SYNTHESIS OF LONG OLIGODEOXYNUCLEOTIDES DOI Creative Commons
Yipeng Yin

Published: Jan. 1, 2024

Synthetic long oligodeoxynucleotides (ODNs) have found wide applications in diverse fields such as chemical biology, synthetic and genes genomes synthesis. Those leading to a significant demand for their production. However, traditional methods purifying ODNs present notable drawbacks, particularly inability purify ODNs, rendering ODN synthesis challenging. To address these issues, techniques coupled with non-chromatographic purification been developed. This technology makes the of feasible offers viable pathway producing extensive repeats or stable secondary structures, which are either unattainable exceedingly complex achieve using conventional methods. Despite advancements, use controlled pore glass (CPG) solid support poses its own limitations. In response, novel surface-functionalized materials identified mitigate challenges. Direct up 1,728-mer on surface has reported. Results indicate that surfaces eliminates steric hindrance reduces errors commonly encountered CPG. Furthermore, while catching-by-polymerization (CBP) method proven effective, affordability polymerizable tagging phosphoramidites (PTPs) remains bottleneck. overcome this hurdle, scalable four nucleoside precursors discovered, offering chromatography-free alternatives making CBP more efficient cost-effective.

Language: Английский

Networks as tools for defining emergent properties of microbiomes and their stability DOI Creative Commons

Kacie Kajihara,

Nicole A. Hynson

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: Sept. 28, 2024

Language: Английский

Citations

8
Sterol‐Targeted Laboratory Evolution Allows the Isolation of Thermotolerant and Respiratory‐Competent Clones of the Industrial Yeast Saccharomyces cerevisiae DOI Creative Commons

Isabel‐Elena Sánchez‐Adriá,

José A. Prieto, Gemma Sanmartín

et al.

Microbial Biotechnology, Journal Year: 2025, Volume and Issue: 18(1)

Published: Jan. 1, 2025

ABSTRACT Sterol composition plays a crucial role in determining the ability of yeast cells to withstand high temperatures, an essential trait biotechnology. Using targeted evolution strategy involving fluconazole (FCNZ), inhibitor sterol biosynthesis pathway, and immunosuppressant FK506, we aimed enhance thermotolerance industrial baker's population by modifying their composition. This approach yielded six isolates capable proliferating liquid YPD with μ max values ranging from 0.072 0.236 h −1 at 41.5°C, temperature that completely inhibits growth parental strain. The clones were categorised into two groups based on respiratory competence or deficiency, latter associated mtDNA loss, event seemingly linked FCNZ heat tolerance. Genome sequencing ploidy‐level analysis all strains revealed aneuploidies, copy number variations (CNVs), single nucleotide polymorphisms (SNPs). Notably, evolved exhibited specific point mutations MPM1 (P50S) PDR1 (F749S). CRISPR‐Cas9 experiments confirmed pdr1 F749S mutation FCNZ‐tolerance phenotype demonstrated Mpm1 is required for temperatures. However, no apparent tolerance benefit was observed combined these genes, supporting hypothesis mediated multiple interacting mechanisms. In this context, altered profiles, differences between respiratory‐competent ‐deficient strains. conclusion, our experimental generated thermotolerant fully competent identified factors could influence growth.

Language: Английский

Citations

0
Designing biochemical circuits with tree search DOI Creative Commons
Pranav S. Bhamidipati, Matt Thomson

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 29, 2025

Abstract Discovering biochemical circuits that exhibit a desired behavior is an outstanding problem in biological engineering. The traditional approach of enumerating every possible circuit topology becomes intractable for with more than four components due to combinatorial scaling the search space. Here, we use Monte Carlo Tree Search (MCTS), reinforcement learning (RL) algorithm, optimize target phenotype by approaching design as sequence assembly decisions. Our RL-based framework, which call CircuiTree, efficiently and comprehensively finds robust designs three-component oscillators prioritizing sparsity. CircuiTree can also infer candidate network motifs from its results, producing similar results enumeration. Using parallel MCTS, scale this workflow up five find highly fault-tolerant novel strategy, motif multiplexing. Multiplexed contain many overlapping each activate different mutational scenarios. evolutionary robustness multiplexing may explain ubiquity multiple sub-oscillators circadian clock circuits. Overall, provides first scalable computational platform designing

Language: Английский

Citations

0
Microbial genetic resource for advanced biofuel production DOI
Rashidin Abdugheni

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 33 - 55

Published: Jan. 1, 2025

Language: Английский

Citations

0
Recent advances in microbial nanomaterials/nanoparticles synthesis and rare earth elements recovery from rare earth mine wastewater: A review DOI

Qiuting Yan,

Zhiman Yang, Zuliang Chen

et al.

Chemical Engineering Journal, Journal Year: 2025, Volume and Issue: unknown, P. 161647 - 161647

Published: March 1, 2025

Language: Английский

Citations

0
A roadmap to understanding and anticipating microbial gene transfer in soil communities DOI
David L. Gillett, Malyn A. Selinidis, Travis R. Seamons

et al.

Microbiology and Molecular Biology Reviews, Journal Year: 2025, Volume and Issue: unknown

Published: April 8, 2025

SUMMARY Engineered microbes are being programmed using synthetic DNA for applications in soil to overcome global challenges related climate change, energy, food security, and pollution. However, we cannot yet predict gene transfer processes assess the frequency of unintentional engineered environmental when applying biology technologies at scale. This challenge exists because complex heterogeneous characteristics soils, which contribute fitness transport cells exchange genetic material within communities. Here, describe knowledge gaps about across microbiomes. We propose strategies improve our understanding communities, highlight need benchmark performance biocontainment measures situ , discuss responsibly engaging community stakeholders. opportunities address gaps, such as creating a set standards studying diverse types measuring host range microbiomes emerging technologies. By comparing rates, range, persistence different posit that community-scale, environment-specific models can be built anticipate biotechnology risks. Such studies will enable design safer biotechnologies allow us realize benefits mitigate risks associated with release

Language: Английский

Citations

0
A CRISPR interference system for engineering biological nitrogen fixation DOI Creative Commons
Steven J. Russell, Amanda K. Garcia, Betül Kaçar

et al.

mSystems, Journal Year: 2024, Volume and Issue: 9(3)

Published: Feb. 20, 2024

ABSTRACT A grand challenge for the next century is in facing a changing climate through bioengineering solutions. Biological nitrogen fixation, globally consequential, nitrogenase-catalyzed reduction of atmospheric to bioavailable ammonia, vital area focus. Nitrogen fixation engineering relies upon extensive understanding underlying genetics microbial models, including broadly utilized gammaproteobacterium, Azotobacter vinelandii ( A. ). Here, we report first CRISPR interference (CRISPRi) system targeted gene silencing that integrates genomically via site-specific transposon insertion. We demonstrate CRISPRi can repress transcription an essential by ~60%. Further, show nitrogenase genes are suitably expressed from insertion site, indicating and engineered be co-integrated combinatorial studies expression engineering. Our established fills important gap desired purposes. IMPORTANCE All life on Earth requires survive. About 78% atmosphere alone nitrogen, yet humans cannot use it directly. Instead, obtain need our survival food eat. For more than 100 years, substantial portion agricultural productivity has relied industrial methods fertilizer synthesis, which consumes significant amounts nonrenewable energy resources exacerbates environmental degradation human-induced change. Promising alternatives these rely only biological pathway generating bioaccessible nitrogen: fixation. Bioengineering strategies require nitrogen-fixing microbes, but genetic tools this critical goal remain lacking. The report, developed bacterial model, , step toward elucidating complexity enabling their manipulation.

Language: Английский

Citations

2
Enhancement of Green Production of Heme by Deleting Odor-Related Genes from Bacillus amyloliquefaciens Based on CRISPR/Cas9n DOI
Cong Jiang, Dian Zou,

Xuedeng Jiang

et al.

Journal of Agricultural and Food Chemistry, Journal Year: 2024, Volume and Issue: 72(29), P. 16412 - 16422

Published: July 10, 2024

Heme is a crucial component in endowing plant-based meat analogs with flavor and color. This study aimed to develop green strategy for heme production by reducing fermentation off-odor accelerating synthesis. First, an efficient CRISPR/Cas9n system was constructed

Language: Английский

Citations

2
Ribozyme-Mediated Gene-Fragment Complementation for Nondestructive Reporting of DNA Transfer within Soil DOI
Malyn A. Selinidis,

Andrew C. Corliss,

James Chappell

et al.

ACS Synthetic Biology, Journal Year: 2024, Volume and Issue: 13(11), P. 3539 - 3547

Published: Aug. 15, 2024

Enzymes that produce volatile metabolites can be coded into genetic circuits to report nondisruptively on microbial behaviors in hard-to-image soils. However, these enzyme reporters remain challenging apply gene transfer studies due leaky off states lead false positives. To overcome this problem, we designed a reporter uses ribozyme-mediated gene-fragment complementation of methyl halide transferase (MHT) regulate the synthesis gases. We split mht two nonfunctional fragments and attached pair splicing ribozyme fragments. While individual mht-ribozyme did not halides when transcribed alone Escherichia coli, coexpression resulted spliced transcript translated MHT reporter. When cells containing one fragment from mobile plasmid were mixed with second fragment, only detected following rare conjugation events. was performed soil, it led 16-fold increase soil headspace. These findings show how achieve tight control protein production, level will critical for monitoring effects conditions fidelity biocontainment measures developed environmental applications.

Language: Английский

Citations

2
Development of bioflocculants for mineral processing DOI Creative Commons

Matthias J. Orchard,

Guangze Yang, Grant B. Webber

et al.

Materials Today Sustainability, Journal Year: 2024, Volume and Issue: 28, P. 100965 - 100965

Published: Aug. 29, 2024

Mining and minerals processing are essential to modern society, the demand for metals is increasing due rapid development of clean energy technologies, such as electric vehicles, solar panels, wind turbines, etc. The mining industry, however, facing significant challenges in meeting sustainability environmental goals. As more extracted, use water increases, leading greater wastewater tailings production. To tackle this issue, flocculants commonly used across sites dewater waste streams by binding settling particles, allow improved solid-liquid separation. While conventional (synthetic polymers often derived from petrochemicals) effective rapidly they present several issues, high levels entrapped water, ineffective fine particle separation, health concerns. address these challenges, bioflocculants have been proposed alternative flocculants. This review explores three main bioflocculant research directions, including plant based, graft copolymers, microbial flocculants, discussing advantages disadvantages each. ratio flocculant dose suspended solids (i.e. ratio) flocculation efficiency studies related mineral separation evaluated. Finally, proposes future opportunities directions mitigate issues that historically made less appealing. These include enhancing recyclability well advancing protein design modification.

Language: Английский

Citations

2