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Article ; Online: Dynamic metabolic engineering: New strategies for developing responsive cell factories.

Brockman, Irene M / Prather, Kristala L J

2015 Volume 10, Issue 9, Page(s) 1360–1369

Abstract: Metabolic engineering strategies have enabled improvements in yield and titer for a variety of valuable small molecules produced naturally in microorganisms, as well as those produced via heterologous pathways. Typically, the approaches have been focused ...

Abstract	Metabolic engineering strategies have enabled improvements in yield and titer for a variety of valuable small molecules produced naturally in microorganisms, as well as those produced via heterologous pathways. Typically, the approaches have been focused on up- and downregulation of genes to redistribute steady-state pathway fluxes, but more recently a number of groups have developed strategies for dynamic regulation, which allows rebalancing of fluxes according to changing conditions in the cell or the fermentation medium. This review highlights some of the recently published work related to dynamic metabolic engineering strategies and explores how advances in high-throughput screening and synthetic biology can support development of new dynamic systems. Dynamic gene expression profiles allow trade-offs between growth and production to be better managed and can help avoid build-up of undesired intermediates. The implementation is more complex relative to static control, but advances in screening techniques and DNA synthesis will continue to drive innovation in this field.
MeSH term(s)	Escherichia coli ; Metabolic Engineering ; Metabolic Networks and Pathways ; Synthetic Biology
Language	English
Publishing date	2015-09
Publishing country	Germany
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	2221885-3
ISSN	1860-7314 ; 1860-6768
ISSN (online)	1860-7314
ISSN	1860-6768
DOI	10.1002/biot.201400422
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Article: Dynamic knockdown of E. coli central metabolism for redirecting fluxes of primary metabolites

Brockman, Irene M / Kristala L.J. Prather

International Metabolic Engineering Society Metabolic engineering. 2015 Mar., v. 28

2015

Abstract: Control of native enzyme levels is important when optimizing strains for overproduction of heterologous compounds. However, for many central metabolic enzymes, static knockdown results in poor growth and protein expression. We have developed a strategy ... ...

Abstract	Control of native enzyme levels is important when optimizing strains for overproduction of heterologous compounds. However, for many central metabolic enzymes, static knockdown results in poor growth and protein expression. We have developed a strategy for dynamically modulating the abundance of native enzymes within the host cell and applied this to a model system for myo-inositol production from glucose. This system relies on controlled degradation of a key glycolytic enzyme, phosphofructokinase-I (Pfk-I). Through tuning Pfk-I levels, we have been able to develop an Escherichia coli strain with a growth mode close to wild type and a production mode with an increased glucose-6-phosphate pool available for conversion into myo-inositol. The switch to production mode is trigged by inducer addition, allowing yield, titer, and productivity to be managed through induction time. By varying the time of Pfk-I degradation, we were able to achieve a two-fold improvement in yield and titers of myo-inositol.
Keywords	enzymes ; Escherichia coli ; glucose ; glucose 6-phosphate ; glycolysis ; metabolites ; myo-inositol ; protein synthesis
Language	English
Dates of publication	2015-03
Size	p. 104-113.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1470383-x
ISSN	1096-7184 ; 1096-7176
ISSN (online)	1096-7184
ISSN	1096-7176
DOI	10.1016/j.ymben.2014.12.005
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Article ; Online: Dynamic knockdown of E. coli central metabolism for redirecting fluxes of primary metabolites.

Brockman, Irene M / Prather, Kristala L J

Metabolic engineering

2014 Volume 28, Page(s) 104–113

Abstract	Control of native enzyme levels is important when optimizing strains for overproduction of heterologous compounds. However, for many central metabolic enzymes, static knockdown results in poor growth and protein expression. We have developed a strategy for dynamically modulating the abundance of native enzymes within the host cell and applied this to a model system for myo-inositol production from glucose. This system relies on controlled degradation of a key glycolytic enzyme, phosphofructokinase-I (Pfk-I). Through tuning Pfk-I levels, we have been able to develop an Escherichia coli strain with a growth mode close to wild type and a production mode with an increased glucose-6-phosphate pool available for conversion into myo-inositol. The switch to production mode is trigged by inducer addition, allowing yield, titer, and productivity to be managed through induction time. By varying the time of Pfk-I degradation, we were able to achieve a two-fold improvement in yield and titers of myo-inositol.
MeSH term(s)	Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Gene Knockdown Techniques ; Glucose-6-Phosphate/genetics ; Glucose-6-Phosphate/metabolism ; Inositol/genetics ; Inositol/metabolism ; Phosphofructokinase-1/genetics ; Phosphofructokinase-1/metabolism
Chemical Substances	Escherichia coli Proteins ; Inositol (4L6452S749) ; Glucose-6-Phosphate (56-73-5) ; Phosphofructokinase-1 (EC 2.7.1.11) ; 1-phosphofructokinase (EC 2.7.1.56)
Language	English
Publishing date	2014-12-24
Publishing country	Belgium
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1470383-x
ISSN	1096-7184 ; 1096-7176
ISSN (online)	1096-7184
ISSN	1096-7176
DOI	10.1016/j.ymben.2014.12.005
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Article ; Online: Improving product yields on D-glucose in Escherichia coli via knockout of pgi and zwf and feeding of supplemental carbon sources.

Shiue, Eric / Brockman, Irene M / Prather, Kristala L J

Biotechnology and bioengineering

2014 Volume 112, Issue 3, Page(s) 579–587

Abstract: The use of lignocellulosic biomass as a feedstock for microbial fermentation processes presents an opportunity for increasing the yield of bioproducts derived directly from glucose. Lignocellulosic biomass consists of several fermentable sugars, ... ...

Abstract	The use of lignocellulosic biomass as a feedstock for microbial fermentation processes presents an opportunity for increasing the yield of bioproducts derived directly from glucose. Lignocellulosic biomass consists of several fermentable sugars, including glucose, xylose, and arabinose. In this study, we investigate the ability of an E. coli Δpgi Δzwf mutant to consume alternative carbon sources (xylose, arabinose, and glycerol) for growth while reserving glucose for product formation. Deletion of pgi and zwf was found to eliminate catabolite repression as well as the ability of E. coli to consume glucose for biomass formation. In addition, the yield from glucose of the bioproduct D-glucaric acid was significantly increased in a Δpgi Δzwf strain.
MeSH term(s)	Biomass ; Bioreactors/microbiology ; Cell Culture Techniques/methods ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Fermentation ; Gene Knockout Techniques ; Glucaric Acid/metabolism ; Glucose/metabolism ; Glucose-6-Phosphate Isomerase/genetics ; Metabolic Engineering/methods
Chemical Substances	Escherichia coli Proteins ; Glucose-6-Phosphate Isomerase (EC 5.3.1.9) ; pgi protein, E coli (EC 5.3.1.9) ; Glucose (IY9XDZ35W2) ; Glucaric Acid (QLZ991V4A2)
Language	English
Publishing date	2014-11-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	280318-5
ISSN	1097-0290 ; 0006-3592
ISSN (online)	1097-0290
ISSN	0006-3592
DOI	10.1002/bit.25470
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Article ; Online: Perspectives of African American Church Leaders in Response to COVID-19 Emergency Preparedness and Risk Communication Efforts Within a Community Engaged Research Partnership: COVID-19 emergency risk communication.

Lalika, Mathias / Salinas, Manisha / Asiedu, Gladys B / Jones, Clarence / Richard, Monisha / Erickson, Jamia / Weis, Jennifer / Abbenyi, Adeline / Brockman, Tabetha A / Sia, Irene G / Wieland, Mark L / White, Richard O / Doubeni, Chyke A / Brewer, LaPrincess C

Disaster medicine and public health preparedness

2023 Volume 17, Page(s) e532

MeSH term(s)	Humans ; Black or African American ; Civil Defense ; Communication ; Community-Based Participatory Research ; COVID-19/epidemiology ; Health Promotion ; Religion ; Leadership
Language	English
Publishing date	2023-10-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2375268-3
ISSN	1938-744X ; 1935-7893
ISSN (online)	1938-744X
ISSN	1935-7893
DOI	10.1017/dmp.2023.182
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Article ; Online: Factors Associated With COVID-19 Vaccine Acceptance Among Patients Receiving Care at a Federally Qualified Health Center.

Lalika, Mathias / Woods, Cynthia / Patel, Aarti / Scott, Christopher / Lee, Alexander / Weis, Jennifer / Jones, Clarence / Abbenyi, Adeline / Brockman, Tabetha A / Sia, Irene G / White, Richard O / Doubeni, Chyke A / Brewer, LaPrincess C

Journal of primary care & community health

2023 Volume 14, Page(s) 21501319231181881

Abstract: Background: COVID-19 vaccine hesitancy in the United States is high, with at least 63 million unvaccinated individuals to date. Socioeconomically disadvantaged populations experience lower COVID-19 vaccination rates despite facing a disproportionate ... ...

Abstract	Background: COVID-19 vaccine hesitancy in the United States is high, with at least 63 million unvaccinated individuals to date. Socioeconomically disadvantaged populations experience lower COVID-19 vaccination rates despite facing a disproportionate COVID-19 burden. Objective: To assess the factors associated with COVID-19 vaccine acceptance among under-resourced, adult patients. Methods: Participants were patients receiving care at a Federally Qualified Health Center (FQHC) in St. Paul, Minnesota. Data were collected via multiple modes over 2 phases in 2020 (self-administered electronic survey) and 2021 (study team-administered survey by telephone, self-administered written survey) to promote diversity and inclusion for study participation. The primary outcome was COVID-19 vaccine acceptance. Using logistic regression analysis, associations between vaccine acceptance and factors including risk perception, concerns about the COVID-19 vaccine, social determinants of health (SDOH), co-morbidities, pandemic-induced hardships, and stress were assessed by adjusted odds ratios (AORs) and 95% confidence intervals (CI). Results: One hundred sixty-eight patients (62.5% female; mean age [SD]: 49.9 [17.4] years; 32% <$20 000 annual household income; 69% <college education) were included in the study. Sixty-one percent of the patients received or were willing to receive the vaccine. Risk perception was positively associated with vaccine acceptance (AOR: 5.3; 95% CI: 2.5, 11.5, <br />Conclusions: Our study in a socioeconomically disadvantaged population suggests that risk perception is associated with an increased likelihood of vaccine acceptance, while concerns about the COVID-19 vaccine are associated with a lower likelihood of vaccine acceptance. As these factors could impact vaccine uptake, consistent, innovative, and context-specific risk communication strategies may improve vaccine coverage in this population.
MeSH term(s)	Adult ; Humans ; Female ; Adolescent ; Male ; COVID-19 Vaccines/therapeutic use ; COVID-19/prevention & control ; Communication ; Electronics ; Health Facilities ; Vaccination
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2023-06-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	2550221-9
ISSN	2150-1327 ; 2150-1319
ISSN (online)	2150-1327
ISSN	2150-1319
DOI	10.1177/21501319231181881
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Article ; Online: Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit.

Gupta, Apoorv / Reizman, Irene M Brockman / Reisch, Christopher R / Prather, Kristala L J

Nature biotechnology

2017 Volume 35, Issue 3, Page(s) 273–279

Abstract: Metabolic engineering of microorganisms to produce desirable products on an industrial scale can result in unbalanced cellular metabolic networks that reduce productivity and yield. Metabolic fluxes can be rebalanced using dynamic pathway regulation, but ...

Abstract	Metabolic engineering of microorganisms to produce desirable products on an industrial scale can result in unbalanced cellular metabolic networks that reduce productivity and yield. Metabolic fluxes can be rebalanced using dynamic pathway regulation, but few broadly applicable tools are available to achieve this. We present a pathway-independent genetic control module that can be used to dynamically regulate the expression of target genes. We apply our module to identify the optimal point to redirect glycolytic flux into heterologous engineered pathways in Escherichia coli, resulting in titers of myo-inositol increased 5.5-fold and titers of glucaric acid increased from unmeasurable to >0.8 g/L, compared to the parent strains lacking dynamic flux control. Scaled-up production of these strains in benchtop bioreactors resulted in almost ten- and fivefold increases in specific titers of myo-inositol and glucaric acid, respectively. We also used our module to control flux into aromatic amino acid biosynthesis to increase titers of shikimate in E. coli from unmeasurable to >100 mg/L.
MeSH term(s)	Computer Simulation ; Escherichia coli/physiology ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Gene Expression Regulation, Bacterial/physiology ; Metabolic Engineering/methods ; Metabolic Flux Analysis/methods ; Metabolome/physiology ; Models, Biological ; Quorum Sensing/physiology ; Signal Transduction/physiology
Chemical Substances	Escherichia coli Proteins
Language	English
Publishing date	2017-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/nbt.3796
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Article ; Online: Longitudinal ex vivo and molecular trends of chloroquine and piperaquine activity against Plasmodium falciparum and P. vivax before and after introduction of artemisinin-based combination therapy in Papua, Indonesia.

International journal for parasitology. Drugs and drug resistance

2021 Volume 17, Page(s) 46–56

Abstract: Drug resistant Plasmodium parasites are a major threat to malaria control and elimination. After reports of high levels of multidrug resistant P. falciparum and P. vivax in Indonesia, in 2005, the national first-line treatment policy for uncomplicated ... ...

Abstract	Drug resistant Plasmodium parasites are a major threat to malaria control and elimination. After reports of high levels of multidrug resistant P. falciparum and P. vivax in Indonesia, in 2005, the national first-line treatment policy for uncomplicated malaria was changed in March 2006, to dihydroartemisinin-piperaquine against all species. This study assessed the temporal trends in ex vivo drug susceptibility to chloroquine (CQ) and piperaquine (PIP) for both P. falciparum and P. vivax clinical isolates collected between 2004 and 2018, by using schizont maturation assays, and genotyped a subset of isolates for known and putative molecular markers of CQ and PIP resistance by using Sanger and next generation whole genome sequencing. The median CQ IC
MeSH term(s)	Antimalarials/pharmacology ; Antimalarials/therapeutic use ; Artemisinins/pharmacology ; Artemisinins/therapeutic use ; Chloroquine/pharmacology ; Chloroquine/therapeutic use ; Drug Resistance/genetics ; Humans ; Indonesia/epidemiology ; Malaria, Falciparum/drug therapy ; Malaria, Falciparum/epidemiology ; Plasmodium falciparum/genetics ; Plasmodium vivax/genetics ; Protozoan Proteins/genetics ; Quinolines
Chemical Substances	Antimalarials ; Artemisinins ; Protozoan Proteins ; Quinolines ; Chloroquine (886U3H6UFF) ; piperaquine (A0HV2Q956Y)
Language	English
Publishing date	2021-06-21
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2751132-7
ISSN	2211-3207 ; 2211-3207
ISSN (online)	2211-3207
ISSN	2211-3207
DOI	10.1016/j.ijpddr.2021.06.002
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Article ; Online: Club Fit: Development of a Physical Activity and Healthy Eating Intervention at a Boys & Girls Club After School Program.

Wieland, Mark L / Biggs, Bridget K / Brockman, Tabetha A / Johnson, Amy / Meiers, Sonja J / Sim, Leslie A / Tolleson, Ellen / Hanza, Marcelo M / Weis, Jennifer A / Rosenman, Jane R / Novotny, Paul J / Patten, Christi A / Clark, Matthew M / Millerbernd, Jodi / Sia, Irene G

The journal of primary prevention

2020 Volume 41, Issue 2, Page(s) 153–170

Abstract: Children and adolescents from minority and low income backgrounds face social and environmental challenges to engaging in physical activity and healthy eating to maintain a healthy weight. In this study, we present pilot work to develop and implement a ... ...

Abstract	Children and adolescents from minority and low income backgrounds face social and environmental challenges to engaging in physical activity and healthy eating to maintain a healthy weight. In this study, we present pilot work to develop and implement a multi-component physical activity and healthy eating intervention at a Boys & Girls Club (BGC) afterschool program. Using a community-based participatory approach, BGC staff and academic researchers developed intervention components informed by formative studies and based on a Social Ecological Theory framework. Components included healthy eating and physical activity policy implementation, staff training, a challenge and self-monitoring program for healthy behaviors, a peer-coaching program for healthy behaviors, and a social marketing campaign. We assessed pilot feasibility through a single group, pre-post study design with measures collected at baseline and 6 months. The sample included 61 children with a mean age of 10.4 years. Mean (SD) body mass index (BMI) percentile was 72.8 (28.9); 47.5% were in the healthy weight range for their age. We found statistically significant improvements of self-efficacy and motivation for physical activity. Self-efficacy and motivation for fruit and vegetable consumption, sugary beverage consumption, and screen time improved but were not statistically different from baseline. We found no improvements of perceived social support, objectively measured physical activity, or self-reported dietary quality. Though BMI did not improve overall, a dose effect was observed such that attendance in Club Fit specific programming was significantly correlated with decreased BMI z scores. Processes and products from this study may be helpful to other communities aiming to address childhood obesity prevention through afterschool programs.
Language	English
Publishing date	2020-02-21
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	622512-3
ISSN	1573-6547 ; 0278-095X
ISSN (online)	1573-6547
ISSN	0278-095X
DOI	10.1007/s10935-020-00582-4
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Article: Improvement of glucaric acid production in

Reizman, Irene M Brockman / Stenger, Andrew R / Reisch, Chris R / Gupta, Apoorv / Connors, Neal C / Prather, Kristala L J

Metabolic engineering communications

2015 Volume 2, Page(s) 109–116

Abstract: D-glucaric acid can be used as a building block for biopolymers as well as in the formulation of detergents and corrosion inhibitors. A biosynthetic route for production ... ...

Abstract	D-glucaric acid can be used as a building block for biopolymers as well as in the formulation of detergents and corrosion inhibitors. A biosynthetic route for production in
Language	English
Publishing date	2015-09-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2821894-2
ISSN	2214-0301
ISSN	2214-0301
DOI	10.1016/j.meteno.2015.09.002
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