Biology subjects

Alvarez, D.

Publications and source records attributed to Alvarez, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Cell Surface Sialoglycan Engineering Through Exogenous mRNA

All human cells display a dense matrix of structurally diverse glycans that often terminate in monosaccharides belonging to the sialic acid family of sugars. While these sialoglycans are now recognized as critical regulators of human immunity, there is a lack of technologies that provide precise, transient control over their biosynthesis and presentation on a live cell surface. Here, we addressed this unmet need by developing an mRNA-based platform for delivery of transcripts coding for the enzymes that assemble sialoglycans - sialyltransferases - to human cells. We demonstrated that mRNA coding for the 2-6-specific sialyltransferase ST6Gal1 produced active, Golgi-resident enzyme that potentiated levels of 2-6-sialoglycans on the surface of human cell lines. Increased presentation of these sialoglycans was transient and tracked with the degradation kinetics of the delivered mRNA. Importantly, this approach minimally perturbed other classes of glycans and did not broadly alter physiological transcriptional networks beyond those involved in cellular responses to exogenous RNA. Similar on-target effects were observed for the O-linked 2-6-specific sialyltransferase ST6GalNAc4; however, the effects from mRNA coding for the 2-3-specific sialyltransferases ST3Gal1 and ST3Gal4 were more complex. Taken together, this mRNA platform provides a framework for cellular sialoglycoengineering endeavours, where precise and reversible control over glycocalyx composition is desired.

bioengineering↗

bioRxiv2026

Capabilities, specificity gaps and training-data dependence of AlphaFold3 across diverse application areas

Structure prediction models have moved from single proteins to assemblies that include diverse biomolecules and their modifications. AlphaFold3 (AF3) and related models extended structural modelling via an all-atom framework, opening many new potential applications in structural biology. We evaluate how well the new capabilities of AF3 translate into application tasks in diverse areas: prediction of ubiquitinated protein structures, T-cell receptor (TCR)-epitope recognition, antibody-antigen complexes, protein-RNA and protein-lipid interactions. We find that, while AF3 can perform well in favourable settings, this performance is uneven across applications. In RNA-target predictions, the model confidence fails to separate genuine from decoy interaction partners and in several tasks accuracy depends on the presence of related complexes in the training set. Taken together, our assessment is more cautious than for AF2, whose gains in modelling monomers and complexes were clear and broadly generalisable. AF3s extension to new biomolecule types shows less consistent performance and generalisation. AF3 can be a powerful tool for hypothesis generation and prioritisation, but its predictions and use of confidence metrics will depend strongly on the specific application area and must be interpreted with respect to training-set overlap. We expect that the benchmarks provided here will serve for testing of future developments in the structure prediction field.

bioinformatics↗

bioRxiv2026

Molecular insights into bulk lipid transport from structural studies of the bridge-like protein VPS13A complexed with the scramblase XKR1

In eukaryotes, bridge-like lipid-transfer proteins (BLTPs) are central in mediating vesicle-independent lipid transfer between organelles. BLTPs span the cytosolic space between organelles at contact sites, featuring hydrophobic channels for lipids to travel between membranes. How BLTPs cooperate with partner proteins to orchestrate lipid delivery remains mysterious. Here we used cryo-electron microscopy to visualize a complex comprising the prototypical BLTP VPS13A and the plasma membrane localized scramblase XKR1 at near-atomic resolution. VPS13A interacts with XKR1 via its PH-domain, priming VPS13As bridge-like lipid-transfer domain to deliver lipids directly to the cytosolic leaflet of the acceptor membrane. In molecular dynamics simulations, such arrangement allows for robust lipid transfer, accelerated by membrane properties. Newly delivered lipids can then be equilibrated between leaflets of the membrane bilayer by the scramblase, allowing for membrane growth. Mechanistic insights regarding lipid delivery by VPS13A are directly applicable to all VPS13 proteins and all BLTP family members more broadly.

cell biology↗

bioRxiv2025

Bioprospecting Native Oleaginous Microalgae for Wastewater Nutrient Remediation and Lipid Production

Subtropical climate in Florida offers a unique opportunity for sustainable biofuel production using native microalgae cultivated in untreated wastewater. This study bioprospected oleaginous microalgal consortia from a wastewater holding tank at the Thomas P. Smith Water Reclamation Facility in Tallahassee, Florida, aiming to identify strains capable of both nutrient remediation and lipid accumulation. Using Fluorescence Activated Cell Sorting (FACS), chlorophyll-containing cells were isolated and cultured on BG-11 media. Shotgun metagenomics revealed that the most robust consortia- labeled C3, C4, and C9, were dominated by Chlamydomonas, Acutodesmus, and Volvox spp., alongside diverse bacterial, fungal, and archaeal communities. Functional gene analysis indicated active pathways for photosynthesis, lipid biosynthesis, and nutrient assimilation. In microcosm experiments, these consortia achieved up to 100% ammonia, 95% phosphorus, and 89% nitrate removal, outperforming control treatments. Lipid screening confirmed significant accumulation, with consortium C9 showing the highest yield. These findings underscore the potential of native microalgal consortia for integrated wastewater treatment and biofuel production, advancing circular bioeconomy strategies for subtropical regions.

microbiology↗

bioRxiv2025

The molecular mechanism of lipid uptake by membrane-anchored bridge-like lipid transfer proteins.

Lipid transport by bridge-like lipid transfer proteins (BLTPs) is emerging as a key process in lipid and cellular metabolism in both physiological and pathological conditions. However, the precise mechanism of lipid transport by BLTPs has remained elusive. Here, we use extensive all-atom molecular dynamics simulations to characterize the precise mechanism of lipid transfer into the BLTP hydrophobic cavity from donor membranes. For multiple BLTPs, we observe the ability to extract and solubilize lipids without lipid selectivity, and we identify membrane destabilization as a critical parameter to achieve effective lipid desorption. We rationally design a mutant BLTP with altered ability to destabilize lipid bilayers, and we show that this abolishes lipid desorption in silico and protein function in vivo. Taken together, our data provide an atomic-level description of the mechanism of lipid transport by BLTPs, ultimately suggesting alternative strategies to interfere with their activity.

biophysics↗

bioRxiv2025

TMEM170 family proteins are lipid scramblases that physically associate with bridge lipid transporters BLTP1/Csf1

Bulk lipid transport between organelles has been proposed to involve the partnership between bridge lipid transport proteins and membrane-embedded lipid scramblases. However, for almost all BLTPs, such physical association has not been fully described, and, in most cases, the identity of the scramblases is unknown. Here, we identify TMEM170 family proteins as endoplasmic reticulum lipid scramblases that physically interact with BLTP1/Csf1 proteins. This finding opens new avenues to understand the complex mechanism involved in lipid transport at membrane contact sites.

cell biology↗

bioRxiv2024

Tensions in tillage: Reduction in tillage intensity associates with lower wheat growth and nutritional grain quality despite enhanced soil biological indicators

Dryland ecosystems are particularly susceptible to the adverse effects of intensive agriculture, with intensive tillage exerting a major impact on soil health and its biotic components. The implementation of less disturbing soil management practices can be essential for preserving the soil environment and maintaining the diverse communities of microorganisms, micro- and mesofauna, which are essential contributors to soil fertility. In this study, we assessed soil chemical properties, soil biodiversity and functionality, and wheat crop growth across a tillage gradient encompassing no-tillage (NT), minimum tillage (MT), and standard tillage (ST). Results showed that NT resulted in increased soil macronutrient levels compared to MT and ST. In general, reduced tillage increased the abundance of soil biota, with significantly higher levels of bacterial and fungal marker genes observed in MT and NT compared to ST. Nematode abundance increased by 25% in MT and 50% in NT, compared to ST and predatory acari were significantly more abundant in NT, while numbers of total acari were higher in both NT and ST compared to MT. Community structure analysis revealed that tillage strongly influenced bacterial, fungal and acari community composition, reflecting a gradient of soil disturbance intensity. Corresponding to the increased abundance of soil biota, reduced tillage increased microbial activity and soil functionality along the disturbance gradient. This was evident in the potential activity of carbon, nitrogen and phosphorus cycling enzymes, as well as the microbial capacity for carbon utilisation. In addition, evidence of the formation of biocrust as a possible source of carbon input was found. Furthermore, we observed important wheat pathogens to decrease and fungal antagonists to increase in NT compared to ST. Despite enhanced soil biological indicators under reduced tillage, wheat growth, nitrogen uptake and grain B vitamin contents were higher in ST compared to NT. In addition, we observed a shift in technological grain properties across tillage practices. The higher root:shoot ratio (an indicator of nitrogen deficiency) and median root diameter (hormone-driven lateral expansion) in NT suggest that soil compaction could be a potential cause of reduced wheat performance. These results suggest that despite improved soil biological indicators, other factors such as a low rates of N mineralization potential and prevalence of soil compaction may be limiting wheat performance in NT systems. HighlightsO_LIEnhanced microbial activity and functionality under reduced tillage C_LIO_LITillage intensity shaped community structure of microbes, nematodes and acari C_LIO_LISoil biocrust development under NT may increase soil organic carbon C_LIO_LIRoot traits revealed soil compaction and nutrient limitation in NT systems C_LIO_LIReduced tillage impaired wheat quality and changed technological grain properties C_LI

ecology↗

bioRxiv2024

Evolution of antiviral resistance captures a transient interdomain functional interaction between chikungunya virus envelope glycoproteins

Envelope proteins drive virus and host-cell membrane fusion to achieve virus entry. Fusogenic proteins are classified into structural classes that function with remarkable mechanistic similarities. Fusion proceeds through coordinated movements of protein domains in a sequence of orchestrated steps. Structures for the initial and final conformations are available for several fusogens, but folding intermediates have largely remained unresolved and interdependency between regions that drive conformational rearrangements is not well understood. Chikungunya virus (CHIKV) particles display heterodimers of envelope proteins E1 and E2 associated as trimeric spikes that respond to acidic pH to trigger fusion. We have followed experimental evolution of CHIKV under the selective pressure of a novel small-molecule entry inhibitor. Mutations arising from selection mapped to two residues located in distal domains of E2 and E1 heterodimer and spikes. Here, we pinpointed the antiviral mode of action to inhibition of fusion. Phenotypic characterization of recombinant viruses indicated that the selected mutations confer a fitness advantage under antiviral pressure, and that the double-mutant virus overcame antiviral inhibition of fusion while single-mutants were sensitive. Further supporting a functional connection between residues, the double-mutant virus displayed a higher pH-threshold for fusion than single-mutant viruses. Finally, mutations implied distinct outcomes of replication and spreading in mice, and infection rates in mosquitoes underscoring the fine-tuning of envelope protein function as a determinant for establishment of infection. Together with molecular dynamics simulations that indicate a link between these two residues in the modulation of the heterodimer conformational rearrangement, our approach captured an otherwise unresolved interaction. ImportanceCHIKV is a reemergent pathogen that has caused large outbreaks in the twenty years. There are no available antiviral therapies and a vaccine has only recently been approved. Here, we describe the mode of action of a novel inhibitor designed against CHIKV envelope proteins heterodimer that blocks entry at the stage of fusion between virus and host membranes. Fusion is common to the entry of enveloped viruses. Virus envelope proteins drive fusion undergoing a series of transitions from an initial metastable conformational state to a more stable post-fusion state. Intermediate conformations are transient and have mostly remained inaccessible to structure determination. In this study, directed evolution of resistance to antiviral inhibition of fusion uncovered a functional interaction between two residues residing in domains that are apart in both the pre-fusion and post-fusion states. Thus, our approach allowed gaining insight into the molecular detail of the inner working of virus fusion machinery.

microbiology↗

bioRxiv2024

Peptipedia v2.0: A peptide sequence database and user-friendly web platform. A major update

In recent years, peptides have gained significant relevance due to their therapeutic properties. The surge in peptide production and synthesis has generated vast amounts of data, enabling the creation of comprehensive databases and information repositories. Advances in sequencing techniques and artificial intelligence have further accelerated the design of tailor-made peptides. However, leveraging these techniques requires versatile and continuously updated storage systems, along with tools that facilitate peptide research and the implementation of machine learning for predictive systems. This work introduces Peptipedia v2.0, one of the most comprehensive public repositories of peptides, supporting biotechnological research by simplifying peptide study and annotation. Peptipedia v2.0 has expanded its collection by over 45% with peptide sequences that have reported biological activities. The functional biological activity tree has been revised and enhanced, incorporating new categories such as cosmetic and dermatological activities, molecular binding, and anti-ageing properties. Utilizing protein language models and machine learning, more than 90 binary classification models have been trained, validated, and incorporated into Peptipedia v2.0. These models exhibit average sensitivities and specificities of 0.877 {+/-} 0.0530 and 0.873 {+/-}0.054, respectively, facilitating the annotation of more than 3.6 million peptide sequences with unknown biological activities, also registered in Peptipedia v2.0. Additionally, Peptipedia v2.0 introduces description tools based on structural and ontological properties and user-friendly machinelearning tools to facilitate the application of machine-learning strategies to study peptide sequences. Peptipedia v2.0 is accessible under the Creative Commons CC BY-NC-ND 4.0 license at https://peptipedia.cl/.

bioinformatics↗

bioRxiv2024

Constitutive immune surveillance of nasal mucosa by three neutrophil subsets with distinct origin, phenotype, and function

The nasal mucosa (NM) has several critical functions, including as a chemosensory organ, as a filter and conditioning surface of inhaled air for the lower airways, and as a first line of defense against airborne infections. Owing to its constant exposure to ever-changing environments, the NM is arguably the most frequently infected tissue in mammals. Consequently, vertebrates harbor an intricate network of subepithelial immune cells that are dispersed throughout the NM. However, the origin, composition, and function of nasal immune cells and their pathophysiological role are poorly understood. Here, we show that murine steady-state NM harbors a prominent population of extravascular neutrophils (EVN) that are abundant in both conventional and germ-free mice, suggesting that their presence is not driven by microbial stimuli. Nasal EVN can be subdivided into three phenotypically distinct subsets: one population that we have termed nN1 is CD11bint Ly6Gint, while the other two subsets are both CD11bhi Ly6Ghi and distinguishable by the absence (nN2) or presence (nN3) of CD11c and SiglecF. nN1 EVN originate in bone marrow (BM) within osseous structures in the skull. These locally produced neutrophils appear to access the adjacent NM via conduits that connect BM cavities to the submucosal lamina propria. nN2 cells reach the NM via the blood and readily engulf infectious microbes. In the absence of infection, nN2 cells differentiate into the nN3 subset, which does not capture microbes but assumes phenotypic and functional features of antigen-presenting cells, including the capacity to cross-present exogenous antigens to CD8 T cells. These findings indicate that steady-state mammalian NM harbors a unique innate cellular immune environment that is unlike any other barrier tissue.

immunology↗

bioRxiv2024

Chromosome-scale pearl millet genomes reveal a CARLACTONOIC ACID METHYL TRANSFERASE as key determinant of strigolactone pattern and Striga susceptibility

The yield of pearl millet, a resilient cereal crop crucial for African food security, is severely impacted by the root parasitic weed Striga hermonthica, which requires host-released strigolactones (SLs) for seed germination. Herein, we identified four SLs present in the Striga-susceptible line SOSAT-C88-P10 (P10), but absent in the resistant 29Aw (Aw). We generated chromosome-scale genome assemblies including four gapless chromosomes for each line. We found the Striga-resistant Aw lacks a 0.7 Mb genome segment containing two putative CARLACTONOIC ACID METHYL TRANSFERASE1 (CLAMT1) genes. Upon transient expression, P10CLAMT1b produced methyl carlactonoate (MeCLA), an intermediate in SL biosynthesis. Feeding Aw with MeCLA resulted in the production of two P10-specific SLs. Screening a diverse pearl millet panel confirmed the pivotal role of the CLAMT1 section for SL diversity and Striga susceptibility. Our results reveal a reason for Striga susceptibility in pearl millet and pave the way for generating resistant lines through marker-assisted breeding or direct genetic modification.

plant biology↗

bioRxiv2024

Admixture with cultivated sunflower likely facilitated establishment and spread of wild sunflower (H. annuus) in Argentina

A better understanding of the genetic and ecological factors underlying successful invasions is critical to mitigate the negative impacts of invasive species. Here, we study the invasion history of Helianthus annuus populations from Argentina, with particular emphasis on the role of post-introduction admixture with cultivated sunflower (also H. annuus) and climate adaptation driven by large haploblocks. We conducted genotyping-by-sequencing of samples of wild populations as well as Argentinian cultivars and compared them with wild (including related annual Helianthus species) and cultivated samples from the native range. We also characterized samples for 11 known haploblocks associated with environmental variation in native populations to test whether haploblocks contributed to invasion success. Population genomics analyses supported two independent geographic sources for Argentinian populations, the central United States and Texas, but no significant contribution of related annual Helianthus species. We found pervasive admixture with cultivated sunflower, likely as result of post-introduction hybridization. Genomic scans between invasive populations and their native sources identified multiple genomic regions with evidence of selection in the invaded range. These regions significantly overlapped between the two native-invasive comparisons and showed disproportionally high crop ancestry, suggesting that crop alleles contributed to invasion success. We did not find evidence of climate adaptation mediated by haploblocks, yet outliers of genome scans were enriched in haploblock regions and, for at least two haploblocks, the cultivar haplotype was favored in the invaded range. Our results show that admixture with cultivated sunflower played a major role in the establishment and spread of H. annuus populations in Argentina.

evolutionary biology↗

bioRxiv2022

Functional mRNA delivery to hematopoietic stem and progenitor cells in vivo.

Gene correction of hematopoietic stem cells (HSC) is a promising therapeutic approach for multiple disorders. Current methods, however, require HSC collection from patients, gene correction during ex vivo culture, and re-infusion of corrected HSC into patients conditioned with chemotherapeutic agents. These approaches are complex, and the conditioning creates toxicities. We show that a lipid nanoparticle (LNP) can deliver mRNA encoding a reporter or a gene editing protein to HSC, with one injection transfecting [~]25% of mouse HSC, and repeated doses resulting in higher editing efficiencies. We also demonstrate LNP-driven in vivo mRNA delivery to HSC in non-human primates and humanized mice. These results demonstrate a translatable approach to deliver mRNA encoding therapeutic proteins, or gene correcting tools, to HSC that do not require cell culture or toxic conditioning. One-Sentence SummaryLNP can deliver functional mRNA to mouse, non-human primate, and human HSC.

immunology↗

bioRxiv2022

Monocyte intrinsic NOD2 signalling inhibits pathogenic macrophage differentiation and its loss in inflammatory macrophages improves intestinal inflammation.

ObjectiveIt is believed that intestinal recruitment of monocytes from Crohns Disease (CD) patients who carry NOD2 risk alleles may repeatedly give rise to recruitment of pathogenic macrophages. We investigated an alternative possibility that NOD2 may rather inhibit their differentiation from intravasating monocytes. DesignThe monocyte fate decision was examined by using germ-free mice, mixed bone marrow chimeras and a culture system yielding macrophages and monocyte-derived dendritic cells (mo-DCs). We next asked whether Nod2 in either monocytes or tissue macrophages have distinct resolving properties in colitis. ResultsDespite a similar abundance of monocytes, the intestinal frequency of mo-DCs from Nod2-deficient mice was lowered independently of the changes in the gut microbiota that are caused by Nod2 deficiency. Similarly, the pool of mo-DCs was poorly reconstituted with mobilized bone marrow Nod2-deficient cells. The use of pharmacological inhibitors revealed that activated NOD2 at an early stage of development dominantly inhibits mTOR-mediated macrophage differentiation in a TNFalpha-dependent manner. These observations were supported by the identification of a TNFalpha-dependent response to MDP that is specifically lost in CD14-expressing blood cells bearing the frameshift mutation in NOD2. Accordingly, loss of NOD2 in monocytes lowers glycolytic reserve, CD115 expression and pro-resolving features. Dietary intake of aryl hydrocarbon receptor (AHR) agonists that promotes mo-DCs generation improves colitis in Nod2-deficient mice to the same extent as what is observed upon macrophage ablation of Nod2. ConclusionNOD2 negatively regulates a macrophage developmental program through a feed-forward loop that could be exploited for overcoming resistance to anti-TNF therapy in CD. Significance of this studyO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LILoss of NOD2 function is predisposing to Crohns disease. C_LIO_LIRapamycin, a serine/THR kinase inhibitor of mammalian target (mTOR) has been reported as potentially effective treatment in discrete subset of CD patients with refractory colitis. C_LIO_LIThe NOD2 protein promotes the chemokine CCL2-dependent recruitment of inflammatory monocytes in response to tissue injury. C_LIO_LIAn accumulation of CCR2-expressing monocytes and inflammatory macrophages is observed within the intestinal mucosa of CD patients including those resistant to anti-TNF therapy. C_LIO_LIActivated NOD2 enhances proinflammatory activity of CX3CR1intLy6Chi effector monocytes. C_LIO_LIThe monocyte fate toward mo-DCs is orchestrated by the aryl hydrocarbon receptor. C_LI What are the new findings?O_LINOD2 has a hierarchically dominant negative role on the mTORC-driven monocyte conversion to inflammatory macrophages independently of the changes in the gut microbiota that are caused by Nod2 deficiency. C_LIO_LIA defect in monocytes fate at the early stage allow the expansion of pathogenic macrophages in Nod2-deficient mice at the expense of mo-DC. C_LIO_LIAdoptive transfer of Nod2-deficient monocytes into wild-type mice was sufficient to exacerbate DSS-induced intestinal damage. C_LIO_LIThe glycolytic reserve of monocytes and their ability to respond to M-CSF is lowered upon loss of NOD2 signalling. C_LIO_LIDeletion of NOD2 in macrophage improves colitis to the same extent as dietary supplementation of AHR agonist in mice. C_LIO_LIThe recognition of the gut microbiota by NOD2 is required for de novo reconstitution of mo-DCs in the lamina propria of the murine intestine, while having minimal effect on the mobilization of their precursors to the intestinal mucosa. C_LI How might it impact on clinical practice in the foreseeable future?This study might contribute to the development of novel mTORC-based therapeutic strategies for improving the response to biologics by restoring the ability of circulating monocytes to reconstitute the pool of mo-DCs during homeostatic turnover and upon tissue injury. It may thereby prevent the accumulation of pathogenic macrophages in patients with loss-of-function NOD2 alleles, which fail to respond to anti-TNF and are at greater risk of developing stricturing disease.

immunology↗

bioRxiv2022

Imaging crossing fibers in mouse, pig, monkey, and human brain using small-angle X-ray scattering

Myelinated axons (nerve fibers) efficiently transmit signals throughout the brain via action potentials. Multiple methods that are sensitive to axon orientations, from microscopy to magnetic resonance imaging, aim to reconstruct the brains structural connectome. As billions of nerve fibers traverse the brain with various possible geometries at each point, resolving fiber crossings is necessary to generate accurate structural connectivity maps. However, doing so with specificity is a challenging task because signals originating from oriented fibers can be influenced by brain (micro)structures unrelated to myelinated axons. X-ray scattering can specifically probe myelinated axons due to the periodicity of the myelin sheath, which yields distinct peaks in the scattering pattern. Here, we show that small-angle X-ray scattering (SAXS) can be used to detect myelinated, axon-specific fiber crossings. We first demonstrate the capability using strips of human corpus callosum to create artificial double- and triple-crossing fiber geometries, and we then apply the method in mouse, pig, vervet monkey, and human brains. Given its specificity, capability of 3-dimensional sampling and high resolution, SAXS can serve as a ground truth for validating MRI as well as microscopy-based methods. Statement of SignificanceTo study how the nerve fibers in our brain are interconnected, scientists need to visualize their trajectories, which often cross one another. Here, we show the unique capacity of small-angle X-ray scattering (SAXS) to study these fiber crossings without use of labelling, taking advantage of SAXSs specificity to myelin - the insulating sheath that is wrapped around nerve fibers. We use SAXS to detect double and triple crossing fibers and unveil intricate crossings in mouse, pig, vervet monkey, and human brains. This non-destructive method can uncover complex fiber trajectories and validate other less specific imaging methods (e.g., MRI or microscopy), towards accurate mapping of neuronal connectivity in the animal and human brain. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/510198v2_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@479368org.highwire.dtl.DTLVardef@11eb0c9org.highwire.dtl.DTLVardef@1e883adorg.highwire.dtl.DTLVardef@1ce024_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2022

An outbreak of SARS-CoV-2 in big hairy armadillos (Chaetophractus villosus) associated with Gamma variant in Argentina three months after being undetectable in humans

The present pandemic produced by SARS-CoV-2 and its variants represents an example of the one health concept in which humans and animals are components of the same epidemiologic chain. Animal reservoirs of these viruses are thus the focus of surveillance programs to monitor their circulation and evolution in potentially new hosts and reservoirs. In this work, we report the detection of SARS-CoV-2 Gamma variant infection in four specimens of Chaetophractus villosus (big hairy armadillo/armadillo peludo) in Argentina. In addition to the finding of a new wildlife species susceptible to SARS-CoV-2 infection, the identification of the Gamma variant three months after its last detection in humans is a noteworthy result, raising the question of potential unidentified viral reservoirs.

microbiology↗

bioRxiv2022

Independent evolution of influenza A virus H1N1 in pigs in Guatemala

Commercial swine farms provide unique systems for interspecies transmission of influenza A viruses (FLUAVs) at the animal-human interface. Bidirectional transmission of FLUAVs between pigs and humans plays a significant role in the generation of novel strains that become established in the new host population. Active FLUAV surveillance was conducted for two years on a commercial pig farm in Southern Guatemala with no history of FLUAV vaccination. Nasal swabs (n=2,094) from fattening pigs (6 to 24 weeks old) with respiratory signs were collected from May 2016 to February 2018. Swabs were screened for FLUAV by RRT-PCR and full virus genomes of FLUAV-positive swabs were sequenced by next-generation sequencing (NGS). FLUAV prevalence was 12.0% (95% CI: 10.6% - 13.4%) with two distinct periods of high infection. All samples were identified as FLUAVs of the H1N1 subtype within the H1 swine clade 1A.3.3.2 and whose ancestors are the human origin 2009 H1N1 influenza pandemic virus (H1N1 pdm09). Compared to the prototypic reference segment sequence, 10 amino acid signatures were observed on relevant antigenic sites on the hemagglutinin. We also found that Guatemalan swine-origin FLUAVs show independent evolution from other H1N1 pdm09 FLUAVs circulating in Central America. The zoonotic risk of these viruses remains unknown, but strongly calls for continued FLUAV surveillance in pigs in Guatemala. ImportanceDespite increased surveillance efforts, the epidemiology of FLUAVs circulating in swine in Latin America remains understudied. For instance, the 2009 H1N1 influenza pandemic strain (H1N1 pdm09) emerged in Mexico, but its circulation remained undetected in pigs. In Central America, Guatemala is the country with the largest swine industry. We found a unique group of H1N1 pdm09 sequences that suggests independent evolution from similar viruses circulating in Central America. These viruses may represent the establishment of a novel genetic lineage with the potential to reassort with other co-circulating viruses, and whose zoonotic risk remains to be determined.

evolutionary biology↗

bioRxiv2021

Robust temporal map of human in vitro myelopoiesis using single-cell genomics

Myeloid cells have a central role in homeostasis and tissue defence. Characterising the current in vitro protocols of myelopoiesis is imperative for their use in research and immunotherapy as well as for understanding the early stages of myeloid differentiation in humans. Here, we profiled the transcriptome of more than 400k cells and generated a robust molecular map of the differentiation of human induced pluripotent stem cells (iPSC) into macrophages. By integrating our in vitro datasets with in vivo single-cell developmental atlases, we found that in vitro macrophage differentiation recapitulates features of in vivo yolk sac hematopoiesis, which happens prior to the appearance of definitive hematopoietic stem cells (HSC). During in vitro myelopoiesis, a wide range of myeloid cells are generated, including erythrocytes, mast cells and monocytes, suggesting that, during early human development, the HSC-independent immune wave gives rise to multiple myeloid cell lineages. We leveraged this model to characterize the transition of hemogenic endothelium into myeloid cells, uncovering poorly described myeloid progenitors and regulatory programs. Taking advantage of the variety of myeloid cells produced, we developed a new protocol to produce type 2 conventional dendritic cells (cDC2) in vitro. We found that the underlying regulatory networks coding for myeloid identity are conserved in vivo and in vitro. Using genetic engineering techniques, we validated the effects of key transcription factors important for cDC2 and macrophage identity and ontogeny. This roadmap of early myeloid differentiation will serve as an important resource for investigating the initial stages of hematopoiesis, which are largely unexplored in humans, and will open up new therapeutic opportunities.

developmental biology↗