Training Program in Quantitative Integrative Biology

项目摘要 加州大学数量综合生物学(QIB)博士前培训计划的总体目标是， 圣地亚哥大学(UCSD)将汇集具有广泛和互补的研究专业知识的教师来培养毕业生 让学生研究系统生理学中的当前问题。中的一组细胞表现出的集体行为 发育、再生和动态平衡的组织和器官实质上超过其各部分的总和，并且需要 细胞、组织和器官之间持续的多层次协作。了解其本质和作用机制 在这种合作的基础上，QIB计划包括使用各种不同 定量工具和方法，以解决与生物发育和再生、组织和 器官生理学，以及这些现象在细胞-细胞交流、相互作用和集体细胞行为中的基础。 认识到生物体的细胞和组织不是孤立地生存，而是与复杂的微生物共生 影响寄主健康的社区，QIB还包括一组具有人类专业知识的教员 微生物组，他们正在开发预测和调节微生物组组成并设计其行为的方法 来影响疾病的进展。QIB项目总共由加州大学圣迭戈分校的27名以数量为导向的教师组成 生物系，物理科学系，医学院和药学院，都位于 在加州大学圣迭戈分校的校园里，彼此距离很近。这群教员拥有惊人的研究成就， 每年带来近2900万美元的研究资金。 QIB项目的中心内容是培训学生开发实验工具和整合现代理论 方法研究他们在数量生理学方面的研究。该计划是更广泛的校园范围的组成部分 数量生物学(QBio)倡议，得到了大量的机构支持，包括2,000平方英尺。英国《金融时报》的 专门的空间和100万美元的独特设备投资，用于一个名为qBio的现代教学实验室，旨在 培养学生不仅使用现代工具和方法进行生命科学研究，而且赋予他们 具有修改现有工具并使其适应特定研究项目的能力和思维定力。这项提案旨在培训6名 每年有博士前学生，另外还有两个由研究生办公室和 常务副校长，从研究生二年级开始，为期12个月。这项建议 为来自以下四个系/方案之一的学生设立特殊课程：物理系、系 化学和生物化学系(均在物理科学系)、生物科学系和 生物医学研究生课程。该课程包括多门定量方法课程。 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 职业成长(批判性阅读、研究报告、个人和职业指导)。符合条件的学生人数众多 因为这个新的培训计划非常好--我们教员实验室71名研究生中有52名(73%) [过去10年内178人中的132人(74%)]将有资格参加该计划。给定 加州大学圣地亚哥分校在跨学科和协作研究方面的优势，优秀的合格学员队伍，以及广泛的 与之配套的培训师资队伍有着精湛的研究、培训和资金记录，我们相信我们的QIB 该计划为在非常重要的领域进行量化研究提供了一个绝佳而独特的培训机会 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.