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PubMed1976

Animal experiments with biogalvanic and biofuel cells.

Animal experiments with biogalvanic cells have demonstrated that an average power of 80 muW can be derived continously for at least 2 years. There is a further scope to stabilize the power at 100 muW for considerable longer periods so that the chances of cardiac pacing with biogalvanic power have become bright. However, large scale efforts are necessary in in establishing the statistical reliability and the secured performance which are expensive and time consuming. Animal experiments with biofuel cells are still in preliminary stages. We derived a continous power of 40 muW (4MUW/cm2) at 575 mV over 150 days so far. This is the longest recorded period with such a high power density. The main problem in deriving higher power over longer period is to properly encapsulate the cell with materials which are hydrophilic and essentially biocompatible.

Animals↗

PubMed2025

Physiological and metabolic responses of Zymomonas mobilis to lignocellulosic hydrolysate.

Zymomonas mobilis is a promising biocatalyst for the sustainable conversion of lignocellulosic sugars into biofuels and bioproducts, yet its response to lignocellulosic hydrolysates remains poorly understood. Here, we investigate the physiological response of Z. mobilis to ammonia fiber expansion (AFEX)-pretreated switchgrass hydrolysate using a systems-level approach integrating LC-MS/MS-based lipidomics and shotgun proteomics. Growth on hydrolysate induced substantial shifts in fatty acid and membrane phospholipid composition, alongside broad proteomic remodeling. Notably, Z. mobilis exhibited a stress response characterized by the upregulation of heat shock proteins and efflux transporters and the downregulation of cell motility proteins. Unexpectedly, hydrolysate exposure also led to a robust upregulation of the Entner-Doudoroff pathway, the ethanol fermentation pathway, and other central carbon metabolism enzymes, indicating a substantial cellular investment potentially driven by additional nutrient availability in hydrolysate. These findings provide new insights into the metabolic adaptations of Z. mobilis to lignocellulosic hydrolysates, informing strategies to enhance its biofuel production capabilities.IMPORTANCEBiomass pretreatment processes release fermentable sugars from lignocellulosic biomass, but they also generate inhibitors that can impact microbial metabolism. This study provides a systems-level evaluation of how Zymomonas mobilis responds to hydrolysate stress, revealing distinct physiological and lipid membrane remodeling responses. While some stress responses overlap with those induced by ethanol and isobutanol toxicity, both valuable biofuels, hydrolysate exposure elicits unique metabolic shifts. These findings offer valuable insights for engineering Z. mobilis strains with improved tolerance and performance for efficient bioconversion of lignocellulosic hydrolysates into biofuels and bioproducts.

Zymomonas↗

PubMedDate not supplied

Bioelectrical conversion in sensors with living cells.

Bacterial metabolism can drive various processes with biotechnological significance, like in the case of biosensors for probing organic compounds, or in biofuel cells. Here we present some of our results connected with the construction of a bacterial electrode with Pseudomonas sp. for probing glucose in body fluids, and those related to biofuel cells with anaerobic bacteria (Clostridium sp.). The output of the bioselective electrode linearly indicates glucose concentrations in the 2.5 x 10(-5)-1.25 x 10(-4) M domain, with a sensitivity limit of 10(-5) M. The time constant is 10 min, and it works for more than ten days. The amperometric response of biofuel cells with Clostridium sp. offers the electrical image of the state of the bacterial culture itself, thus being a promising tool for the automated control of the bacterial suspensions used in fermentative reactors.

Biosensing Techniques↗

PubMed2025

Engineering of xylose metabolic pathways in Rhodotorula toruloides for sustainable biomanufacturing.

The oleaginous yeast Rhodotorula toruloides is a promising microbial cell factory for the sustainable production of biofuels and value-added chemicals from renewable carbon sources. Unlike the conventional yeast Saccharomyces cerevisiae, R. toruloides can naturally metabolize xylose, the second most abundant sugar in lignocellulosic hydrolysates. However, its native xylose metabolism is inefficient, characterized by slow xylose uptake and accumulation of D-arabitol. Moreover, despite its phenotype, research on the enzymes involved in xylose metabolism has yet to reach a consensus. Therefore, this review provides a comprehensive analysis of the non-canonical xylose metabolism in R. toruloides, focusing on the properties of key enzymes involved in xylose metabolism. Native xylose reductase and xylitol dehydrogenase exhibit broad substrate promiscuity compared to their counterparts in the xylose-fermenting Scheffersomyces stipitis. Additionally, the absence of xylulokinase expression under xylose-utilizing conditions redirects metabolism toward D-arabitol accumulation. Consequently, D-arabitol dehydrogenases and ribulokinase play essential roles in the xylose metabolism of R. toruloides. These findings highlight the fundamental differences between R. toruloides xylose metabolism and the oxidoreductase pathways observed in other xylose-fermenting yeast, providing insights for metabolic engineering strategies to improve xylose utilization and enhance bioconversion of cellulosic hydrolysates to different bioproducts by R. toruloides.

Xylose↗

PubMed2024

Genetic modification of the shikimate pathway to reduce lignin content in switchgrass (Panicum virgatum L.) significantly impacts plant microbiomes.

UNLABELLED: Switchgrass (Panicum virgatum L.) is considered a sustainable biofuel feedstock, given its fast-impact growth, low input requirements, and high biomass yields. Improvements in bioenergy conversion efficiency of switchgrass could be made by reducing its lignin content. Engineered switchgrass that expresses a bacterial 3-dehydroshikimate dehydratase (QsuB) has reduced lignin content and improved biomass saccharification due to the rerouting of the shikimate pathway towards the simple aromatic protocatechuate at the expense of lignin biosynthesis. However, the impacts of this QsuB trait on switchgrass microbiome structure and function remain unclear. To address this, wild-type and QsuB-engineered switchgrass were grown in switchgrass field soils, and samples were collected from inflorescences, leaves, roots, rhizospheres, and bulk soils for microbiome analysis. We investigated how QsuB expression influenced switchgrass-associated fungal and bacterial communities using high-throughput Illumina MiSeq amplicon sequencing of ITS and 16S rDNA. Compared to wild-type, QsuB-engineered switchgrass hosted different microbial communities in roots, rhizosphere, and leaves. Specifically, QsuB-engineered plants had a lower relative abundance of arbuscular mycorrhizal fungi (AMF). Additionally, QsuB-engineered plants had fewer Actinobacteriota in root and rhizosphere samples. These findings may indicate that changes in the plant metabolism impact both AMF and Actinobacteriota similarly or potential interactions between AMF and the bacterial community. This study enhances understanding of plant-microbiome interactions by providing baseline microbial data for developing beneficial bioengineering strategies and by assessing nontarget impacts of engineered plant traits on the plant microbiome. IMPORTANCE: Bioenergy crops provide an important strategy for mitigating climate change. Reducing the lignin in bioenergy crops could improve fermentable sugar yields for more efficient conversion into bioenergy and bioproducts. In this study, we assessed how switchgrass engineered for low lignin impacted aboveground and belowground switchgrass microbiome. Our results show unexpected reductions in mycorrhizas and actinobacteria in belowground tissues, raising questions on the resilience and function of genetically engineered plants in agricultural systems.

Panicum↗

PubMed2026

Genomic and bioreactor evaluation of newly isolated cellulase-producing bacteria.

Cellulose is a renewable resource with broad biotechnological potential, and its hydrolysis by cellulases underpins applications such as biofuel production and biowaste valorization. This study combined isolation, screening, molecular identification, enzyme assays, genome sequencing, and bioreactor evaluation to characterize novel cellulase-producing bacteria. Preliminary screening identified and selected bacterial isolates by hydrolysis halo formation, with strains showing halos ≥ 20 mm selected for further quantitative assays. Streptomyces olivaceus C1_7A, Bacillus thuringiensis FBB7BB, and Bacillus licheniformis strains AT081C and AT082C showed the highest endoglucanase activities (from 0.11 to 0.26 U mL-1). Further testing on Arundo donax and Avicel led to the selection of B. thuringiensis FBB7BB and S. olivaceus C1_7A as the most promising strains for biotechnological application. Whole genome sequencing confirmed the presence of genes involved in polysaccharide degradation. Finally, lab-scale fermentation trials using 1-2% CMC showed that B. thuringiensis FBB7BB reached a maximum endo-1,4-β-glucanase activity of 0.30 ± 0.04 U mL-1 after 8 h at 37 °C, whereas S. olivaceus C1_7A achieved 0.36 ± 0.03 U mL-1 after 216 h at 30 °C.

Cellulase↗

PubMed2025

Orthogonal replication with optogenetic selection evolves yeast JEN1 into a mevalonate transporter.

The in vivo continuous evolution system OrthoRep (orthogonal replication) is a powerful strategy for rapid enzyme evolution in Saccharomyces cerevisiae that diversifies genes at a rate exceeding the endogenous genome mutagenesis rate by several orders of magnitude. However, it is difficult to neofunctionalize genes using OrthoRep partly because of the way selection pressures are applied. Here we combine OrthoRep with optogenetics in a selection strategy we call OptoRep, which allows fine-tuning of selection pressure with light. With this capability, we evolved a truncated form of the endogenous monocarboxylate transporter JEN1 (JEN1t) into a de novo mevalonate importer. We demonstrate the functionality of the evolved JEN1t (JEN1tY180C/G) in the production of farnesene, a renewable aviation biofuel, from mevalonate fed to fermentation media or produced by microbial consortia. This study shows that the light-induced complementation of OptoRep may improve the ability to evolve functions not currently accessible for selection, while its fine tunability of selection pressure may allow the continuous evolution of genes whose desired function has a restrictive range between providing effective selection and cellular viability.

Saccharomyces cerevisiae↗

PubMed2024

Organ-delimited gene regulatory networks provide high accuracy in candidate transcription factor selection across diverse processes.

Organ-specific gene expression datasets that include hundreds to thousands of experiments allow the reconstruction of organ-level gene regulatory networks (GRNs). However, creating such datasets is greatly hampered by the requirements of extensive and tedious manual curation. Here, we trained a supervised classification model that can accurately classify the organ-of-origin for a plant transcriptome. This K-Nearest Neighbor-based multiclass classifier was used to create organ-specific gene expression datasets for the leaf, root, shoot, flower, and seed in Arabidopsis thaliana. A GRN inference approach was used to determine the: i. influential transcription factors (TFs) in each organ and, ii. most influential TFs for specific biological processes in that organ. These genome-wide, organ-delimited GRNs (OD-GRNs), recalled many known regulators of organ development and processes operating in those organs. Importantly, many previously unknown TF regulators were uncovered as potential regulators of these processes. As a proof-of-concept, we focused on experimentally validating the predicted TF regulators of lipid biosynthesis in seeds, an important food and biofuel trait. Of the top 20 predicted TFs, eight are known regulators of seed oil content, e.g., WRI1, LEC1, FUS3. Importantly, we validated our prediction of MybS2, TGA4, SPL12, AGL18, and DiV2 as regulators of seed lipid biosynthesis. We elucidated the molecular mechanism of MybS2 and show that it induces purple acid phosphatase family genes and lipid synthesis genes to enhance seed lipid content. This general approach has the potential to be extended to any species with sufficiently large gene expression datasets to find unique regulators of any trait-of-interest.

Arabidopsis↗

PubMed2026

Genome analysis of the glycosphingolipid-producing green alga tetraselmis sp. NKG400013.

Microalgae are gaining attention as sustainable resources for the production of valuable compounds, including biofuels, pigments, and bioactive metabolites. To support metabolic engineering and genome editing approaches aimed at enhancing these traits, high-quality genome assemblies are essential; however, genomic information remains limited for many microalgal lineages. Tetraselmis sp. NKG400013 is a green alga known for high glycosphingolipid accumulation with distinctive structural features. Here, we report a draft genome assembly of this strain generated using PacBio HiFi sequencing and transcriptome-supported annotation. The assembled genome spans 423.7 Mbp, with 74.5% repetitive sequences and 15,322 predicted protein-coding genes. Comparative analyses across 11 green algal species revealed a positive correlation between genome sizes and repeat contents, indicating that transposable element expansion, particularly long terminal repeat retrotransposons, has substantially contributed to genome enlargement in Tetraselmis. Genome-wide functional annotation and ortholog inference identified core enzymes required for glycosylceramide biosynthesis. Both sphingolipid Δ4 and Δ8 desaturases were identified in Tetraselmis and their coexistence suggests an expanded capacity for long-chain base modification that may underlie its distinctive glycosphingolipid profile. These results establish a genomic framework for understanding the high glycosphingolipid-producing capacity of NKG400013 and provide insights into the evolutionary diversification of sphingolipid metabolism in green algae.

Chlorophyta↗

PubMed2025

Hierarchical metabolic engineering for rewiring cellular metabolism.

Metabolic engineering is a key enabling technology for rewiring cellular metabolism to enhance production of chemicals, biofuels, and materials from renewable resources. However, how to make cells into efficient factories is still challenging due to its robust metabolic networks. To open this door, metabolic engineering has realized great breakthroughs through three waves of technological research and innovations, especially the third wave. To understand the third wave of metabolic engineering better, we discuss its mainstream strategies and examples of its application at five hierarchies, including part, pathway, network, genome, and cell level, and provide insights as to how to rewire cellular metabolism in the context of maximizing product titer, yield, and productivity. Finally, we highlight future perspectives on metabolic engineering for the successful development of cell factories.

Metabolic Engineering↗

PubMed2025

Targeted, Genome-scale Overexpression in Proteobacteria.

Targeted, genome-scale gene perturbation screens using Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi) and activation (CRISPRa) have revolutionized eukaryotic genetics, advancing medical, industrial, and basic research. Although CRISPRi knockdowns have been broadly applied in bacteria, options for genome-scale gene overexpression face key limitations. Here, we develop a facile approach for genome-scale overexpression in bacteria we call, "CRISPRtOE" (CRISPR transposition and OverExpression). We first create a platform for comprehensive gene targeting using CRISPR-associated transposons (CAST) and show that transposition occurs at a higher frequency in non-transcribed DNA. We then demonstrate that CRISPRtOE can upregulate gene expression in Proteobacteria with medical and industrial relevance by integrating synthetic promoters of varying strength upstream of target genes. Finally, we employ CRISPRtOE screening at the genome-scale in the model bacterium Escherichia coli and the non-model biofuel producer Zymomonas mobilis, recovering known and novel antibiotic and engineering targets. We envision that CRISPRtOE will be a valuable overexpression tool for antibiotic mode of action, industrial strain optimization, and gene function discovery in bacteria.

Journal Article↗

PubMed2016

Characterization of Class III Peroxidases from Switchgrass.

Class III peroxidases (CIIIPRX) catalyze the oxidation of monolignols, generate radicals, and ultimately lead to the formation of lignin. In general, CIIIPRX genes encode a large number of isozymes with ranges of in vitro substrate specificities. In order to elucidate the mode of substrate specificity of these enzymes, we characterized one of the CIIIPRXs (PviPRX9) from switchgrass (Panicum virgatum), a strategic plant for second-generation biofuels. The crystal structure, kinetic experiments, molecular docking, as well as expression patterns of PviPRX9 across multiple tissues and treatments, along with its levels of coexpression with the majority of genes in the monolignol biosynthesis pathway, revealed the function of PviPRX9 in lignification. Significantly, our study suggested that PviPRX9 has the ability to oxidize a broad range of phenylpropanoids with rather similar efficiencies, which reflects its role in the fortification of cell walls during normal growth and root development and in response to insect feeding. Based on the observed interactions of phenylpropanoids in the active site and analysis of kinetics, a catalytic mechanism involving two water molecules and residues histidine-42, arginine-38, and serine-71 was proposed. In addition, proline-138 and gluntamine-140 at the 137P-X-P-X140 motif, leucine-66, proline-67, and asparagine-176 may account for the broad substrate specificity of PviPRX9. Taken together, these observations shed new light on the function and catalysis of PviPRX9 and potentially benefit efforts to improve biomass conservation properties in bioenergy and forage crops.

Amino Acid Sequence↗

PubMed2026

Periplasmic SacB as a robust counter-selection tool for genome engineering in the polyploid bacterium Zymomonas mobilis.

UNLABELLED: The alpha-proteobacterium Zymomonas mobilis exhibits exceptional ethanologenic physiology, which makes it a traditional alcoholic beverage producer and a promising chassis for biofuel production. Although genetic tools for this organism have expanded in recent years, a fundamental aspect of its chromosome organization remains to be understood. In particular, Z. mobilis has been suggested to exhibit polyploidy, but this feature is not fully confirmed because of discrepancies among studies reporting the copy number of chromosomes. Here, we tagged the chromosome-partitioning protein ParB with a fluorescent marker to visualize its cellular localization and estimate chromosome copy number in individual cells. Imaging showed that Z. mobilis exhibits several distinctive ParB foci throughout the cytoplasm and an accumulated focus at the pole, indicating that a single Z. mobilis cell contains >5 copies of the chromosome at the oriC regions. We then sought to establish an efficient counter-selection system, which is crucial for engineering multiple copies of the chromosome. We assessed the efficacy of levan-sucrase (SacB) toxicity in Z. mobilis. We found that, despite Z. mobilis secreting a native extracellular sucrase SacB, heterologous periplasmically localized Bacillus subtilis SacB rendered Z. mobilis cells sensitive to sucrose. We successfully used this effect for counter-selection when deleting and inserting targeted DNA sequences into the Z. mobilis genome. Together, this work provides important insights and tools for advancing Z. mobilis genetics and its biotechnological applications. IMPORTANCE: Zymomonas mobilis is a promising industrial bacterium with the capacity to convert sugars into ethanol at nearly maximum theoretical yield. With its expanding use in industrial applications, it is crucial to clarify if individual Z. mobilis cells carry multiple copies of the chromosome, as this has important implications for genome engineering. Two previous studies have used quantitative PCR to address this question, but their reported chromosome copy numbers varied widely from 20 to 100. Here, we used a cell biological approach to estimate the copy number and confirmed that a single Z. mobilis cell possesses multiple copies. In addition, we show that a SacB-based counter-selection works in Z. mobilis, enabling efficient and complete mutation of all chromosome copies.

Zymomonas↗

PubMed2026

Unveiling the Molecular Secrets of Seaweeds: A Comprehensive Review of Bioinformatics Applications in Algal Research.

Recent advances in high-throughput sequencing, bioinformatics, and multi-omics technologies have transformed seaweed research by overcoming long-standing challenges associated with complex genomes, diverse life cycles, and limited genomic resources. This review provides a comprehensive overview of bioinformatics approaches used to investigate seaweed genomics, transcriptomics, proteomics, metabolomics, microbiomes, and functional genomics, with emphasis on the computational tools and databases that support these analyses. Applications of bioinformatics in phylogenetics, drug discovery, microbiome characterization, and the development of biofuels, nutraceuticals, pharmaceuticals, and sustainable agriculture are also discussed. Particular attention is given to emerging strategies involving multi-omics integration, genome editing, artificial intelligence, machine learning, and synthetic biology that are reshaping seaweed research. The review further examines current challenges, including incomplete genomic resources, data standardization, and the need for experimental validation of computational predictions. Collectively, these advances highlight the growing role of bioinformatics in enabling systems-level understanding of seaweed biology and accelerating their translation into sustainable biotechnological and marine bioeconomy applications.

macroalgal genomics↗

PubMed1978

Electrochemical behavior of amino acids and their influence on the anodic oxidation of glucose in neutral media.

Body fluids contain a large number of amino acids along with glucose. Therefore, the electrochemical behavior of amino acids should be considered in studying the anodic oxidation reaction of glucose for biological applications. Potential-sweep and steady-state measurements with different platinum electrodes under neutral conditions have shown that the oxidation of amino acids is basically possible. However, their presence, especially as a mixture, has a remarkable influence on the glucose oxidation and the anodic reaction is strongly inhibited. With respect to the degree of inhibition, they can be classified into two groups. The inhibiting effect is particularly drastic in the case of basic and unsaturated amino acids as well as the ones containing sulphur because of their strong absorption at the electrode surface. The glucose currents are inhibited by about 90% under steady-state. In addition to the direct electrochemical inhibition, the following bacterial decomposition of amino acids is probably also responsible for the drastic effect. However, about 10% of the glucose currents still remain measurable indicating that glucose is detectable at physiological concentrations even under extremly unfavorable conditions. This result is of basic importance in operating a biofuel cell or in measuring glucose concentrations.

Amino Acids↗

PubMed2025

Advances in the Genus Ulva Research: From Structural Diversity to Applied Utility.

The green macroalgae Ulva Linnaeus, 1753, also known as sea lettuce, is one of the most ecologically and economically significant algal genera. Its representatives occur in marine, brackish, and freshwater environments worldwide and show high adaptability, rapid growth, and marked biochemical diversity. These traits support their ecological roles in nutrient cycling, primary productivity, and habitat provision, and they also explain their growing relevance to the blue bioeconomy. This review summarizes current knowledge of Ulva biodiversity, taxonomy, and physiology, and evaluates applications in food, feed, bioremediation, biofuel, pharmaceuticals, and biomaterials. Particular attention is given to molecular approaches that resolve taxonomic difficulties and to biochemical profiles that determine nutritional value and industrial potential. This review also considers risks and limitations. Ulva species can act as hyperaccumulators of heavy metals, microplastics, and organic pollutants, which creates safety concerns for food and feed uses and highlights the necessity of strict monitoring and quality control. Technical and economic barriers restrict large-scale use in energy and material production. By presenting both opportunities and constraints, this review stresses the dual role of Ulva as a promising bioresource and a potential ecological risk. Future research must integrate molecular genetics, physiology, and applied studies to support sustainable utilization and ensure safe contributions of Ulva to biodiversity assessment, environmental management, and bioeconomic development.

algal bloom↗

PubMed1992

Indoor air pollution.

This article summarizes the health effects of indoor air pollutants and the modalities available to control them. The pollutants discussed include active and passive exposure to tobacco smoke; combustion products of carbon monoxide; nitrogen dioxide; products of biofuels, including wood and coal; biologic agents leading to immune responses, such as house dust mites, cockroaches, fungi, animal dander, and urine; biologic agents associated with infection such as Legionella and tuberculosis; formaldehyde; and volatile organic compounds. An approach to assessing building-related illness and "tight building" syndrome is presented. Finally, the article reviews recent data on hospital-related asthma and exposures to potential respiratory hazards such as antineoplastic agents, anesthetic gases, and ethylene oxide.

Air Pollutants↗

PubMed1991

Lipid bilayer-based sensors and biomolecular electronics.

The lipid bilayer postulated as the basic structural matrix of biological membranes is widely accepted. Experiments in the early 1960s have made direct studies of lipid bilayers possible. At present, the planar bilayer lipid membrane (BLM) together with spherical lipid bilayers (liposomes), upon suitable modification, serves as a most appropriate model for biological membranes. In recent years, advances in microelectronics and interest in ultrathin organic films, including BLMs, have resulted in a unique fusion of ideas toward the development of biosensors and transducers. Furthermore, recent trends in interdisciplinary studies in chemistry, electronics, and biology have led to a new field of research: biomolecular electronics. This exciting new field of scientific-technological endeavor is part of a more general approach toward the development of a new, postsemiconductor electronic technology, namely, molecular electronics with a long-term goal of molecular computers. Experimental BLMs have been mainly used in the past as models of biological membranes. The methods of BLM studies may not be familiar to those outside biomedical research. Therefore, a brief description of the experimental techniques will be given in Section IV. Recently, it has been demonstrated that BLMs, after suitable modification, can function as electrodes and exhibit nonlinear electronic properties. These and other experimental findings relevant to sensor development and to "biomolecular electronic devices" (BED) will be covered in Section V, after a brief description of biomembranes which have been suggested as nature's molecular devices (Section III). In the last section, the potential use of the BLM system together with its modifications in the development of a new class of organic diodes, switches, biosensors, electrochemical photocells, and biofuel cells will be presented (Section VI). Additionally, this paper, besides presenting a review of our work and those of others on BLMs and liposomes in relation to biosensors and molecular electronics, reports a novel technique for obtaining BLMs (or lipid bilayers) on solid supports. The presence of solid support on one side of the BLM greatly enhances its mechanical stability, while retaining the dynamic properties of the lipid bilayer. Advantages of the new technique for self-assembling amphiphilic molecules on rigid substrates are discussed in terms of their possible uses. That is, the new BLM system (s-BLMs) is potentially useful for technological applications in the area of biosensors, enzyme electrodes, and molecular electronics as well as biochips (Section IV.C). The dividing line between the present microscopic and the future molecular electronics is 1 micron.(ABSTRACT TRUNCATED AT 400 WORDS)

Biological Transport, Active↗