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Yan, J.

Publications and source records attributed to Yan, J..

At least 145 records · Page 8Linked to original sources

Hoi1 targets the yeast BLTP2 protein to ER-PM contact sites to regulate lipid homeostasis

Membrane contact sites between organelles are important for maintaining cellular lipid homeostasis. Members of the recently identified family of bridge-like lipid transfer proteins (BLTPs) span opposing membranes at these contact sites to enable the rapid transfer of bulk lipids between organelles. While the VPS13 and ATG2 family members use organelle-specific adaptors for membrane targeting, the mechanisms that regulate other bridge-like transporters remain unknown. Here, we identify the conserved protein Ybl086c, which we name Hoi1 (Hob interactor 1), as an adaptor that targets the yeast BLTP2-like proteins Fmp27/Hob1 and Hob2 to ER-PM contact sites. Two separate Hoi1 domains interface with alpha-helical projections that decorate the central hydrophobic channel on Fmp27, and loss of these interactions disrupts cellular sterol homeostasis. The mutant phenotypes of BLTP2 and HOI1 orthologs indicate these proteins act in a shared pathway in worms and flies. Together, this suggests that Hoi1-mediated recruitment of BLTP2-like proteins represents an evolutionarily conserved mechanism for regulating lipid transport at membrane contact sites.

cell biology↗

Unveiling Cognitive Processes in Mice through Reinforcement Learning Models in the FST and TST

Simple behavioral tests like the forced swim test (FST) and tail suspension test (TST) are widely used to assess depression-like behaviors in rodents, primarily measuring immobility time. However, this approach oversimplifies behavioral readouts and overlooks the cognitive processes driving behavior, leaving the relationship between increased immobility and cognitive biases unclear. Here, we developed the SwimStruggleTracker (SST) to extract fine-grained behavioral trajectories and integrate computational modeling to methodically analyze behavior. Our findings reveal that behavior in the FST and TST follows reinforcement learning principles involving learning, consequence perception, and decision-making. Notably, the cognitive processes underlying behavior differ between the two tests, challenging the assumption that they are interchangeable for cross-validation. Regression analyses identify distinct behavior phases: early behavior is primarily influenced by learning-related factors, while later stages are more affected by consequence sensitivity. These findings suggest traditional analyses focusing final minutes may underestimate the role of learning and overemphasize consequence sensitivity. MotivationThe forced swim test (FST) and tail suspension test (TST) are among the most widely used paradigms for assessing depression-like behaviors in rodents. Yet, traditional analyses typically quantify only immobility during the final minutes, discarding rich temporal structure in the data and hindering efforts to uncover the cognitive mechanisms underlying these behaviors. To address this gap, we developed an automated tool that captures behavioral trajectories with fine temporal resolution and integrates computational modeling to dissect the cognitive processes driving behavior. Using this approach, we demonstrate that the FST and TST engage overlapping but partially distinct cognitive processes, and that the dominant cognitive components shift across different stages of the tests. HighlightsO_LISwimStruggleTracker (SST) accurately rejects passive movements, such as pendulum-like motion. C_LIO_LIReinforcement learning models capture the behavioral dynamics of mice in the FST and TST. C_LIO_LIDistinct winning models indicate that the FST and TST engage partially dissociable cognitive processes. C_LIO_LILearning factors dominate early stages, whereas consequence-sensitivity factors dominate later stages. C_LI

animal behavior and cognition↗

TOC1 phosphorylation disproportionally enhances chromatin binding at rhythmic gene promoters

Protein phosphorylation is a key regulatory mechanism in circadian systems. TIMING OF CAB EXPRESSION 1(TOC1) is a core transcriptional repressor in the plant circadian system that is phosphorylated near its N-terminus. Phenotype testing of single and multi-phosphosite mutants shows incomplete rescue of the short period toc1 mutant. We establish that TOC1 phosphorylation (particularly at S175) is necessary for optimal interaction with FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and PHYTOCHROME INTERACTING FACTOR 5 (PIF5) at the CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) promoter to downregulate CCA1 expression. At the same time, expression of the closely related LATE ELONGATED HYPOCOTYL (LHY) also requires TOC1, but is independent of the TOC1 phosphorylation state, suggesting different TOC1-dependent mechanisms in the repression of these two genes. We additionally show how phosphorylation-dependent interactions of TOC1 at specific clock gene promoters selectively regulate these circadian system components more acutely than non-rhythmic genes. Our genome-wide analysis shows that the phosphostate of TOC1 is important for optimal chromatin presence and robust rhythmic gene expression.

plant biology↗

Nematode-Trapping Fungus Arthrobotrys oligospora is Hungry for COQ7 to Alleviate Environmentally Triggered Iron Overload

Choosing the right and appropriate amount of substances in a changing environment is essential for the growth and survival of all species. We found that elevated oxygen levels significantly enhanced the iron-rich trapping devices of a nematode-trapping fungus (NTF), Arthrobotrys oligospora. Interestingly, genomic analysis revealed that all NTFs lacked coq7, a key gene involved in ubiquinol (UQ) biosynthesis and iron chelation. Notably, A. oligospora utilizes UQ instead of UQ for low-aerobic respiration. Transcriptional, metabolic, mutational, and phenotypic analyses revealed that A. oligospora produces a chemotaxonomic class of highly oxygenated arthrobotrins with characteristics similar to UQ skeleton, for high-aerobic respiration. Disruption of arthrobotrin biosynthesis in the {Delta}art mutant not only enhanced UQ biosynthesis, but also triggered trapping device formation and nematicidal activity under elevated oxygen conditions. The addition of UQ to both wild-type and {Delta}art mutants strongly inhibited trapping device development. Remarkably, the iron-rich trapping devices preferentially capture N2 nematodes harboring iron-chelating COQ7 with ferritin properties. Time-calibrated evolutionary analyses, combined with geological data, indicated that the NTF ancestor lost the coq7 gene after acquiring the arthrobotrin biosynthetic gene cluster during the "superoligotrophy" period, characterized by dramatic shifts in global oxygen levels and temperature changes. Our results demonstrate that oxygen is a critical factor in inducing iron overload, highlighting the origin and role of coq7 loss in the evolution of predatory behavior of NTFs. Our finding that NTFs capture nematodes for iron chelation therapy, rather than for food, explains a long standing debate about the limited carnivorous ability of trapping devices.

microbiology↗

Discovery of NANOG enhancers and their essential roles in self-renewal and differentiation in human embryonic stem cells

Human embryonic stem cells (hESCs) are notable for their ability to self-renew and to differentiate into all tissue types in the body. NANOG is a core regulator of hESC identity, and dynamic control of its expression is crucial to maintain the balance between self-renewal and differentiation. Transcriptional regulation depends on enhancers, but NANOG enhancers in hESCs are not well characterized. Here we report two NANOG enhancers discovered from a CRISPR interference screen in hESCs. Deletion of a single copy of either enhancer significantly reduced NANOG expression, compromising self-renewal and increasing differentiation propensity. Interestingly, these two NANOG enhancers are involved in a tandem duplication event found in certain primates including humans but not in mice. However, the duplicated counterparts do not regulate NANOG expression. This work expands our knowledge of functional enhancers in hESCs, and highlights the sensitivity of the hESC state to the dosage of core regulators and their enhancers.

developmental biology↗

Restoration of PKM1 improves functional maturation of human stem-cell derived-β cell by regulating PEP metabolism

Human stem cell-derived {beta} (SC-{beta}) cells still exhibit limited glucose response required for insulin secretion due to glycolytic bottlenecks, yet how these metabolic abnormalities impact glucose response and functional maturation of SC-{beta} cells remains unclear. In this study, we identified a metabolic checkpoint located at PEP accumulation that impeded the functional maturation, which was rescued by restoration of pyruvate kinase 1 (PKM1). Glucose-tracing metabolomics in human stem cell-derived islets revealed abnormal glycolytic PEP accumulation at resting condition, resulting in impaired calcium response and insulin secretion upon high glucose or glycolytic metabolite stimulation. Mechanistically, elevated PEP significantly raised intracellular basal calcium levels, leading to downregulated expression of genes involved in TCA cycle elucidated by single cell transcriptomics. Furthermore, the activity of pyruvate kinase, which metabolizes PEP, was notably reduced due to low PKM1 expression. By overexpressing PKM1, the impairment of TCA-related genes caused by PEP accumulation was reversed via modulating PEP metabolism, resulting in enhanced calcium responses and insulin secretion upon high glucose stimulation. Together, we discovered a novel role of PKM1-regulated PEP metabolism in mediating the functional maturation of human SC-{beta} cells. This study highlights the importance of metabolic reprogramming in human SC-{beta} cell maturation, advancing cell therapy approaches for diabetes treatment.

cell biology↗

Multi-view BLUP: a promising solution for post-omics data integrative prediction

Phenotype prediction is a promising strategy for accelerating molecular plant breeding. Data from multiple sources (called multi-view data) can provide complementary information to characterize a biological object from various aspects. By integrating multi-view information into phenotype prediction, a multi-view best linear unbiased prediction (MVBLUP) method was proposed in this paper. By assigning different weights to measure the importance of different views of data and using a differential evolution algorithm with an early stopping mechanism to adjust the weight vector adaptively, a multi-view kinship matrix was obtained first and then incorporated into the BLUP model for phenotype prediction. To validate the efficiency of MVBLUP, we conducted numerical experiments on four multi-view datasets. Compared to the average performance of the single-view method, the prediction accuracy of the MVBLUP method has improved by a range of 0.038 to 0.201.The results demonstrate that the MVBLUP model is an effective method of integrating multi-view data.

genetics↗

Surface remodeling and inversion of cell-matrix interactions underlies community recognition and dispersal in Vibrio cholerae biofilms

Biofilms are ubiquitous surface-associated bacterial communities embedded in an extracellular matrix. While it is commonly assumed that biofilm-dwelling cells are glued together by the matrix, how the cell-matrix interaction depends on the specific biochemistry of the matrix components and how this interaction varies during biofilm growth remains unclear. Here, we investigated cell-matrix interactions in Vibrio cholerae (Vc), the causative agent of cholera. We combine genetics, microscopy, simulation, and biochemical tools to show that Vc cells are not attractive to Vibrio polysaccharide (VPS), the main matrix component, but they can be bridged with each other and to the VPS network through crosslinking by Bap1. Downregulation of VPS and surface trimming by the polysaccharide lyase RbmB cause surface remodeling as biofilms age, shifting the nature of cell-matrix interactions from attractive to repulsive and facilitating cell dispersal as aggregated groups. Our results suggest a new conceptual model in understanding the intricate cell-matrix interaction as the major driver for biofilm development, which is potentially generalizable to certain other biofilm-forming species and exopolysaccharides.

biophysics↗

Pan-cistrome analysis of the leaf accessible chromatin regions of 214 maize inbred lines

Characterizing the noncoding regions of the genome, particularly the cis-regulatory elements (CREs) located in accessible chromatin regions (ACRs) in gene promoters, is crucial for understanding how gene expression is regulated and how genotype contributes to phenotypic diversity in plants.In this study, we used ATAC-seq to resequence and map the ACRs of 214 maize inbred lines. We identified 82,174 ACRs and reported that 39.55% of them exhibited significant variation across the population. Next, we used the accessibility of ACRs as a quantitative feature and performed a chromatin associability GWAS (caGWAS), resulting in 27,004 caQTLs. Among them, 2,463 were predicted to disrupt the cis-regulatory elements that TF binds in these ACRs, suggesting that TF binding affects chromatin accessibility. Specifically, we identified two caACRs that regulate the expression of fad7, which encodes a fatty acid desaturase and affects the linolenic acid content.Our findings highlight the dynamic nature of maize ACRs and demonstrate that chromatin accessibility information could be used for GWASs, offering key insights into the genetic and regulatory mechanisms of chromatin accessibility and its impact on complex traits in plants.

genomics↗

B cell c-Maf signaling promotes tumor progression in animal models of pancreatic cancer and melanoma

BackgroundThe role of B cells in anti-tumor immunity remains controversial, with studies suggesting the pro-tumor and anti-tumor activity. This controversy may be due to the heterogeneity in B cell populations, as the balance among the subtypes may impact tumor progression. The immunosuppressive regulatory B cells (Breg) release IL-10 but only represent a minor population. Additionally, tumor-specific antibodies (Ab) also exhibit anti-tumor and pro-tumor function dependent on the Ab isotype. Transcription factor c-Maf has been suggested to contribute to the regulation of IL-10 in Breg, but the role of B cell c-Maf signaling in anti-tumor immunity and regulating antibody responses remain unknown. MethodsConditional B cell c-Maf knockout (KO) and control mice were used to establish a KPC pancreatic cancer model and B16.F10 melanoma model. Tumor progression was evaluated. B cell and T cell phenotypes were determined by flow cytometry, mass cytometry, and cytokine/chemokine profiling. Differentially expressed genes in B cells were examined by using RNA-seq. Peripheral blood samples were collected from healthy donors and melanoma patients for B cell phenotyping. ResultsCompared to B cells from spleen and lymph nodes, B cells in the pancreas exhibited significantly less follicular phenotype and higher IL-10 production in naive mice. c-Maf deficiency resulted in a significant reduction of CD9+ IL-10-producing Breg in the pancreas. PDAC progression resulted in accumulation of circulating B cells with follicular phenotype and less IL-10 production in the pancreas. Notably, B cell c-Maf deficiency delayed PDAC tumor progression and resulted in pro-inflammatory B cells. Further, tumor volume reduction and increased effective T cells in the tumor-draining lymph node (TDLN) were observed in B cell c-Maf KO mice in the B16.F10 melanoma model. RNA-seq analysis of isolated B cells revealed that B cell c-Maf signaling modulates immunoglobulin (Ig)-associated genes and tumor specific antibody production. We furthermore demonstrated c-Maf-positive B cell subsets and increase of IL-10-producing B cells after incubation with IL-4 and CD40L in the peripheral blood of melanoma patients. ConclusionOur study highlights that B cell c-Maf signaling drives tumor progression through the modulation of Breg, inflammatory responses, and tumor-specific Ab responses. What is already known on this topicThe net effect of B cells on tumor immunity depends on the balance of various B cell subtypes. c-Maf has been suggested to contribute to the regulation of IL-10 in regulatory B cells (Breg), but the role of B cell c-Maf signaling in anti-tumor immunity remains unknown. What this study addsThis study shown that B cell c-Maf signaling drives tumor progression in pancreatic cancer and melanoma. We defined different anti-tumor mechanisms of B cell c-Maf deficiency in two tumor models. Specifically, c-Maf signaling modulates the pro-inflammatory phenotype of B cells in the KPC tumor-bearing pancreas and tumor-specific antibody responses in tumor draining lymph nodes (TDLN) of melanoma. How this study might affect research, practice or policyThese studies indicate that inhibition of c-Maf signaling is a novel and promising approach for immunotherapy in pancreatic cancer and melanoma.

immunology↗

Sustained exposure to multivalent antigen-decorated nanoparticles generates broad anti-coronavirus responses

The threat of future coronavirus pandemics requires developing cost-effective vaccine technologies that provide broad and long-lasting protection against diverse circulating and emerging strains. Here we report a multivalent liposomal hydrogel depot vaccine technology comprising the receptor binding domain (RBD) of up to four relevant SARS and MERS coronavirus strains non-covalently displayed on the surface of the liposomes within the hydrogel structure. The multivalent presentation and sustained exposure of RBD antigens improved the potency, neutralizing activity, durability, and consistency of antibody responses across homologous and heterologous coronavirus strains in a naive murine model. When administrated in animals previously exposed to the wild-type SARS-CoV-2 antigens, liposomal hydrogels elicited durable antibody responses against the homologous SARS and MERS strains for over 6 months and elicited neutralizing activity against the immune-evasive SARS-CoV-2 variant Omicron BA.4/BA.5. Overall, the tunable antigen-decorated liposomal hydrogel platform we report here generates robust and durable humoral responses across diverse coronaviruses, supporting global efforts to effectively respond to future viral outbreaks. Progress and PotentialRapidly mutating infectious diseases such as influenza, HIV, and COVID-19 pose serious threats to human health. Yet, most vaccines still do not mount durable protection against mutagenic viruses and fail to induce broad responses to protect against emergent strains. Materials approaches to vaccine design, such as employing sustained delivery approaches or decorating nanoparticle constructs with multiple antigens, have shown promise in improving the breadth and potency of vaccines. Yet, these approaches typically require cumbersome chemistries and have not been explored in pre-exposed populations over clinically relevant time scales. Here, we report the development of an injectable liposomal hydrogel depot technology capable of prolonged presentation of multiple coronavirus antigens non-covalently coordinated on the surface of the liposomes forming the hydrogel structure. These hydrogels improve the potency, durability and breadth of vaccine response and are easy to fabricate, enabling the rapid design of next generation vaccines that confer protection against rapidly evolving pandemics.

bioengineering↗

Achieving Single Cell Acoustic Localisation with Deactivation Super Resolution

Super-resolution optical microscopy enables optical imaging of cells, molecules and other biological structures beyond the diffraction limit. However, no similar method exists to super-resolve specific cells with ultrasound. Here we introduce Deactivation Super Resolution (DSR), an ultrasound imaging method that uses the acoustic deactivation of genetically encodable contrast agents to super-resolve individual cells with ultrasound as they navigate through structures that cannot be resolved by conventional imaging methods. DSR takes advantage of gas vesicles, which are air-filled sub-micron protein particles that can be expressed in genetically engineered cells to produce ultrasound contrast. Our experimental results show that DSR can distinguish sub-wavelength microstructures that standard B-mode ultrasound images fail to resolve by super- localizing individual mammalian cells. This study provides a proof of concept for the potential of DSR to serve as a super- resolution ultrasound technique for individual cell localization, opening new horizons in the field.

bioengineering↗

Vibrio cholerae RbmB is an α-1,4-polysaccharide lyase with biofilm-dispersal activity against Vibrio Polysaccharide (VPS)

Many pathogenic bacteria form biofilms as a protective measure against environmental and host hazards. The underlying structure of the biofilm matrix consists of secreted macromolecules, usually including exopolysaccharides. To escape the biofilm, bacteria may produce a number of matrix-degrading enzymes, including glycosidic enzymes that digest exopolysaccharide scaffolds. The human pathogen Vibrio cholerae assembles and secretes an exopolysaccharide called VPS (Vibrio polysaccharide) which is essential in most cases for the formation of biofilms and consists of a repeating tetrasaccharide unit. Previous studies have indicated that a secreted glycosidase called RbmB is involved in Vibrio cholerae biofilm dispersal, although the mechanism by which this occurs is not understood. To approach the question of RbmB function, we recombinantly expressed and purified RbmB and tested its activity against purified VPS. Using a fluorescence-based biochemical assay, we show that RbmB specifically cleaves VPS in vitro under physiological conditions. Analysis of the cleavage products using mass spectrometry, solid-state NMR, and solution NMR indicates that RbmB cleaves VPS at a specific site (at the -1,4 linkage between D-galactose and a modified L-guluronic acid) into a mixture of tetramers and octamers. We demonstrate that the product of the cleavage contains a double bond in the modified-guluronic acid ring, strongly suggesting that RbmB is cleaving using a glycoside lyase mechanism. Finally, we show that recombinant RbmB from Vibrio cholerae and the related aquatic species Vibrio coralliilyticus are both able to disperse living Vibrio cholerae biofilms. Our results support the role of RbmB as a polysaccharide lyase involved in biofilm dispersal as well as an additional glycolytic enzyme to add to the toolbox of potential therapeutic antibacterial enzymes. Author summaryBiofilms are protective sheaths produced by many bacteria that play important roles in survival in the environment and in hosts during infection. Understanding how biofilms form and disperse is essential in the fight against harmful bacterial pathogens. Vibrio cholerae is a historically significant human pathogen that forms biofilms made of a polysaccharide called VPS and secreted accessory proteins. Within the V. cholerae biofilm gene cluster is a gene encoding a protein called RbmB, which is known to play a role in biofilm dispersal. Using a combination of biochemical and analytical tools, we show that RbmB indeed cleaves VPS into 4- and 8-monosaccharide fragments at a unique site and demonstrate that it falls into the family of polysaccharide lyase enzymes (as opposed to the more common hydrolases). Furthermore, recombinant RbmB disperses living V. cholerae biofilms further indicating that it may play a role in VPS processing or degradation.

biochemistry↗

Comprehensive Genomic and Evolutionary Analysis of Biofilm Matrix Clusters and Proteins in the Vibrio Genus

Vibrio cholerae pathogens cause cholera, an acute diarrheal disease resulting in significant morbidity and mortality worldwide. Biofilms in vibrios enhance their survival in natural ecosystems and facilitate transmission during cholera outbreaks. Critical components of the biofilm matrix include the Vibrio polysaccharides produced by the vps-1 and vps-2 gene clusters and the biofilm matrix proteins encoded in the rbm gene cluster, together comprising the biofilm matrix cluster. However, the biofilm matrix clusters and their evolutionary patterns in other Vibrio species remain underexplored. In this study, we systematically investigated the distribution, diversity, and evolution of biofilm matrix clusters and proteins across the Vibrio genus. Our findings reveal that these gene clusters are sporadically distributed throughout the genus, even appearing in species phylogenetically distant from V. cholerae. Evolutionary analysis of the major biofilm matrix proteins RbmC and Bap1 shows that they are structurally and sequentially related, having undergone structural domain and modular alterations. Additionally, a novel loop-less Bap1 variant was identified, predominantly represented in two phylogenetically distant Vibrio cholerae subspecies clades that share specific gene groups associated with the presence or absence of the protein. Furthermore, our analysis revealed that rbmB, a gene involved in biofilm dispersal, shares a recent common ancestor with Vibriophage tail proteins, suggesting that phages may mimic host functions to evade biofilm-associated defenses. Our study offers a foundational understanding of the diversity and evolution of biofilm matrix clusters in vibrios, laying the groundwork for future biofilm engineering through genetic modification.

evolutionary biology↗

Trapping Devices of Carnivorous Fungus Arthrobotrys oligospora Can Isolate Heat-Triggered Excess Irons

Under low-nutrient conditions, Arthrobotrys oligospora and other NTFs can differentiate their mycelia into specialized trapping devices for capturing prey as their nutritional source. Using energy-dispersive X-ray spectroscopy (EDX) in conjunction with transmission electron microscopy (TEM), we identified that the characteristic electron-dense bodies in trapping devices contained more iron than vacuoles and mitochondria. Meanwhile, fungal mycelial cells used effective desferriferrichromes for iron chelation and storage. Complex bioassays showed that electron-dense bodies represent a novel type of microbial iron storage particle and trapping devices in A. oligospora function as an unprecedented phenotypic system for iron storage. Unexpectedly, all NTFs lack a crucial Ccc1-mediated vacuolar iron detoxification mechanism, which is conserved in most fungi. Inserting the Ccc1 gene cloned from yeast into A. oligospora significantly reduced formation of trapping devices and inhibited nematicidal activity. Notably, Bayesian relaxed molecular clock analysis indicated that the loss of Ccc1-mediated vacuolar iron storage occurred during the Late Paleozoic Ice Age, while the origin of the trapping devices and the acquisition of desferriferrichrome biosynthesis were strongly associated with significantly elevated temperatures. Temperature bioassays demonstrated that the formation of trapping devices is highly temperature-dependent, with free iron content in mycelial cells being inversely proportional to temperature, consistent with that A. oligospora is sensitive to high temperatures and fails to grow above 30{degrees}C. Our findings revealed that global temperature fluctuations are a crucial driver of the genetic evolution of NTFs, as a catalyst for the origin of trapping devices, which are a novel phenotypic indicator of eukaryotic iron overload. Author summaryWe found that a unique group of carnivorous fungi has evolved specialized trapping devices to sequester excess iron, compensating for the absence of the crucial Ccc1-mediated vacuolar iron detoxification pathway, which is conserved in most fungi. Furthermore, we report for the first time that elevated temperature is a non-trophic factor that induces iron overload in eukaryotes, as iron content and composition in fungal mycelia are negatively correlated with temperature. Our findings suggest that nematode-trapping fungi could serve as a potential eukaryotic model for investigating the dynamic regulation mechanisms of iron homeostasis, which could contribute to the development of therapies for iron overload-related diseases in humans. In humans, iron overload leads to tissue damage, particularly in the cardiovascular system. It has long been assumed that iron overload occurs when iron intake is increased over an extended period, either through repeated red blood cell transfusions or enhanced absorption from the gastrointestinal tract. Caucasians are particularly susceptible to iron overload and the complications of hemochromatosis due to a higher incidence of mutations in the homeostatic iron regulation gene within this population. The discovery of eukaryotes exhibiting an iron overload phenotype when exposed to heat holds significant implications for developing treatments and strategies for human iron overload disorders.

evolutionary biology↗

Efficient Genome Editing with Chimeric Oligonucleotide-Directed Editing

Prime editing has emerged as a precise and powerful genome editing tool, offering a favorable gene editing profile compared to other Cas9-based approaches. Here we report new nCas9-DNA polymerase fusion proteins to create chimeric oligonucleotide-directed editing (CODE) systems for search-and-replace genome editing. Through successive rounds of engineering, we developed CODEMax and CODEMax(exo+) editors that achieve efficient genome modifications in human cells with low unintended edits. CODEMax and CODEMax(exo+) contain an engineered Bst DNA polymerase derivative known for its robust strand displacement ability. Additionally, CODEMax(exo+) features a 5 to 3 exonuclease activity that promotes effective strand invasion and repair outcomes favoring the incorporation of the desired edit. We demonstrate CODEs can perform small insertions, deletions, and substitutions with improved efficiency compared to PEMax at many loci. Overall, CODEs complement existing prime editors to expand the toolbox for genome manipulations without double-stranded breaks.

bioengineering↗

NSP4 mutation T492I drives rapid evolution of SARS-CoV-2 toward Omicron

T492I, a mutation encountered in SARS-CoV-2 nonstructural protein 4 (NSP4), enhances viral replication and alters nonstructural protein cleavage, causing potential evolutionary impacts. Through comprehensive comparative analyses based on evolve-and-resequence experiments of SARS-CoV-2 wild-type and Delta strains with or without T492I, we demonstrate that NSP4 T492I not only increases the mutation rate, but also accelerates the emergence of many mutations characteristic for Omicron variants. Accordingly, viral populations that evolved from ancestors with T492I, show Omicron-biased selective forces and increases in viral replication, infectivity, immune evasion capacity, potentials for cross-species transmission and receptor-binding affinity. Aside from enhanced replication, we observed stronger epistasis regarding viral replication and infectivity in T492I than in S N501Y and NSP6 {Delta}SGF; this facilitates the regulation of mutation types, which can drive fast evolution of Omicron specific mutations. Our results highlight the role of an important replication-enhancing mutation in regulating the evolutionary rates and mutational trends of SARS-CoV-2.

evolutionary biology↗

Association between Adolescent Brain Morphometry and Cognitive Function: Insights from a Cross-Sectional Analysis of ABCD Data from 9 to 15 Years Old

Significant changes occur in brain structure and cognitive abilities during adolescence. Investigating their association can provide insight into brain-based cognitive development, yet previous studies were limited by narrow brain measures, small samples, and lacking focus on age-related variation. Here, we analyzed a large cohort (N = 8,534, age 9-15) from the Adolescent Brain Cognitive Development dataset. Using structural MRI and diffusion imaging, we derived 16 regional structural measures and integrated them via morphometric similarity networks to characterize 16,563 regional, connectivity, and hub features. We applied large-scale computational models to investigate their associations with performance on seven cognitive subtests and general intelligence (g), as well as age-related changes. Brain areas most strongly associated with cognitive ability also showed the greatest age-related variability in these associations, located primarily in the frontal, temporal, and occipital lobes. Structural MRI measures exhibited stronger associations with cognition and greater age-related variability than diffusion-derived metrics, while global hub measures showed stronger and more variable associations than local measures. Overall, our study provides a comprehensive and reliable understanding of brain structure-cognition associations during adolescence.

neuroscience↗