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PubMed1990

Immobilization of microbial cells by adsorption.

Immobilized cells cover a wide area of applications and are essential components of many biotechnological processes. In general it can be distinguished between two immobilization methods: (1) entrapment into polymers and (2) natural adsorption onto porous and inert support materials. The immobilization by adsorption is discussed by the following criteria: biomass loading, strength of adhesion, enzymatic stability/specific activity of the biocatalyst, effectivity/reaction engineering and operational stability.

Adsorption↗
PubMed2001

Phage R4 integrase mediates site-specific integration in human cells.

The R4 integrase is a site-specific, unidirectional recombinase derived from the genome of phage R4 of Streptomyces parvulus. Here we define compact attB and attP recognition sites for the R4 integrase and express the enzyme in mammalian cells. We demonstrate that R4 integrase functions in human cells, performing efficient and precise recombination between R4 attB and attP sites cloned on an extrachromosomal vector. We also provide evidence that the enzyme can mediate integration of an incoming plasmid bearing an attB or attP site into endogenous sequences in the human genome. Furthermore, when R4 attB and attP sites are placed into the human genome, either by random integration or at a specific sequence by using the phi C31 integrase, they act as targets for integration of incoming plasmids bearing R4 att sites. The R4 integrase has immediate utility as a site-specific integration tool for genome engineering, as well as potential for further development.

Attachment Sites, Microbiological↗
PubMed1989

[Microorganisms in our food: yesterday, today and tomorrow].

The development of fermented foodstuffs can be considered as one of the greatest achievements of human civilization and goes back thousands of years. It arose from the necessity to conserve foods, to make them more digestible and also more enjoyable. During the centuries man learned by trial and error to conduct the fermentation processes by changing physical and chemical parameters in the basic food ingredients. It took much longer, however, to discover the cause of fermentation processes: only towards the end of the 19th century it was demonstrated, for example, that baker's yeast is the cause of alcoholic fermentation. Through the development of the technique of "pure microbial culture", developed again with yeast, the basis for a controlled use of microbes in food industry was established. The movement from artisan to industrial scale fermentations made necessary a systematic strain development by the "classical" techniques of "mutation, selection and recombination". The modern techniques of genetic engineering have hardly been applied to food microorganisms so far. These methods, which usually have been developed with laboratory strains, would give us the possibility to change or disrupt genes very specifically and even to introduce new genes into established food microorganisms. Some possible applications with the baker's yeast are discussed in this article.

Bacteria↗
PubMed2002

Biotransformations using prokaryotic P450 monooxygenases.

Recent studies on microbial cytochrome P450 enzymes have covered several new areas. Advances have been made in structure-function analysis and new non-enzymatic/electrochemical systems for the replacement of NAD(P)H in biocatalysis have been developed. Furthermore, the properties of some enzymes have been re-engineered by site-directed mutagenesis or by methods of directed evolution and new P450s have been functionally expressed and characterized. It is thought that a combination of these approaches will facilitate the use of isolated P450 monooxygenases in biocatalysis.

Bacteria↗
PubMed2006

Microbial fuel cells: methodology and technology.

Microbial fuel cell (MFC) research is a rapidly evolving field that lacks established terminology and methods for the analysis of system performance. This makes it difficult for researchers to compare devices on an equivalent basis. The construction and analysis of MFCs requires knowledge of different scientific and engineering fields, ranging from microbiology and electrochemistry to materials and environmental engineering. Describing MFC systems therefore involves an understanding of these different scientific and engineering principles. In this paper, we provide a review of the different materials and methods used to construct MFCs, techniques used to analyze system performance, and recommendations on what information to include in MFC studies and the most useful ways to present results.

Bacteria↗
PubMed2004

Rational pathway engineering of type I fatty acid synthase allows the biosynthesis of triacetic acid lactone from D-glucose in vivo.

Metabolic pathway engineering is a powerful tool to synthesize structurally diverse and complex chemicals via genetic manipulation of multistep catalytic systems involved in cell metabolism. Here, we report the rational design of a fatty acid biosynthetic pathway, Brevibacterium ammoniagenes fatty acid synthase B (FAS-B), that allows the microbial synthesis of triacetic acid lactone (TAL) from an inexpensive feedstock, d-glucose. TAL can be chemically converted to phloroglucinol, which is a core structure for the synthesis of various high value bioactive compounds and energetic compounds such as 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Synthesis of phloroglucinol from d-glucose using this combined biological and chemical synthesis may offer significant advantages over the current phloroglucinol manufacture, including environmental friendliness and reduction in the cost of phloroglucinol. More importantly, it represents a novel strategy for the benzene-free synthesis of aromatic chemicals.

Bacterial Proteins↗
PubMed2006

Role of toll-like receptors on human adipose-derived stromal cells.

Adult mesenchymal stem cells (MSCs) are promising tools for such applications as tissue engineering and cellular therapy. It is not clear how stem cells exposed to unfavorable conditions (e.g., hypoxia or inflammation) respond to signals of danger after in vivo transplantation. Toll-like receptors (TLRs) play a major role in the immune system, participating in the initial recognition of microbial pathogens and pathogen-associated components. This study was designated to determine the role of TLRs in human MSCs. Reverse transcriptase-polymerase chain reaction (RT-PCR) and flow cytometry analysis demonstrated that MSCs derived from human adipose tissue and bone marrow express TLR-1, TLR-2, TLR-3, TLR-4, TLR-5, TLR-6, and TLR-9. We investigated induction of the differentiation and proliferation of human adipose tissue stromal cells (hADSCs) by TLR agonists, including flagellin, peptidoglycans (PGN), lipopolysaccharide (LPS), the synthetic double-stranded RNA analog poly(I:C), and synthetic CpG oligodeoxydinucleotide (CpG-ODN). None of these agonists, except ODN, affected the proliferation of hADSCs. LPS and PGN increased osteogenic differentiation, but CpG-ODN decreased it. Poly(I:C) itself did not affect adipogenic or osteogenic differentiations, but exerted a synergistic effect on LPS- or PGN-induced osteogenic differentiation. RT-PCR analysis demonstrated that LPS and PGN induce osteogenic markers in hADSCs. TLR agonists affected the expression of chemokines and cytokines differentially. Furthermore, hADSCs affected the expression of specific TLRs in vitro under hypoxic conditions. These data provide evidence of a nonimmune role for TLR signaling on MSCs and may provide clues to the behavior of transplanted MSCs in vivo.

Adipogenesis↗
PubMed2026

Agricultural sprinkler irrigation systems as environmental reservoirs and airborne dissemination sources of Legionella pneumophila.

Sprinkler irrigation systems are critical for modern agriculture but represent largely unrecognized aquatic environments capable of sustaining opportunistic human pathogens. Among them, Legionella pneumophila is of particular concern due to its ability to colonize engineered water systems, persist under fluctuating environmental conditions, and be transmitted through aerosols. In this study, we conducted a comprehensive microbiological and genomic investigation of irrigation ponds and ditches in a rural area of north-east Spain where two zones were sampled. Metagenomic profiling revealed highly diverse microbial communities encompassing more than 20,000 species, including 21 airborne-transmissible bacterial pathogens of clinical relevance. Notably, L. pneumophila was detected in both zones, with a relative abundance of up to 4.6 %. Culture-based isolation confirmed the presence of L. pneumophila serogroup 1, Pontiac group, Benidorm subgroup, sequence type 15. Phylogenetic analysis demonstrated a close relationship between this environmental strain and clinical isolates obtained during a Legionnaires' disease outbreak occurred in 2015, which had remained without a confirmed environmental source. Meteorological data from the exposure period revealed wind conditions favouring long-distance aerosol dispersion from irrigated fields toward residential areas. Our findings provide evidence that irrigation infrastructures can act as environmental reservoirs and dissemination routes of L. pneumophila among other airborne pathogens. These results underscore the need to incorporate agricultural irrigation systems into routine environmental surveillance, outbreak investigations, and public health risk assessments.

Legionella pneumophila↗
PubMedDate not supplied

Control of secondary metabolite congener distributions via modulation of the dissolved oxygen tension.

Many secondary metabolites, including various polyketides, require complex enzymatic pathways for modification into their final biologically active forms. Limitation of the dissolved oxygen supplied during cultivation of various microbial strains can decrease the activity of cytochrome P-450 monooxygenases required for the processing of pathway intermediates into their final forms, resulting in the accumulation of these intermediates as the primary products. Here, a generalized oxygen-limited cultivation strategy is specifically demonstrated with a myxobacterial strain engineered to heterologously express the epothilone polyketide synthase (PKS) gene cluster under either an excess (the dissolved oxygen tension is maintained at 50% of saturation) or a depleted (no residual dissolved oxygen detected) level of oxygenation during cultivation. Cultivation of this myxobacterial strain with excess oxygenation resulted in the production of epothilones A and B as the primary products, while cultivation of this same strain under depleted oxygenation resulted in the production of epothilones C and D as the primary products. Additionally, the peak cell density in the oxygen-depleted cultivations was 60% higher than that observed in oxygen-excess cultivations. Finally, an active EpoK epoxidase was found to catalyze the production of a novel epothilone (Epo506) with an unexpected structure during the cultivation of another myxobacterial strain expressing a genetically modified epothilone PKS under excess oxygenation. The structure of Epo506 was determined by high-resolution mass spectrometry and one- and two-dimensional NMR.

Bioreactors↗
PubMed2004

Heat-induced production of human growth hormone by high cell density cultivation of recombinant Escherichia coli.

The temperature-induced, over-expression of the human growth hormone gene in a recombinant E. coli during high cell density cultivation is reported. Human growth hormone (hGH) production and stability were tested under different heat shock conditions. Cell densities were 25 and 60 g l(-1) in a pH-stat fed-batch mode in defined and complex medium, respectively, and the fermentation time was decreased from 41 to 32 h. hGH was produced at 2 g l(-1) in complex medium. By using glycerol as main carbon source in the complex medium with exponential feeding, cell density and hGH production were increased to 100 g l(-1) and 2.7 g l(-1), respectively.

Bioreactors↗
PubMed1996

Immunopotency of a viral peptide assembled on the carbohydrate moieties of self immunoglobulins.

The T-cell receptor recognizes peptides bound to the major histocompatibility complex antigens. Synthetic peptides corresponding to microbial epitopes can efficiently stimulate the in vitro proliferation of T-cell hybridoma or in vivo primed T cells. However, the in vivo immune responses elicited by synthetic peptides are weak because of their short half-life and poor immunogenicity. We previously showed that a genetically engineered immunoglobulin (Ig-HA), in which the CDR3 region of VH gene was replaced with a viral peptide recognized by CD4+ T cells, was able to deliver this epitope in the correct frame to antigen-processing cells that efficiently presented the peptide to T cells. Recently, we developed an enzymatic method to assemble viral peptides on the sugar moieties of immunoglobulins without alteration of the biological functions of either molecule. The viral peptide carried by these conjugates was twenty times more efficient in activating a T-cell hybridoma than the free peptide as calculated on a molar basis. We show that such conjugates are able to prime in vivo the precursors of peptide-specific T cells and to induce proliferation of naive lymphocytes from transgenic mice expressing a peptide-specific T-cell receptor in both CD4 and CD8 T-cell subsets. Our results suggest that peptides enzymatically linked to the carbohydrate moieties of immunoglobulins, using galactose residues as peptide acceptor, can be used as a safe and efficient delivery system of protective epitopes for the prevention of infectious diseases. The enzymatic engineering of immunoglobulins may also allow the development of immunotherapeutic agents to deliver antagonist peptides to autoreactive T cells or to direct immunomodulatory agents such as interleukins or cytolytic drugs to tumor cells.

Animals↗
PubMed2026

Integrating multi-omics technologies to decipher microbiome functions.

Multi-omics approaches have revolutionized our understanding of microbial communities by enabling simultaneous interrogation of genomic, transcriptomic, proteomic, and metabolomic data. The systematic integration and analysis of these deep datasets help decipher the functional roles of microbiomes, providing critical insights into microbial activities, interactions, and dynamics across diverse environments. Biological complexity makes multi-omics analysis of a single, isolated organism demanding but highly informative, yet this complexity increases further when samples comprise hundreds to thousands of individual species. As microbiome research continues to expand into clinical, environmental, and engineered systems, standardized workflows, benchmarked datasets, and community-driven initiatives are essential to ensure reproducibility, standardization and interpretability. Establishing and disseminating best practices for experimental design, data processing, and integrative analyses will be critical for maximizing comparability and scientific rigor across studies. This perspective highlights recent advances in multi-omics microbiome research, outlines key obstacles in data integration and metadata harmonization, and proposes a collaborative roadmap for scalable, FAIR-compliant multi-omics investigations and potentially disruptive Artificial Intelligence (AI) advances comparable to those of AlphaFold in the field of microbiome science.

Multiomics↗
PubMed2004

Recent developments in the maytansinoid antitumor agents.

Maytansine and its congeners have been isolated from higher plants, mosses and from an Actinomycete, Actinosynnema pretiosum. Many of these compounds are antitumor agents of extraordinary potency, yet phase II clinical trials with maytansine proved disappointing. The chemistry and biology of maytansinoids has been reviewed repeatedly in the late 1970s and early 1980s; the present review covers new developments in this field during the last two decades. These include the use of maytansinoids as "warheads" in tumor-specific antibodies, preliminary metabolism studies, investigations of their biosynthesis at the biochemical and genetic level, and ecological issues related to the occurrence of such typical microbial metabolites in higher plants.

Animals↗
PubMed2003

The microbiology of biological phosphorus removal in activated sludge systems.

Activated sludge systems are designed and operated globally to remove phosphorus microbiologically, a process called enhanced biological phosphorus removal (EBPR). Yet little is still known about the ecology of EBPR processes, the microbes involved, their functions there and the possible reasons why they often perform unreliably. The application of rRNA-based methods to analyze EBPR community structure has changed dramatically our understanding of the microbial populations responsible for EBPR, but many substantial gaps in our knowledge of the population dynamics of EBPR and its underlying mechanisms remain. This review critically examines what we once thought we knew about the microbial ecology of EBPR, what we think we now know, and what still needs to be elucidated before these processes can be operated and controlled more reliably than is currently possible. It looks at the history of EBPR, the currently available biochemical models, the structure of the microbial communities found in EBPR systems, possible identities of the bacteria responsible, and the evidence why these systems might operate suboptimally. The review stresses the need to extend what have been predominantly laboratory-based studies to full-scale operating plants. It aims to encourage microbiologists and process engineers to collaborate more closely and to bring an interdisciplinary approach to bear on this complex ecosystem.

Aerobiosis↗
PubMed1992

Natural genetic engineering in evolution.

The results of molecular genetics have frequently been difficult to explain by conventional evolutionary theory. New findings about the genetic conservation of protein structure and function across very broad taxonomic boundaries, the mosaic structure of genomes and genetic loci, and the molecular mechanisms of genetic change all point to a view of evolution as involving the rearrangement of basic genetic motifs. A more detailed examination of how living cells restructure their genomes reveals a wide variety of sophisticated biochemical systems responsive to elaborate regulatory networks. In some cases, we know that cells are able to accomplish extensive genome reorganization within one or a few cell generations. The emergence of bacterial antibiotic resistance is a contemporary example of evolutionary change; molecular analysis of this phenomenon has shown that it occurs by the addition rearrangement of resistance determinants and genetic mobility systems rather than by gradual modification of pre-existing cellular genomes. In addition, bacteria and other organisms have intricate repair systems to prevent genetic change by sporadic physicochemical damage or errors of the replication machinery. In their ensemble, these results show that living cells have (and use) the biochemical apparatus to evolve by a genetic engineering process. Future research will reveal how well the regulatory systems integrate genomic change into basic life processes during evolution.

Animals↗
PubMed2002

Maintenance and impacts of an inoculated mer/luc-tagged Pseudomonas fluorescens on microbial communities in birch rhizospheres developed on humus and peat.

Antagonistic bacteria represent promising biocontrol agents for improving forest production in seedling nurseries or forest soils. The fate of an introduced mer/luc-tagged antagonistic Pseudomonas fluorescens 31K3 was monitored in the rhizosphere of silver birch (Betula pendula) seedlings grown in microcosms containing forest humus or nursery peat. The inoculated strain (10(8) cfu g(-1) soil) was unable to establish in significant numbers in either soil type and turned nonculturable in humus. Detection in both soils was possible only via luminescence of enrichment cultures 80 days post-inoculation. Despite low P. fluorescens survival, inoculation had a positive effect on seedling growth. Limited impact of inoculation on the indigenous microbial communities was identified following analyses of respiration and denitrification potential, community-level physiological profiles and molecular fingerprinting of fungi and eubacteria, and Pseudomonas community structures. The minor changes observed in the indigenous microbial communities, including mycorrhiza development, were not consistent between humus and peat growth substrates. It was concluded that the rhizosphere-related microbial communities developed in both of these highly organic soil systems are highly buffered against introduction of foreign bacteria.

Betula↗
PubMed1987

Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors.

Fragments of exogenous DNA that range in size up to several hundred kilobase pairs have been cloned into yeast by ligating them to vector sequences that allow their propagation as linear artificial chromosomes. Individual clones of yeast and human DNA that have been analyzed by pulsed-field gel electrophoresis appear to represent faithful replicas of the source DNA. The efficiency with which clones can be generated is high enough to allow the construction of comprehensive libraries from the genomes of higher organisms. By offering a tenfold increase in the size of the DNA molecules that can be cloned into a microbial host, this system addresses a major gap in existing experimental methods for analyzing complex DNA sources.

Chromosomes↗
PubMed2001

Comparison of response of six different luminescent bacterial bioassays to bioremediation of five contrasting oils.

The performance of six different bioluminescent bacteria for the assessment of oil bioremediation was compared. Three contained lux genes linked to promoters from hydrocarbon degradation pathways: Pseudomonas fluorescens HK44 (pUTK21), Escherichia coli HMS174 (pOS25) and E. coli DH5 alpha (pGEc74, pJAMA7), responding to naphthalene, isopropylbenzene and octane, respectively. The other three expressed lux constitutively: E. coli HB101 (pUCD607) and P. putida F1 (pUCD607) are genetically engineered, while Vibrio fischeri is naturally bioluminescent and was included to facilitate comparison with previous work. Five different oils (four crude oils plus diesel) were spiked into soil, and the progress of remediation was followed over a period of 119 d by monitoring both hydrocarbon disappearance and changes in the microbial response to soil extracts. The octane bioassay was the only one of the hydrocarbon-responsive bacterial assays to show any appreciable response, with up to 20-fold induction by light crude oils. Heavy crude oil and diesel elicited a much weaker response. The metabolic (lux constitutively expressed) bioassays showed that there was a general increase in toxicity over the course of the experiment, although toxicity to E. coli HB101 (pUCD607) appeared to be decreasing by the final sampling point. The metabolic bioassay response was much less variable between the different oils than for the first three, catabolic, strains.

Benzene Derivatives↗