Biology subjects

Sanchez, J.

Publications and source records attributed to Sanchez, J..

30 records · Page 2Linked to original sources

bioRxiv2023

Stratigraphic distribution of ammonoids and other macrofossils from the upper Albian-lower Cenomanian interval in Putumayo, Colombia, northern South America: new data for mid-Cretaceous basin correlation

Despite the rich paleontological heritage of Colombia, in the equatorial Neotropics, one of the least explored regions in terms of its fossil record is the Putumayo region near Ecuador, largely due to its considerable ground cover, thick vegetation, rock weathering, geographic remoteness, and overall inaccessibility to well-exposed outcrops. This precludes detailed comparisons with neighboring basins, and thus the generation of more comprehensive biostratigraphic correlations for western northern South America and other paleobiogeographic regions, e.g., Mediterranean Tethys, northern Africa, Western Interior Basin. Here, we report 67 occurrences of mid- Cretaceous ammonoids and other macrofossils (e.g., bivalves, decapod crustaceans, fish remains, plant remains), from the middle Albian of the uppermost Caballos Formation and the upper Albian-lower Cenomanian of the lower Villeta Formation, collected in-situ from a stratigraphic section cropping out on the Mocoa-San Francisco road in the Department of Putumayo, Colombia. Among the ammonoid taxa recovered are several morphotypes assignable to ?Schloenbachia sp., cf. Engonoceras sp., Oxytropidoceras (Venezoliceras) sp., Oxytropidoceras (Laraiceras) sp., cf. Oxytropidoceras sp., Mortoniceras (Mortoniceras) cf. vespertinum, Mortoniceras (Mortoniceras) sp., Algericeras sp., Hysteroceras sp. 1, Hysteroceras sp. 2, cf, Hysteroceras sp., cf. Forbesiceras sp., Graysonites sp., Hamites sp., and two isolated aptychi. The occurrence of the ammonoid genera Oxytropidoceras, Mortoniceras, and Schloenbachia, suggest interconnection of the Putumayo Basin during the mid-Cretaceous with the Upper Magdalena Valley in Colombia and the Oriente Basin in Ecuador, which, together with the rest of the ammonoid assemblage, provide biostratigraphic data to define the upper Albian-lower Cenomanian in the basin and thus in northwestern South America.

paleontology↗

bioRxiv2023

Leveraging IFNγ/CD38 regulation to unmask and target leukemia stem cells in acute myelogenous leukemia

Elimination of drug-resistant leukemia stem cells (LSCs) represents a major challenge to achieve a cure in acute myeloid leukemia (AML). Although AML blasts generally retain high levels of surface CD38 (CD38pos), the presence of CD34 and lack of CD38 expression (CD34posCD38neg) are immunophenotypic features of both LSC-enriched AML blasts and normal hematopoietic stem cells (HSCs). We report that IFN-{gamma} induces CD38 upregulation in LSC-enriched CD34posCD38neg AML blasts, but not in CD34posCD38neg HSCs. To leverage the IFN-{gamma} mediated CD38 up-regulation in LSCs for clinical application, we created a compact, single-chain CD38-CD3-T cell engager (CD38-BIONIC) able to direct T cells against CD38pos blasts. Activated CD4pos and CD8pos T cells not only kill AML blasts but also produce IFN{gamma}, which leads to CD38 expression on CD34posCD38neg LSC-enriched blasts. These cells then become CD38-BIONIC targets. The net result is an immune-mediated killing of both CD38neg and CD38pos AML blasts, which culminates in LSC depletion. Statement of significanceThis work represents a potential advancement in the treatment of AML, as it involves the release of IFN-{gamma} by T cells to induce CD38 expression and thus sensitizing leukemia stem cells, which have been resistant to current treatment regimens, to CD38-directed T cell engagers.

cancer biology↗

bioRxiv2023

APOE3 Christchurch modulates tau phosphorylation and regulates β-catenin/Wnt/Cadherin signaling in induced pluripotent stem cell-derived cerebral organoids from Alzheimer's cases

Alzheimers disease (AD) is the most common cause of dementia among older adults. APOE3 Christchurch (R136S, APOE3Ch) variant homozygosity was reported in an individual with extreme resistance to autosomal dominant AD due to the PSEN1 E280A mutation. This subject had a delayed clinical age at onset and resistance to tauopathy and neurodegeneration despite extremely high amyloid plaque burden. We established induced pluripotent stem (iPS) cell-derived cerebral organoids from this resistant case and from a non-protected kindred control (with PSEN1 E280A and APOE3/3). We used CRISPR/Cas9 gene editing to successfully remove the APOE3Ch to wild type in iPS cells from the protected case and to introduce the APOE3Ch as homozygote in iPS cells from the non-protected case to examine causality. We found significant reduction of tau phosphorylation (pTau 202/205 and pTau396) in cerebral organoids with the APOE3Ch variant, consistent with the strikingly reduced tau pathology found in the resistant case. We identified Cadherin and Wnt pathways as signaling mechanisms regulated by the APOE3Ch variant through single cell RNA sequencing in cerebral organoids. We also identified elevated {beta}-catenin protein, a regulator of tau phosphorylation, as a candidate mediator of APOE3Ch resistance to tauopathy. Our findings show that APOE3Ch is necessary and sufficient to confer resistance to tauopathy in an experimental ex-vivo model establishing a foundation for the development of novel, protected case-inspired therapeutics for tauopathies, including Alzheimers.

neuroscience↗

bioRxiv2022

Systems biology illuminates alternative metabolic niches in the human gut microbiome

Human gut bacteria perform diverse metabolic functions with consequences for host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta performs several unusual chemical transformations, but it does not metabolize sugars and its core growth strategy remains unclear. To obtain a comprehensive view of the metabolic network of E. lenta, we generated several complementary resources: defined culture media, metabolomics profiles of strain isolates, and a curated genome-scale metabolic reconstruction. Stable isotope-resolved metabolomics revealed that E. lenta uses acetate as a key carbon source while catabolizing arginine to generate ATP, traits which could be recapitulated in silico by our updated metabolic model. We compared these in vitro findings with metabolite shifts observed in E. lenta-colonized gnotobiotic mice, identifying shared signatures across environments and highlighting catabolism of the host signaling metabolite agmatine as an alternative energy pathway. Together, our results elucidate a distinctive metabolic niche filled by E. lenta in the gut ecosystem.

microbiology↗

bioRxiv2022

Characterization of the Pace-and-Drive Capacity of the Human Sinoatrial Node: a 3D in silico Study

The sinoatrial node (SAN) is a complex structure that spontaneously depolarizes rhythmically ("pacing") and excites the surrounding non-automatic cardiac cells ("drive") to initiate each heart beat. However, the mechanisms by which the SAN cells can activate the large and hyperpolarized surrounding cardiac tissue are incompletely understood. Experimental studies demonstrated the presence of an insulating border that separates the SAN from the hyperpolarizing influence of the surrounding myocardium, except at a discrete number of sinoatrial exit pathways (SEP). We propose a highly detailed 3D model of the human SAN, including 3D SEPs to study the requirements for successful electrical activation of the primary pacemaking structure of the human heart. A total of 788 simulations investigate the ability of the SAN to pace and drive with different heterogeneous characteristics of the nodal tissue (gradient and mosaic models) and myocyte orientation. A sigmoidal distribution of the tissue conductivity combined with a mosaic model of SAN and atrial cells in the SEP was able to drive the right atrium (RA). Additionally, we investigated the influence of the SEPs by varying their number, length and width. SEPs created a transition zone of transmembrane voltage (TMV) and ionic currents to enable successful pace and drive. Unsuccessful simulations showed a hyperpolarized TMV (-66 mV), which blocked the L-type channels and attenuated the sodium-calcium exchanger. The fiber direction influenced the SEPs that preferentially activated the crista terminalis (CT). The location of the leading pacemaker site (LPS) shifted towards the SEP-free areas. LPSs were located closer to the SEP-free areas (3.46{+/-}1.42 mm), where the hyperpolarizing influence of the CT was reduced, compared to a larger distance from the LPS to the areas where SEPs were located (7.17{+/-}0.98 mm). This study identified the geometrical and electrophysiological aspects of the 3D SAN-SEP-CT structure required for successful pace-and-drive in silico. SIGNIFICANCEThe human sinoatrial node (SAN) is the intrinsic natural pacemaker of the heart. Despite its remarkable robustness to failure, the electrophysiological properties, and mechanisms by which the SAN overcomes the source-sink mismatch towards the hyperpolarized surrounding cardiac tissue remains a mystery. The SAN is electrically isolated from the hyperpolarized cardiac tissue, except at a discrete number of sinoatrial exit pathways (SEP). Using in silico experiments, we explore the influence of the fiber orientation, the SEPs number, geometry and location on the activation of the SAN and the surrounding atrial tissue. We provide the mechanisms in a first 3D model of the human SAN-SEP structure that can successfully drive the working myocardium.

physiology↗

bioRxiv2021

Ecological relevance of abundant and rare taxa in a high-diverse elastic hypersaline microbial mat, using a small-scale sampling

We evaluated the microbial diversity and metabolome profile of an uncommon hypersaline elastic microbial mat from Cuatro Cienegas Basin (CCB) in the Chihuahuan Desert of Coahuila, Mexico. We collected ten samples on a small scale transect (1.5-meters) and described its microbial diversity through NGS-based ITS and 16S rDNA gene sequencing. A very low number of taxa comprised a considerable proportion of the mat and were shared across all sampling points, whereas the rare biosphere was more phylogenetically diverse (Faiths Phylogenetic Diversity (FPD) index) and phylogenetically disperse (using a null model distribution of Phylogenetic Species Clustering (nmdPSC)) than the abundant (high read count) taxa for both analyzed libraries. We also found a distinctive metabolome profile for each sample and were able to tentatively annotate several classes of compounds with relevant biological properties.

microbiology↗

bioRxiv2021

The openCARP Simulation Environment for Cardiac Electrophysiology

Background and ObjectiveCardiac electrophysiology is a medical specialty with a long and rich tradition of computational modeling. Nevertheless, no community standard for cardiac electrophysiology simulation software has evolved yet. Here, we present the openCARP simulation environment as one solution that could foster the needs of large parts of this community. Methods and ResultsopenCARP and the Python-based carputils framework allow developing and sharing simulation pipelines which automate in silico experiments including all modeling and simulation steps to increase reproducibility and productivity. The continuously expanding openCARP user community is supported by tailored infrastructure. Documentation and training material facilitate access to this complementary research tool for new users. After a brief historic review, this paper summarizes requirements for a high-usability electrophysiology simulator and describes how openCARP fulfills them. We introduce the openCARP modeling workflow in a multi-scale example of atrial fibrillation simulations on single cell, tissue, organ and body level and finally outline future development potential. ConclusionAs an open simulator, openCARP can advance the computational cardiac electrophysiology field by making state-of-the-art simulations accessible. In combination with the carputils framework, it offers a tailored software solution for the scientific community and contributes towards increasing use, transparency, standardization and reproducibility of in silico experiments.

bioinformatics↗

bioRxiv2021

Yield Maintenance Under Drought is Orchestrated by the qDTY12.1-Encoded DECUSSATE Gene of Rice Through a Network With Other Flowering-Associated Genes Across the Genetic Background

Introgression of major-effect QTLs is an important component of rice breeding for yield-retention under drought. While largely effective, the maximum potentials of such QTLs have not been consistent across genetic backgrounds. We hypothesized that synergism or antagonism with additive-effect peripheral genes across the background could either enhance or undermine the QTL effects. To elucidate the molecular underpinnings of such interaction, we dissected qDTY12.1 synergy with numerous peripheral genes in context of network rewiring effects. By integrative transcriptome profiling and network modeling, we identified the DECUSSATE (OsDEC) within qDTY12.1 as the core of the synergy and shared by two sibling introgression lines in IR64 genetic background, i.e., LPB (low-yield penalty) and HPB (high-yield penalty). OsDEC is expressed in flag leaves and induced by progressive drought at booting stage in LPB but not in HPB. The unique OsDEC signature in LPB is coordinated with 35 upstream and downstream peripheral genes involved in floral development through the cytokinin signaling pathway, which are lacking in HPB. Results further support the differential network rewiring effects through genetic coupling-uncoupling between qDTY12.1 and other upstream and downstream peripheral genes across the distinct genetic backgrounds of LPB and HPB. We propose that the functional DEC-network in LPB defines a mechanism for early flowering as a means for avoiding the depletion of photosyntate needed for reproductive growth due to drought. Its impact on yield-retention is likely through the timely establishment of stronger source-sink dynamics that sustains a robust reproductive transition under drought. Author summaryWhile the Green Revolution of the 1960s significantly increased rice grain yields through the creation of high-yielding varieties for high input systems, current marginal climates pose a significant challenge for providing consistent yield. In rice growing regions of the world, drought affects the livelihood of small-scale and subsistence farmers by inflicting significant yield penalties to their production systems. Breeding of next-generation rice varieties with optimal balance of survivability and productivity traits will be key to providing consistent yields year to year. Within this paradigm, the use of large effect QTLs such as qDTY12.1 to improve yield retention under drought have been largely successful. By integrating the use of high resolution transcriptome datasets with a focused biological interrogation of agronomic results from this and previous studies, we uncovered a putative functional genetic network, anchored by the DECUSSATE gene (OsDEC) within qDTY12.1, that effectively minimizes drought penalties to yield by driving cellular processes that culminate in timely flowering that maximizes the use of photosynthetic sources for efficient reproduductive transition and ultimately seed development. Our study further illuminates the qDTY12.1 function and speaks to the misconception that qDTY introgression alone is sufficient for providing consistently large positive effects to yield retention under reproductive stage drought.

genetics↗

bioRxiv2020

High-resolution Crystal Structures of Transient Intermediates in the Phytochrome Photocycle

Phytochromes are red/far-red light photoreceptors in bacteria to plants, which elicit a variety of important physiological responses. They display a reversible photocycle between the resting (dark) Pr state and the light activated Pfr state, in which light signals are received and transduced as structural change through the entire protein to modulate the activity of the protein. It is unknown how the Pr-to-Pfr interconversion occurs as the structure of intermediates remain notoriously elusive. Here, we present short-lived crystal structures of the classical phytochrome from myxobacterium Stigmatella aurantiaca captured by an X-ray Free Electron Laser 5 ns and 33ms after light illumination of the Pr state. We observe large structural displacements of the covalently bound bilin chromophore, which trigger a bifurcated signaling pathway. The snapshots show with atomic precision how the signal progresses from the chromophore towards the output domains, explaining how plants, bacteria and fungi sense red light.

biophysics↗

bioRxiv2019

α-synuclein aggregates induce c-Abl activation and neurodegeneration by a redox stress mechanism

ObjectiveRedox stress, c-Abl activation, and -synuclein aggregates each independently contribute to neurodegeneration in Parkinsons disease. Interactions between these factors may underlie convergent and feed-forward mechanisms of disease progression. Methods-synuclein aggregate formation was induced in neuronal cultures and mouse substantia nigra by exposure to pre-formed human -synuclein fibrils or by AAV-mediated over-expression of -synuclein. Aggregate formation, c-Abl activation, redox stress, and neurodegeneration were evaluated by immunohistochemistry and Western blots, and mouse motor function was evaluated using the rota-rod and pole tests. To suppress redox stress, cultures and mice were treated with N-acetyl cysteine, a thiol repletion agent that supports neuronal glutathione metabolism. ResultsIn primary neuron cultures, the formation of -synuclein aggregates led to redox stress and c-Abl activation. Redox stress alone, in the absence of -synuclein aggregates, was also sufficient to induced c-Abl activation. N-acetyl cysteine suppressed redox stress, and likewise suppressed both c-Abl activation and -synuclein aggregation. A similar pattern was observed in the two mouse models of Parkinsons disease. In both models, -synuclein aggregates in the substantia nigra were accompanied by redox stress, c-Abl activation, dopaminergic neurodegeneration and motor impairment, all of which were attenuated in mice treated with oral N-acetyl cysteine. InterpretationThese results indicate that -synuclein aggregates induce c-Abl activation by a redox stress mechanism. c-Abl in turn promotes -synuclein aggregation, and this potentially feed-forward process can be blocked by N-acetyl cysteine. The findings thus add mechanistic support for N-acetyl cysteine as a therapeutic for Parkinsons disease.

neuroscience↗

bioRxiv2019

AML ImmunoPET: 64Cu-DOTA-anti-CD33 PET-CT imaging of AML in Xenograft mouse model

PurposeAcute myeloid leukemia (AML) is a highly aggressive form of leukemia that results in poor survival outcomes. Currently, diagnosis and prognosis are based on invasive single-point bone marrow biopsies (iliac crest). There is currently no AML-specific non-invasive imaging method to assess disease in the whole body, including in extramedullary organs, representing an unmet clinical need. About 85-90% of human myeloid leukemia cells express CD33 (an accepted biomarker for AML) cell surface receptors, highlighting CD33 as an ideal candidate for AML immunoPET.\n\nExperimental DesignIn this study, we evaluated if 64Cu-DOTA-anti-CD33 murine monoclonal antibody (mAb) can be used for ImmunoPET-CT imaging of AML in preclinical model. For translational purpose, a humanized anti-CD33 antibody was produced, and after confirming its anti-CD33 PET-CT imaging ability we further explored its therapeutic potential.\n\nResults64Cu-DOTA-anti-CD33 based PET-CT imaging detected CD33+ AML in mice with high sensitivity (95.65%) and specificity (100%). In the entire skeletal system, CD33+ PET activity was significantly high in the bones of AML bearing mice over non-leukemic control mice; femur (p<0.00001), tibia (p=0.0001), humerus (p=0.0014), and lumber spine (p<0.00001). Interestingly, the imaging showed CD33+ PET activity prevelant in epiphysis/diaphysis of the bones, indicating spatial heterogeneity. Anti-CD33 therapy using newly developed humanized anti-CD33 mAb as an ADC (p=0.02) and 225Ac-anti-CD33-RIT (p<0.00001), significantly reduced disease burden over that of respective controls.\n\nConclusionWe have successfully developed a novel anti-CD33 immunoPET-CT based non-invasive imaging tool for diagnosis of AML and its spatial distribution, which indicates a preferential skeletal niche.\n\nTranslational RelevanceAcute myeloid leukemia (AML) exhibits extensive heterogeneity in therapeutic response, even in patients sharing similar characteristics, indicating the inadequacy of currently used biopsy-based prognostic tools. There is a critical need for non-invasive quantitative imaging modality specific to AML, which is able to assess this disease in the whole body, including in extramedullary organs and to longitudinally monitor treatment response. CD33, an accepted AML biomarker is expressed on more than 85-90% of blast cells and Mylotarg (anti-CD33-ADC) is FDA approved immunotherapy for AML. In this preclinical study using anti-human CD33 mAb (64Cu-DOTA-anti-CD33), a CD33 PET-CT imaging modality was developed that detected AML with high sensitivity and specificity. The approach also indicated spatial heterogeneity in leukemic disease, dependent on disease burden, which warrants caution in analyzing results from single point bone marrow biopsies. Therefore, this imaging modality can be used to non-invasively detect AML in humans and also monitor treatment response, an unmet clinical need.

cancer biology↗

bioRxiv2017

Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems

Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the [~]7500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequenced across a diversity of taxa. We designed and tested 16,308 RNA baits to capture 720 Ultraconserved Element loci and 1,071 exon loci. Library preparation and target enrichment was performed on 33 taxa from all orders within the class Anthozoa. Following Illumina sequencing and Trinity assembly, we recovered 1,774 of 1,791 targeted loci. The mean number of loci recovered from each species was 638 {+/-} 222, with more loci recovered from octocorals (783 {+/-} 138 loci) than hexacorals (475 {+/-}187 loci). Phylogenetically informative sites ranged from 26-49% for alignments at differing hierarchical taxonomic levels (e.g., Anthozoa, Octocorallia, Hexacorallia). The percent of variable sites within each of three genera (Acropora, Alcyonium, and Sinularia) for which multiple species were sequenced ranged from 4.7-30%. Maximum likelihood analyses recovered highly resolved trees with topologies matching those supported by other studies, including the monophyly of the order Scleractinia. Our results demonstrate the utility of this target-enrichment approach to resolve phylogenetic relationships from relatively old to recent divergences. Re-designing the baits with improved affinities to capture loci within each sub-class will provide a valuable toolset to address systematic questions and further our understanding of the timing of diversifications in the class Anthozoa.

genomics↗