A5021185093- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Fungal and yeast genetics research
- Microbial Metabolic Engineering and Bioproduction
- RNA and protein synthesis mechanisms
- Molecular Biology Techniques and Applications
- Chromosomal and Genetic Variations
- RNA modifications and cancer
- Gut microbiota and health
- Algal biology and biofuel production
- Enzyme Production and Characterization
- Microbial Community Ecology and Physiology
- Studies on Chitinases and Chitosanases
- Probiotics and Fermented Foods
- Cocoa and Sweet Potato Agronomy
- Protist diversity and phylogeny
- Viral gastroenteritis research and epidemiology
- Integrated Circuits and Semiconductor Failure Analysis
- Epigenetics and DNA Methylation
- Pharmaceutical and Antibiotic Environmental Impacts
- Biocrusts and Microbial Ecology
- Phytase and its Applications
- Respiratory viral infections research
- Ethics in Clinical Research
Max Planck Institute for Terrestrial Microbiology
2022-2024
CorpoGen (Colombia)
2019-2021
Abstract Synthetic biology offers the opportunity to build solutions for improved capture and conversion of carbon dioxide (CO 2 ) that outcompete those evolved by nature. Here we demonstrate design construction a new-to-nature CO -fixation pathway, reductive tricarboxylic acid branch/4-hydroxybutyryl-CoA/ethylmalonyl-CoA/acetyl-CoA (THETA) cycle. The THETA cycle encompasses 17 enzymes from 9 organisms revolves around two most efficient -fixing described in nature, crotonyl-CoA...
Modern biological science, especially synthetic biology, relies heavily on the construction of DNA elements, often in form plasmids. Plasmids are used for a variety applications, including expression proteins subsequent purification, heterologous pathways production valuable compounds, and study functions mechanisms. For all critical step after plasmid is its sequence validation. The traditional method determination Sanger sequencing, which limited to approximately 1000 bp per reaction....
Abstract Lytic bacteriophages hold substantial promise in medical and biotechnological applications. CRISPR-Cas systems offer a way to explore these mechanisms via site-specific phage mutagenesis. However, phages can resist Cas-mediated cleavage through extensive DNA modifications like cytosine glycosylation, hindering mutagenesis efficiency. Our study utilizes the eukaryotic enzyme NgTET temporarily reduce modifications, facilitating Cas nuclease enhancing This approach enables precise...
Abstract The global demand for fine-flavour cocoa has increased worldwide during the last years. Fine-flavour offers exceptional quality and unique fruity floral flavour attributes of high by world's elite chocolatiers. Several studies have highlighted relevance fermentation to produce such attributes. Nevertheless, little is known regarding microbial interactions biochemistry that lead production these on farms industrial relevance, where traditional methods been pre-standardized scaled up....
Abstract The increase in antibiotic resistant bacteria has raised global concern regarding the future effectiveness of antibiotics. Human activities that influence microbial communities and environmental resistomes can generate additional risks to human health. In this work, we characterized aquatic their samples collected at three sites along Bogotá River from wastewaters city hospitals, investigated community profiles resistance genes (ARGs) as a function anthropogenic contamination....
Abstract Highly specific interactions between proteins are a fundamental prerequisite for life, but how they evolve remains an unsolved problem. In particular, initially unrelated require that matching surfaces. It is unclear whether such surface compatibilities can only be built by selection in small incremental steps, or also emerge fortuitously. Here, we used molecular phylogenetics, ancestral sequence reconstruction and biophysical characterization of resurrected to retrace the evolution...
Golden Gate cloning has revolutionized synthetic biology. Its concept of modular, highly characterized libraries parts that can be combined into higher order assemblies allows engineering principles to applied biological systems. The basic parts, typically stored in level 0 plasmids, are sequence validated by the method choice and on demand. Higher transcriptional units, multiple units assembled multi-gene constructs. assembly based defined usually does not introduce changes. Therefore,...
Highlights•A library-based approach for synthetic sRNAs with varying seed region length (SRL)•Synthetic RybB are processed by RNase E at AU-rich sequence motifs•Accessibility of SgrS regions is an important determinant functionality•Importance Hfq and SRL regulatory efficiency depends on the sRNA scaffoldSummaryAll organisms must respond to environmental changes. In bacteria, small RNAs (sRNAs) aspect regulation network underlying adaptation such base-pair their target mRNAs, allowing rapid...
Microbial diversity is magnificent and essential to almost all life on Earth. Microbes are an part of every human, allowing us utilize otherwise inaccessible resources. It no surprise that humans started, initially unconsciously, domesticating microbes for food production: one may call this microbial domestication 1.0. Sourdough bread just the miracles performed by fermentation, extraction more nutrients from flour at same time creating a fluffy delicious loaf. There broad range products...
Microbiomes are vast communities of microbes and viruses that populate all natural ecosystems. Viruses have been considered the most variable component microbiomes, as supported by virome surveys examples high genomic mosaicism. However, recent evidence suggests human gut is remarkably stable compared to other environments. Here we investigate origin, evolution, epidemiology crAssphage, a widespread virus. Through global collaboratory, obtained DNA sequences crAssphage from over one-third...
Synthetic Sc2.0 yeast strains contain hundreds to thousands of loxPsym recombination sites that allow restructuring the Saccharomyces cerevisiae genome by SCRaMbLE. Thus, a highly diverse population can arise from single genotype. The selection genetically candidates with rearranged synthetic chromosomes for downstream analysis requires an efficient and straightforward workflow. Here we present loxTags, set qPCR primers genotyping across detect not only deletions but also inversions...
Abstract All organisms must respond to environmental changes. In bacteria, small RNAs (sRNAs) are an important aspect of the regulation network underlying adaptation such sRNAs base-pair with their target mRNAs, allowing rapid modulation proteome. This post-transcriptional is usually facilitated by RNA chaperones, as Hfq. have a potential synthetic regulators that can be modulated rational design. this study, we use library-based approach and oxacillin susceptibility assays investigate...
Lytic bacteriophages hold substantial promise in medical and biotechnological applications. Therefore a comprehensive understanding of phage infection mechanisms is crucial. CRISPR-Cas systems offer way to explore these via site-specific mutagenesis. However, phages can resist Cas-mediated cleavage through extensive DNA modifications like cytosine glycosylation, hindering mutagenesis efficiency. Our study utilizes the eukaryotic enzyme NgTET temporarily reduce modifications, facilitating Cas...
The vast microbial diversity on the planet represents an invaluable source for identifying novel activities with potential industrial and therapeutic application. In this regard, metagenomics has emerged as a group of strategies that have significantly facilitated analysis DNA from multiple environments expanded limits known diversity. However, functional characterization enzymes, metabolites, products encoded by diverse genomes is limited inefficient heterologous expression foreign genes....
Abstract Background Komagataella phaffii (Pichia pastoris ) is a methylotrophic commercially important non-conventional species of yeast that grows in fermentor to exceptionally high densities on simple media and secretes recombinant proteins efficiently. Genetic engineering strategies are being explored this organism facilitate cost-effective biomanufacturing. Small, stable artificial chromosomes K. could offer unique advantages by accommodating multiple integrations extraneous genes their...
ABSTRACT Nicotinamide adenine dinucleotide (NAD) serves as a cap-like structure on cellular RNAs (NAD-RNAs) in all domains of life including the bacterium Escherichia coli . NAD also acts key molecule phage-host interactions, where bacterial immune systems deplete to abort phage infection. Nevertheless, NAD-RNAs have not yet been identified during infections bacteria and mechanisms their synthesis degradation are unknown this context. The T4 that specifically infects E. presents an important...
Abstract Optimization of the metabolic flux through heterologous pathways to improve bioproduction or utilization alternative substrates requires both fine-tuning non-native gene expression levels and improvement host genome. The SCRaMbLE system incorporated into synthetic Sc2.0 yeast strains enables a rapid approach rearrange genome Saccharomyces cerevisiae in order create optimized chassis. Here, we show that light-inducible Cre recombinase L-SCRaMbLE can efficiently generate diverse...
ABSTRACT Background Komagataella phaffii (Pichia pastoris ) is a methylotropic commercially important non-conventional species of yeast that grows in fermentor to exceptionally high densities on simple media and secretes recombinant proteins efficiently. Genetic engineering strategies are being explored this organism facilitate cost-effective biomanufacturing. Small, stable artificial chromosomes K. could offer unique advantages by accommodating multiple integrations extraneous genes their...