Regional, institutional, and departmental factors associated with gender diversity among BS-level chemical and electrical engineering graduates

Engineering remains the least gender diverse of the science, technology, engineering and mathematics fields. Chemical engineering (ChE) and electrical engineering (EE) are exemplars of relatively high and low gender diversity, respectively. Here, we investigate departmental, institutional, and regional factors associated with gender diversity among BS graduates within the US, 2010–2016. For both fields, gender diversity was significantly higher at private institutions (p \u3c 1x10-6) and at historically black institutions (p \u3c 1x10-5). No significant association was observed with gender diversity among tenure-track faculty, PhD-granting status, and variations in departmental name beyond the standard “chemical engineering” or “electrical engineering”. Gender diversity among EE graduates was significantly decreased (p = 8x10-5) when a distinct degree in computer engineering was available; no such association was observed between ChE gender diversity and the presence of biology-associated degrees. States with a highly gender diverse ChE workforce had a significantly higher degree of gender diversity among BS graduates (p = 3x10-5), but a significant association was not observed for EE. State variation in funding of support services for K-12 pupils significantly impacted gender diversity of graduates in both fields (p \u3c 1x10-3), particularly in regards to instructional staff support (p \u3c 5x10-4). Nationwide, gender diversity could not be concluded to be either significantly increasing or significantly decreasing for either field

Metabolic engineering of biocatalysts for carboxylic acids production

Fermentation of renewable feedstocks by microbes to produce sustainable fuels and chemicals has the potential to replace petrochemical-based production. For example, carboxylic acids produced by microbial fermentation can be used to generate primary building blocks of industrial chemicals by either enzymatic or chemical catalysis. In order to achieve the titer, yield and productivity values required for economically viable processes, the carboxylic acid-producing microbes need to be robust and wellperforming. Traditional strain development methods based on mutagenesis have proven useful in the selection of desirable microbial behavior, such as robustness and carboxylic acid production. On the other hand, rationally-based metabolic engineering, like genetic manipulation for pathway design, has becoming increasingly important to this field and has been used for the production of several organic acids, such as succinic acid, malic acid and lactic acid. This review investigates recent works on Saccharomyces cerevisiae and Escherichia coli , as well as the strategies to improve tolerance towards these chemicals

Engineering inhibitor tolerance for the production of biorenewable fuels and chemicals

Metabolic Engineering has enabled the production of biorenewable fuels and chemicals from biomass using recombinant bacteria. The economic viability of these processes is often limited by inhibition of the biocatalyst by the metabolic product, such as a carboxylic acid or alcohol, or by contaminant compounds in the biomass-derived sugars, such as acetic acid or furans. Historically, selection-based methods have been used to improve biocatalyst tolerance to these inhibitors. But recently, genome-wide analysis has been used to both identify the mechanism of inhibition and reverse engineer inhibitor-tolerant strains, enabling the rational, predictive manipulation of bacteria in order to increase inhibitor tolerance. Here we review recent work in this area, particularly in relation to carboxylic acids, furfural and butanol

Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities

<p>Abstract</p> <p>Background</p> <p>Gene regulatory networks play essential roles in living organisms to control growth, keep internal metabolism running and respond to external environmental changes. Understanding the connections and the activity levels of regulators is important for the research of gene regulatory networks. While relevance score based algorithms that reconstruct gene regulatory networks from transcriptome data can infer genome-wide gene regulatory networks, they are unfortunately prone to false positive results. Transcription factor activities (TFAs) quantitatively reflect the ability of the transcription factor to regulate target genes. However, classic relevance score based gene regulatory network reconstruction algorithms use models do not include the TFA layer, thus missing a key regulatory element.</p> <p>Results</p> <p>This work integrates TFA prediction algorithms with relevance score based network reconstruction algorithms to reconstruct gene regulatory networks with improved accuracy over classic relevance score based algorithms. This method is called Gene expression and Transcription factor activity based Relevance Network (GTRNetwork). Different combinations of TFA prediction algorithms and relevance score functions have been applied to find the most efficient combination. When the integrated GTRNetwork method was applied to <it>E. coli </it>data, the reconstructed genome-wide gene regulatory network predicted 381 new regulatory links. This reconstructed gene regulatory network including the predicted new regulatory links show promising biological significances. Many of the new links are verified by known TF binding site information, and many other links can be verified from the literature and databases such as EcoCyc. The reconstructed gene regulatory network is applied to a recent transcriptome analysis of <it>E. coli </it>during isobutanol stress. In addition to the 16 significantly changed TFAs detected in the original paper, another 7 significantly changed TFAs have been detected by using our reconstructed network.</p> <p>Conclusions</p> <p>The GTRNetwork algorithm introduces the hidden layer TFA into classic relevance score-based gene regulatory network reconstruction processes. Integrating the TFA biological information with regulatory network reconstruction algorithms significantly improves both detection of new links and reduces that rate of false positives. The application of GTRNetwork on <it>E. coli </it>gene transcriptome data gives a set of potential regulatory links with promising biological significance for isobutanol stress and other conditions.</p

Understanding biocatalyst inhibition by carboxylic acids

Carboxylic acids are an attractive biorenewable chemical in terms of their flexibility and usage as precursors for a variety of industrial chemicals. It has been demonstrated that such carboxylic acids can be fermentatively produced using engineered microbes, such as Escherichia coli andSaccharomyces cerevisiae. However, like many other attractive biorenewable fuels and chemicals, carboxylic acids become inhibitory to these microbes at concentrations below the desired yield and titer. In fact, their potency as microbial inhibitors is highlighted by the fact that many of these carboxylic acids are routinely used as food preservatives. This review highlights the current knowledge regarding the impact that saturated, straight-chain carboxylic acids, such as hexanoic, octanoic, decanoic, and lauric acids can have on E. coli and S. cerevisiae, with the goal of identifying metabolic engineering strategies to increase robustness. Key effects of these carboxylic acids include damage to the cell membrane and a decrease of the microbial internal pH. Certain changes in cell membrane properties, such as composition, fluidity, integrity, and hydrophobicity, and intracellular pH are often associated with increased tolerance. The availability of appropriate exporters, such as Pdr12, can also increase tolerance. The effect on metabolic processes, such as maintaining appropriate respiratory function, regulation of Lrp activity and inhibition of production of key metabolites such as methionine, are also considered. Understanding the mechanisms of biocatalyst inhibition by these desirable products can aid in the engineering of robust strains with improved industrial performance

Growth condition optimization for docosahexaenoic acid (DHA) production by Moritella marina MP-1

The marine organism Moritella marina MP-1 produces the polyunsaturated fatty acid docosahexaenoic acid (DHA). While the basic metabolic pathway for DHA production in this organism has been identified, the impact of growth conditions on DHA production is largely unknown. This study examines the effect of supplemental carbon, nitrogen and salts, growth temperature and media composition and pH on DHA and biomass production and the fatty acid profile. The addition of supplemental nitrogen significantly increased the overall DHA titer via an increase in biomass production. Supplemental glucose or glycerol increased biomass production, but decreased the amount of DHA per biomass, resulting in no net change in the DHA titer. Acidification of the baseline media pH to 6.0 increased DHA per biomass. Changes in growth temperature or provision of supplemental sodium or magnesium chloride did not increase DHA titer. This organism was also shown to grow on defined minimal media. For both media types, glycerol enabled more DHA production per biomass than glucose. Combination of these growth findings into marine broth supplemented with glycerol, yeast extract, and tryptone at pH 6.0 resulted in a final titer of 82 ± 5 mg/L, a nearly eightfold increase relative to the titer of 11 ± 1 mg/L seen in the unsupplemented marine broth. The relative distribution of other fatty acids was relatively robust to growth condition, but the presence of glycerol resulted in a significant increase in myristic acid (C14:0) and decrease in palmitic acid (C16:0). In summary, DHA production by M. marina MP-1 can be increased more than fivefold by changing the growth media. Metabolic engineering of this organism to increase the amount of DHA produced per biomass could result in additional increases in titer

Engineering ethanologenic Escherichia coli for levoglucosan utilization

Levoglucosan is a major product of biomass pyrolysis. While this pyrolyzed biomass, also known as bio-oil, contains sugars that are an attractive fermentation substrate, commonly-used biocatalysts, such as Escherichia coli, lack the ability to metabolize this anhydrosugar. It has previously been shown that recombinant expression of the levoglucosan kinase enzyme enables use of levoglucosan as carbon and energy source. Here, ethanologenic E. coli KO11 was engineered for levoglucosan utilization by recombinant expression of levoglucosan kinase from Lipomyces starkeyi. Our engineering strategy uses a codon-optimized gene that has been chromosomally integrated within the pyruvate to ethanol (PET) operon and does not require additional antibiotics or inducers. Not only does this engineered strain use levoglucosan as sole carbon source, but it also ferments levoglucosan to ethanol. This work demonstrates that existing biocatalysts can be easily modified for levoglucosan utilization

Hybrid thermochemical processing: Fermentation of pyrolysis-derived bio-oil

Thermochemical processing of biomass by fast pyrolysis provides a nonenzymatic route for depolymerization of biomass into sugars that can be used for the biological production of fuels and chemicals. Fermentative utilization of this bio-oil faces two formidable challenges. First is the fact that most bio-oil-associated sugars are present in the anhydrous form. Metabolic engineering has enabled utilization of the main anhydrosugar, levoglucosan, in workhorse biocatalysts. The second challenge is the fact that bio-oil is rich in microbial inhibitors. Collection of bio-oil in distinct fractions, detoxification of bio-oil prior to fermentation, and increased robustness of the biocatalyst have all proven effective methods for addressing this inhibition

Quantifying Attachment and Antibiotic Resistance of Escherichia coli from Conventional and Organic Swine Manure

Broad-spectrum antibiotics are often administered to swine, contributing to the occurrence of antibiotic-resistant bacteria in their manure. During land application, the bacteria in swine manure preferentially attach to particles in the soil, affecting their transport in overland flow. However, a quantitative understanding of these attachment mechanisms is lacking, and their relationship to antibiotic resistance is unknown. The objective of this study is to examine the relationships between antibiotic resistance and attachment to very fine silica sand inEscherichia coli collected from swine manure. A total of 556 isolates were collected from six farms, two organic and four conventional (antibiotics fed prophylactically). Antibiotic resistance was quantified using 13 antibiotics at three minimum inhibitory concentrations: resistant, intermediate, and susceptible. Of the 556 isolates used in the antibiotic resistance assays, 491 were subjected to an attachment assay. Results show that E. coli isolates from conventional systems were significantly more resistant to amoxicillin, ampicillin, chlortetracycline, erythromycin, kanamycin, neomycin, streptomycin, tetracycline, and tylosin (P \u3c 0.001). Results also indicate that E. coli isolated from conventional systems attached to very fine silica sand at significantly higher levels than those from organic systems (P \u3c 0.001). Statistical analysis showed that a significant relationship did not exist between antibiotic resistance levels and attachment in E. coli from conventional systems but did for organic systems (P \u3c 0.001). Better quantification of these relationships is critical to understanding the behavior of E. coli in the environment and preventing exposure of human populations to antibiotic-resistant bacteria