Oncogenes,protein tyrosine kinases,and signal transduction

Many oncogenes encode protein tyrosine kinases (PTKs). Oncogenic mutations of these genes invariably result in constitutive activation of these PTKs. Autophosphorylation of the PTKs and tyrosine phosphorylation of their cellular substrates are essential events for transmission of the mitogenic signal into cells. The recent discovery of the characteristic amino acid sequences, of thesrc homology domains 2 and 3 (SH2 and SH3), and extensive studies on proteins containing the SH2 and SH3 domains have revealed that protein tyrosine-phosphorylation of PTKs provides phosphotyrosine sites for SH2 binding and allows extracellular signals to be relayed into the nucleus through a chain of protein-protein interactions mediated by the SH2 and SH3 domains. Studies on oncogenes, PTKs and SH2/SH3-containing proteins have made a tremendous contribution to our understanding of the mechanisms for the control of cell growth, oncogenesis, and signal transduction. This review is intended to provide an outline of the most recent progress in the study of signal transduction by PTKs.     

Managing the pattern of forest harvest: lessons from wildfire

Managing forests for sustainable use requires that both the biological diversity of the forests and a viable forest industry be maintained. A current approach towards maintaining biological diversity is to pattern forest management practices after those of natural disturbance events. This paradigm hypothesizes that ecological processes will be maintained best where active management approximates natural disturbance events. The forest management model now used in most sub-boreal and boreal forests calls for regularly dispersed clearcuts no greater than 60–100 ha in size. However, the spatial characteristics of the landscape produced by this model are distinctly different from the historic pattern generated by wildfire, which was heretofore the dominant stand-replacing process in these forests. Wildfire creates a more complex landscape spatial pattern with greater range in patch size and more irregular disturbance boundaries. Individual wildfires are often over 500 ha but leave patches of unburned forest within them. The combination of these attributes is not present in recent clearcuts. Allowing a proportion of larger (i.e.>500ha) harvest units may provide distinct economic advantages that could outweight the opportunity costs of leaving some patches of forest behind. For the forest type examined, further evaluation of modelling forest harvest patterns more closely after the patterns created by wildfire is required as it may achieve a good balance and strike a suitable compromise between certain ecological and economic objectives of sustainable development.     

Risks of Avian Influenza Transmission in Areas of Intensive Free-Ranging Duck Production with Wild Waterfowl

For decades, southern China has been considered to be an important source for emerging influenza viruses since key hosts live together in high densities in areas with intensive agriculture. However, the underlying conditions of emergence and spread of avian influenza viruses (AIV) have not been studied in detail, particularly the complex spatiotemporal interplay of viral transmission between wild and domestic ducks, two major actors of AIV epidemiology. In this synthesis, we examine the risks of avian influenza spread in Poyang Lake, an area of intensive free-ranging duck production and large numbers of wild waterfowl. Our synthesis shows that farming of free-grazing domestic ducks is intensive in this area and synchronized with wild duck migration. The presence of juvenile domestic ducks in harvested paddy fields prior to the arrival and departure of migrant ducks in the same fields may amplify the risk of AIV circulation and facilitate the transmission between wild and domestic populations. We provide evidence associating wild ducks migration with the spread of H5N1 in the spring of 2008 from southern China to South Korea, Russia, and Japan, supported by documented wild duck movements and phylogenetic analyses of highly pathogenic avian influenza H5N1 sequences. We suggest that prevention measures based on a modification of agricultural practices may be implemented in these areas to reduce the intensity of AIV transmission between wild and domestic ducks. This would require involving all local stakeholders to discuss feasible and acceptable solutions.     

鸭C4BPα的克隆、表达及其与鸭疫里默氏菌的互作

为研究鸭C4结合蛋白(C4b-binding protein,C4BP)与鸭疫里默氏菌(Riemerella anatipestifer,RA)的相互作用,对鸭C4BPα进行克隆、原核表达,免疫小鼠制备多克隆抗体,并利用间接免疫荧光试验及斑点杂交试验验证C4BP与RA的相互作用。结果显示,鸭C4BPα核苷酸序列全长为1230bp,与鸡C4BPα的相似性最高(82.1%);系统进化树分析发现,鸭C4BPα与鸡C4BPα处于同一系统进化树分支上,两者遗传进化关系最近;C4BPα在大肠杆菌Escherichia coli BL21 (DE3)中能高效表达,重组蛋白以胞内可溶性形式存在;多克隆抗体效价超过1∶10000,并且可以与重组蛋白发生特异性反应;间接免疫荧光试验和斑点杂交试验结果显示RA与鸭C4BP可以发生相互作用。研究结果为进一步揭示RA的致病机制奠定了基础。     

培养时间对蛹拟青霉(Paecilomyces militaris)菌丝体中代谢产物的影响

[目的]通过测定不同培养时间蛹拟青霉(Paecilomyces militaris)菌丝体中次级代谢产物的变化,分析蛹拟青霉次级代谢产物与培养时间之间的关系.[方法]液体种子接入SDAY固体培养基 ;培养温度为25℃,培养周期为9d,从第2天开始每天取样 ;用甲醇与乙酸乙酯分别提取菌丝体中次级代谢产物,离心、过滤后合并提取液,用液质联用仪进行分析,用MetaboAnalyst software软件进行数据采集分析.[结果]主成分分析结果表明供试菌株在不同培养时间内其菌丝中次级代谢产物差异显著.聚类分析结果显示,供试拟青霉对生物碱、肽类和核苷等易形成阳离子类物质的代谢物可分为前中后三个阶段.供试拟青霉对糖类和有机酸等易形成阴离子类物质的代谢主要分为前后两个阶段.差异代谢物及热图分析结果表明,在培养的第2和第3天含量显著增加的代谢产物种类较多,主要有酯类及其水解产物、细胞破坏素B和拟青霉素,以及多种尚未鉴定的含氮化合物等 ;在培养第4和第5天含量显著增加的差异代谢物质种类较少,主要有细胞破坏素A和团囊虫草素等肽类抗菌杀虫物质 ;在培养第6天至第9天含量显著增加的代谢物种类较多,除多种白僵菌交酯和细胞破坏素等肽类抗生素外,显著增加的还有多种脂肪酸、氨基酸、鼠李糖、海藻糖、脑苷脂类化合物和核黄素等物质.[结论]培养时间对蛹拟青霉菌丝中次级代谢产物的产生有显著影响.在培养初期,菌体中酯类及细胞破坏素B和拟青霉素等含氮化合物的合成旺盛.在培养中期,次生代谢物明显减少,但细胞破坏素A2和团囊虫草素等肽类抗生素的合成却仍显著增多.在培养后期,供试蛹拟青霉除代谢出多种白僵菌交酯等肽类抗生素外,还大量产生有机酸、氨基酸和海藻糖等物质.虽然在整个培养过程中都有肽类抗生素产生,但这些抗生素并不相同,同时后一阶段新的抗生素的产生常常伴随着前一阶段的抗生素减少,因此前期的抗生素可能是后期产生的抗生素的前体.     

REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding

Background

More than 7000 papers related to “protein refolding” have been published to date, with approximately 300 reports each year during the last decade. Whilst some of these papers provide experimental protocols for protein refolding, a survey in the structural life science communities showed a necessity for a comprehensive database for refolding techniques. We therefore have developed a new resource – “REFOLDdb” that collects refolding techniques into a single, searchable repository to help researchers develop refolding protocols for proteins of interest.

Results

We based our resource on the existing REFOLD database, which has not been updated since 2009. We redesigned the data format to be more concise, allowing consistent representations among data entries compared with the original REFOLD database. The remodeled data architecture enhances the search efficiency and improves the sustainability of the database. After an exhaustive literature search we added experimental refolding protocols from reports published 2009 to early 2017. In addition to this new data, we fully converted and integrated existing REFOLD data into our new resource. REFOLDdb contains 1877 entries as of March 17^th, 2017, and is freely available at http://p4d-info.nig.ac.jp/refolddb/.

Conclusion

REFOLDdb is a unique database for the life sciences research community, providing annotated information for designing new refolding protocols and customizing existing methodologies. We envisage that this resource will find wide utility across broad disciplines that rely on the production of pure, active, recombinant proteins. Furthermore, the database also provides a useful overview of the recent trends and statistics in refolding technology development.

     

ArfGAP1 inhibits mTORC1 lysosomal localization and activation

The mammalian target of rapamycin complex 1 (mTORC1) integrates nutrients, growth factors, stress, and energy status to regulate cell growth and metabolism. Amino acids promote mTORC1 lysosomal localization and subsequent activation. However, the subcellular location or interacting proteins of mTORC1 under amino acid‐deficient conditions is not completely understood. Here, we identify ADP‐ribosylation factor GTPase‐activating protein 1 (ArfGAP1) as a crucial regulator of mTORC1. ArfGAP1 interacts with mTORC1 in the absence of amino acids and inhibits mTORC1 lysosomal localization and activation. Mechanistically, the membrane curvature‐sensing amphipathic lipid packing sensor (ALPS) motifs that bind to vesicle membranes are crucial for ArfGAP1 to interact with and regulate mTORC1 activity. Importantly, ArfGAP1 represses cell growth through mTORC1 and is an independent prognostic factor for the overall survival of pancreatic cancer patients. Our study identifies ArfGAP1 as a critical regulator of mTORC1 that functions by preventing the lysosomal transport and activation of mTORC1, with potential for cancer therapeutics.     

Metapopulation Dynamics Enable Persistence of Influenza A,Including A/H5N1, in Poultry

Highly pathogenic influenza A/H5N1 has persistently but sporadically caused human illness and death since 1997. Yet it is still unclear how this pathogen is able to persist globally. While wild birds seem to be a genetic reservoir for influenza A, they do not seem to be the main source of human illness. Here, we highlight the role that domestic poultry may play in maintaining A/H5N1 globally, using theoretical models of spatial population structure in poultry populations. We find that a metapopulation of moderately sized poultry flocks can sustain the pathogen in a finite poultry population for over two years. Our results suggest that it is possible that moderately intensive backyard farms could sustain the pathogen indefinitely in real systems. This fits a pattern that has been observed from many empirical systems. Rather than just employing standard culling procedures to control the disease, our model suggests ways that poultry production systems may be modified.     

The Clinical Significance and Risk Factors of Anti-Platelet Factor 4/heparin Antibody on Maintenance Hemodialysis Patients: A Two-Year Prospective Follow-up

Background

Heparin-induced thrombocytopenia is an immune response mediated by anti-PF4/heparin antibody, which is clinically characterized by thrombocytopenia and thromboembolic events. In this study, a prospective and multi-center clinical investigation determined the positive rate of anti-PF4/heparin antibody in maintenance hemodialysis patients in China, identified the related risk factors, and further explored the effect of the anti-PF4/heparin antibody on bleeding, thromboembolic events, and risk of death in the patients.

Methods

The serum anti-PF4/heparin antibody was measured in 661 patients from nine hemodialysis centers, detected by IgG-specific ELISA and followed by confirmation with excess heparin. Risk factors of these patients were analyzed. Based on a two-year follow-up, the association between the anti-PF4/heparin antibody and bleeding, thromboembolic events, and risk of death in the patients was investigated.

Results

The positivity rate of the anti-PF4/heparin antibody in maintenance hemodialysis patients was 5.6%. With diabetes as an independent risk factor, the positivity rate of the anti-PF4/heparin antibody decreased in the patients undergoing weekly dialyses ≥3 times. The positivity rate of the anti-PF4/heparin antibody was not related to the occurrence of clinical thromboembolic events and was not a risk factor for death within two years in maintenance hemodialysis patients. Negativity for the anti-PF4/heparin antibody combined with a reduction of the platelet count or combined with the administration of antiplatelet drugs yielded a significant increase in bleeding events. However, the composite determination of the anti-PF4/heparin antibody and thrombocytopenia, as well as the administration of antiplatelet drugs, was not predictive for the risk of thromboembolic events in the maintenance hemodialysis patients.

Conclusions

A single detection of the anti-PF4/heparin antibody did not predict the occurrence of clinical bleeding, thromboembolic events, or risk of death in the maintenance hemodialysis patients.