Nature子刊《Communications Biology》杂志论文发表者Nick Y. Larsen专访

  • 张晴
  • 2022-01-07
  • 1695

2021 92日,《Communications Biology》杂志在线发表了由中国科学院生物物理所蛋白质科学研究平台生物成像中心、丹麦奥胡斯大学、中国科学院大学中丹学院共同合作的技术创新成果"Cellular 3D-reconstruction and analysis in human cerebral cortex using automatic serial sections"

该项技术创新成果是由2017级中丹学院博士毕业生 Nick Y. Larsen 在中科院生物物理所孙飞研究员与奥胡斯大学的 Jens R.Nyengaard共同指导下完成的,该团队建立了一种基于连续半薄切片自动收集的光学显微成像(automatic collector of serialsections for Light microscopyAutoCUTS-LM)三维重构新技术,并通过该技术对储存的人类大脑皮层组织中的锥体细胞进行了三维重构分析。该研究获得国家自然科学基金、中科院前沿科学重点研究项目等基金的资助。

 



个人简介

Nick Y. Larsen, 2017级中丹学院博士研究生,由中丹学院、生物物理研究所、奥胡斯大学联合培养。神经科学与神经影像专业,主要研究方向为三维结构生物技术及其应用。博士期间,教授神经科学与神经影像研究生项目的基础课程:神经科学、高级神经科学、基础生物医学信号处理等课程。他的教学经验使他在哥本哈根大学和奥胡斯大学分别担任两个研究生的合作导师。

Nick Y. Larsen, a 2017 Ph.D. graduate in SDC, was jointly trained by Institute of Biophysics, University of Chinese Academy of Sciences and Aarhus University, majoring in Neuroscience and Neuroimaging. His main research field is three-dimensional structural biology technology and its applications. During his Ph.D. study, he taught courses offered by the Neuroscience & Neuroimaging graduate program, such as Basic Neuroscience, Advanced Neuroscience, and Fundamental Biomedical Signal Processing. His previous teaching experience served him well as a co- supervisor for two graduate students from the University of Copenhagen and Aarhus University, respectively.

 

导师简介

孙飞,中国科学院生物物理研究所生物大分子国家实验室首席研究员,生物成像中心主任、首席科学家。生物成像中心是中国科学院生物物理研究所蛋白质科学的核心设施。孙老师的主要研究方向是生物大分子的结构和功能,包括膜蛋白和超大分子组装体。孙老师是一位杰出的青年长江学者,并于2017年获得首届中国低温电子显微镜杰出贡献奖。

Sun Fei, the Principal Investigator of the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS) also serves as Director and Chief Scientist in Center for Biological Imaging, which is a core facility for Protein Sciences in Institute of Biophysics, CAS. Prof. Fei Suns research interest mainly focuses on the structure and functions of biological macromolecules including membrane proteins and supra macromolecular assemblies. Prof. Sun is a talented young scientist, who was the winner for National "Outstanding Youth Fund"; "Cheung Kong Scholars Program" for Young Scholars, and achieved  the first China Cryo-electron Microscopy Outstanding Contribution Award in 2017.

      Jens R. Nyengaard博士是奥胡斯大学分子形态学核心中心的教授和负责人,从事全职研究。Jens R. Nyengaard是中丹中心的客座教授和课程组织者。他的实验室专门研究光显微镜技术、先进的荧光方法、各种电子显微镜、分子技术,并将其与复杂的采样方法、定量图像分析技术和机器学习相结合,用于各种神经科学和转化研究问题。奖项和荣誉:奥胡斯大学参与多项大型国家和国际研究计划的合作伙伴;欧洲食品安全局(EFSA)科学顾问,国际立体学和图像分析学会前主席。

Jens R. Nyengaard is MD and performs full-time research as Professor and Head of the Core Centre for Molecular Morphology at Aarhus University. Jens is a Guest Professor and course organizer at Sino-Danish Center. His laboratory specializes in light microscopic techniques, advanced fluorescence methods, various types of electron microscopy, molecular techniques, and combines this with complex sampling methods, quantitative image analysis techniques and machine learning for various neuroscience and translational research questions. Awards and honors: Partner in several large national and international research initiatives involving Aarhus University; Scientific adviser in the European Food Safety Authority (EFSA), previous President of International Society for Stereology and Image Analysis

 

Nick专访

问题一:你在中国的研究内容是什么?

Nick本研究项目旨在调查和扩大定量显微镜的适用性,以估计和测量一些极有价值的存档的基于尸检的人类大脑形态变化。研究人员在处理旧的组织样本时面临着难以置信的机遇和巨大的挑战,因为许多免疫标记技术无法用于识别和定位抗原,因为在长期固定过程中,细胞质中的可溶性蛋白通常会受损或丢失。

This research project aimed to investigate and broaden the applicability of quantitative microscopy for estimating and measuring morphological changes in some extremely valuable archived autopsy-based human brains. Researchers face an incredible opportunity as well as a massive challenge when working with old archived tissue samples because many immunolabeling techniques cannot be used to identify and localize antigens due to soluble proteins in the cytoplasm that are commonly damaged or lost during long-term fixation.

 

问题二:在实验中有没有遇到问题?

Nick:在AutoCUTS-LM的开发和优化过程中,我们遇到了一些技术障碍,导致在收集切片时出现了折叠和褶皱。在这里,我们测试了多个可能影响剖面质量的参数,然而,这并没有使任何现实分析成为不可能。经过几个月的测试后,我们意识到,在北京夏季的几个月里,切片上的褶皱数量要比冬季少得多,因此我考虑了这些部分可能会受到环境条件的影响。我们发现北京的湿度在夏天和冬天之间变化很大,然后我买了一个加湿器来提高房间的湿度,这大大改善了部分。在我看来,这个不大不小的发现说明了一个科学问题,一个大家都可能会在科学项目中遇到的普遍未知的科学问题。

During the development and optimization of the AutoCUTS-LM, we ran into some technical obstacles that resulted in folds and wrinkles on the sections while collecting them. Here we tested multiple parameters which could influence the quality of the section, however, that did not make any realistic analysis impossible. We then realized after months of testing that the number of wrinkles on the sections was much less during the summer months compared to the winter months in Beijing. Then I considered how the sections might be affected by environmental conditions. We discovered that the humidity in Beijing changed greatly between the summer and winter seasons. I then bought a humidifier to raise the humidity of the room, which improved the sections greatly. In my opinion,this modest discovery illustrates a common unknown scientific problem that one might come across during a scientific project.

 

问题三:为什么选择中丹学院?你认为中丹学院的培养模式对你的项目和个人发展有什么作用?

Nick国际经验可以帮助你的职业发展。它开阔了一个人的视野,教你如何与来自不同科学领域的人建立关系。以我为例,我们利用了中丹双方的所有资源来完成我的博士研究生学位。在这里,我从丹麦获得了在中国无法获得的生物样本,然后在中国使用一种我帮助开发的新技术对它们进行了采样。因此,如果没有这次合作,我不可能取得我在博士阶段所取得的成果和经历,对此我非常感激。

International experience can help you to advance your career. It broadens one's horizons and teaches you how to form relationships with people from various scientific fields. In my case, we used every available resource available on both the Chinese and Danish sides to complete my Ph.D . research. Here, I acquired biological samples from Denmark that could not be accessed in China and then sampled them in China using a novel technology that I helped develop. Therefore, I would not have been able to achieve the results and experiences that I did during my Ph.D. without this collaboration, for which I am extremely grateful.

我在中丹学院完成了神经科学和神经成像的硕士学位,在那里我获得了更深入的基础、分子、认知和临床神经科学,基于PET/MR的神经成像技术,以及基本的机器学习知识。我在国际化的教育环境中学习了一系列的技术,这使我在与不同研究领域的研究人员更好地互动和形成跨学科合作方面受益匪浅。在中国的工作和学习提升了我的跨文化意识,也给了我提高我的外语技能的机会。

I completed a Master's Degree in Neuroscience & Neuroimaging here in SDC where I obtained a deeper knowledge in basic, molecular, cognitive and clinical neuroscience, PET/MR based neuroimaging techniques, and basic machine learning. As I learned a range of techniques during my education in an international environment, it has benefited me in better interacting and forming interdisciplinary collaborations with researchers across different research areas. Working and studying in China has broadened my cross-cultural awareness while also giving me the opportunity to improve my foreign language skills.

 

问题四:如何评价你的导师?

Nick我要感谢Jens R. Nyengaard教授,我的丹方导师,允许我继续这个博士项目。Jens R. Nyengaard是我见过的最专注、最勤奋的人之一,他完全相信我做出正确决定和独立工作的能力。在我整个博士项目中,他鼓励我相信自己的判断。当我感到沮丧时,他会倾听我的意见,他总是会及时回复我,并为我的挑战提供现实的解决方案。

I would like to thank Professor Jens R. Nyengaard, my principal supervisor, for allowing me to pursue this Ph.D. project. Jens is one of the most dedicated and hardworking individuals I have ever met, and he has complete faith in my ability to make good decisions and work on my own. Throughout my Ph.D. project, his attitude has encouraged me to trust my judgment. He listened to me when I was frustrated, was always approachable around the clock, and provided realistic solutions to challenges .

我的另一位导师,孙飞老师,生物物理所的首席研究员,从一开始就是我博士研究的重要成员。他参与了我在中国工作的每一个阶段。当我因为工作没有如期进行而感到沮丧时,他给了我精神上的支持。他也给了我关于研究的自由,并给我提供了相关的反馈,使我可以成为一个更独立的研究者。
My other supervisor, Dr. Fei Sun, the department's Principal Investigator, has been an integral member of my Ph.D. study from the start. He has been there for me at every stage of my work in China, both technically and personally. When I became discouraged due to the work not progressing as anticipated, he provided me with moral support. He has also given me the freedom to make my own decisions regarding the research and has provided me with relevant feedback so that I may become a more independent researcher.

 

问题五:你对低年级学生有什么建议?

Nick在我看来,作为研究生,找到一个有趣的项目是在开始实验室工作之前要做的最重要的事情。多年来,我遇到过一些学生,他们没有动力去做他们的项目,因为他们觉得很无聊。因此,做一些你感兴趣的事情是非常必要的。

Finding an interesting project to work on as a graduate or Ph.D. student is, in my opinion, one of the most crucial things to do before starting work in a lab. Over the years, I have encountered students who are unmotivated to work on their projects because they find it boring. Therefore, doing something that interests you is very essential.

 

问题六:为什么选择这个项目?

Nick这个科学项目吸引我的是实际工作、数据分析和叙事要清晰的平衡。我必须去奥胡斯的脑库收集精神障碍患者的脑组织。在我们使用人工智能检测和研究组织中的神经元之前,组织必须被处理、嵌入和切割,图像必须被数字化。因此,这个项目有一个明确的路径,我很欣赏。

What attracted me to this scientific project was the balance of practical work, data analysis, and a clear story to tell. I had to go to the brain bank in Aarhus and collect brain tissue from subjects with mental disorders. The tissue had to be processed , embedded, and cut, and the images had to be digitalized before we could use artificial intelligence to detect and study neurons in the tissue.Therefore, there was a clear path of what to do for this project, which I appreciated.

 

问题七:如何评估你的研究的意义?

Nick如果更多的人对我的研究感兴趣,我就认为我的工作是成功的,然后我将把这个方法应用到其他的研究中。但是,现在就下结论还为时过早。

I will consider my work to be a success if more people become interested in my studies, and I will then apply this methodology to other studies. But, it is too early to tell for the time being.

 

导师采访

问题一:孙老师,您觉得中丹学院的项目有哪些优势呢?

孙飞:中丹学院为中方和丹方的老师提供了课题合作的机会。丹方学生加入我们的课题组,不仅为实验室带来了人手,也带来了不同的文化和思想,为双方架起沟通和学习的桥梁;同时中方学生也有机会去到丹麦,这也可以丰富他们的人生经历。

问题二:孙老师,这篇论文的研究成果有哪些重要意义呢?

孙飞:由于中丹学院为双方提供了合作的机会,Nick带来的科学问题和我们成像中心的技术得以结合,从而不仅解决了Nick的科学问题,也促进了我们新技术的发展。这个课题的研究成果是在原有技术的基础上,又建立了一种基于连续半薄切片自动收集的光学显微成像三维重构技术,并通过该技术对储存的人类大脑皮层组织中的锥体细胞进行了三维重构分析。由于患有抑郁症等某些精神疾病的人的脑组织成像与正常人是不同的,通过这个技术,我们可以对死者的脑组织成像进行分析,从而为法医鉴定提供科学依据。

 

Nick Y. Larsen的技术创新成果发表的文章链接:https://www.nature.com/articles/s42003-021-02548-6

 

 

英文/董俊娜 马悦舒 翻译/张宜