Biological Responses of Pacific Herring Embryos to Crude Oil Are Quantifiable at Exposure Levels Below Conventional Limits of Quantitation for PAHs in Water and Tissues DOI Creative Commons
John P. Incardona,

Tiffany L. Linbo,

James Cameron

et al.

Environmental Science & Technology, Journal Year: 2023, Volume and Issue: 57(48), P. 19214 - 19222

Published: Nov. 14, 2023

Pacific herring (Clupea pallasii), a cornerstone of marine food webs, generally spawn on macroalgae in shallow nearshore areas that are disproportionately at risk from oil spills. Herring embryos also highly susceptible to toxicity chemicals leaching stranded intertidal and subtidal zones. The water-soluble components crude trigger an adverse outcome pathway involves disruption the physiological functions cardiomyocytes embryonic heart. In previous studies, impaired ionoregulation (calcium potassium cycling) response specific polycyclic aromatic hydrocarbons (PAHs) corresponds lethal embryolarval heart failure or subtle chamber malformations high low ends PAH exposure range, respectively. Sublethal cardiotoxicity, which abnormal outgrowth (ballooning) cardiac ventricular soon after hatching, subsequently compromises juvenile structure function, leading pathological hypertrophy ventricle reduced individual fitness, measured as cardiorespiratory performance. Previous studies have not established threshold for these sublethal delayed-in-time effects, even with total (∑)PAH exposures 29 ng/g wet weight (tissue dose). Here, we extend earlier findings showing (1) cyp1a gene expression provides metric is more sensitive than typical quantitation PAHs via GC-MS (2) morphometrics provide similarly measure toxic response. Early life stage injury (impaired development) thus occurs below limits both water tissues conventional basis assessing oil-induced losses coastal ecosystems.

Language: Английский

Biosensors Characterisation: Formal methods from the Perspective of Proteome Fractions DOI Creative Commons
Nicolás A. Vaccari, Dahlin Zevallos-Aliaga, Tom H. Peeters

et al.

Synthetic Biology, Journal Year: 2025, Volume and Issue: 10(1)

Published: Jan. 1, 2025

Abstract Many studies characterize transcription factors and other regulatory elements to control gene expression in recombinant systems. However, most lack a formal approach analyse the inherent context-specific variations of these components. This study addresses this gap by establishing framework from which convenient methods are inferred circuits. We modelled bacterial cell as collection proteome fractions. Deriving time-dependent fraction, we obtained general theorem that describes its change function specific portion total biosynthesis flux cell. Formal deduction reveals when fraction reaches maximum, it becomes equivalent fraction. equation enables reliable measurement through direct protein quantification. In addition, experimental data demonstrate linear correlation between production rate growth over significant time period. suggests constant within window. For an Isopropyl β- d-1-thiogalactopyranoside (IPTG) biosensor, five cellular contexts, fractions determined maximum method slope produced strikingly similar dose–response parameters independently fit Hill function. Furthermore, analysing two more biosensors, for mercury cumate detection, can be applied effectively various Therefore, concepts presented here provide obtaining parameters, clearly defining interval their validity offering interpreting typical biosensor outputs terms physiology. Graphical Nutrients, transformed action Nutrient Fixators (purple arrow), used at ρ Protein biosynthesis. The is multiplied fR, fC, fH, fQ obtain (black arrows) each ΦR, ΦC, ΦH, ΦQ, respectively. graph Growth versus Proteome Fraction Production Rate, (green lines) observed, equal condition.

Language: Английский

Citations

0
Identification and Characterization of Anaerobically Activated Promoters in Escherichia coli DOI
Sen Yang, Chengxian Guo,

Wen-Yue Tong

et al.

Journal of Biotechnology, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

Citations

0
Precision Quantification and Rational Regulation of Protein Expression with Bicistronic Cassette for Efficient Biotin Production DOI
Shun Li, Xuan Zhou, Ye Chen‐Izu

et al.

Journal of Agricultural and Food Chemistry, Journal Year: 2025, Volume and Issue: 73(11), P. 6854 - 6866

Published: March 5, 2025

Identifying optimal enzyme expression levels is critical for microbial cell factories, as metabolic imbalances can impede the synthesis of target products. However, current screening strategies often rely on trial-and-error approaches, which are labor-intensive and have limited applicability. Here we developed a quantitative strategy utilizing bicistronic design (BCD) library screening, requiring no more than 17 tests in two steps: profiling focused selection. The BCD encoded 992-fold range, protein abundances were quantified based fluorescence intensities due to strong correlation (r = 0.96). This was employed fine-tune rate-limiting BioB biotin synthesis, whose overexpression inhibits growth production. Consequently, BCD6 identified strength overexpressed bio operon, while BCD7 + isc operons, resulting 1.47-fold 3.03-fold increases titer compared original strain. Western Blot analysis confirmed 2.38-fold 2.71-fold increase abundance, respectively. pioneering application establishes it versatile tool rational tuning construction any factory.

Language: Английский

Citations

0
Microbial Transcription Factor-Based Biosensors: Innovations from Design to Applications in Synthetic Biology DOI Creative Commons

Kyeongseok Song,

Hyunju Ji, Ji‐Won Lee

et al.

Biosensors, Journal Year: 2025, Volume and Issue: 15(4), P. 221 - 221

Published: March 31, 2025

Transcription factor-based biosensors (TFBs) are powerful tools in microbial biosensor applications, enabling dynamic control of metabolic pathways, real-time monitoring intracellular metabolites, and high-throughput screening (HTS) for strain engineering. These systems use transcription factors (TFs) to convert metabolite concentrations into quantifiable outputs, precise regulation fluxes biosynthetic efficiency cell factories. Recent advancements TFB, including improved sensitivity, specificity, range, have broadened their applications synthetic biology industrial biotechnology. Computational such as Cello further revolutionized TFB design, silico optimization construction complex genetic circuits integrating multiple signals achieving gene regulation. This review explores innovations biosensors, role engineering adaptive evolution, future integration with artificial intelligence advanced technologies overcome critical challenges bioproduction.

Language: Английский

Citations

0
Computation-guided transcription factor biosensor specificity engineering for adipic acid detection DOI Creative Commons
Chester Pham, P.J. Stogios, Alexei Savchenko

et al.

Computational and Structural Biotechnology Journal, Journal Year: 2024, Volume and Issue: 23, P. 2211 - 2219

Published: May 15, 2024

Transcription factor (TF)-based biosensors that connect small-molecule sensing with readouts such as fluorescence have proven to be useful synthetic biology tools for applications in biotechnology. However, the development of specific TF-based is hindered by limited repertoire TFs molecules interest since current construction methods rely on a set characterized TFs. In this study, we present an approach engineering specificity through computation-based workflow using molecular docking enables targeted alteration TF ligand specificity. Using method, engineer LysR family BenM alter its from cognate cis,cis-muconic acid adipic single amino substitution identified our computational workflow. When implemented cell-free system, engineered biosensor shows higher sensitivity, expanding potential circuit. We further investigate binding dynamics analyze substitution, elucidating impact modulating position mechanism binding. This study represents first application biomolecular modeling altering and gaining insights into how mutations influence structural BenM. Such can potentially applied other responsible these changes, highlighting applicability informing experiments. addition, developed identification enzymes produce acid.

Language: Английский

Citations

3
State-of-the-art in engineering small molecule biosensors and their applications in metabolic engineering DOI Creative Commons

Patarasuda Chaisupa,

R Clay Wright

SLAS TECHNOLOGY, Journal Year: 2023, Volume and Issue: 29(2), P. 100113 - 100113

Published: Nov. 1, 2023

Genetically encoded biosensors are crucial for enhancing our understanding of how molecules regulate biological systems. Small molecule biosensors, in particular, help us understand the interaction between chemicals and processes. They also accelerate metabolic engineering by increasing screening throughput eliminating need sample preparation through traditional chemical analysis. Additionally, they offer significantly higher spatial temporal resolution cellular analyte measurements. In this review, we discuss recent progress vivo control systems-biosensor-based controllers-for engineering. We specifically explore protein-based that utilize less commonly exploited signaling mechanisms, such as protein stability induced degradation, compared to more prevalent transcription factor allosteric regulation mechanism. propose these lesser-used mechanisms will be significant eukaryotic systems slower-growing prokaryotic where turnover may facilitate rapid reliable measurement current state. Lastly, emphasize utilization cutting-edge state-of-the-art techniques development achieved rational design, directed evolution, collaborative approaches.

Language: Английский

Citations

8
DetSpace: a web server for engineering detectable pathways for bio-based chemical production DOI Creative Commons
Hèctor Martín Lázaro, R. Bautista, Pablo Carbonell

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(W1), P. W476 - W480

Published: April 18, 2024

Tackling climate change challenges requires replacing current chemical industrial processes through the rational and sustainable use of biodiversity resources. To that end, production routes to key bio-based chemicals for bioeconomy have been identified. However, their still remains inefficient in terms titers, rates, yields; because hurdles found when scaling up. In order make more efficient, strategies like automated screening dynamic pathway regulation biosensors applied as part strain optimization. date, no systematic way exists design a genetic circuit is responsive concentrations given target compound. Here, DetSpace web server provides set integrated tools allows user select biological performs sensing molecule interest by its enzymatic conversion detectable transcription factor. way, synthetic biologists easily biosensing metabolic pathways applications ranging from circuits design, screening, production, bioremediation chemicals, diagnostics drug delivery.

Language: Английский

Citations

2
Challenges and possibilities for the qualitative and quantitative analysis of phosphate metabolites DOI

Pei Zhang,

Meiyu Gao,

Zunjian Zhang

et al.

TrAC Trends in Analytical Chemistry, Journal Year: 2024, Volume and Issue: 180, P. 117934 - 117934

Published: Aug. 29, 2024

Language: Английский

Citations

2
A review of the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle DOI
Belete Kuraz Abebe, Hongbao Wang, Anning Li

et al.

Journal of Animal Breeding and Genetics, Journal Year: 2023, Volume and Issue: 141(3), P. 235 - 256

Published: Dec. 25, 2023

Abstract In the past few decades, genomic selection and other refined strategies have been used to increase growth rate lean meat production of beef cattle. Nevertheless, fast rates cattle breeds are often accompanied by a reduction in intramuscular fat (IMF) deposition, impairing quality. Transcription factors play vital roles regulating adipogenesis lipogenesis Meanwhile, understanding role transcription has gained significant attention IMF deposition Therefore, aim this paper was provide comprehensive summary valuable insight into complex This review summarizes contemporary studies lipogenesis, genome‐wide analysis factors, epigenetic regulation nutritional metabolic signalling pathways, functional genomics methods, transcriptomic profiling adipose tissues, quality comparative with livestock species. conclusion, crucial promoting adipocyte development fatty acid biosynthesis They control tissue formation metabolism, thereby improving maintaining balance. Understanding processes which these regulate lipid metabolism will simplify marbling or composition

Language: Английский

Citations

4
Synthetic cell-based biosensors and methods for discovering novel sensing elements DOI

Yichen Zhan

Published: Jan. 8, 2024

With the advancement of synthetic biology, cells can be modified and engineered through gene recombination, editing protein engineering. Given that many elements in expression are environmental-sensitive, biosensor based on has been proposed studies have validated this concept. Synthetic biosensors facilitate research revelation biomolecular activity living systems. And it advantages easy operation, energy economy, adaptability. This review introduces three types including transcriptional biosensors, translational post-translational biosensors. Then topic will focus approaches help discovery biosensing cells, which is vital but still challenging for development Cell-free assays, directed revolution, high through-put screening computational methods discussed review. Subsequently, application summarized, presenting utility them. At last, future direction discussed, hoping to provide prospects or advice field.

Language: Английский

Citations

1