Biology subjects

Huang, Y.

Publications and source records attributed to Huang, Y..

At least 307 records · Page 17Linked to original sources

bioRxiv2025

Widespread distribution of the BpfA-carrying bacteria involved in the bisphenol F degradation in Pseudomonadota and Actinomycetota

The global use of bisphenol F (BPF) has led to widespread environmental contamination, posing significant threats to ecosystems and human health. However, the genes involved in BPF degradation remained unknown. In this study, a novel oxidase gene, bpfA, was obtained from strain Microbacterium sp. F2 through a four-step purification strategy. BpfA is classified as a member of the 4-phenol oxidizing (4PO) subfamily and contains a conserved FAD-binding domain (Asp152 and His393) as well as a Tyr-Tyr-Arg triad (Tyr93, Tyr474, Arg475). BpfA catalyzes the conversion of BPF to 4,4-dihydroxydibenzophenone (DHBP) through a series of three consecutive reactions. In addition, BpfA exhibits catalytic activity towards 4-alkylphenols, such as vanillyl alcohol (VA), 4-n-propylguaiacol (4PG), and 4-(methoxymethyl)phenol (4MOP). BpfA homologs are widely distributed in the environment, particularly in soil. Bioinformatics-based taxonomic profiling revealed that BpfA homologs are widely distributed in metagenomes from cultivated land and forests, mainly belonging to Pseudomonadota and Actinomycetota. This study enhances our understanding of the microbial degradation mechanism of BPF, elucidates the catalytic function of the novel oxidase gene bpfA and its distribution pattern in the environment, and provides important insights into the evolutionary origin of BPF degradation genes and the targeted mining of environmental microbial resources.

microbiology↗

bioRxiv2025

The XPF-like domain in SHOC1 required for homologous recombination and safeguarding autosome from meiotic silencing of unsynapsed chromatin

During meiosis, a group of evolutionarily conserved ZMM proteins plays essential roles in stabilizing the recombination intermediates and promoting crossover (CO) formation. In mice, SHOC1 forms a trimeric complex with the other two ZMM proteins, SPO16 and TEX11, to bind recombination intermediates after strand invasion. Although genetic variants of SHOC1 are clinically associated with meiotic arrest and male infertility, their precise molecular mechanisms and evolutionarily conserved functions in human gametogenesis remain enigmatic. Here, we delineated species-specific divergences between human and mouse SHOC1 complex, and identified a missense variant within the XPF-like domain in SHOC1 (c.A1769G:p.Q590R) that was associated with meiotic arrest and non-obstructive azoospermia (NOA). The disorder of the XPF-like domain in SHOC1 impaired DNA double-strand breaks repair by compromising its ability to bind branched DNA structures and the recruitment of M1AP, REDIC1, and ZMM factors to recombination intermediates, ultimately abolishing CO formation. Furthermore, the variant disrupted dynamic 3D chromatin structure in pachytene spermatocytes and induced defects in homologous chromosome synapsis. More importantly, the XPF-like domain in SHOC1 was revealed to prevent autosome intrusion into the sex body compartment, thereby safeguarding critical autosomal loci from meiotic silencing of unsynapsed chromatin (MSUC). Overall, our study demonstrated that the XPF-like domain in SHOC1 is required for homologous recombination and safeguarding autosome from MSUC in meiosis.

developmental biology↗

bioRxiv2025

Phylogenomics of Aristolochia subg. Siphisia (Aristolochiaceae) reveals widespread incomplete lineage sorting and supports a novel pollinator-filtering hypothesis

Aristolochia subgenus Siphisia constitutes a monophyletic lineage of predominantly lianescent species, with occasional shrubs or herbs, and is characterized by remarkable diversity in perianth morphology. Members of Siphisia serve as larval hosts for endangered Lepidoptera and are widely used in traditional medicine. Despite its ecological and ethnobotanical significance, Siphisia systematics remains unresolved due to limited genomic resources and insufficient phylogenetic signal across previously sampled loci. Here, we present a phylogenomically informed framework for Siphisia, integrating 46 newly collected accessions and seven public datasets across 44 taxa. Using genome skimming ([~]30x coverage) and HybPiper, we recovered Angiosperms353 nuclear loci, including supercontigs, for phylogenetic reconstruction via concatenation and coalescent approaches. The resulting species trees resolve seven strongly supported monophyletic clades, each defined by distinct biogeographic patterns and morphological synapomorphies. Comparative plastome analyses from de novo assemblies explored quadripartite structure, plastid phylogeny, GC content, and gene synteny. Cytonuclear discordance was concentrated in species-rich Asian clades, while hybridization signals were rare and limited to deep backbone nodes in North American lineages. These results indicate that incomplete lineage sorting, rather than introgression, accounts for most gene-species tree conflicts and likely reflects strong reproductive isolation following speciation. We also revise a previously taxonomically ambiguous complex--the now well-supported A. versicolor species group--based on integrated phylogenomic and morphological evidence. Within this group, we describe five previously unrecognized cryptic species and identify a novel pollination syndrome involving floral adaptations for pollinator filtering. This syndrome may contribute to prezygotic isolation and recent diversification, and it challenges the prevailing assumption that Aristolochia pollination is universally governed by a trapping-release mechanism--suggesting this model may not apply to subg. Siphisia.

evolutionary biology↗

bioRxiv2025

The mGluR5 Agonist, CHPG, Enhances Numbers of Differentiated Human Oligodendrocytes

Previous studies on adult mice indicate that the mGluR5 agonist 2-chloro-5-hydroxyphenyl glycine (CHPG), reduces cuprizone-elicited losses in myelin. This effect is partly mediated by CHPG binding to mGluR5 receptors on reactive astrocytes, triggering the release of brain derived neurotrophic factor (BDNF), which results in an increase in myelin, and alleviates behavioral deficits. However, it remains unclear whether CHPG has similar beneficial effects on human cells. To address this issue, we examined effects of CHPG on human cells using both human induced pluripotent stem cell (hiPSC)-derived oligodendrocytes and primary human fetal brain cells. Treatment of hiPSCs (30M, 5 days) or primary cells (30 M, 3 days) with CHPG increases the percent of MBP+O4+ mature oligodendrocytes relative to total O4+cells, without affecting survival. When effects of CHPG were evaluated on proliferating OPCs, effects on proliferation are observed. In contrast, when CHPG was evaluated in young oligodendrocytes, effects on proliferation were gone, suggesting that in this population CHPG is influencing differentiation. Interestingly, in contrast to observations in mice, mGluR5 expression in humans is localized on PDGFR+ oligodendrocyte precursor cells (OPCs) and O4+ immature oligodendrocytes, but not astrocytes. Moreover, using purified human OPC cultures, we show a direct effect of CHPG in enhanced differentiation. To identify potential cellular targets of CHPG in the adult human brain, we analyzed postmortem tissue from individuals with multiple sclerosis (MS) and healthy controls. In contrast to the hiPSCs or fetal cells, demyelinated white matter from MS patients showed elevated mGluR5 mRNA expression in astrocytes. Taken together, our findings suggest that CHPG enhances the differentiation of human OPCs during development through a mechanism distinct from that observed in adult cuprizone-treated mice. Moreover, astrocytes in MS pathology upregulate mGluR5, suggesting they may become responsive to CHPG under disease conditions.

neuroscience↗

bioRxiv2025

A lineage-specific heat-induced feedback loop controls HrcA to promote chlamydial fitness under stress

Bacterial stress responses rely on transcriptional regulation by sigma factors and repressors. In Chlamydia, which lacks a dedicated heat shock sigma factor, repressor HrcA limits chaperone gene expression under non-stressed conditions. While HrcA function may be enhanced by the chaperone GroESL in a positive feedback loop, here we identify a heat-induced negative feedback loop mediated by HagF, a protein unique to Chlamydiota and conserved across Chlamydia species. We show that HrcA represses hagF, but heat shock induces hagF expression, leading to HagF accumulation and binding to HrcA. Structural modeling and pulldown assays indicate that HagF blocks HrcA dimerization, impairing DNA binding. This relieves repression of the hrcA-grpE-dnaK operon and promotes secondary differentiation in the developmental cycle, enabling infectious elementary bodies to form under heat stress. Our findings reveal dual feedback regulation that tunes chaperone gene expression and illustrate how transcriptional repression can be modulated in a minimal-genome pathogen.

microbiology↗

bioRxiv2025

Marker genes for predicting cytokine release syndrome in vitro before CAR T cell infusion

Cytokine release syndrome (CRS) and neurotoxicity are common adverse events of the Chimeric antigen receptor (CAR) T cell therapy. Assessing the cytotoxicity associated biomarkers would be essential for therapy design to avoid developing severe toxicities. In this study, we re-analyzed previously published RNAseq results of CAR T cells before infusion and combined it with the clinical response post infusion. We observed that CAR T cells from patients who developed severe CRS displayed a higher expression of TCL6, HPCAL4, CCDC144B, and SIRPG, but lower levels of IL2, IL21, and HSPA1B when stimulated with anti-CAR19 idiotypic antibody in vitro. Interestingly, the upregulated gene SIRPG is positively correlated with CRS severity. In addition, without stimulation, CAR T cells from CRS group showed a higher levels of IFNAR1, IL7R, ZNF69, and USP32P1 but lower levels of CCL3, IL4, IL17A, IL23R, IL13, CD70, and IFNGR2. These results provided insights to evaluate the adverse events of CAR T products before treatments, which could be beneficial for designing therapy plans.

immunology↗

bioRxiv2025

Genetically Programmable Adhesive Protein Hydrogels for Sealing Perforating Corneal Trauma

The cornea, situated at the forefront of the eyeball, is often subjected to varying degrees of mechanical laceration injuries due to various traumatic incidents. Timely and precise suturing of corneal wounds to prevent the leakage of intraocular contents is a significant clinical challenge. Although some studies have attempted to use hydrogels to accurately cover corneal injuries, most of these hydrogels are only suitable for adhering to focal stromal defects that do not involve the corneal stroma. Here, a fully protein-based hydrogel, based on SpyTag-SpyCatcher chemistry, was investigated for repairing corneal perforating injury models in rats and rabbits. The hydrogel formation relies on covalent bonding between SpyTag (A) and SpyCatcher (B) under physiologically mild conditions, eliminating requirements for organic solvents, elevated temperatures, or photoactivation Notably, integration of recombinant mussel foot protein 3 (Mfp3) endowed the hydrogels with exceptional water-resistant adhesiveness, while maintaining their original mechanical properties and biocompatibility. This study demonstrates the great potential of Mfp hydrogels in the timely and precise repair of corneal perforating injuries in complex physicochemical environments. TeaserBioinspired protein hydrogel rapidly seals corneal perforations, minimizing scarring and inflammation without sutures in animal models.

bioengineering↗

bioRxiv2025

PSMtags improve peptide sequencing and throughput in sensitive proteomics

Mass spectrometry-based proteomics enables comprehensive characterization of protein abundance, function, and interactions. Label-free approaches are simple to implement but challenging to scale to thousands of samples per day. Multiplexed techniques, such as plexDIA, can address these limitations but remain restricted by the lack of mass tags optimized for data-independent acquisition (DIA) workflows. Here, we present a systematic approach screening a library of 576 compounds that identifies several small molecules that, when conjugated to peptides, improve their detection and sequence identification by mass spectrometry. The lead molecule, PSMtag, substantially increases the detection of fragment b-ions, which increases the confidence of sequence identification and enhances de novo sequencing. PSMtags allow 9-plexDIA, using only stable isotopes of carbon, oxygen and nitrogen. As a result, it allows simultaneously increasing proteome coverage and sample throughput for plexDIA workflows without compromising quantitative accuracy. We demonstrate 240 samples-per-day with 9-plexDIA, while acquiring 28,359 protein data points in the same time label-free methods acquire 4,340. Our approach constitutes an expandable framework for designing mass tags to overcome existing limitations in multiplexed proteomics and provides plexDIA reagents capable of analyzing over 1,000 samples per day when using 10 minute runs. By facilitating higher throughput and improved identification, this innovation holds significant potential for accelerating proteomic studies across diverse biological and clinical applications.

bioengineering↗

bioRxiv2025

Bridging Scales: Spectral Theory Reveals How Local Connectivity Rules Sculpt Global Neural Dynamics in Spatially Extended Networks

The brains diverse spatiotemporal activity patterns are fundamental to cognition and consciousness, yet how these macroscopic dynamics emerge from microscopic neural circuitry remains a critical challenge. We address this by developing a spatially extended neural network model integrated with a spectral theory of its connectivity matrix. Our theory quantitatively demonstrates how local structural parameters, such as E/I neuron projection ranges, connection strengths, and density determine distinct features of the eigenvalue spectrum, specifically outlier eigenvalues and a bulk disk. These spectral signatures, in turn, precisely predict the networks emergent global dynamical regime, encompassing asynchronous states, synchronous states, oscillations, localized activity bumps, traveling waves, and chaos. Motivated by observations of shifting cortical dynamics in mice across arousal states, our framework not only explains this repertoire of behaviors but also offers a principled approach to inferring underlying effective connectivity changes from macroscopic brain activity. By mechanistically linking neural structure to dynamics, this work provides a powerful tool for understanding brain function and paves the way for identifying potential biomarkers for neurological disorders.

biophysics↗

bioRxiv2025

Scaled multidimensional assays of variant effect identify sequence-function relationships in hypertrophic cardiomyopathy

BackgroundAn estimated 1 in 500 people live with hypertrophic cardiomyopathy (HCM), a disease for which genetic diagnosis can identify family members at risk, and increasingly guide therapy. Mutations in the myosin binding protein C3 (MYBPC3) gene account for a significant proportion of HCM cases. However, many of these variants are classified as variants of uncertain significance (VUS), complicating clinical decision-making. Scalable methods for variant interpretation in disease-specific cell types are crucial for understanding variant impact and uncovering disease mechanisms. MethodsWe developed a scaled multidimensional mapping strategy to evaluate the functional impact of variants across a critical domain of MYBPC3. We incorporate saturation base editing at the native MYBPC3 locus, a long-read RNA sequencing-enabled assay of variant splice effects, and measurements of HCM-relevant phenotypes, including MYBPC3 abundance, hypertrophic signaling, and ubiquitin-proteasome function in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). ResultsOur multidimensional mapping strategy enabled high-resolution functional analysis of MYBPC3 variants in iPSC-CMs. Targeted transient base editing generated a comprehensive variant library at the native locus, capturing diverse variant effects on cellular HCM-relevant phenotypes. Our massively parallel splicing assay identified novel splice-disrupting variants. Integration of functional assays revealed that decreased MYBPC3 abundance is a key driver of HCM-related phenotypes. In parallel, downregulation of protein degradation was observed as a compensatory response to MYBPC3 loss of function, and novel disease mechanisms were identified for missense variants near a critical binding domain, underscoring their contribution to pathogenesis. Bayesian estimates of variant effects enable the reclassification of clinical variants. ConclusionsThis work provides a platform for extending genome engineering in iPSCs to multiplexed assays of variant effects across diverse disease-relevant cellular phenotypes, enhancing the understanding of variant pathogenicity and uncovering novel biological mechanisms that could inform therapeutic strategies.

genetics↗

bioRxiv2025

Scaling law links plant growth variation to grain yield in wheat stands

Growth rate, a fundamental biological trait influencing plant resource use, scales predictably with plant mass, following remarkably consistent allometric power laws shaped by biophysical constraints and natural selection. However, how these laws apply to crop plants shaped by artificial selection, and how they manifest in agronomic traits, remains undefined. Under controlled greenhouse conditions, we quantified the relationship between plant mass and growth rate in 195 European winter wheat cultivars. We uncovered genetic variation in allometry linked to plant size, where increased leaf allocation and faster development elevated allometric exponents. Phenotypic and genetic analyses revealed adaptive strategies, ranging from large, slow-growing genotypes that support reproductive initiation to small, fast-growing genotypes that enhance reproductive effort. A shared genetic basis--associated with Photoperiod response-1 (Ppd-1)--linked growth allometry in the greenhouse to genotype-by-environment interactions for grain yield in field trials. This variation in growth allometry, shaped by breeding in diverse environments, reflects strategies that enhance adaptation to weather conditions. Our findings demonstrate that growth allometry is biologically robust and agronomically important because it scales to wheat yield under diverse, realistic field conditions.

plant biology↗

bioRxiv2025

Testicular mRNA-LNP Delivery: A Novel Therapy for Genetic Spermatogenic Disorders

Uniform testicular maturation arrest is a severe form of male infertility characterized by the presence of germ cells that do not complete spermatogenic development. It is usually caused by meiotic arrest with genetic variants and difficult to treat via drugs or surgery. mRNA-lipid nanoparticle (LNP) delivery is a promising therapeutic option for maturation arrest with monogenic variants via protein replacement therapy. Herein, a spermatocytes-tropic LNP (Pool1-LNP3) was identified via a library of 30 ionizable lipids screening. And in vivo delivery of this novel LNP composition using rete testis microinjection was showed to be high spermatocytes targeting with high transfection efficiency. Thereafter, it was revealed that in vivo delivery of Pool1-LNP3 encapsulating Msh5 mRNA could promote crossover formation and restore spermatogenesis in Msh5D486Y/D486Y mouse models with DSB recombination defects. Notably, the offspring without genomic integration was born using intracytoplasmic sperm injection (ICSI) derived from rescue of Msh5D486Y/D486Ymouse and embryo transfer. Furthermore, no obvious inflammation and histologic damage in any tissue were detected after in vivo delivery of mRNA-LNP. In addition, it was demonstrated that Maps mRNA-LNP3 recovered spermatogenesis in Maps KO mouse with meiotic arrest. Altogether, these findings suggested that this spermatocytes-tropic mRNA-LNP delivery could become a viable and broad applicable strategy for treatment of spermatogenic disorders with genetic defects, providing a foundation for future clinical application.

molecular biology↗

bioRxiv2025

Aligning Neural Population Patterns Facilitates Motor Learning Transfer

Motor learning transfer, the ability to apply skills acquired in one task to enhance performance in a related task, is driven by changes in neural ensemble activities. However, the long-term evolution of neural population dynamics during motor learning transfer remains unclear. Specifically, how do the neural patterns reorganize and stabilize over an extended learning period in the new task? To investigate the neural mechanisms in the motor cortex that enable such transfer, we employed a Brain-Machine Interface (BMI) paradigm in rats. In the experiment, rats first mastered a lever-pressing task before proceeding to a more complex but related lever-discrimination task. We analyzed neural ensemble activities by projecting them into a low-dimensional linear feature space that captures the most prominent dynamic structure. Within this space, we represented neural patterns as clusters and developed an iterative method to align similar clusters between the two tasks. Leveraging this alignment, we introduced a novel decoding approach, Clustering Alignment-based Transfer on Kernel Reinforcement Learning (CATKRL), which utilizes parameters learned from the initial task to enhance efficiency in the new task. Our results revealed that neural patterns for learned actions form distinct clusters with consistent shapes and centroid distances across tasks, and these patterns exhibit rotational evolution during learning. By integrating the cluster alignment mechanism into the RL decoder, we achieved a faster training speed with less data in the lever-discrimination task. Our results suggest that aligning neural pattern clusters can enhance BMI decoding efficiency by leveraging consistent neural representations. This approach not only provides valuable insights into the brain mechanisms underlying motor learning transfer but also holds promise for advancing multi-task learning in neuroprosthetics.

neuroscience↗

bioRxiv2025

Bona fide hematopoietic stem cells in zebrafish originate from the supra-intestinal artery

Hematopoietic stem cells (HSCs) in vertebrates are widely believed to originate from hemogenic endothelial cells (HECs) in the dorsal aorta (DA) through endothelial-to-hematopoietic transition. However, conclusive in vivo DA-specific lineage-tracing studies to confirm this origin are lacking. Here, leveraging infrared light-mediated temporospatial-resolution lineage-tracing technology, we demonstrate that in zebrafish, HSCs do not originate from the DA. Instead, following the DA hematopoiesis, which produces hematopoietic precursors with limited renewal potential, lifelong renewable HSCs emerge from the supra-intestinal artery (SIA). Remarkably, while the DA produces hematopoietic cells from unipotent HECs, the SIA generates hematopoietic cells from both unipotent HECs and bipotent vessel-resident hemangioblasts (VRHs). These VRHs undergo multiple rounds of division and budding, generating both hematopoietic cells and SIA-resident endothelial cells. The distinct characteristics of DA and SIA cells are further reinforced by single-cell transcriptomic profiling. Our findings challenge the current paradigm of HSC development, underscoring the complexity of vertebrate hematopoiesis.

developmental biology↗

bioRxiv2025

Deep Blood Proteomics Identifies over 12,000 Proteins Providing Valuable Information about the State of the Human Body

Blood is a valuable resource for clinical research, offering insight into physiological and pathological states. However, the specific proteins detectable in blood and the optimal proteomic methods for their detection have not been rigorously investigated and documented. To address this, we conducted various blood proteomic strategies, including directly blood proteomic analysis, high-abundance protein depletion, low-abundance protein enrichment, and extracellular vesicle enrichment using data-independent acquisition or targeted proteomics. These approaches identified 11,679 protein groups in plasma from healthy individuals. In 136 pancreatic ductal adenocarcinoma whole blood samples, 6,956 protein groups were found, including 678 not seen in healthy samples, expanding the total to 12,357 blood proteins. This represents the most comprehensive blood proteome to date. To support broader access and analysis, we developed the Human Blood Proteome (HuBP) database, detailing protein detectability, abundance, and reproducibility across workflows, sample types, and disease contexts.

systems biology↗

bioRxiv2025

Lipid nanoparticle-mediated CRISPR/Cas9 delivery enables efficient trabecular meshwork gene editing in mice

Lipid nanoparticles (LNPs) have emerged as a transformative platform for mRNA delivery, enabling vaccines and gene editing with transient expression and high cargo capacity. However, their potential for ocular gene editing remains underexplored. In this study, we assessed the transduction efficiency, inflammatory response, and gene editing capability of LNP-encapsulated mRNA in murine eyes. Intravitreal delivery of LNPs achieved targeted mRNA expression in the trabecular meshwork (TM) with superior specificity and efficiency compared to adenoviral or adeno-associated viral vectors, while inducing minimal microglial activation in the retina. Using LNPs co-encapsulating SpCas9 mRNA and sgRNA, we demonstrated efficient CRISPR-mediated knockout (KO) of Matrix Gla Protein (Mgp), a key inhibitor of TM calcification. Mgp-KO eyes exhibited sustained intraocular pressure (IOP) elevation and anterior chamber deepening with normal anterior chamber angle, recapitulating key features of primary open-angle glaucoma (POAG). Chronic IOP elevation led to reactive Muller gliosis and ganglion cell complex thinning, reflecting retinal stress and progressive neurodegeneration. Our findings establish LNP-CRISPR as a safe and efficient system for TM-targeted gene editing, with broad applicability in glaucoma pathogenesis modelling and therapeutic discovery.

neuroscience↗

bioRxiv2025

scDenorm: a denormalisation tool for integrating single-cell transcriptomics data

Integrating single-cell omics data at an atlas scale enhances our understanding of cell types and disease mechanisms. However, the integration of data processed by different normalisation methods can lead to biases, such as unexpected batch effects and gene expression distortion, leading to misinterpretations in downstream analysis. To address these challenges, we present scDenorm, an algorithm that reverts normalised single-cell omics data to raw counts, preserving the integrity of the original measurements and ensuring consistent data processing during integration. We evaluated scDenorms performance on large-scale datasets and benchmarked its impact on data integration and downstream analysis across three datasets.

bioinformatics↗

bioRxiv2025

Generative AI-driven artificial DNA design for enhancing inter-species gene activation and enzymatic degradation of PET

Conventional approaches to heterologous gene expression rely on codon optimization, which is limited to swapping synonymous codons and often fails to capture deeper adaptive changes. In contrast, naturally evolved orthologous genes between species often differ by more than just synonymous substitutions - they can include non-synonymous mutations, insertions, and deletions that confer functional adaptation to different host contexts. Here we present OrthologTransformer, a Transformer-based deep learning model that converts orthologous genes between species by learning from large-scale orthologous gene datasets curated for high-quality sequence alignments. The model recapitulates the full spectrum of evolutionary differences - from synonymous codon swaps to amino acid-changing mutations and indels - to predict a coding sequence optimized for a target species while preserving the proteins function. In extensive validation across diverse bacterial species pairs, OrthologTransformer significantly increased the conversion accuracy of generated genes to native target sequences compared to the original source genes, even for pairs with stark disparities in GC content and optimal growth temperature. The Transformers context-aware designs also favored conservative amino acid substitutions, maintaining protein functional integrity. As a proof-of-concept, an OrthologTransformer-designed PETase gene for Bacillus subtilis from the host species Ideonella sakaiensis was synthesized and expressed, yielding robust PET plastic-degradation activity that surpassed synonymous codon-optimized controls. These results establish OrthologTransformer as a powerful tool for de novo cross-species gene adaptation, transcending the limits of traditional codon optimization and enabling more effective heterologous gene performance in synthetic biology applications.

bioinformatics↗