Collaborative Research: ABI Innovation: Biofilm Resource and Information Database (BRaID): A Tool to Fuse Diverse Biofilm Data Types

合作研究：ABI 创新：生物膜资源和信息数据库 (BRaID)：融合多种生物膜数据类型的工具

• 批准号: 2027203
• 负责人: Thiruvarangan Ramaraj
• 金额: $ 13.83万
• 依托单位: DePaul University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-11-01 至 2023-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2027203&HistoricalAwards=false
• 关键词: Collaborative; Research; ABI; Innovation; Biofilm

The "Biofilm Resource and Information Database (BRaID)" project is a collaboration between the Center for Biofilm Engineering (CBE) at Montana State University, Bozeman, MT and the Gianforte School of Computing at MSU and the National Center for Genome Resources (NCGR), Santa Fe, NM. Biofilms are microbial communities that have important impacts on water quality, food production, energy-making processes, and various aspects of human and animal health. BRaID serves as a community resource, containing both data and the metadata (where or how data was collected, processed, and interpreted). Some examples of metadata include: a geographical location, such as the Bozeman Water Reclamation Facility; microenvironments such as water chemistry; environmental factors such as changes in temperature, perturbations such as adding corrosion inhibitors; and interventions such as antibiotic treatments. BRaID has utility to a broad range of stakeholders in basic and applied research, as such it is expected to enhance the competitiveness of US industry, basic research, and defense, as well as assist with advancements in human health, environmental health, and energy production. Outreach activities will include (1) dissemination of research outcomes to local community members and industry stakeholders at conferences and legislator engagements; (2) involvement of underrepresented Native American students from high schools and tribal colleges in summer research activities as well as undergraduate researchers at MSU-Bozeman; and (3) educational activities in undergraduate and graduate courses at MSU, as well as summer internship, outreach and training activities at the NCGR.Awareness of the importance of microbial biofilms - microorganisms growing as aggregates attached to surfaces, interfaces, or each other - has exploded in the past decade. Diverse microbial communities grow as biofilms in such settings as dental plaque, heart valves, natural watercourses, wastewater treatment processes, cooling systems, oil and gas pipelines, and persistent infections. Biofilms can have significant impacts on human health, industrial productivity, and natural resources, spanning natural, engineered, and medical systems. Despite the importance of biofilms, there is no public web portal and database dedicated to storage, analysis, and communication of biofilm-specific data. Part of the reason for this is the sheer breadth of data types used to describe biofilms, including nucleotide sequences, images, video, chemistry (water, surface, and extracellular polymer matrix), remediation history, clinical outcomes, and geospatial data. BRaID will complement existing microbial databases by developing a data representation paradigm that solves the problems posed by the challenge arising from the unique combination of data, and will implement new metrics and algorithms for the formal description and analysis of biofilms data. This project aims to provide the premier resource that offers users the ability to ask complex questions (including those currently impossible to answer), permitting quantitative comparisons among biofilms, supporting remediation efforts, and enabling predictions about outcomes. Results of the project can be found at: http://ncgr.org/braid.

“生物膜资源和信息数据库（Braid）”项目是蒙大拿州立大学的生物膜工程中心（CBE），Bozeman，MT，MT，MSU的Gianforte计算学院与国家基因组资源中心（NCGR）（NCGR）的Gianforte Computing Schooling，NM。生物膜是微生物群落，对水质，粮食生产，能源生产过程以及人类和动物健康的各个方面产生重要影响。编织物是一种社区资源，其中包含数据和元数据（收集，处理和解释的数据或方式）。 元数据的一些例子包括：地理位置，例如Bozeman水回开垦设施；微环境，例如水化学；环境因素，例如温度变化，扰动，例如增加腐蚀抑制剂；以及诸如抗生素治疗之类的干预措施。 Braid在基础研究和应用研究方面具有广泛的利益相关者，因此有望提高美国行业，基础研究和防御的竞争力，并协助在人类健康，环境健康和能源生产方面取得进步。外展活动将包括（1）将研究成果传播给会议和立法者参与的当地社区成员和行业利益相关者； （2）来自高中和部落学院的美国原住民学生参与夏季研究活动以及MSU-Bozeman的本科研究人员； （3）MSU的本科和研究生课程的教育活动，以及NCGR的暑期实习，外展和培训活动。在过去的十年中，微生物生物膜的重要性 - 微生物生物膜的重要性 - 随着表面，界面或其他方面的聚集体而生长的微生物。在牙菌斑，心脏瓣膜，天然水道，废水处理过程，冷却系统，石油和天然气管道以及持续感染等环境中，各种微生物群落随着生物膜的生长而生长。生物膜可能会对人类健康，工业生产力和自然资源产生重大影响，涵盖自然，工程和医疗系统。尽管生物膜很重要，但没有专门用于生物膜特定数据的存储，分析和通信的公共网站和数据库。其原因的一部分是用于描述生物膜的数据类型的绝对广度，包括核苷酸序列，图像，视频，化学（水，表面和细胞外聚合物基质），修复历史，临床结果和地理空间数据。 Braid将通过开发一个数据表示范式来补充现有的微生物数据库，该数据表示范式解决了由数据的独特组合引起的挑战所带来的问题，并将实施新的指标和算法，以正式描述和分析生物膜数据。该项目旨在提供主要资源，使用户能够提出复杂问题（包括目前无法回答的问题），允许在生物膜之间进行定量比较，支持补救工作以及对结果的预测。该项目的结果可以在以下网址找到：http：//ncgr.org/braid。

项目成果

Thresholding Approach for Automatic Detection of Pseudomonas aeruginosa Biofilms from Fluorescence in situ Hybridization Images

从荧光原位杂交图像自动检测铜绿假单胞菌生物膜的阈值方法

• 发表时间: 2021
• 期刊: International Journal of Biomedical and Biological Engineering
• 作者: Zonglin Yang, Tatsuya Akiyama