Training Program in Quantitative Integrative Biology

项目摘要 加州大学定量整合生物学（QIB）博士前培训计划的总体目标， 圣地亚哥大学（UCSD）将汇集具有广泛和互补研究专长的教师， 学生研究系统生理学中的当前问题。细胞群的集体行为表现在 组织和器官的发育、再生和自我平衡远远超过其各部分的总和， 细胞、组织和器官之间持续的多层次协作。为了理解 在这种合作的基础上，QIB计划包括一个多样化的培训教师集合，他们使用各种 定量工具和方法，以解决与生物体发育和再生，组织和 器官生理学，以及细胞间通讯、相互作用和集体细胞行为中这些现象的基础。 认识到生物体的细胞和组织不是孤立地生活，而是与复杂的微生物共生， 影响宿主健康的社区，QIB还包括一组具有人类健康专业知识的教师。 微生物组，他们正在开发预测和调节微生物组组成的方法，并设计其行为 影响疾病的发展总的来说，QIB计划包括27个定量导向的教师从加州大学圣地亚哥分校 生物学系，物理科学系，以及医学院和药学院，都位于 在加州大学圣地亚哥分校校园里彼此非常接近。这群教师拥有惊人的研究成就， 每年带来近2900万美元的研究经费总额。 QIB计划的核心要素是培养学生开发实验工具，并将现代理论 他们在定量生理学的研究方法。该计划是一个更广泛的校园范围的组成部分 定量生物学（qBio）倡议，该倡议得到了大量的机构支持，包括2,000平方米。英尺的 专门的空间和100万美元的独特设备投资，为现代教学实验室被称为qBio“黑客实验室”，旨在 培养学生不仅要使用现代工具和方法进行生命科学研究，而且要赋予他们 修改现有工具并使其适应特定研究项目的能力和心态。该项目旨在培养6名 博士前的学生，每年有2个额外的匹配插槽与研究生研究办公室和 执行副校长，从研究生学习的第二年开始，为期12个月。该提案 为四个部门/计划之一的学生建立了特殊的课程：物理系，系 化学与生物化学（均在物理科学部），生物科学部，以及 生物医学科学研究生课程。该课程包括定量方法的多门课程， 生理学，为期一年的实验工具开发和应用培训（qBio黑客实验室），以及 专业成长（批判性阅读、研究报告、个人和职业指导）。合格的学生 对于这个新的培训计划是优秀的- 52出的71（73%），目前在我们学院的实验室研究生 [or在过去10年内，178人中有132人（74%）有资格参加该计划。鉴于 UCSD在跨学科和合作研究方面的实力，合格学员的优秀人才库，以及广泛的 和互补的培训教师与一流的研究，培训和资金记录，我们相信，我们的QIB 该计划提供了一个非常重要的领域定量导向的研究优秀和独特的培训机会 系统生理学。

Project Summary The overall goal of the pre-doctoral training program in Quantitative Integrative Biology (QIB) at University of California, San Diego (UCSD) is to bring together faculty with broad and complementary research expertise to train graduate students to investigate current questions in systems physiology. The collective behavior exhibited by groups of cells in developing, regenerating and homeostatic tissues and organs is substantially more than the sum of its parts, and requires continuous multi-level collaborations between cells, tissues, and organs. To understand the nature and mechanisms underlying such collaborations, the QIB program includes a diverse collection of training faculty who use a variety of quantitative tools and approaches to address questions related to organismal development and regeneration, tissue and organ physiology, and the basis of these phenomena in cell-cell communication, interactions and collective cell behaviors. Recognizing that cells and tissues of an organism do not live in isolation, but in a symbiotic state with complex microbial communities affecting the health of the host, QIB also includes a group of faculty with expertise in the human microbiome, who are developing approaches to predict and modulate microbiome composition, and engineer its behavior to affect disease progression. Altogether, the QIB program comprise of 27 quantitatively-oriented faculty from the UCSD Division of Biology, Division of Physical Sciences, and from the Medical School and Pharmacy School, all located in close proximity to each other on the UCSD campus. This group of faculty boasts of spectacular research accomplishments, bringing almost $29M annually in total research funding. The central element of the QIB program is to train students to develop experimental tools and integrate modern theoretical methods into their research in quantitative physiology. This program is a component of a broader campus wide Quantitative Biology (qBio) initiative, which has received substantial institutional support, including 2,000 sq. ft. of dedicated space and $1M investment in unique equipment for a modern teaching lab dubbed the qBio “hacker lab”, aimed to train students not only to work with modern tools and methodology for life science studies, but to endow them with the ability and mind-set to modify existing tools and adapt them to specific research projects. This proposal aims to train 6 pre-doctoral students each year, with 2 additional matching slots with funds from the Office of Graduate Studies and the Executive Vice Chancellor, starting in their second year of graduate studies for a 12-month period. The proposal establishes a special curriculum for students from one of four departments/programs: Department of Physics, Department of Chemistry & Biochemistry (both in the Division of Physical Sciences), Division of Biological Sciences, and the Graduate Program in Biomedical Sciences. The curriculum includes multiple courses in quantitative methods in physiology, year-long training in experimental tool development and application (the qBio hacker lab), and mentoring in professional growth (critical reading, research presentation, personal and career guidance). The pool of students qualified for this new training program is excellent – 52 out of the 71 (73%) of the current graduate students in our faculty's labs [or 132 out of 178 (74%) within the past 10 years] would have been eligible to participate in the program. Given the strength of UCSD in interdisciplinary and collaborative research, the outstanding pool of qualified trainees, and a broad and complementary set of training faculty with superb research, training, and funding record, we believe that our QIB program offers an excellent and unique training opportunity for quantitative-oriented research in the very important field of systems physiology.