Department of Biological Systems Engineering

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https://hdl.handle.net/10919/24227

Biological Systems Engineering (BSE) is the engineering discipline that applies concepts of biology, chemistry and physics, along with engineering science and design principles, to solve problems in biological systems. Our faculty and students work in a broad range of biological systems, from natural systems, such as watersheds with a focus on water resources, to built systems, such as bioreactors and bioprocessing facilities. We work from the nanoscale to the macroscale. We seek to improve animal, human, and environmental health through development and design of healthy food products, vaccines, bioenergy, biomaterials, and water quality management practices. We convert biological resources, such as switchgrass, plant proteins, and animal manure, into value-added products, such as biopharmaceuticals, biofuels, and biomaterials, in a sustainable manner.

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Now showing 1 - 20 of 2035

13C-Metabolic Flux Analysis: An Accurate Approach to Demystify Microbial Metabolism for Biochemical Production
Guo, Weihua; Sheng, Jiayuan; Feng, Xueyang (MDPI, 2015-12-25)
Metabolic engineering of various industrial microorganisms to produce chemicals, fuels, and drugs has raised interest since it is environmentally friendly, sustainable, and independent of nonrenewable resources. However, microbial metabolism is so complex that only a few metabolic engineering efforts have been able to achieve a satisfactory yield, titer or productivity of the target chemicals for industrial commercialization. In order to overcome this challenge, ¹³C Metabolic Flux Analysis (¹³C-MFA) has been continuously developed and widely applied to rigorously investigate cell metabolism and quantify the carbon flux distribution in central metabolic pathways. In the past decade, many ¹³C-MFA studies have been performed in academic labs and biotechnology industries to pinpoint key issues related to microbe-based chemical production. Insightful information about the metabolic rewiring has been provided to guide the development of the appropriate metabolic engineering strategies for improving the biochemical production. In this review, we will introduce the basics of ¹³C-MFA and illustrate how ¹³C-MFA has been applied via integration with metabolic engineering to identify and tackle the rate-limiting steps in biochemical production for various host microorganisms
Accelerating structure-function mapping using the ViVa webtool to mine natural variation
Hamm, Morgan; Moss, Britney; Leydon, Alexander; Gala, Hardik; Lanctot, Amy; Ramos, Román; Klaeser, Hannah; Lemmex, Andrew; Zahler, Mollye; Nemhauser, Jennifer L.; Wright, R. Clay (Wiley, 2018-12-05)
Thousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of this data remains inaccessible to researchers without significant bioinformatics experience. Here, we present a webtool called ViVa (Visualizing Variation) which aims to empower any researcher to take advantage of the amazing genetic resource collected in the Arabidopsis thaliana 1001 Genomes Project (http://1001genomes.org). ViVa facilitates data mining on the gene, gene family or gene network level. To test the utility and accessibility of ViVa, we assembled a team with a range of expertise within biology and bioinformatics to analyze the natural variation within the well-studied nuclear auxin signaling pathway. Our analysis has provided further confirmation of existing knowledge and has also helped generate new hypotheses regarding this well studied pathway. These results highlight how natural variation could be used to generate and test hypotheses about less studied gene families and networks, especially when paired with biochemical and genetic characterization. ViVa is also readily extensible to databases of interspecific genetic variation in plants as well as other organisms, such as the 3,000 Rice Genomes Project (http://snp-seek.irri.org/) and human genetic variation (https://www.ncbi.nlm.nih.gov/clinvar/).
Advancements in the development of HIF-1α-activated protein switches for use in enzyme prodrug therapy
Wright, R. Clay; Khakhar, Arjun; Eshleman, James R.; Ostermeier, Marc (2014-01)
While gene-directed enzyme prodrug therapy has shown potential as a cancer therapeutic in animal and clinical trials, concerns over the efficacy, selectivity, and safety of gene delivery vehicles have restricted its advance. In an attempt to relieve some of the demands on targeted gene delivery vehicles and achieve the full potential of enzyme prodrug therapy, cancer-targeted activity can be engineered into the enzyme itself. We previously engineered a switchable prodrug-activating enzyme that selectively kills human cancer cells accumulating the cancer marker hypoxia-inducible factor-1α (HIF-1α). This HIF-1α-activated protein switch (Haps59) is designed to increase its ability to convert the prodrug 5-fluorocytosine into the chemotherapeutic 5-fluorouracil in a HIF-1α-dependent manner. However, in cancer cell lines expressing Haps59 the 5FC sensitivity difference between the presence and absence of HIF-1α was not as large as desired. In this work, we aimed to improve the cancer specificity of this switch via a directed evolution approach utilizing random mutagenesis, linker mutagenesis, and random insertion and circular permutation. We identified improved HIF-1α-activated protein switches that confer E. coli with modest increases in HIF-1α-dependent 5FC toxicity. Additionally, the current bottleneck in the development of improved HIF-1α-activated protein switches is screening switch candidates in mammalian cells. To accommodate higher throughput and reduce experimental variability, we explored the use of Flp recombinase-mediated isogenic integration in 293 cells. These experiments raised the possibility that Haps59 can be activated by other interactors of the CH1 domain, and experiments in E. coli indicated that CITED2 can also activate Haps59. Although many CH1 binding partners are also oncogenes, CH1's promiscuous binding and subsequent off-target activation of Haps59 needs to be examined under normal physiological conditions to identify off-target activators. With aberrant activating molecules identified, further directed evolution can be performed to improve the cancer specificity of HIF-1α-activated protein switches.
Advances in Biochemical Engineering-Biotechnology
Zhang, Y. H. Percival; Rollin, Joseph A.; Ye, Xinhao; Del Campo, Julia S. Martin; Adams, Michael W. W. (Springer, 2014-07-15)
In vitro hydrogen generation represents a clear opportunity for novel bioreactor and system design. Hydrogen, already a globally important commodity chemical, has the potential to become the dominant transportation fuel of the future. Technologies such as in vitro synthetic pathway biotransformation (SyPaB)—the use of more than 10 purified enzymes to catalyze unnatural catabolic pathways—enable the storage of hydrogen in the form of carbohydrates. Biohydrogen production from local carbohydrate resources offers a solution to the most pressing challenges to vehicular and bioenergy uses: small-size distributed production, minimization of CO2 emissions, and potential low cost, driven by high yield and volumetric productivity. In this study, we introduce a novel bioreactor that provides the oxygen-free gas phase necessary for enzymatic hydrogen generation while regulating temperature and reactor volume. A variety of techniques are currently used for laboratory detection of biohydrogen, but the most information is provided by a continuous low-cost hydrogen sensor. Most such systems currently use electrolysis for calibration; here an alternative method, flow calibration, is introduced. This system is further demonstrated here with the conversion of glucose to hydrogen at a high rate, and the production of hydrogen from glucose 6-phosphate at a greatly increased reaction rate, 157 mmol/L/h at 60 [degrees] C.
Advances in Watershed Management: Modeling, Monitoring, and Assessment
Benham, Brian L.; Yagow, Eugene R.; Chaubey, I.; Douglas-Mankin, K. R. (American Society of Agricultural and Biological Engineers, 2011)
This article introduces a special collection of nine articles that address a wide range of topics all related to improving the application of watershed management planning. The articles are grouped into two broadly defined categories.. modeling applications, and monitoring and assessment. The modeling application articles focus on one of two widely used watershed-scale water quality modeling packages: HSPF or SWAT The HSPF article assesses the model's robustness when applied to watersheds across a range of topographic settings and climatic conditions. In the SWAT-related articles, researchers used the model to inform watershed management efforts in a variety of ways, including subwatershed prioritization in the context of achieving broader watershed management goals, examining the utility of applying SWAT in a watershed receiving groundwater inputs from outside the topographic watershed boundaries, and estimating the uncertainty and risk associated with meeting TMDL target loads. The monitoring and assessment articles cover such diverse topics as an examination of how best management practice effectiveness is assessed, examination of estimated nutrient loads to a reservoir where a nutrient TMDL has been developed, examination of the sources of fecal indicator bacteria in an urban watershed, and detailed accounting of issues related to flow measurements in small watersheds. The articles in this collection contribute to the body of literature that seeks to inform and advance sound watershed management planning and execution.
AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata
Liang, Xiao; Akers, Kyle; Keenum, Ishi M.; Wind, Lauren L.; Gupta, Suraj; Chen, Chaoqi; Aldaihani, Reem; Pruden, Amy; Zhang, Liqing; Knowlton, Katharine F.; Xia, Kang; Heath, Lenwood S. (2021-03-10)
Background Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of antibiotic resistance. However, the ability to compare the distribution and prevalence of antibiotic resistance genes (ARGs) across multiple studies and environments is currently impossible without a complete re-analysis of published datasets. This challenge must be addressed for metagenomics to realize its potential for helping guide effective policy and practice measures relevant to agricultural ecosystems, for example, identifying critical control points for mitigating the spread of antibiotic resistance. Results Here we introduce AgroSeek, a centralized web-based system that provides computational tools for analysis and comparison of metagenomic data sets tailored specifically to researchers and other users in the agricultural sector interested in tracking and mitigating the spread of ARGs. AgroSeek draws from rich, user-provided metagenomic data and metadata to facilitate analysis, comparison, and prediction in a user-friendly fashion. Further, AgroSeek draws from publicly-contributed data sets to provide a point of comparison and context for data analysis. To incorporate metadata into our analysis and comparison procedures, we provide flexible metadata templates, including user-customized metadata attributes to facilitate data sharing, while maintaining the metadata in a comparable fashion for the broader user community and to support large-scale comparative and predictive analysis. Conclusion AgroSeek provides an easy-to-use tool for environmental metagenomic analysis and comparison, based on both gene annotations and associated metadata, with this initial demonstration focusing on control of antibiotic resistance in agricultural ecosystems. Agroseek creates a space for metagenomic data sharing and collaboration to assist policy makers, stakeholders, and the public in decision-making. AgroSeek is publicly-available at https://agroseek.cs.vt.edu/ .
Analysis of crab meat volatiles as possible spoilage indicators for blue crab (Callinectes sapidus) meat by gas chromatography-mass spectrometry
Sarnoski, Paul J.; O'Keefe, Sean F.; Jahncke, Michael L.; Mallikarjunan, Parameswarakumar; Flick, George J. Jr. (Elsevier, 2010-10-01)
Traditionally crab meat spoilage has been evaluated using sensory panels. A method was developed using solid-phase microextraction–gas chromatography–mass spectrometry (SPME–GC–MS) to examine the aroma profile of blue crab (Callinectes sapidus) for chemical indicators of spoilage. The chemicals found to correlate best with spoilage were trimethylamine (TMA), ammonia, and indole over a period of 7 days. In addition, chemicals previously not identified in the aroma profile of blue crab were tentatively detected. Scan mode of the mass spectrometer was used to qualitatively determine compounds extracted from the volatile profile of spoiling blue crab by the SPME fiber. Selected ion monitoring (SIM) mode of the mass spectrometer improved resolution, identified compounds at low concentrations, and allowed spoilage related compounds to be detected in one chromatographic run without sample heating. TMA increased linearly. A significant difference in TMA concentrations were found for day 0 and day 4 samples. Indole concentrations corresponded well with sensory and microbial evaluations, in early, mid, and highly spoiled crab meat samples.
Annual Report of AE Extension Project 10, with Project Statements
Seitz, Charles E. (1924)
Annual Report for Project 10 detailing Virginia Cooperative Extension activities in 1924, with project statements.
Annual Report of Agricultural Engineering Department, Extension Division
Seitz, Charles E. (1920)
Summary of extension projects coordinated through the Agricultural Engineering Department for 1919-20.
Annual Report of Agricultural Engineering Department, Extension Division
(1921)
Summary of extension projects coordinated through the Agricultural Engineering Department for 1920-21.
Annual Report of Agricultural Engineering Extension Project 10
Seitz, Charles E. (1924)
Annual Report for Project 10 detailing Virginia Cooperative Extension activities in 1924.
Annual Report of Agricultural Engineering Extension Project 10, (copy 2)
Seitz, Charles E. (1923)
Annual Report for Project 10 detailing Virginia Cooperative Extension activities in 1923.
Annual Report of Agricultural Engineering Extension Project 10, with photos
Seitz, Charles E. (1923)
Annual Report for Project 10 detailing Virginia Cooperative Extension activities in 1923.
Annual Report of Agricultural Engineering Resident Instruction
Seitz, Charles E. (1930)
Summary of activities related to instruction provided through the Agricultural Engineering Department.
Annual Report of Drainage Work for 1914
Seitz, Charles E. (1914)
Report of drainage work and drainage tile system surveys as applied to farms in Virginia.
Annual Report of Extension Work in Land Drainage for 1915 (2nd copy)
Seitz, Charles E. (1915)
Summary of drainage work related to farm land, swamp lands, and river and creek bed lands for Virginia Farmers.
Annual Report of Extension Work in Land Drainage for 1915, and plan for 1916
Seitz, Charles E. (1915)
Summary of drainage work related to farm land, swamp lands, and river and creek bed lands for Virginia Farmers.
Annual Report of Soil and Water Conservation Research, 1942
(1942)
Summary report of soil and water conservation research for 1941 – 1942.
Annual Report of Soil and Water Conservation Research, 1943
(1943)
Summary report of soil and water conservation research for 1942 – 1943.
Annual Report of Soil and Water Conservation Research, 1944 (semi-final)
(1944)
Summary report of soil and water conservation research for 1943 – 1944.

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