A5024291940- Fungal and yeast genetics research
- Antifungal resistance and susceptibility
- Fungal Infections and Studies
- DNA Repair Mechanisms
- Fermentation and Sensory Analysis
- Botanical Research and Applications
- Probiotics and Fermented Foods
- Microbial Natural Products and Biosynthesis
- Yeasts and Rust Fungi Studies
- CRISPR and Genetic Engineering
- Bioinformatics and Genomic Networks
- Evolution and Genetic Dynamics
- Microbial Metabolites in Food Biotechnology
- Cassava research and cyanide
- Gut microbiota and health
- Plant Gene Expression Analysis
- Gene Regulatory Network Analysis
- Genetic Mapping and Diversity in Plants and Animals
- Food composition and properties
- Synthesis and Biological Evaluation
- Fungal Biology and Applications
- Biochemical and Molecular Research
- Plant-Microbe Interactions and Immunity
- Microbial Metabolic Engineering and Bioproduction
- Monoclonal and Polyclonal Antibodies Research
Instituto Tecnológico Superior de Irapuato
2020-2025
Center for Research and Advanced Studies of the National Polytechnic Institute
2019-2025
Instituto Politécnico Nacional
2019-2022
University of California, San Francisco
2013-2017
University of California System
2017
European Molecular Biology Laboratory
2009-2011
Wellcome Trust
2009
European Bioinformatics Institute
2009
European Molecular Biology Laboratory
2007-2008
Universidad Nacional Autónoma de México
2005
ABSTRACT The production of traditional agave spirits in Mexico, such as mezcal, involves a process that uses environmental microorganisms to ferment the cooked must from plants. By analysing these microorganisms, researchers can understand dynamics microbial communities at interface natural and human‐associated environments. This study involved 16S ITS amplicon sequencing 99 fermentation tanks 42 distilleries across Mexico. Agave species used, methods, climatic conditions biogeographic...
Accurate estimates of mutation rates provide critical information to analyze genome evolution and organism fitness. We used whole-genome DNA sequencing, pulse-field gel electrophoresis, comparative hybridization determine in diploid vegetative meiotic accumulation lines Saccharomyces cerevisiae. The underwent only mitotic divisions while the a cycle every ∼20 divisions. Similar base substitution were estimated for both lines. Given our experimental design, these measures indicated that rate...
The rewiring of gene regulatory networks can generate phenotypic novelty. It remains an open question, however, how the large number connections needed to form a novel network arise over evolutionary time. Here, we address this question using controlled by fungal transcription regulator Ndt80. This conserved protein has undergone dramatic switch in function—from ancestral role regulating sporulation derived biofilm formation. function corresponded large-scale genes regulated However,...
We examine how a complex transcription network composed of seven 'master' regulators and hundreds target genes evolved over span approximately 70 million years. The controls biofilm formation in several Candida species, group fungi that are present humans both as constituents the microbiota opportunistic pathogens. Using variety approaches, we observed two major types changes have occurred since four extant species examined last shared common ancestor. Master regulator 'substitutions'...
Abstract Fungi from the genus Candida are common members of human microbiota; however, they also important opportunistic pathogens in immunocompromised hosts. Several morphological transitions have been linked to ability these fungi occupy different ecological niches body. The transcription factor Efg1 APSES family plays a central role circuits underlying several changes. In albicans, for example, is regulator filamentation, biofilm formation, and white-opaque switching, processes associated...
The human fungal pathogen Candida albicans can reversibly switch between two cell types named "white" and "opaque," each of which is stable through many divisions. These differ in their ability to mate, metabolic preferences interactions with the mammalian innate immune system. A highly interconnected network eight transcriptional regulators has been shown control switching these types. To identify additional switch, we systematically quantitatively measured white-opaque rates 196 strains,...
Abstract Yeasts are a diverse group of fungal microorganisms that widely used to produce fermented foods and beverages. In Mexico, open fermentations obtain spirits from agave plants. Despite the prevalence this traditional practice throughout country, yeasts have only been isolated studied limited number distilleries. To systematically describe diversity yeast species fermentations, here we generate YMX‐1.0 culture collection by isolating 4524 strains 68 sites with climatic, geographical,...
<title>Abstract</title> Background The NUDIX superfamily encompasses highly diverse enzymes involved in a plethora of biological functions such as mRNA metabolism, DNA repair, and lipid peroxidation. These hydrolases are found all domains life show surprising versatility terms the substrates that they process. knowledge about diversity fungal proteins is fragmentary, being largely limited to small number characterized from yeasts. To address this gap systematically, we performed detailed...
The common yeast Saccharomyces cerevisiae is widely associated with anthropogenic habitats and dominates agave fermentations in Mexico, despite the absence of starter cultures artisanal production. Yet, origins dispersal microorganisms involved this fermentation system—including wild S. its sister species paradoxus —remain poorly understood. Here, we analyzed distribution these two across three regions Mexico by collecting a total 861 samples from 15 traditional distilleries 25 nearby...
Heritable epigenetic changes underlie the ability of cells to differentiate into distinct cell types. Here, we demonstrate that fungal pathogen Candida tropicalis exhibits multipotency, undergoing stochastic and reversible switching between three cellular states. The states exhibit unique morphologies, growth rates, global gene expression profiles. Genetic analysis identified six transcription factors play key roles in regulating differentiation. In particular, show forced Wor1 or Efg1 can...
Frequently during evolution, new phenotypes evolved due to novelty in gene regulation, such as that caused by genome rewiring. This has been demonstrated comparing common regulatory sequences among species and identifying single mutations are associated with phenotypes. However, while a mutation changes element, regulation is accomplished network involving multiple interactive elements. Therefore, better understand we have studied how contributed the adaptation of cells challenge. We created...
When mismatches in heteroduplex DNA formed during meiotic recombination are left unrepaired, post-meiotic segregation of the two mismatched alleles occurs ensuing round mitosis. This gives rise to somatic mosaicism multicellular organisms and leads unexpected allelic combinations among progeny. Despite its implications for inheritance, has been studied at only a few loci. By genotyping tens thousands genetic markers yeast segregants their clonal progeny, we analyzed genome-wide scale. We...
Species from the genus Candida are among most important human fungal pathogens. Several of them frequent commensals microbiota but also able to cause a variety opportunistic infections, especially when host becomes immunocompromised. By far, research understand molecular underpinnings pathogenesis these species has focused on albicans, virulent member genus. However, epidemiological data indicates that related clinically important. Here, we describe generation set strains and plasmids...
The ascomycetous yeast Kazachstania humilis is an active species in backslopped sourdough and the spontaneous fermentation of several traditional foods beverages. Here, we report draft genome sequence a
Fungal pathogens can be lethal, especially among immunocompromised populations, such as patients with AIDS and recipients of tissue transplantation or chemotherapy. Prolonged usage antifungal reagents lead to drug resistance treatment failure. Understanding mechanisms that underlie by pathogenic microorganisms is thus vital for dealing this emerging issue. In study, we show dramatic sequence changes in PDR5, an ABC (ATP-binding cassette) efflux transporter protein gene opportunistic fungal...
ABSTRACT Yeasts are a diverse group of fungal microorganisms that widely used to produce fermented foods and beverages. In Mexico, open fermentations obtain spirits from agave plants. Despite the prevalence this traditional practice throughout country, yeasts have only been isolated studied limited number distilleries. To systematically describe diversity yeast species fermentations, here we generate YMX.1.0 culture collection by isolating 4,524 strains 68 sites in climatic, geographical,...
Candida maltosa is closely related to important pathogenic species, especially C. tropicalis and albicans, but it has been rarely isolated from humans. For this reason, through comparative studies, could be a powerful model understand the genetic underpinnings of pathogenicity species. Here, we generated cohesive assembly genome developed engineering tools that will facilitate studying species at molecular level. We used combination short long-read sequencing build polished genomic draft...
From yeasts to humans, introgressive hybridization significantly influences the evolutionary history of living organisms by introducing new genetic diversity. Strains Saccharomyces cerevisiae worldwide exhibit introgressions from sister species S. paradoxus , despite average sequence identity between these being lower than 90%. While isolates Neotropics are known for their high levels introgression, events leading unusually prevalence them remain unclear. Here, we sequenced 216 in open agave...
Microarrays provide an accurate and cost-effective method for genotyping large numbers of individuals at high resolution. The resulting data permit the identification loci which genetic variation is associated with quantitative traits, or fine mapping meiotic recombination, a key determinant diversity among individuals. Several issues inherent to short oligonucleotide arrays -- cross-hybridization, variability in probe response target have potential produce errors. There need improved...