Biology subjects

Hernandez, M.

Publications and source records attributed to Hernandez, M..

44 records · Page 3Linked to original sources

bioRxiv2020

Reconstructing genomes of carbon monoxide oxidisers in volcanic deposits including members of the class Ktedonobacteria

Microorganisms can potentially colonize volcanic rocks using the chemical energy in reduced gases such as methane, hydrogen (H2) and carbon monoxide (CO). In this study, we analysed soil metagenomes from Chilean volcanic soils, representing three different successional stages with ages of 380, 269 and 63 years, respectively. A total of 19 metagenome-assembled genomes (MAGs) were retrieved from all stages with a higher number observed in the youngest soil (1640: 2 MAGs, 1751: 1 MAG, 1957: 16 MAGs). Genomic similarity indices showed that several MAGs had amino-acid identity (AAI) values >50% to the phyla Actinobacteria, Acidobacteria, Gemmatimonadetes, Proteobacteria and Chloroflexi. Three MAGs from the youngest site (1957) belonged to the class Ktedonobacteria (Chloroflexi). Complete cellular functions of all the MAGs were characterised, including carbon fixation, terpenoid backbone biosynthesis, formate oxidation and CO oxidation. All 19 environmental genomes contained at least one gene encoding a putative carbon monoxide dehydrogenase (CODH). Three MAGs had form I coxL operon (encoding the large subunit CO-dehydrogenase). One of these MAGs (MAG-1957-2.1, Ktedonobacterales) was highly abundant in the youngest soil. MAG-1957-2.1 also contained genes encoding a [NiFe]-hydrogenase and hyp genes encoding accessory enzymes and proteins. Little is known about the Ktedonobacterales through cultivated isolates, but some species can utilize H2 and CO for growth. Our results strongly suggest that the remote volcanic sites in Chile represent a natural habitat for Ktedonobacteria and they may use reduced gases for growth.

microbiology↗

bioRxiv2020

Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19

SARS-CoV-2, the virus responsible for COVID-19, causes widespread damage in the lungs in the setting of an overzealous immune response whose origin remains unclear. We present a scalable, propagable, personalized, cost-effective adult stem cell-derived human lung organoid model that is complete with both proximal and distal airway epithelia. Monolayers derived from adult lung organoids (ALOs), primary airway cells, or hiPSC-derived alveolar type-II (AT2) pneumocytes were infected with SARS-CoV-2 to create in vitro lung models of COVID-19. Infected ALO-monolayers best recapitulated the transcriptomic signatures in diverse cohorts of COVID-19 patient-derived respiratory samples. The airway (proximal) cells were critical for sustained viral infection, whereas distal alveolar differentiation (AT2[->]AT1) was critical for mounting the overzealous host immune response in fatal disease; ALO monolayers with well-mixed proximodistal airway components recapitulated both. Findings validate a human lung model of COVID-19, which can be immediately utilized to investigate COVID-19 pathogenesis and vet new therapies and vaccines. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=176 SRC="FIGDIR/small/344002v4_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@1d1507aorg.highwire.dtl.DTLVardef@faa17forg.highwire.dtl.DTLVardef@80ceb1org.highwire.dtl.DTLVardef@81d61c_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIHuman lung organoids with mixed proximodistal epithelia are created C_LIO_LIProximal airway cells are critical for viral infectivity C_LIO_LIDistal alveolar cells are important for emulating host response C_LIO_LIBoth are required for the overzealous response in severe COVID-19 C_LI IN BRIEFAn integrated stem cell-based disease modeling and computational approach demonstrate how both proximal airway epithelium is critical for SARS-CoV-2 infectivity, but distal differentiation of alveolar pneumocytes is critical for simulating the overzealous host response in fatal COVID-19.

cell biology↗

bioRxiv2020

Mobilization of a Kluyvera-like arnBCADTEF operon, besides mcr genes, confers colistin resistance to Escherichia coli isolated from healthy animals

The use of colistin as a last resort antimicrobial is compromised by the emergence of resistant enterobacteria with acquired determinants like mcr genes, mutations that activate the PmrAB two-component system and also by some other(s) still unknown mechanism(s). This work analyzed 74 E. coli isolates from healthy swine, turkey or bovine animals, characterizing their colistin resistance determinants. The mcr-1 gene, detected in 69 isolates, was the main determinant found among which 45% were carried by highly mobile plasmids, followed by four strains lacking previously known resistance determinants or two with mcr-4 (one in addition to mcr-1), whose phenotypes were not transferred by conjugation. Although a fraction of isolates carrying mcr-1 or mcr-4 genes also presented missense polymorphisms in pmrA or pmrB, constitutive activation of PmrAB was not detected, in contrast to control strains carrying mutations that confer colistin resistance. The expression of mcr genes negatively controls arnBCADTEF expression, a down-regulation that was also observed in the four isolates lacking known resistance determinants, three of them sharing the same macrorestriction and plasmid profiles. Genomic sequencing of one of these strains, isolated from a bovine in 2015, revealed a IncFII plasmid of 60 Kb encoding an arnBCADTEF operon closely related to Kluyvera ascorbata homologs. This element, named pArnT1, was cured by ethidum bromide and lost in parallel to colistin resistance. This work reveals that, besides mcr genes and chromosomal mutations, mobilization of arnBCADTEF operon represents a colistin resistance mechanism whose spread and relevance for public health should be carefully surveyed. Abstract ImportanceColistin is an old antibiotic that has returned to first-line fighting against (Gram negative) microorganisms after pandemic rising of antimicrobial resistance. However, low susceptibility to colistin is also becoming spread, mainly by plasmid mobilization of one of the enzymes (encoded by mcr genes) that modify covalently the external layer (the lipid A component of the lipopolysaccharide) of bacterial envelope, interfering antibiotic effectiveness. The second enzymatic system that performs envelope modification and confers colistin resistance when overexpressed is encoded by arnBCADTEF operon, a set of seven genes with location restricted (up to now) to the chromosome of Gram negative bacteria. This work describes plasmid mobilization of this operon between enterobacteria, from Kluyvera to Escherichia coli, where a Kluyvera-like arnBCADTEF operon carried by pArnT1 might represent, besides mcr genes, a potential risk for antimicrobial therapy and might require careful surveillance.

microbiology↗

bioRxiv2020

Factors influencing taxonomic unevenness in scientific research: A mixed-methods case study of non-human primate genomic sequence data generation

Scholars have often noted major disparities in the extent of scientific research conducted among taxonomic groups. Such trends may cascade if future scientists gravitate towards study species with more data and resources already available. As new technologies emerge, do research studies employing these technologies continue these disparities? Here, using non-human primates as a case study, we first identified disparities in recently-generated massively-parallel genomic sequencing data and we then conducted interviews with the scientists who produced these data to learn their motivations when selecting species for study. Specifically, we tested whether variables including publication history and conservation status were significantly correlated with publicly-available sequence data in the NCBI Sequence Read Archive. Of the 179.6 terabases (Tb) of sequence data in this database for 519 non-human primate species, 135 Tb (~75%) were from only five species: rhesus macaques, olive baboons, green monkeys, chimpanzees, and crab-eating macaques. The strongest individual predictors of the amount of genomic data were the total number of non-medical scholarly publications (linear regression; r2=0.37; P=6.15x10-12) and number of medical publications (r2=0.27; P=9.27x10-9). In a generalized linear model, the number of non-medical publications (P=0.00064) and closer phylogenetic distance to humans (P=0.024) were the most predictive of the amount of genomic sequence data. We interviewed 33 authors of genomic data-producing publications and analyzed their responses using a grounded theory approach. Consistent with our quantitative results, authors mentioned that their choices of species were motivated by sample accessibility, prior published work, and perceived relevance (especially health-related) to humans. Our mixed-methods approach helped us to identify and contextualize some of the driving factors behind species-uneven patterns of scientific research, which can now be considered by funding agencies, scientific societies, and research teams aiming to align their broader goals with future data generation efforts. SIGNIFICANCE STATEMENTOur study sheds lights on the species-uneven distribution of genomic sequence data generation across the order Primates. We used a combination of quantitative data analyses and qualitative interviews with authors of data-producing studies to identify factors that have driven the observed pattern of unevenness; these included the extent of prior research conducted on each species, the relevance to human medicine, phylogenetic distance to humans, and sample accessibility. While our study focused on factors influencing non-human primate genomic sequence data, similar questions can be asked about how the scientific community engages with research projects more broadly. Our goal is to bring attention to the diversity of factors that influence scientists as they plan their projects, so that this process can be considered in the future by research groups and funding agencies aiming to align their broader goals with future data generation efforts.

genomics↗

bioRxiv2019

Global Genetic Cartography of Urban Metagenomes andAnti-Microbial Resistance

We have created a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities across 3 years. This is the first systematic, worldwide study cataloging the urban microbial ecosystem. We identify taxonomically-defined microorganisms collected across three years. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics AMR markers, and novel genetic elements, including 10,928 viral, 1302 bacteria, and 2 archaea novel species. We identify 4,424 species of urban microorganisms and a consistent "core" of 31 species found in nearly all samples that is largely distinct from any human commensal microbiome. Profiles of AMR genes show geographic variation in type and density. Together, these results constitute a high-resolution, global metagenomic atlas, which enables the discovery of new genetic components, highlights potential forensic applications, and provides an essential first draft of the global AMR burden of the worlds cities.

microbiology↗

bioRxiv2019

Resourceful mice do not starve: feeding efforts and decision-making process under a restricted unknown food source

Foraging decisions must balance the energy gained, the time investment and the influence of key environmental factors. In our work, we aimed to examine the importance of predation risk cues and experience in the feeding efforts and decision-making process when a novel food resource is presented. To achieve this, free ranging wood mice Apodemus sylvaticus were live-trapped in "Monte de Valdelatas" (Madrid) by setting 80 Sherman traps in 4 plots. Traps were subjected to two food access difficulties three-night consecutive treatments: open plastic bottles and closed bottles, both using corn as bait. To generate predation risk, we set fox faeces in half of the traps in each plot. Also, we considered indirect predator cues as the moon phase. We analyse whether mice had bitten the bottles and the area gnawed of each bottle was measured. We discovered that mice feeding decisions and efforts were driven by food access difficulty, experience and predation risk. The ability of mice to properly balance their energy budget was probed since they bit and performed bigger orifices in the closed bottles, hence, individuals can adapt the feeding effort when a new food source is available. Moreover, experience was determinant in the use of this new resource since recaptured mice gnawed the bottles more successfully and the skill was improved each time an individual was recaptured. Additionally, direct predation risk cues prompt mice to bite the bottles whereas the effect of different moon phases varied among the treatments. This is the first study that provides direct evidence of wild mice formidable efficacy to exploit a new nutrient resource while deepening in crucial environmental factors that shape decision-making procedure.

animal behavior and cognition↗

bioRxiv2018

New insights of the local immune response against both fertile and infertile hydatid cysts

BackgroundCystic echinococcosis is caused by the metacestode of the zoonotic flatworm Echinococcus granulosus. Within the viscera of the intermediate host, the metacestode grows as a unilocular cyst known as hydatid cyst. This cyst is comprised of two layers of parasite origin: germinal and laminated layers, and one of host origin: the adventitial layer, that encapsulates the parasite. This adventitial layer is composed of collagen fibers, epithelioid cells, eosinophils and lymphocytes. To establish itself inside the host, the germinal layer produces the laminated layer, and to continue its life cycle, generates protoscoleces. Some cysts are unable to produce protoscoleces, and are defined as infertile cysts. The molecular mechanisms involved in cyst fertility are not clear, however, the host immune response could play a crucial role.\n\nMethodology/Principal fidingsWe collected hydatid cysts from both liver and lungs of slaughtered cattle, and histological sections of fertile, infertile and small hydatid cysts were stained with haematoxylin-eosin. A common feature observed in infertile cysts was the disorganization of the laminated layer by the infiltration of host immune cells. These infiltrating cells eventually destroy parts of laminated layer. Immunohistochemical analysis of both parasite and host antigens, identify these cells as cattle macrophages and are present inside the cysts associated to germinal layer.\n\nConclusions/SignificanceThis is the first report that indicates to cell from immune system present in adventitial layer of infertile bovine hydatid cysts could disrupt the laminated layer, infiltrating and probably causing the infertility of cyst.\n\nAuthor SummaryCystic echinococcosis is caused by the zoonotic flatworm Echinococcus granulosus. Within the viscera of the intermediate host, mainly liver and lungs of herbivores such as cows and sheep as well as human beings, the parasite grows as a unilocular cyst known as hydatid cyst. These cysts develop in their inner chamber a structure known as protoscolex, when consumed by the definitive host (e.g. dogs), it grows into a worm that resides in the small intestine and produces eggs that contaminate the environment. In cattle, most hydatid cysts are unable to produce protoscoleces, and thus are termed infertile hydatid cysts. The molecular mechanisms that explain the causes of hydatid cyst infertility remain unknown. We routinely collected cattle hydatid cysts from both liver and lugs and processed them for histological analysis. We found that there is a subset of fertile hydatid cysts that have low protoscolex viability and high immune infiltration surrounding the cyst. All infertile cysts have high immune infiltration, and many of them show disruption of the laminated layer and immune cells of host origin inside the cyst. This is the first report that shows that the cyst can be infiltrated by the host immune system.

immunology↗

bioRxiv2017

Detecting pathogen exposure during the non-symptomatic incubation period using physiological data

Early pathogen exposure detection allows better patient care and faster implementation of public health measures (patient isolation, contact tracing). Existing exposure detection most frequently relies on overt clinical symptoms, namely fever, during the infectious prodromal period. We have developed a robust machine learning based method to better detect asymptomatic states during the incubation period using subtle, sub-clinical physiological markers. Starting with high-resolution physiological waveform data from non-human primate studies of viral (Ebola, Marburg, Lassa, and Nipah viruses) and bacterial (Y. pestis) exposure, we processed the data to reduce short-term variability and normalize diurnal variations, then provided these to a supervised random forest classification algorithm and post-classifier declaration logic step to reduce false alarms. In most subjects detection is achieved well before the onset of fever; subject cross-validation across exposure studies (varying viruses, exposure routes, animal species, and target dose) lead to 51h mean early detection (at 0.93 area under the receiver-operating characteristic curve [AUCROC]). Evaluating the algorithm against entirely independent datasets for Lassa, Nipah, and Y. pestis exposures un-used in algorithm training and development yields a mean 51h early warning time (at AUCROC=0.95). We discuss which physiological indicators are most informative for early detection and options for extending this capability to limited datasets such as those available from wearable, non-invasive, ECG-based sensors.

physiology↗