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Diaz, D.

Publications and source records attributed to Diaz, D..

At least 19 recordsLinked to original sources

Bone Marrow-Derived Cells Fuse with Bergmann Glia in Experimental Autoimmune Encephalomyelitis

Bone marrow-derived cells (BMDCs) can infiltrate the brain and adopt new identities through transdifferentiation or fusion, yet their interactions with specific neural cells remain poorly defined. We examined BMDC fusion with Bergmann glia (BG), a key cerebellar support cell, in a mouse model of multiple sclerosis. After bone marrow transplantation, BMDCs fused with BG to form heterokaryons, retaining BG morphology and molecular markers. These heterokaryons contained donor and host nuclei that differed in both morphology and transcriptional activity. Remarkably, the BMDC nucleus localized not only to the soma but also along BG processes. This discovery identifies BMDC-BG fusion as a previously unrecognized form of glial plasticity, opening avenues for therapeutic strategies aimed at potentiating glial-mediated repair.

neuroscience↗

Oncogenic transformation proceeds through a transient state of cellular plasticity constrained by lineage-specific barriers.

Normal tissues frequently harbor oncogenic mutations without progressing to cancer, but the cellular basis of this resistance remains poorly defined. We asked whether transformation requires selection of a rare, permissive state within normal-like cell populations. Dermal fibroblasts and mammary epithelial cells responded uniformly to combined HRAS-G12V expression and p53 disruption. Cellular barcoding revealed no loss or enrichment of clones during morphological transformation, arguing against clonal selection as the primary driver of neoplastic reprogramming. Instead, all transduced cells underwent an early, shared transcriptional transition characterized by loss of differentiation markers, induction of RAS-associated and inflammatory programs, activation of alternative-lineage signatures, increased single-cell entropy, and chromatin decondensation. These changes were transient: entropy and chromatin accessibility subsequently declined, and some cells moved toward the control transcriptional state, whereas others stabilized in altered states. The two lineages followed distinct trajectories. Fibroblasts showed greater initial transcriptional plasticity but subsequently reverted more strongly toward the normal state, whereas epithelial cells changed more gradually and continued to diverge from it, suggesting a stronger barrier to transformation in the mesenchymal lineage. Thus, oncogenic perturbation initiated reprogramming throughout the population but did not uniformly produce a stable transformed state. Together, these findings support a model in which normal-like cells tolerate oncogenic mutations not because most cells fail to respond, but because a p53-independent, cell-intrinsic barrier limits the stabilization of malignant transformation following a transient period of heightened plasticity. This framework may facilitate the identification of mechanisms that constrain tumor initiation.. Significance StatementLoss of TP53 and activation of oncogenic RAS are common drivers of human cancer and frequently coexist in the same tumor. Nevertheless, these alterations often fail to induce malignant transformation. To investigate why, we introduced both alterations into fibroblasts and epithelial cells and tracked their responses using clonal barcoding, single-cell transcriptomics, and phenotypic assays. Initially, cells uniformly reprogrammed their transcriptional and chromatin states without detectable clonal selection. They then diverged: some reacquired transcriptional profiles resembling those of the original normal cells, whereas others became transformed. Thus, normal cells resist transformation through an intrinsic barrier that operates despite p53 disruption. Because this transition is transient and reversible, it provides a tractable window for studying the earliest stages of cancer development.

cancer biology↗

Engineering a Novel Bacterial Encapsulin for Programmable Surface Functionalization: From Single-Target to Mosaic Nanovaccines

Encapsulins are prokaryotic self-assembling protein nanocages with promise as nanovaccine scaffolds. Their utility as modular platforms require tolerance to surface engineering, high-yield soluble production, formulation stability, and controlled antigen (co-)display. Herein, a previously uncharacterized encapsulin from Alkaliphilus metalliredigens is engineered into a SpyCatcher-decorated nanoscaffold (Am-S) that enables controlled surface display of SpyTagged antigens. Cryo-EM confirms that the native encapsulin forms a T = 1 icosahedral nanocage, and that C-terminal SpyCatcher fusion yields Am-S without compromising nanocage assembly, symmetry, or structural integrity. Notably, Am-S exhibits high-yield soluble production in Escherichia coli, remains monodisperse after freeze-thaw and extended storage, and supports efficient SpyTagged peptide conjugation for single- and multi-antigen display. As a proof-of-concept, Am-S is functionalized with Alzheimers disease-associated amyloid-{beta} and/or hyperphosphorylated tau epitopes to generate single-target nanocages displaying either antigen and dual-target mosaic nanocages co-displaying both. In mice, Am-S antigen display enhances antigen-specific IgG responses relative to free antigens and induces predominantly IgG1-biased humoral immunity. Mosaic nanocages elicit antibodies against both targets, with immune sera selectively recognizing amyloid-{beta}- and phosphorylated tau-associated pathology in ex vivo brain sections from Alzheimers disease mouse models. These findings position Am-S as a manufacturable scaffold for developing multi-targeting nanovaccines against complex diseases.

synthetic biology↗

The selective OX1R antagonist 1-SORA-51 reduces binge-like feeding behavior in male and female mice without detectable changes in dopamine.

Binge eating disorder (BED) is characterized by episodic overconsumption of palatable food and involves dysregulated motivational and arousal processes. The orexin (hypocretin) system, through its widespread projections to mesolimbic circuits, has been implicated in cue-driven reward seeking and escalated intake, raising the possibility that orexin receptor antagonists may modulate binge-like behavior. Here we evaluated the effects of a dual orexin receptor antagonist (DORA-22) and an OX1R-selective antagonist (1-SORA-51) in a cyclic intermittent high-fat access model that generates robust and reproducible binge-like intake in male and female mice. DORA-22 produced no detectable effect on consumption at either early (2 h) or extended (24 h) binge timepoints. In contrast, 1-SORA-51 significantly reduced high-fat intake during the initial 2 hours of access in both sexes, with no effect on 24-hour consumption, indicating a selective attenuation of the early phase of binge intake. Fiber photometry recordings of GRABDA2m fluorescence in the nucleus accumbens revealed that 1-SORA-51 did not alter baseline dopamine signals or the dopamine increase triggered by high-fat pellet delivery, demonstrating that its behavioral effects occur without detectable modulation of mesolimbic dopamine dynamics. Together, these findings identify OX1R antagonism as a strategy for suppressing the initiation of binge-like feeding and highlight the receptor-level specificity of orexin contributions to maladaptive overconsumption.

neuroscience↗

Concomitant ablation of SOS1 and SOS2 triggers a lethal phenotype involving compromised intestinal integrity and widespread septicemia

The RAS guanine nucleotide exchange factors Son of Sevenless 1 and 2 (SOS1 and SOS2) are key regulators of RAS signaling pathways controlling cellular proliferation, differentiation, and survival processes that are essential for correct tissue homeostasis. While mice lacking both SOS1 and SOS2 die precipitously, we demonstrate herein that the combined genetic ablation of SOS1 and SOS2 triggers spontaneous, gut-derived, lethal bacteremia. Double-knockout (DKO) SOS1/2 mice exhibit extensive intestinal tissue damage, massive bacterial leakage out of the gut, and rapid progression to multi-organ failure and death. At the cellular level, loss of both SOS1 and SOS2 leads to profound immune cell depletion and a marked reduction in intestinal stem cell abundance and proliferative capacity, which is accompanied by severe disruption of intestinal architecture and increased epithelial permeability, indicating a breakdown of gut barrier integrity. Notably, therapeutic interventions aimed at enhancing cellular stemness significantly improve survival in SOS1/2 DKO mice, restoring intestinal proliferation and tissue organization. Collectively, our findings identify SOS1 and SOS2 as critical regulators of intestinal homeostasis and regenerative capacity during systemic infection and reveal stemness reinforcement as a potential strategy to overcome lethal susceptibility to sepsis.

cell biology↗

Enzyme Classification via Semi-Supervised Functional ResidueLearning

Predicting enzymatic function from a protein sequence is a fundamental task in protein discovery and engineering. In this paper, we present Semi-supervised Learning for Enzyme Classification (SLEEC): a semi-supervised learning framework that learns a function-aware protein representation for Enzyme Commision (EC) number prediction. SLEEC achieves SOTA performance on standard bench-marks and provides interpretable, residue-level annotations. We further demonstrate that our framework is robust to benign sequence modifications routinely observed in protein engineering workflows- such as appending functional tags- a desirable property that current ML frameworks lack. Our main technical contribution is a multiple sequence alignment (MSA)-based data augmentation technique for discovering sparse residue activations within a given enzyme sequence.

bioengineering↗

Unveiling the Toxicological and Allelopathic Effects of Pteridium aquilinum: Chemical Profiling and Biological Assays

The fern Pteridium aquilinum (bracken) is among the world most widespread plants and poses serious ecological and health risks due to the presence of illudane glycosides (IGs), carcinogenic compounds that particularly affect grazing livestock. This study determined the presence of IGs in plant extracts and in water samples from the Asturias region (northern Spain), an area characterized by intensive cattle farming, and assessed the genotoxic potential, and allelopathic effects of these samples. The glycosides ptaquiloside (PTA) and ptesculentoside (PTE), together with the degradation products pterosin A and pterosin B, were quantified in in vitro-cultured gametophytes and young sporophytes, spring-collected croziers, and autumn water samples from several bracken-infested sites. All sampling locations contained IGs in both plant and water samples, with particularly high concentrations of PTA detected in croziers from Brana Vieja (Somiedo), where cattle deaths had been reported. In vivo genotoxicity assays, using Drosophila melanogaster, revealed induction of somatic mutations and recombination events by aqueous plant extracts and of somatic mutations by water samples. The genotoxic activity of plant extracts, but not that of water samples, was associated with pterosins A and B. Moreover, comet assays in cultured human cells confirmed the genotoxic activity of plant extracts. Unexpectedly, allelopathic bioassays indicated a possible phytostimulatory rather than inhibitory effect of bracken extracts on the germination of meadow species. These findings underscore the widespread presence and biological activity of bracken in northern Spain and highlight the urgent need for management strategies to mitigate the ecological and toxicological threats posed by bracken proliferation.

pharmacology and toxicology↗

Evolution of the conformational ensemble and allosteric networks of apoptotic caspases in chordates

Caspases, known for their role in apoptosis and inflammation, have recently emerged as potential regulators of cell differentiation and proliferation. The regulation of caspase conformations to affect these specific pathways is not well understood. Understanding the conformational landscapes, intermediate states, and mechanisms for fine-tuning these ensembles is critical for unraveling their diverse regulatory functions. We combined experimental and computational techniques to characterize the evolution of conformational ensemble in caspases. Using ancestral protein reconstruction, molecular dynamics simulations, and network analysis, we identify a network of residues that serve as a scaffold for conformational variation, and the network has been faithfully passed down over 500 million years of apoptotic caspase evolution. In addition, investigations of free energy landscapes provide thermodynamic insights into how initiator and effector caspase subfamilies stabilize monomeric and dimeric conformations while undergoing conformational dynamics. We find, through mutational in-vitro folding analysis, that the small subunit and amino acid networks at the base of the structure are essential for conformational dynamics beyond a ubiquitous intermediate present in the conformational ensemble of all apoptotic chordate caspases. We identify key allosteric hub residues that regulate the equilibrium in the conformational ensembles of all apoptotic caspases in chordates. Lastly, by combining our new data set with previous folding studies we provide a comprehensive model for folding of all apoptotic caspases in chordates.

biochemistry↗

Tenascin-C potentiates Wnt signaling in thyroid cancer

Tenascin-C (TNC) is a secreted extracellular matrix protein that is highly expressed during embryonic development and re-expressed during wound healing, inflammation, and neoplasia. Studies in developmental models suggest that TNC may regulate the Wnt signaling pathway. Our lab has shown high levels of Wnt signaling and TNC expression in anaplastic thyroid cancer (ATC), a highly lethal cancer with an abysmal [~]3-5 month median survival. Here, we investigated the role of TNC in facilitating ligand-dependent Wnt signaling in thyroid cancer. We utilized bulk RNA-sequencing from three independent multi-institutional thyroid cancer patient cohorts. TNC expression was spatially localized in patient tumors with RNA in situ hybridization. The role of TNC was investigated in vitro using Wnt reporter assays and in vivo with a NOD.PrkdcscidIl2rg-/- mouse ATC xenograft tumor model. TNC expression was associated with aggressive thyroid cancer behavior, including anaplastic histology, extrathyroidal extension, and metastasis. Spatial localization of TNC in patient tissue demonstrated a dramatic increase in expression within cancer cells along the invasive edge, adjacent to Wnt ligand-producing fibroblasts. TNC expression was also increased in areas of intravascular invasion. In vitro, TNC bound Wnt ligands and potentiated Wnt signaling. Finally, in an ATC mouse model, TNC increased Wnt signaling, tumor burden, invasion, and metastasis. Altogether, TNC potentiated ligand driven Wnt signaling and promotes cancer cell invasion and metastasis in a mouse model of thyroid cancer. Understanding the role of TNC and its interaction with Wnt ligands could lead to the development of novel biomarkers and targeted therapeutics for thyroid cancer.

cancer biology↗

Neuroprotective Effects Of VEGF-B In A Murine Model Of Aggressive Neuronal Loss With Childhood Onset

In recent decades, the scientific community has faced a major challenge in the search for new therapies that can slow down or alleviate the process of neuronal death that accompanies neurodegenerative diseases. This study aimed at identifying an effective therapy using neurotrophic factors to delay the rapid and aggressive cerebellar degeneration experienced by the Purkinje Cell Degeneration (PCD) mouse, a model of childhood-onset neurodegeneration with cerebellar atrophy (CONDCA). Initially, we analyzed the changes in the expression of several neurotrophic factors related to the degenerative process itself, identifying changes in insulin-like growth factor 1 (IGF-1) and Vascular Endothelial Growth Factor B (VEGF-B) in the affected animals. Then, we administered pharmacological treatments using human recombinant IGF-1 (rhIGF-1) or VEGF-B (rhVEGF-B) proteins, considering their temporal variations during the degenerative process. The effects of these treatments on motor, cognitive, and social behavior, as well as on cerebellar destructuration were analyzed. Whereas treatment with rhIGF-1 did not demonstrate any neuroprotective effect, rhVEGF-B administration at moderate dosages stopped the process of neuronal death and restored motor, cognitive, and social functions altered in PCD mice (and CONDCA patients). Additionally, we demonstrate that this neuroprotective effect was achieved through a partial inhibition or delay of apoptosis. These findings provide strong evidence supporting the use of rhVEGF-B as a pharmacological agent to limit severe cerebellar neurodegenerative processes.

neuroscience↗

In vivo fate of systemically administered encapsulin protein nanocages and implications for their use in targeted drug delivery

Encapsulins, self-assembling protein nanocages derived from prokaryotes, are promising nanoparticle-based drug delivery systems (NDDS). However, the in vivo behavior and fate of encapsulins are poorly understood. In this pre-clinical study, we probe the interactions between the model encapsulin from Thermotoga maritima (TmEnc) and key biological barriers encountered by NDDS. Here, a purified TmEnc formulation that exhibited colloidal stability, storability, and blood compatibility was intravenously injected into BALB/c mice. TmEnc had an excellent nanosafety profile, with no abnormal weight loss or gross pathology observed, and only temporary alterations in toxicity biomarkers detected. Notably, TmEnc demonstrated immunogenic properties, inducing the generation of nanocage-specific IgM and IgG antibodies, but without any prolonged pro-inflammatory effects. An absence of antibody cross-reactivity also suggested immune-orthogonality among encapsulins systems. Moreover, TmEnc formed a serum-derived protein corona on its surface which changed dynamically and appeared to play a role in immune recognition. TmEncs biodistribution profile further revealed its sequestration from the blood circulation by the liver and then biodegraded within Kupffer cells, thus indicating clearance via the mononuclear phagocyte system. Collectively, these findings provide critical insights into how encapsulins behave in vivo, thereby informing their future design, modification, and application in targeted drug delivery. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/549228v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1691ecaorg.highwire.dtl.DTLVardef@647c31org.highwire.dtl.DTLVardef@115a146org.highwire.dtl.DTLVardef@10f2b6f_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

β-hydroxybutyrate is a metabolic regulator of proteostasis in the aged and Alzheimer disease brain

Loss of proteostasis is a hallmark of aging and Alzheimer disease (AD). Here, we identify {beta}-hydroxybutyrate ({beta}HB), a ketone body, as a regulator of protein solubility in the aging brain. {beta}HB is a small molecule metabolite which primarily provides an oxidative substrate for ATP during hypoglycemic conditions, and also regulates other cellular processes through covalent and noncovalent protein interactions. We demonstrate {beta}HB-induced protein insolubility across in vitro, ex vivo, and in vivo mouse systems. This activity is shared by select structurally similar metabolites, is not dependent on covalent protein modification, pH, or solute load, and is observable in mouse brain in vivo after delivery of a ketone ester. Furthermore, this phenotype is selective for pathological proteins such as amyloid-{beta}, and exogenous {beta}HB ameliorates pathology in nematode models of amyloid-{beta} aggregation toxicity. We have generated a comprehensive atlas of the {beta}HB-induced protein insolublome ex vivo and in vivo using mass spectrometry proteomics, and have identified common protein domains within {beta}HB target sequences. Finally, we show enrichment of neurodegeneration-related proteins among {beta}HB targets and the clearance of these targets from mouse brain, likely via {beta}HB-induced autophagy. Overall, these data indicate a new metabolically regulated mechanism of proteostasis relevant to aging and AD.

physiology↗

BCL7 proteins, metazoan-specific subunits of the mammalian SWI/SNF complex, bind the nucleosome core particle

BCL7 proteins are among the most recently identified subunits of the mammalian SWI/SNF (mSWI/SNF) chromatin remodeling complex and are absent from the unicellular version of the complex. Mutations in BCL7 proteins are associated with different kind of cancers including blood malignancies. The information on the molecular function and on the structure of BCL7 proteins is to date very limited. Here we report that BCL7 proteins directly bind the nucleosome core particle (NCP) and free DNA with high affinity. We demonstrate that BCL7 proteins form defined complexes with the NCP and we identify the conserved N-terminal part of BCL7 proteins as sufficient to nucleosome binding. We further characterize the impact of BCL7 protein mutations reported in cancer patients on NCP binding and show that the R11S driver mutation reduces the affinity for the nucleosome. Our findings clarify the molecular function of BCL7 proteins and help rationalize the impact of cancer-associated mutations.

biochemistry↗

Genome assembly with variable order de Bruijn graphs

Choosing an order for constructing a de Bruijn graph (DBG) is a crucial step in de novo assembly, as no single value allows complete genome reconstruction. The variable-order de Bruijn graph (voDBG) addresses this limitation by combining DBGs of multiple orders in a single structure connected by contextual relationships. This representation enables new connections to be identified or ambiguities to be resolved during assembly. However, voDBGs currently lack a formal definition of contigs. In this paper, we give the first formal definition of contigs for voDBGs. We show that, for a frequency range [{ell}, h] with{ell} > h/2, nodes whose labels occur with frequency f [isin] [{ell}, h] in the reads spell sequences of the genome with high probability under uniform sampling assumptions. We call these sequences ({ell}, h)-tigs. We also present an efficient algorithm to enumerate ({ell}, h)-tigs from a voDBG that accounts for homopolymer errors. Experiments on PacBio HiFi data show that our method significantly improves contiguity compared to fixed-order DBGs while remaining considerably lighter than full genome assemblers.

bioinformatics↗

High sensitivity single cell RNA sequencing with split pool barcoding

Single cell RNA sequencing (scRNA-seq) has become a core tool for researchers to understand biology. As scRNA-seq has become more ubiquitous, many applications demand higher scalability and sensitivity. Split-pool combinatorial barcoding makes it possible to scale projects to hundreds of samples and millions of cells, overcoming limitations of previous droplet based technologies. However, there is still a need for increased sensitivity for both droplet and combinatorial barcoding based scRNA-seq technologies. To meet this need, here we introduce an updated combinatorial barcoding method for scRNA-seq with dramatically improved sensitivity. To assess performance, we profile a variety of sample types, including cell lines, human peripheral blood mononuclear cells (PBMCs), mouse brain nuclei, and mouse liver nuclei. When compared to the previously best performing approach, we find up to a 2.6-fold increase in unique transcripts detected per cell and up to a 1.8-fold increase in genes detected per cell. These improvements to transcript and gene detection increase the resolution of the resulting data, making it easier to distinguish cell types and states in heterogeneous samples. Split-pool combinatorial barcoding already enables scaling to millions of cells, the ability to perform scRNA-seq on previously fixed and frozen samples, and access to scRNA-seq without the need to purchase specialized lab equipment. Our hope is that by combining these previous advantages with the dramatic improvements to sensitivity presented here, we will elevate the standards and capabilities of scRNA-seq for the broader community.

genomics↗

Exploring the Self-Assembly of Encapsulin Protein Nanocages from Different Structural Classes

Encapsulins, self-assembling icosahedral protein nanocages derived from prokaryotes, represent a versatile set of tools for nanobiotechnology. However, a comprehensive understanding of the mechanisms underlying encapsulin self-assembly, disassembly, and reassembly is lacking. Here, we characterise the disassembly/reassembly properties of three encapsulin nanocages that possess different structural architectures: T = 1 (24 nm), T = 3 (32 nm), and T = 4 (42 nm). Using spectroscopic techniques and electron microscopy, encapsulin architectures were found to exhibit varying sensitivities to the denaturant guanidine hydrochloride (GuHCl), extreme pH, and elevated temperature. While all encapsulins showed the capacity to reassemble following GuHCl-induced disassembly (within 75 min), only the smallest T = 1 nanocage reassembled after disassembly in basic pH (within 15 min). Furthermore, atomic force microscopy revealed that all encapsulins showed a significant loss of structural integrity after undergoing sequential disassembly/reassembly steps. These findings provide insights into encapsulins disassembly/reassembly dynamics, thus informing their future design, modification, and application.

biophysics↗

Molecular architecture determines brain delivery of a transferrin-receptor targeted lysosomal enzyme

Delivery of biotherapeutics across the blood-brain barrier (BBB) is a challenge. Many approaches fuse biotherapeutics to platforms that bind the transferrin receptor (TfR), a brain endothelial cell target, to facilitate receptor-mediated transcytosis across the BBB. Here, we characterized the pharmacological behavior of two distinct TfR-targeted platforms fused to iduronate 2-sulfatase (IDS), a lysosomal enzyme deficient in mucopolysaccharidosis type II (MPS II), and compared the relative brain exposures and functional activities of both approaches in mouse models. IDS fused to a moderate-affinity, monovalent TfR binding enzyme transport vehicle (ETV:IDS) resulted in widespread brain exposure, internalization by parenchymal cells, and significant substrate reduction in the CNS of an MPS II mouse model. In contrast, IDS fused to a standard high-affinity bivalent antibody (IgG:IDS) resulted in lower brain uptake, limited biodistribution beyond brain endothelial cells, and reduced brain substrate reduction. These results highlight important features likely to impact the clinical development of TfR-targeting platforms in MPS II and potentially other CNS diseases. SummaryBrain delivery, biodistribution and pharmacodynamics of a lysosomal enzyme fused to a moderate-affinity transferrin receptor-directed blood-brain barrier enzyme transport vehicle are superior to a traditional high-affinity anti-TfR monoclonal antibody fusion.

neuroscience↗

Bioengineering a light-responsive encapsulin nanoreactor: a potential tool for photodynamic therapy

Encapsulins, a prokaryotic class of self-assembling protein nanocompartments, are being re-engineered to serve as ‘nanoreactors’ for the augmentation or creation of key biochemical reactions. However, approaches that allow encapsulin nanoreactors to be functionally activated with spatial and temporal precision is lacking. We report the construction of a light-responsive encapsulin nanoreactor for “on-demand” production of reactive oxygen species (ROS). Herein, encapsulins were loaded with the fluorescent flavoprotein mini-Singlet Oxygen Generator (miniSOG), a biological photosensitizer that is activated by blue-light to generate ROS, primarily singlet oxygen (1O2). We established that the nanocompartments stably encased miniSOG, and in response to blue-light were able to mediate the photoconversion of molecular oxygen into ROS. Using an in vitro model of lung cancer, ROS generated by the nanoreactor was shown to trigger photosensitized oxidation reactions that exerted a toxic effect on tumour cells, suggesting utility in photodynamic therapy. This encapsulin nanoreactor thus represents a platform for the light-controlled initiation and/or modulation of ROS-driven processes in biomedicine and biotechnology.Competing Interest StatementThe authors have declared no competing interest.View Full Text

synthetic biology↗