Cancer biomarker discovery and translation: proteomics and beyond

Introduction: Cancer is often diagnosed at late stages when the chance of cure is relatively low and although research initiatives in oncology discover many potential cancer biomarkers, few transition to clinical applications. This review addresses the current landscape of cancer biomarker discovery and translation with a focus on proteomics and beyond.

Areas covered: The review examines proteomic and genomic techniques for cancer biomarker detection and outlines advantages and challenges of integrating multiple omics approaches to achieve optimal sensitivity and address tumor heterogeneity. This discussion is based on a systematic literature review and direct participation in translational studies.

Expert commentary: Identifying aggressive cancers early on requires improved sensitivity and implementation of biomarkers representative of tumor heterogeneity. During the last decade of genomic and proteomic research, significant advancements have been made in next generation sequencing and mass spectrometry techniques. This in turn has led to a dramatic increase in identification of potential genomic and proteomic cancer biomarkers. However, limited successes have been shown with translation of these discoveries into clinical practice. We believe that the integration of these omics approaches is the most promising molecular tool for comprehensive cancer evaluation, early detection and transition to Precision Medicine in oncology.     

长白山区阔叶红松林经营历史与研究历程

长白山区位于中国东北东部的山地森林区,地带性植被是阔叶红松林,是我国珍贵木材生产和东北森林带的重要载体,孕育着丰富的物种资源.短短120年来,长白山区广袤的原始森林几乎消失殆尽,被次生林、过伐林和人工林等替代.建国以来,东北的阔叶红松林经营理论与技术在红松更新规律、皆伐与择伐的争论中,在人们对阔叶红松林结构和功能认识不断深入的过程中逐渐完善.但目前红松更新问题依然存在,森林经营依然十分粗放.本文梳理了过去70年来阔叶红松林的经营历史及研究历程,分析当前森林资源类型和经营制度的形成过程,以期为该区天然林可持续经营和质量的精准提升等提供借鉴.     

基于文献计量的生态宜居研究热点和趋势分析

基于CNKI数据库和Web of Science数据库,利用网页检索功能分析了生态宜居研究的年发文量、基金资助机构及国家地区分布、研究方向及研究机构状况;利用Citespace对2002—2017年生态宜居研究关键词进行共现性和可视化图谱聚类分析。结果表明:近年生态宜居研究逐渐成为人们关注的热点,但该方面研究获得国家及相关部门基金资助的比例仍然较小;当前生态宜居研究主要集中在宏观经济管理与可持续发展学科,研究机构排名中,天津地区相关机构发文量相对较多。就目前研究来看,研究热点集中于新型城镇化、城镇化、指标体系、生态宜居度、生态文明等。在未来的研究发展趋势方面,新型城镇化和生态宜居标准的制定仍然是重要的研究领域,必须在此持续发力,为生态宜居建设提供必要的理论支撑和政策依据。     

2019环境生物技术专刊序言

环境生物技术,作为一门由现代生物技术与环境工程相结合的新兴交叉学科,已经在环境污染治理、环境监测中得到了广泛的应用,环境友好、高效地处理有机及无机污染,同时变废为宝生产高值化合物为从根本上解决环境问题提供了希望与支持。本专刊报道了环境生物技术在多环芳烃、抗生素、石油基塑料等环境污染物降解领域的基础与应用研究,介绍了吲哚、微生物铁载体等分子在生物修复中的应用,为全面认识环境污染现状、深入开展环境生物技术研究并制定综合治理策略等提供参考。     

基于文献计量分析的珊瑚礁研究现状与热点

珊瑚礁生态系统在全球海洋生态中扮演着重要角色,它为热带海洋动物提供栖息地,为人类提供食物药物资源,是全球生产力最高的生态系统之一。为了解当前国内外珊瑚相关研究的现状与热点,利用文献计量的方法统计分析了珊瑚的相关研究。文章分别以WEB OF SCIENCE数据库和中国期刊全文数据库(CNKI)中期刊论文为国际和国内的数据源,从文献计量的角度出发,利用Excel按年份统计论文的发文数量,通过Bibexcel得出高频词共词矩阵,并用Ucinet和Netdraw得出共词网络可视化图谱。利用SPSS进行聚类分析,分别将国内外相关研究分为四大类,分析珊瑚相关研究趋势与热点。研究表明:①国际与国内的珊瑚研究除个别年份有所回落,均基本成逐年上升趋势,大致于20世纪90年代开始进入成熟阶段,但国内的研究略迟于国际;②国际上对珊瑚的研究更倾向于探究珊瑚礁退化的原因,而国内则以提高珊瑚礁的造礁能力为研究热点;③通过共词分析得出,国际研究高频词中的coral reefs,corals,climate change,sedimentation,一定程度上也可视为研究热点;④通过聚类分析,国内外的珊瑚研究有一定的相似性,主要集中在珊瑚礁生态系统、影响珊瑚的环境因子、气候因子等几个方面,但国内外研究又各有侧重。总结得出,有关珊瑚、珊瑚礁研究在国内外均以珊瑚礁为重点,近年来和未来珊瑚礁研究注重于珊瑚礁修复或帮助珊瑚礁生态系统自行恢复。     

药用白及资源再生策略初探

白及为兰科白及属植物。作为著名中药,白及功效多样、用途广泛,具有较高的药用价值和经济价值。随资源利用强度的增加,野生白及资源日渐萎缩,人工规模化种植是实现白及药用资源可持续利用的必由之路。优良种质及繁育技术是种植业的关键问题。为了更好地推动白及资源研究和可持续利用,本文就白及种质及快繁技术研究进展作一综述,并就白及资源再生策略进行初步探讨,为相关研究和生产提供参考。     

Current methods for the maturation of induced pluripotent stem cellderived cardiomyocytes

Induced pluripotent stem cells(iPSCs) were first generated by Yamanaka and colleagues over a decade ago. Since then, iPSCs have been successfully differentiated into many distinct cell types, enabling tissue-, disease-, and patientspecific in vitro modelling. Cardiovascular disease is the greatest cause of mortality worldwide but encompasses rarer disorders of conduction and myocardial function for which a cellular model of study is ideal. Although methods to differentiate iPSCs into beating cardiomyocytes(iPSC-CMs) have recently been adequately optimized and commercialized, the resulting cells remain largely immature with regards to their structure and function,demonstrating fetal gene expression, disorganized morphology, reliance on predominantly glycolytic metabolism and contractile characteristics that differ from those of adult cardiomyocytes. As such, disease modelling using iPSC-CMs may be inaccurate and of limited utility. However, this limitation is widely recognized, and numerous groups have made substantial progress in addressing this problem. This review highlights successful methods that have been developed for the maturation of human iPSC-CMs using small molecules,environmental manipulation and 3-dimensional(3 D) growth approaches.     

Site fertility drives temporal turnover of vegetation at high latitudes

Experimental evidence shows that site fertility is a key modulator underlying plant community changes under climate change. Communities on fertile sites, with species having fast dynamics, have been found to react more strongly to climate change than communities on infertile sites with slow dynamics. However, it is still unclear whether this generally applies to high‐latitude plant communities in natural environments at broad spatial scales. We tested a hypothesis that vegetation of fertile sites experiences greater changes over several decades and thus would be more responsive under contemporary climate change compared to infertile sites that are expected to show more resistance. We resurveyed understorey communities (vascular plants, bryophytes, and lichens) of four infertile and four fertile forest sites along a latitudinal bioclimatic gradient. Sites had remained outside direct human disturbance. We analyzed the magnitude of temporal community turnover, changes in the abundances of plant morphological groups and strategy classes, and changes in species diversity. In agreement with our hypothesis, temporal turnover of communities was consistently greater on fertile sites compared to infertile sites. However, our results suggest that the larger turnover of fertile communities is not primarily related to the direct effects of climatic warming. Furthermore, community changes in both fertile and infertile sites showed remarkable variation in terms of shares of plant functional groups and strategy classes and measures of species diversity. This further emphasizes the essential role of baseline environmental conditions and nonclimatic drivers underlying vegetation changes. Our results show that site fertility is a key determinant of the overall rate of high‐latitude vegetation changes but the composition of plant communities in different ecological contexts is variously impacted by nonclimatic drivers over time.     

基于计量学方法分析数字PCR技术的临床应用现状与技术热点

近年来数字PCR技术作为第三代PCR技术迅猛发展,已被应用于无创产前筛查、病毒核酸检测及肿瘤液体活检等领域。以中国生物医学文献数据库、PubMed医学文献检索服务系统及Incopat专利数据库收录的与“数字PCR技术临床应用”相关的中英文论文和专利文献为数据源,利用计量学方法分析了数字PCR临床应用现状与技术热点趋势,明确该技术的主要研究机构包括美国弗雷德-哈钦森肿瘤研究中心、哈佛医学院丹娜法伯癌症研究所和Bio-Rad公司等。中文文献发表机构中检验检疫部门和疾控中心占比较高。国内外数字PCR技术研究主要聚焦于肿瘤伴随诊断、病毒检测和基因表达分析等方面。中国数字PCR技术研究热情较高,专利申请已展现出国际领先趋势。     

Applications of a new subspace clustering algorithm (COSA) in medical systems biology

A novel clustering approach named Clustering Objects on Subsets of Attributes (COSA) has been proposed (Friedman and Meulman, (2004). Clustering objects on subsets of attributes. J. R. Statist. Soc. B 66, 1–25.) for unsupervised analysis of complex data sets. We demonstrate its usefulness in medical systems biology studies. Examples of metabolomics analyses are described as well as the unsupervised clustering based on the study of disease pathology and intervention effects in rats and humans. In comparison to principal components analysis and hierarchical clustering based on Euclidean distance, COSA shows an enhanced capability to trace partial similarities in groups of objects enabling a new discovery approach in systems biology as well as offering a unique approach to reveal common denominators of complex multi-factorial diseases in animal and human studies. Doris Damian, Matej Orešič, and Elwin Verheij contributed equally to this work.