Biology subjects

Salazar, A.

Publications and source records attributed to Salazar, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Expanding the catabolic capacity of Pseudomonas putida to acetovanillone, 5-carboxyvanillate, and vanillyl glyoxylate for muconate production from kraft lignin-derived aromatics

The pulp and paper industry produces large volumes of condensed kraft lignin, which is challenging to convert to single chemical products. For this purpose, tandem chemical depolymerization and bioconversion to a single atom-efficient product is a potentially promising strategy. In this study, we conducted copper-catalyzed oxidative depolymerization using pine-derived kraft lignin to generate multiple bioavailable aromatic monomers at a yield of 4.5 weight% (wt%; g monomers per g lignin) from both C--O and C--C bond cleavage, followed by counter-current extraction with a 52 wt% monomer recovery. This resulted in an oxidized lignin product containing vanillin, vanillate, 4-hydroxybenzaldehyde, 4-hydroxybenzoate, 5-formylvanillin, 5-carboxyvanillin, 5-carboxyvanillate, acetovanillone, and vanillyl glyoxylate. Based on this stream composition, we engineered the industrially relevant soil bacterium Pseudomonas putida KT2440 to catabolize the latter five compounds via overexpression of ten heterologous genes (acvABCDEFSYK-6, vceABSYK-6, ligW2SYK-6, and mdlCPP). We combined these engineered pathways with previously reported strategies for muconate production from G- and H-type monomers to generate P. putida KMM428, which utilized 93.6 {+/-} 0.2 mol% of the quantified aromatic monomers in a depolymerized kraft lignin mixture, and produced muconate at a yield of 99 {+/-} 3 mol%, on a quantified monomer basis. Together, this work increases the theoretical carbon conversion efficiency of this process by 37.6 {+/-} 0.1 mol% through incorporation of three {beta}-5 cleavage products, in addition to traditional G-type monomers.

synthetic biology↗

bioRxiv2026

snpXplorer: an interactive platform for haplotype-aware exploration and integrated annotation of GWAS data

BackgroundGenome-wide association studies (GWAS) have identified thousands of loci associated with complex traits and diseases, yet translating these signals into biological insight remains challenging. Most associated variants are non-coding and reside in linkage disequilibrium (LD) blocks, where multiple correlated variants jointly contribute to association signals. These clusters, or haplotypes, may capture shared regulatory and functional contexts. Interpreting GWAS signals thus requires approaches that integrate regulatory, functional, and cross-trait evidence, while preserving the broader haplotypic context of disease-associated loci. At the same time, the rapid growth of publicly available GWAS summary statistics has enabled large-scale cross-trait analyses, but also introduced redundancy across closely related phenotypes. Efficient interpretation of GWAS data therefore requires tools that integrate heterogeneous data sources while preserving genomic and biological contexts. ResultsWe present snpXplorer, an interactive web platform for haplotype-aware exploration and annotation of GWAS data. The platform incorporates >10,000 GWAS datasets from OpenGWAS and enables multi-scale analysis across variants, haplotypes, genes, and traits. Key features include (i) a haplotype-based representation of association signals derived from LD structure, (ii) a unified variant annotation framework integrating clinical annotations (ClinVar), allele frequencies (gnomAD), functional predictions (CADD, AlphaGenome), quantitative trait loci (GTEx), structural variation, and GWAS associations, and (iii) cross-trait exploration using semantic similarity-based clustering of phenotypes. Use cases centered on Alzheimers disease illustrate this utility: for example, at the TMEM106B locus, snpXplorer identified a haplotype linked to eleven distinct traits, revealing synergistic pleiotropy across neurological and behavioral phenotypes alongside antagonistic pleiotropy with height. ConclusionssnpXplorer allows users to browse, filter, and inspect variant-, haplotype-, gene- and trait-level evidence, lowering the barrier to biological interpretation of GWAS results. Compared with existing tools that focus on specific aspects of GWAS interpretation, the strength of snpXplorer is that it reduces the need for fragmented queries across databases.

genetics↗

bioRxiv2026

TabularQual: A spreadsheet-based format for annotating and curating logical models in SBML-qual

Logical models are widely used to study regulatory and signaling systems, yet their reuse, annotation, and exchange across tools remain challenging. Although SBML Level 3 Qualitative Models (SBML-qual) provides a standard representation, its XML-based syntax is difficult to inspect and edit directly. Here we introduce TabularQual, a spreadsheet-based, community-driven representation for Boolean and multi-valued logical models, together with a bidirectional converter between spreadsheets and SBML-qual. The converter is accessible programmatically and via a web interface to support diverse user workflows. We further describe two integration strategies that enable existing modeling tools to operate with TabularQual, either through SBML-qual exchange or via direct support. Case studies using the Stress Knowledge Map and CaSQ demonstrate how this integration supports model construction, curation, and reuse. TabularQual provides a practical bridge between human-readable model representations and standardized executable formats, supporting reproducibility, interoperability, and community-driven model development.

systems biology↗

bioRxiv2024

Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure

Biomolecular condensates play key roles in the spatiotemporal regulation of cellular processes. Yet, the relationship between atomic features and condensate function remains poorly understood. We studied this relationship using the polar organizing protein Z (PopZ) as a model system, revealing how its material properties and cellular function depend on its ultrastructure. We revealed PopZs hierarchical assembly into a filamentous condensate by integrating cryo-electron tomography, biochemistry, single-molecule techniques, and molecular dynamics simulations. The helical domain drives filamentation and condensation, while the disordered domain inhibits them. Phase-dependent conformational changes prevent interfilament contacts in the dilute phase and expose client binding sites in the dense phase. These findings establish a multiscale framework that links molecular interactions and condensate ultrastructure to macroscopic material properties that drive cellular function.

cell biology↗

bioRxiv2024

Spinal motor neuron development and metabolism are transcriptionally regulated by Nuclear Factor IA

Neural circuits governing all motor behaviors in vertebrates rely on the proper development of motor neurons and their precise targeting of limb muscles. Transcription factors are essential for motor neuron development, regulating their specification, migration, and axonal targeting. While transcriptional regulation of the early stages of motor neuron specification is well-established, much less is known about the role of transcription factors in the later stages of maturation and terminal arborization. Defining the molecular mechanisms of these later stages is critical for elucidating how motor circuits are constructed. Here, we demonstrate that the transcription factor Nuclear Factor-IA (NFIA) is required for motor neuron positioning, axonal branching, and neuromuscular junction formation. Moreover, we find that NFIA is required for proper mitochondrial function and ATP production, providing a new and important link between transcription factors and metabolism during motor neuron development. Together, these findings underscore the critical role of NFIA in instructing the assembly of spinal circuits for movement.

developmental biology↗

bioRxiv2024

Characterising tandem repeat complexities across long-read sequencing platforms with TREAT

Tandem repeats (TR) play important roles in genomic variation and disease risk in humans. Long-read sequencing allows for the accurate characterisation of TRs, however, the underlying bioinformatics perspectives remain challenging. We present otter and TREAT: otter is a fast targeted local assembler, cross-compatible across different sequencing platforms. It is integrated in TREAT, an end-to-end workflow for TR characterisation, visualisation and analysis across multiple genomes. In a comparison with existing tools based on long-read sequencing data from both Oxford Nanopore Technology (ONT, Simplex and Duplex) and PacBio (Sequel 2 and Revio), otter and TREAT achieved state-of-the-art genotyping and motif characterisation accuracy. Applied to clinically relevant TRs, TREAT/otter significantly identified individuals with pathogenic TR expansions. When applied to a case-control setting, we significantly replicated previously reported associations of TRs with Alzheimers Disease, including those near or within APOC1 (p=2.63x10-9), SPI1 (p=6.5x10-3) and ABCA7 (p=0.04) genes. We finally used TREAT/otter to systematically evaluate potential biases when genotyping TRs using diverse ONT and PacBio long-read sequencing datasets. We showed that, in rare cases (0.06%), long-read sequencing suffers from coverage drops in TRs, including the disease-associated TRs in ABCA7 and RFC1 genes. Such coverage drops can lead to TR mis-genotyping, hampering the accurate characterisation of TR alleles. Taken together, our tools can accurately genotype TR across different sequencing technologies and with minimal requirements, allowing end-to-end analysis and comparisons of TR in human genomes, with broad applications in research and clinical fields.

bioinformatics↗

bioRxiv2024

MotifScope: a multi-sample motif discovery and visualization tool for tandem repeats

Tandem repeats (TRs) constitute a significant portion of the human genome, exhibiting high levels of polymorphism due to variations in size and motif composition. These variations have been associated with various neuropathological disorders, underscoring the clinical importance of TRs. Furthermore, the motif structure of these repeats can offer valuable insights into evolutionary dynamics and population structure. However, analysis of TRs has been hampered by the limitations of short-read sequencing technology, which lacks the ability to fully capture the complexity of these sequences. With long-read data becoming more accessible, there is now also a need for tools to explore and characterize these TRs. In this study, we introduce MotifScope, a novel algorithm for visualization of TRs in their population context based on a de novo k-mer approach for motif discovery. Comparative analysis against three established tools, uTR, TRF, and vamos, reveals that MotifScope can identify a greater number of motifs and more accurately represent the actual repeat sequence. Additionally, MotifScope enables comparison of sequencing reads within an individual and assemblies across different individuals, showing its applicability in diverse genomic contexts. We demonstrate potential applications of MotifScope in diverse fields, including population genetics, clinical settings, and forensic analyses.

genomics↗

bioRxiv2024

Comparison of the performance of multiple whole-genome sequence-based tools for the identification of Bacillus cereus sensu stricto biovar Thuringiensis

The Bacillus cereus sensu stricto (s.s.) species comprises strains of biovar Thuringiensis (Bt) known for their bioinsecticidal activity, as well as strains with foodborne pathogenic potential. Bt strains are identified (i) based on the production of insecticidal crystal proteins also known as Bt toxins or (ii) based on the presence of cry, cyt, and vip genes, which encode Bt toxins. Multiple bioinformatics tools have been developed for the detection of crystal protein-encoding genes based on whole-genome sequencing (WGS) data. However, the performance of these tools is yet to be evaluated using phenotypic data. Thus, the goal of this study was to assess the performance of four bioinformatics tools for the detection of crystal protein-encoding genes. The accuracy of sequence-based identification of Bt was determined in reference to phenotypic microscope-based screening for production of crystal proteins. A total of 58 diverse B. cereus s.l. strains isolated from clinical, food, environmental, and commercial biopesticide products were underwent WGS. Isolates were examined for crystal protein production using phase contrast microscopy. Crystal protein-encoding genes were detected using BtToxin_Digger, BTyper3, IDOPS, and Cry_processor. Out of 58 isolates, the phenotypic production of crystal proteins was confirmed for 18 isolates. Specificity and sensitivity of Bt identification based on sequences were 0.85 and 0.94 for BtToxin_Digger, 0.97 and 0.89 for BTyper3, 0.95 and 0.94 for IDOPS, and 0.88 and 1.00 for Cry_processor, respectively. Cry_processor predicted crystal protein production with highest specificity, and BtToxin_Digger and IDOPS predicted crystal protein production with the highest sensitivity. Three out of four tested bioinformatic tools performed well overall, with IDOPS achieving both high sensitivity and specificity (>0.90). IMPORTANCEBacillus cereus s.s. biovar Thuringiensis (Bt) is used as an organic biopesticide. It is differentiated from the foodborne pathogen Bacillus cereus s.s. by the production of insecticidal crystal proteins. Thus, reliable genomic identification of biovar Thuringiensis is necessary to ensure food safety and facilitate risk assessment. This study assessed the accuracy of WGS-based identification of Bt compared to phenotypic microscopy-based screening for crystal protein production. Multiple bioinformatics tools were compared to assess their performance in predicting crystal protein production. Among them, IDOPS performed best overall at WGS- based Bt identification.

bioinformatics↗

bioRxiv2022

Excessive Mechanotransduction in Sensory Neurons Causes Joint Contractures in a Mouse Model of Arthrogryposis

Distal arthrogryposis (DA) is a collection of rare disorders characterized by congenital joint contractures. Most DA mutations are in muscle- and joint-related genes, and the anatomical defects originate cell-autonomously within the musculoskeletal system. However, gain-of-function (GOF) mutations in PIEZO2, a principal mechanosensor in somatosensation, cause DA subtype 5 via unknown mechanisms. We show that expression of a GOF PIEZO2 mutation in proprioceptive sensory neurons mainly innervating muscle spindles and tendons is sufficient to induce DA5-like phenotypes in mice. Overactive PIEZO2 causes anatomical defects via increased activity within the peripheral nervous system during postnatal development. Remarkably, Botox and a dietary fatty acid that modulates PIEZO2 activity markedly reduce DA5-like deficits. This reveals an unexpected role for somatosensory neurons: excessive mechanosensation within these neurons disrupts musculoskeletal development.

neuroscience↗

bioRxiv2022

Moss functional traits are important drivers for moss and underlying soil bacterial communities: evidence from a chronosequence in an Icelandic glacier forefield

Mosses are among the first colonizing organisms after glacier retreat and can develop into thick moss mats during later successional stages. They are key players in N2 fixation through their microbiome, which is an important process for nutrient build-up during primary succession. How these moss-microbe interactions develop during succession is not well-studied and is relevant in the light of climate change and increased glacier retreat. We examined how the bacterial communities associated with two moss species of the genus Racomitrium and the underlying substrate, as well as moss traits and nitrogen fixation, develop along a successional gradient in the glacier forefield of Flaajokull in southeast Iceland. In addition, tested whether moss functional traits, such as total carbon (TC) and nitrogen contents (TN) are drivers of moss and underlying soil bacterial communities. Although time since deglaciation did not affect TN and moisture content, TC and shoot length increased with time since deglaciation. Moss and underlying soil bacterial communities were distinct. While the soil bacterial community structure was driven by the time since deglaciation and moss C/N ratios, the moss bacterial community structure was linked to time since deglaciation and moss moisture content. Moss N2-fixation rates were linked to bacterial community composition and nifH gene abundance rather than moss TN or time since deglaciation. This was accompanied by a shift from autotrophic to heterotrophic diazotrophs. Overall, our results suggest that there is little lateral transfer between moss and soil bacterial communities and that moss traits and time since deglaciation affect moss and soil bacterial community structure. In addition, moss N2-fixation rates are determined by bacterial community structure, rather than moss traits or time since deglaciation.

ecology↗

bioRxiv2022

Environmental change alters nitrogen fixation rates and microbial parameters in a subarctic biological soil crust

Together, Biological Soil Crust (BSC) and other cryptogamic groundcovers can contribute up to half of the global nitrogen (N) fixation. BSC also stabilizes the soil (reducing erosion and dust emissions), fixes carbon (C), retains moisture, and acts as a hotspot of microbial diversity and activity. Much of the knowledge about how climate change is affecting the composition and functioning of BSC comes from hot arid and semiarid regions. The comparatively smaller body of research on BSC from cold and mesic environments has been primarily observational, for example along chronosequences after a glacier retreat. Few studies have experimentally investigated the effects of the environment on BSC from high latitudes. Such experiments allow unraveling of relationships at a resolution that can only be achieved by controlling for confounding factors. We measured short-term (2-4 days) responses of a liverwort-based (Anthelia juratzkana) BSC from the south of Iceland to a range of temperature, moisture and light conditions. Warming increased N fixation rates, especially when moisture was at a saturation level, and only when light was not limiting. A correlation analysis suggests that increases in N fixation rates were linked to cyanobacterial abundance on the BSC surface and to the rates of their metabolic activity. Warming and moisture changes also induced compositional and structural modification of the bacterial community, with consequences at the functional level. In contrast to many observations on BSC from hot drylands, the BSC from our cold and mesic study site is more limited by low temperature and light than by moisture. Our findings show possible ways in which BSC from cold and mesic ecosystems can respond to short-term manifestations of climate change, such as increasingly frequent heat waves.

microbiology↗

bioRxiv2021

A novel hybrid protein promotes Aβ clearance and reduces inflammatory response through MerTK

Alzheimers disease (AD) is the worlds leading cause of dementia and the most common neurodegenerative disorder. Its major pathological features are amyloid beta (A{beta}) plaques, tau tangles, and neuroinflammation that eventually leads to massive death of nerve cells. Even with the multifactorial aspect of AD, the most accepted theory is that A{beta} is the driving force of AD pathogenesis. We engineered a novel hybrid protein that facilitates the phagocytosis of A{beta} and redirect its clearance to the noninflammatory Mer tyrosine kinase (MerTK) pathway. The novel hybrid protein facilitates robust uptake and clearance of A{beta} in BV2 microglia through MerTK receptor with reduced production of inflammatory factors and oxidative products. In APP/PS1 transgenic AD mouse model, intraperitoneal administration of the hybrid protein for two months results in significant reduction of A{beta} burden in the brain and protection of nerve cells from dying. Taken together, our results suggest that the novel hybrid may have the potential for AD treatment by targeting both A{beta} clearance and reduction of inflammation.

molecular biology↗

bioRxiv2021

Neutralizing antibody-independent immunity to SARS-CoV-2 in hamsters and hACE-2 transgenic mice immunized with a RBD/Nucleocapsid fusion protein

The nucleocapsid (N) and the receptor binding domain (RBD) of the Spike (S) proteins elicit robust antibody and T cell responses either in vaccinated or COVID-19 convalescent individuals. We generated a chimeric protein that comprises the sequences of RBD from S and N antigens (SpiN). SpiN was highly immunogenic and elicited a strong IFN{gamma} response from T cells and high levels of antibodies to the inactivated virus, but no neutralizing antibodies. Importantly, hamsters and the human Angiotensin Convertase Enzyme-2-transgenic mice immunized with SpiN were highly resistant to challenge with the wild type SARS-CoV-2, as indicated by viral load, clinical outcome, lung inflammation and lethality. Thus, the N protein should be considered to induce T-cell-based immunity to improve SARS-CoV-2 vaccines, and eventually to circumvent the immune scape by variants.

immunology↗

bioRxiv2021

Probing Loop-Mediated Isothermal Amplification (LAMP) targeting two gene-fragments of rose rosette virus

This study explores the development of Loop-mediated isothermal amplification of DNA (LAMP) for detection of rose rosette emaravirus (RRV), a technique with the potential to be translated to rose nurseries. RRV is a negative-sense single-stranded RNA Emaravirus and causal agent of the rose rosette disease (RRD). Transmission of RRV is by Phyllocoptes fructiphilus, an eriophyid mite. Although RRV symptoms are characteristics, early visual diagnosis of RRD can be misleading and confusing since it may appear similar to herbicide damage. Two sets of RRV gene sequences composed of twenty-two accessions of RRV-P3 (RNA 3) and another twenty-four from RRV-P4 (RNA 4) were analyzed and two sets of four LAMP primers were designed for broad-range detection of RRV isolates. The direct antigen-capture method for direct trapping of RRV in plastic was used for RNA extraction followed by cDNA synthesis. LAMP reactions were optimized for Bst 2.0 DNA polymerase using the outer RRV-F3/RRV-B3 primers, and internal RRV-FIP/RRV-BIP primers. LAMP reactions were for 1 hour at 64{degrees}C (RRV-P3) and 66.5{degrees}C (RRV-P4) using either a thermocycler or a portable dry bath. LAMP was also optimized using DNA polymerase GspSSD LD using the same RRV sets of primers. RRV was detected in symptomatic and non-symptomatic RRD tissue from Oklahoma. The limit of detection (LoD) using Bst 2.0 LAMP was 1pg/L and 1 fg/L with GspSSD LD quantitative LAMP. The LoD of pre-reaction hydroxy naphthol blue (HNB, 120 M) for colorimetric (visual) reactions was 10 pg/L and 0.1 pg/L using SYBR green I (1:10 dilution) in colorimetric post-reactions. No cross-reactivity was detected in LAMP reaction testing cDNAs of eight commonly co-infecting rose viruses (INSV, ArMV, MSpV, TSWV, ApMV, PNRSV, ToRSV, and TMV), and one virus taxonomically related to RRV (HPWMoV). RNA from healthy rose tissues and non-template controls (water) were included in all LAMP assays.

molecular biology↗

bioRxiv2021

The effects of long duration spaceflight on sensorimotor control and cognition

Astronauts returning from spaceflight typically show transient declines in mobility and balance. These whole-body postural control behaviors have been investigated thoroughly, while study of the effects of spaceflight on other sensorimotor behaviors is prevalent. Here, we tested the effects of the spaceflight environment of microgravity on various sensorimotor and cognitive tasks during and after missions to the International Space Station (ISS). We obtained mobility (Functional Mobility Test), balance (Sensory Organization Test-5), bimanual coordination (bimanual Purdue Pegboard), cognitive-motor dual-tasking and various cognitive measures (Digit Symbol Substitution Test, Cube Rotation, Card Rotation, Rod and Frame Test) before, during and after 15 astronauts completed 6+ month missions aboard the ISS. We used linear mixed effect models to analyze performance changes due to entering the microgravity environment, behavioral adaptations aboard the ISS and subsequent recovery from microgravity. We identified declines in mobility and balance from pre- to post-flight, suggesting possible disruption and/or downweighting of vestibular inputs; these behaviors recovered to baseline levels within 30 days post-flight. We also identified bimanual coordination declines from pre- to post-flight and recovery to baseline levels within 30 days post-flight. There were no changes in dual-task performance during or following spaceflight. Cube rotation response time significantly improved from pre- to post-flight, suggestive of practice effects. There was a trend for better in-flight cube rotation performance on the ISS when crewmembers had their feet in foot loops on the "floor" throughout the task. This suggests that tactile inputs to the foot sole aided orientation. Overall, these results suggest that sensory reweighting due to the microgravity environment of spaceflight affected sensorimotor performance, while cognitive performance was maintained. A shift from exocentric (gravity) spatial references on Earth towards an egocentric spatial reference may also occur aboard the ISS. Upon return to Earth, microgravity adaptions become maladaptive for certain postural tasks, resulting in transient sensorimotor performance declines that recover within 30 days.

neuroscience↗

bioRxiv2020

Mucosal immune stimulation with HSV-2 and polyICLC boosts control of viremia in SIVΔNef vaccinated rhesus macaques with breakthrough SIV infection

Development of an effective human immunodeficiency virus (HIV) vaccine is among the highest priorities in the biomedical research agenda. Adjuvants enhance vaccine efficacy, but in the case of HIV, strong or inappropriate immune activation may undermine protection by increasing HIV susceptibility. Co-infection with immunomodulatory pathogens may also impact vaccine efficacy. In the rhesus macaque rectal SIV{Delta}Nef live attenuated vaccine model, we utilized a low virulence HSV-2 infection and the double-stranded RNA viral mimic polyICLC as tools to probe the effects of distinct types of immune activation on HIV vaccine efficacy and explore novel correlates of protection from wild type SIV. Rectally administered HSV-2 and polyICLC impacted the protection conferred by mucosal SIV{Delta}Nef vaccination by favoring partial protection in animals with breakthrough infection following virulent SIV challenge ("Controllers"). However, SIV{Delta}Nef persistence in blood and tissues did not predict protection in this rectal immunization and challenge model. Non-controllers had similar SIV{Delta}Nef viremia as completely protected macaques, and while they tended to have less replication competent SIV{Delta}Nef in lymph nodes, controllers had no recoverable virus in the lymph nodes. Non-controllers differed from protected macaques immunologically by having a greater frequency of pro-inflammatory CXCR3+CCR6+ CD4 T cells in blood and a monofunctional IFN{gamma}-dominant CD8 T cell response in lymph nodes. Controller phenotype was associated with heightened IFN production during acute SIV infection and a greater frequency of CXCR5+ CD4 T cells in blood pre-challenge despite a lower frequency of cells with the T follicular helper (Tfh) cell phenotype in blood and lymph nodes. Our results establish novel correlates of immunological control of SIV infection while reinforcing the potential importance of T cell functionality and location in SIV{Delta}Nef efficacy. Moreover, this work highlights that triggering of mucosal immunity can aid mucosal vaccine strategies rather than undermine protection. AUTHOR SUMMARYAn efficacious HIV vaccine is essential to contain the HIV pandemic. Vaccine-mediated protection from HIV may be either enhanced or obstructed by mucosal immune activation; thus, the impact of adjuvants and underlying co-infections that lead to immune activation needs to be evaluated. Using the SIV macaque model, we set out to study the impact of underlying infection with HSV-2 or treatment with the adjuvant polyICLC on rectal immunization with the live attenuated vaccine SIV{Delta}Nef. We found that neither stimulus impacted complete protection from SIV; however, the combination of HSV-2 and polyICLC improved control of infection in animals that were not completely protected. Compared with non-controller macaques, controllers had less inflammatory T cells before SIV challenge as well as greater gene expression of IFN and more functional SIV-specific T cells after infection. The results add to our understanding of the mechanisms of SIV{Delta}Nef protection and demonstrate that mucosal immune activation does not necessarily undermine protection in mucosal vaccination against HIV.

immunology↗

bioRxiv2019

Human CardioChimeras: Creation of a Novel \"Next Generation\" Cardiac Cell

BackgroundCardioChimeras (CCs) produced by fusion of murine c-kit+ cardiac interstitial cells (cCIC) with mesenchymal stem cells (MSCs) promote superior structural and functional recovery in a mouse model of myocardial infarction (MI) compared to either precursor cell alone or in combination. Creation of human CardioChimeras (hCC) represents the next step in translational development of this novel cell type, but new challenges arise when working with cCICs isolated and expanded from human heart tissue samples. The objective of the study was to establish a reliable cell fusion protocol for consistent optimized creation of hCCs and characterize fundamental hCC properties.\n\nMethods and ResultsCell fusion was induced by incubating human cCICs and MSCs at a 2:1 ratio with inactivated Sendai virus. Hybrid cells were sorted into 96-well microplates for clonal expansion to derive unique cloned hCCs, which were then characterized for various cellular and molecular properties. hCCs exhibited enhanced survival relative to the parent cells and promoted cardiomyocyte survival in response to serum deprivation in vitro.\n\nConclusionsThe generation of hCC is demonstrated and validated in this study, representing the next step toward implementation of a novel cell product for therapeutic development. Feasibility of creating human hybrid cells prompts consideration of multiple possibilities to create novel chimeric cells derived from cells with desirable traits to promote healing in pathologically damaged myocardium.\n\nClinical PerspectiveO_LI\"Next generation\" cell therapeutics will build upon initial findings that demonstrate enhanced reparative action of combining distinct cell types for treatment of cardiomyopathic injury.\nC_LIO_LIDifferential biological properties of various cell types are challenging for optimization of delivery, engraftment, persistence, and synergistic action when used in combination.\nC_LIO_LICreation of a novel hybrid cell called a CardioChimera overcomes limitations inherent to use of multiple cell types.\nC_LIO_LICardioChimeras exhibit unique properties relative to either parental cell anticipated to be advantageous in cellular therapeutic applications.\nC_LIO_LICardioChimeras have now been created and characterized using cells derived from human heart tissue, advancing initial proof of concept previously demonstrated with mice.\nC_LIO_LICardioChimeras represent an engineered solution that can be implemented as a path forward for improving the outcome of myocardial cell therapy.\nC_LI

cell biology↗

bioRxiv2019

Alpaca: a kmer-based approach for investigating mosaic structures in microbial genomes

SummaryMicrobial genomes are often mosaic: different regions can possess different evolutionary origins due to genetic recombination. The recent feasibility to assemble microbial genomes completely and the availability of sequencing data for complete microbial populations, means that researchers can now investigate the potentially rich evolutionary history of a microbe at a much higher resolution. Here, we present Alpaca: a method to investigate mosaicism in microbial genomes based on kmer similarity of large sequencing datasets. Alpaca partitions a given assembly into various sub-regions and compares their similarity across a population of genomes. The result is a high-resolution map of an entire genome and the most similar scoring clades across the given population. Availabilityhttps://github.com/AbeelLab/Alpaca Contactt.abeel@tudelft.nl

bioinformatics↗