deepomics.org/pipelines/3DCD6955FEF2E64A/.

     

Isolation and culture of hepatic stellate cells from mouse liver

Hepatic stellate cells （HSCs） are the primary extracellular matrix-producing cells within the river and have numerous vital functions. A robust protocol for the isolation and culture of HSCs is important for further investigations of cell functions and related mechanisms in river disease. The volume of the mouse river is much smaller than that of the rat river, which makes it much more difficult to isolate mouse HSCs （mHSCs） than rat HSCs. At present, isolating mHSCs is still a challenge because there is no efficient, robust method to isolate and culture these cells. In the present study, C57BL/6J mice were intravenously injected with riposomeencapsulated dichloromethylene diphosphate （CL2MDP） to selectively eliminate Kupffer cells from the river. The mouse livers were then perfused in situ, and the mHSCs were isolated with an optimized density gradient centrifugation technique. In the phosphate buffer solution （PBS）-liposome group, the yield of mHSCs was （1.37 ±0.23） × 10^6/g river, the cell purity was （90.18 ± 1.61）%, and the cell survival rate was （94.51 ±1.61）%. While in the CL2MDP-liposome group, the yield of mHSCs was （1.62 ±0.34）× 10^6/g liver, the cell purity was （94.44 ± 1.89）%, and the cell survival rate was （94.41 ±1.50）%. Based on the yield and purity of mHSCs, the CL2MDP-riposome treatment was superior to the PBS-liposome treatment （P 〈 0.05, P 〈 0.01）. This study established successfully a robust and efficient protocol for the separation and purification of mHSCs, and both a high purity and an adequate yield of mHSCs were obtained.     

肠道微生物菌株资源库的构建与应用开发

肠道微生物组在组成和功能上都具有极高的复杂性,大量基于免培养的微生物组学研究表明肠道菌群失调与多种疾病都存在密切关联,肠道菌群的稳态与宿主健康密切相关已是共识。同时,越来越多的研究者认识到,可培养微生物菌株资源是肠道微生物组研究从关联分析向功能验证、机理解析和应用开发方向深入发展的基础和保障。本文主要对近年来完成的一些具有代表性的人肠道微生物大规模分离培养和菌株资源库构建工作,进行整理,总结回顾肠道微生物分离培养技术和方法的进展;并通过几个有代表性的基于可培养微生物菌株资源开展的肠道微生物数据挖掘、宿主–微生物互作机理研究和应用开发的成果,展示肠道微生物菌株资源库的应用价值和开发潜力。