Biology subjects

Shi, R.

Publications and source records attributed to Shi, R..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

3D Printed Nerve Guidance Conduit for Biologics-Free Nerve Regeneration and Vascular Integration

There is a clinical need for an effective nerve guidance conduit to treat peripheral nerve injuries. Many studies have explored different materials and active cues to guide neural regeneration, with some success. However, none have demonstrated a comparable or better functional recovery than the clinical standard autograft. Autografts are often insufficient for reconstruction of an injury to long nerves such as the sciatic or brachial plexus. Synthetic nerve guidance conduits (NGCs) have been investigated for these injuries to guide axonal regeneration and lead to functional recovery. We have designed a biologics-free hydrogel-based multi-channel conduit with defined microscale features to guide axonal outgrowth. To investigate extraneural vascular infiltration and its effects on functional recovery, we also designed a multi-microchannel conduit with defined regularly spaced micropores, orthogonal to the axon guidance channels. Using our custom-built Rapid Projection, Image-guided, Dynamic (RaPID) bioprinting system, we are able to fabricate each hydrogel conduit within minutes from a milliliter-volume prepolymer vat. With our state-of-the-art printing platform, we have achieved NGCs with a consistent channel wall width of 10 microns. We implanted the NGCs for 17 weeks in a murine sciatic nerve transection injury model. We assessed the functional recovery by dynamic gait analysis throughout the recovery period and by compound muscle action potential (CMAP) electrophysiology before NGC harvesting. Both the non-porous and micro-porous conduit groups led to functional nerve regeneration on par with the autograft group. Further, both conduit groups resulted in restoration of bulk motor function to pre-injury performance. Translational Impact StatementWe have developed a synthetic therapeutic that can be implanted to aid nerve regeneration after a debilitating injury that performs similarly to the current clinical standard treatment. One major hurdle to clinically translating an implantable therapeutic is needing to include biologics such as cells or active biomolecules, which increases the regulatory burden. With this in mind, we systematically developed a biologics-free synthetic hydrogel nerve guidance conduit, composed of polymer backbones that have been used in many FDA-approved applications, capable of restoring motor function.

bioengineering↗

bioRxiv2025

OmniEM: Unifying the EM Multiverse through a Large-scale Foundation Model

Accurate analysis of electron microscopy (EM) images is essential for exploring nanoscale biological structures, yet data heterogeneity and fragmented workflows hinder scalable insights. Pretrained on large, diverse datasets, image foundation models provide a robust framework for learning transferable representations across tasks. Here, we introduce EM-DINO, the first EM image foundational model pretrained on EM-5M, a large curated and standardized EM corpus (5 million images) encompassing multiple species, tissues, protocols, and resolutions. EM-DINOs multi-scale embeddings capture rich image features that support multiple applications, including organ-specific pattern recognition, image deduplication, and high quality image restoration. Building on these representations, we developed OmniEM, a U-shaped architecture for unified dense prediction that achieves superior performance compared with task-specific models in both image restoration and segmentation. In restoration benchmarks, OmniEM matches the performance of the EM-specific diffusion model while reducing spurious structural artifacts that could mislead interpretation. It also outperforms previous methods across 2D and 3D mitochondrial segmentation, as well as multi-class organelle segmentation tasks. Furthermore, we demonstrate OmniEMs integrated capability to generate high-resolution segmentations from low-resolution inputs, offering the potential to enable fine-scale subcellular analysis in legacy and high-throughput EM datasets. Together, EM-5M, EM-DINO, OmniEM, and an integrated Napari plugin comprise a comprehensive end-to-end toolkit for standardized EM analysis, advancing cellular and subcellular understanding and accelerating the discovery of novel organelle morphologies and disease-related alterations.

bioengineering↗

bioRxiv2025

Manganese suppresses tumor growth through hyper-activating IRE1α

IRE1 and its downstream XBP1 signal is the most conserved unfolded protein response pathway that cells utilize to combat endoplasmic reticulum stress, also known to be utilized by tumor cells to adapt to harsh environment, leading to tumor progression. Several inhibitors against IRE1 have been developed, some of which show promising effect in clinical trial for cancer therapy, but none of them have been used in practice. Considering that hyper-activation of IRE1 induces cell death, we hypothesize that activation of IRE1 could be an alternative way for tumor suppression. Here, we identified divalent manganese ion as a potent activator to IRE1, which interacts with the cytosolic part of IRE1 directly, augmenting the downstream pro-apoptotic pathway but not the pro-survival outcome. Mn2+ limits tumor growth in xenograft model in an IRE1-dependent way. Our finding suggests pharmacological activation of IRE1 as an underestimated but promising way in cancer therapy. HighlightsO_LIMn2+ binds to cytosolic segment of IRE1 and promotes its oligomerization C_LIO_LIMn2+ hyper-activates IRE1 and induces downstream terminal UPR under ER stress C_LIO_LIMn2+ does not elevate XBP1s expression C_LIO_LIMn2+ as an IRE1 activator impairs tumor growth in xenograft model C_LI

cancer biology↗

bioRxiv2025

Multivariable Mendelian Randomization adjusting for heritable confounding analyzes the causal effects of C-reactive protein on multiple diseases

BackgroundC-reactive protein (CRP) is a marker of inflammation associated with autoimmune, cardiovascular, and neuropsychiatric disorders. However, it remains unclear whether CRP causally affects these traits or if observed associations result from reverse causation or confounding. Mendelian randomization (MR) uses genetic variants as instrumental variables to estimate causal effects and avoid the biases present in observational studies. Prior MR studies have suggested causal effects of CRP on several traits, including schizophrenia, bipolar disorder, and colorectal cancer. However, MR may produce biased results if factors that confound the exposure and outcome are heritable, resulting in horizontal pleiotropy. This is a major concern for studies of CRP, because CRP levels may increase in response to inflammation caused by a wide range of heritable conditions. MethodsMultivariable Mendelian randomization (MVMR) can be used to eliminate bias from heritable confounding when GWAS summary data are available for confounders. In this study, we use MVMR to estimate the causal effects of CRP on 12 outcomes with prior evidence of a causal or associational link to CRP. We use a novel computational pipeline to identify a broad set of potential heritable confounders between CRP and each outcome trait from studies in the MRC-IEU OpenGWAS database. We compare MVMR results with computationally selected confounders to univariable MR results and MVMR using a narrower, literature derived set of confounders. ResultsWe find that univariable MR suggests evidence of a potential risk-increasing effect of CRP on coronary artery disease, knee osteoarthritis, and rheumatoid arthritis, and a protective effect on schizophrenia. However, after adjusting for computationally selected heritable confounders, only the causal effects on rheumatoid arthritis (OR 1.18, 95% CI [1.07,1.31], p=0.0010 by GRAPPLE) and schizophrenia (OR 0.87, 95% CI [0.79,0.96], p=0.0038 by GRAPPLE) remain significant. Additionally, after adjusting for confounders we find evidence of a potential protective effect of CRP on bipolar disorder at the nominal significance level, which is not observed in the univariable analysis. ConclusionThese results suggest that univariable MR analyses of CRP may be biased by high levels of heritable confounding, though CRP may indeed play a causal role in development of some diseases, potentially mediated by its role in innate immunity. These results also high-light the potential for automatic confounder selection to improve the robustness of Mendelian randomization analyses. Key MessagesO_LIWe used multivariable Mendelian randomization to estimate the causal effect of CRP levels on various diseases after adjusting for heritable confounders. C_LIO_LIWe proposed a novel computational pipeline for phenome-wide heritable confounder selection using traits from the MRC-IEU OpenGWAS database. C_LIO_LIOur study did not find evidence of a causal effect of CRP on multiple diseases, except rheuma-toid arthritis and schizophrenia. C_LIO_LIOur study highlights the role of CRP as an indicator of inflammation rather than a causal factor in disease risk, suggesting that previous MR analyses may have been biased by heritable confounding. C_LI

genetics↗

bioRxiv2024

Small molecule modulator of neuronal lysosome positioning and function resolves Alzheimers Disease-linked pathologies in cultured human neurons

Abnormal increase in axonal lysosome abundance is associated with multiple neurodegenerative diseases including Alzheimers disease. However, the underlying mechanisms and disease relevance are not fully understood. We have recently identified RH1115 as a small molecule modulator of the autophagy-lysosomal pathway that regulates lysosome positioning in neurons. This allowed us to manipulate neuronal lysosome distribution including in axons and interrogate its contribution to both optimal neuronal functioning and to disease pathology. We demonstrate that the small molecule not only rescues aberrant buildup of both axonal autophagic and lysosomal intermediates but also reduces secreted A{beta}42 levels in human iPSC-derived neurons lacking the lysosomal adaptor, JIP3. We thus demonstrate that restoring efficient axonal lysosome transport has an anti-amyloidogenic effect in human neurons and is a promising therapeutic strategy for Alzheimers disease. Furthermore, we show that the small molecule enhances neuronal lysosome degradation, requires the lysosomal adaptor JIP4 to rescue the axonal lysosome pathology in the JIP3 KO neurons and increases levels of the JIP4-interacting lysosomal membrane protein, TMEM55B. Lastly, treatment with the small molecule led to a striking rescue of locomotor defects in JIP3 KO zebrafish larvae. Thus, we have identified a small molecule which can be impactful in neurodegenerative diseases that have a lysosomal pathology and have determined its molecular targets in modulating axonal lysosome abundance.

cell biology↗

bioRxiv2024

Orthrus: Towards Evolutionary and Functional RNA Foundation Models

In the face of rapidly accumulating genomic data, our ability to accurately predict key mature RNA properties that underlie transcript function and regulation remains limited. Pre-trained genomic foundation models offer an avenue to adapt learned RNA representations to biological prediction tasks. However, existing genomic foundation models are trained using strategies borrowed from textual domains that do not leverage biological domain knowledge. Here, we introduce Orthrus, a Mamba-based mature RNA foundation model pre-trained using a novel self-supervised contrastive learning objective with biological augmentations. Orthrus is trained by maximizing embedding similarity between curated pairs of RNA transcripts, where pairs are formed from splice isoforms of 10 model organisms and transcripts from orthologous genes in 400+ mammalian species from the Zoonomia Project. This training objective results in a latent representation that clusters RNA sequences with functional and evolutionary similarities. We find that the generalized mature RNA isoform representations learned by Orthrus significantly outperform genomic foundation models on mRNA property prediction tasks, and requires only a fraction of fine-tuning data to do so. Finally, we show that Orthrus is capable of capturing divergent biological function of individual transcript isoforms.

genomics↗

bioRxiv2024

Stochastic growth and selective stabilization generate stereotyped dendritic arbors

Stereotyped dendritic arbors are shaped by dynamic and stochastic growth during neuronal development. It remains unclear how guidance receptors and ligands coordinate branch dynamic growth, retraction, and stabilization to specify dendritic arbors. We previously showed that extracellular ligand SAX-7/LICAM dictates the shape of the PVD sensory neuron via binding to the dendritic guidance receptor DMA-1, a single transmembrane adhesion molecule. Here, we perform structure-function analyses of DMA-1 and unexpectedly find that robust, stochastic dendritic growth does not require ligand-binding. Instead, ligand-binding inhibits growth, prevents retraction, and specifies arbor shape. Furthermore, we demonstrate that dendritic growth requires a pool of ligand-free DMA-1, which is maintained by receptor endocytosis and reinsertion to the plasma membrane via recycling endosomes. Mutants defective of DMA-1 endocytosis show severely truncated dendritic arbors. We present a model in which ligand-free guidance receptor mediates intrinsic, stochastic dendritic growth, while extracellular ligands instruct dendrite shape by inhibiting growth.

neuroscience↗

bioRxiv2024

HEPN-AbiV is an RNase in the antiphage system AbiV

Prokaryotes and eukaryotes possess defense systems, which can be either innate or acquired, to protect against viral infections. At the bacterial population level, abortive infection (Abi) serves as an innate immune defense mechanism against phage invasion. The AbiV antiviral system is prevalent in several bacterial genomes and exhibits diverse characteristics in terms of gene composition and evolution. Our investigation into the Lactococcus AbiV system revealed a novel two-component system, abiV1 and abiV2, both of which are essential for its function as a type III toxin-antitoxin system. The toxin component AbiV (product of abiV1) is an RNase belonging to the HEPN (Higher Eukaryotes and Prokaryotes Nucleotide-binding) superfamily as it carries the consensus Rx4-6H motif. In vivo assays coupled with mass spectrometry showed that the lactococcal AbiV was expressed in the presence or absence of phages while in vitro experiments demonstrated that AbiV1 degraded ribosomal RNA but not mRNA. On the other hand, the antitoxin component (abiV2) was found to function as an RNA molecule that inhibited the nuclease activity of the AbiV1 toxin. The structural characterization of AbiV revealed that this RNase utilizes a large patch of positively charged area across the dimer to anchor RNA molecules. In addition, we showed that the AbiV N-terminal region (amino acids 1 to 23) is crucial for its RNase activity as a truncated AbiV lacking this segment adopted distinct conformational states incompatible with RNA binding. This study provided novel insights into the mode of action of the antiviral system AbiV.

biochemistry↗

bioRxiv2024

The longitudinal behavioral effects of acute exposure to galactic cosmic radiation in female C57BL/6J mice: implications for deep space missions, female crews, and potential antioxidant countermeasures

Galactic cosmic radiation (GCR) is an unavoidable risk to astronauts that may affect mission success. Male rodents exposed to 33-beam-GCR (33-GCR) show short-term cognitive deficits but reports on female rodents and long-term assessment is lacking. Here we asked: What are the longitudinal behavioral effects of 33-GCR on female mice? Also, can an antioxidant/anti-inflammatory compound mitigate the impact of 33-GCR? Mature (6-month-old) C57BL/6J female mice received the antioxidant CDDO-EA (400 {micro}g/g of food) or a control diet (vehicle, Veh) for 5 days and either Sham-irradiation (IRR) or whole-body 33-GCR (0.75Gy) on the 4th day. Three-months post-IRR, mice underwent two touchscreen-platform tests: 1) location discrimination reversal (which tests behavior pattern separation and cognitive flexibility, two abilities reliant on the dentate gyrus) and 2) stimulus-response learning/extinction. Mice then underwent arena-based behavior tests (e.g. open field, 3-chamber social interaction). At the experiment end (14.25-month post-IRR), neurogenesis was assessed (doublecortin-immunoreactive [DCX+] dentate gyrus neurons). Female mice exposed to Veh/Sham vs. Veh/33-GCR had similar pattern separation (% correct to 1st reversal). There were two effects of diet: CDDO-EA/Sham and CDDO-EA/33-GCR mice had better pattern separation vs. their respective control groups (Veh/Sham, Veh/33-GCR), and CDDO-EA/33-GCR mice had better cognitive flexibility (reversal number) vs. Veh/33-GCR mice. Notably, one radiation effect/CDDO-EA countereffect also emerged: Veh/33-GCR mice had worse stimulus-response learning (days to completion) vs. all other groups, including CDDO-EA/33-GCR mice. In general, all mice show normal anxiety-like behavior, exploration, and habituation to novel environments. There was also a change in neurogenesis: Veh/33-GCR mice had fewer DCX+ dentate gyrus immature neurons vs. Veh/Sham mice. Our study implies space radiation is a risk to a female crews longitudinal mission-relevant cognitive processes and CDDO-EA is a potential dietary countermeasure for space-radiation CNS risks.

neuroscience↗

bioRxiv2024

Quantitative tests of albendazole resistance in beta-tubulin mutants

Benzimidazole (BZ) anthelmintics are among the most important treatments for parasitic nematode infections in the developing world. Widespread BZ resistance in veterinary parasites and emerging resistance in human parasites raise major concerns for the continued use of BZs. Knowledge of the mechanisms of resistance is necessary to make informed treatment decisions and circumvent resistance. Benzimidazole resistance has traditionally been associated with mutations and natural variants in the C. elegans beta-tubulin gene ben-1 and orthologs in parasitic species. However, variants in ben-1 alone do not explain the differences in BZ responses across parasite populations. Here, we examine the roles of five C. elegans beta-tubulin genes (tbb-1, mec-7, tbb-4, ben-1, and tbb-6) to identify the role each gene plays in BZ response. We generated C. elegans strains with a loss of each beta-tubulin gene, as well as strains with a loss of tbb-1, mec-7, tbb-4, or tbb-6 in a genetic background that also lacks ben-1 to test beta-tubulin redundancy in BZ response. We found that only the individual loss of ben-1 conferred a substantial level of BZ resistance, although the loss of tbb-1 was found to confer a small benefit in the presence of albendazole (ABZ). The loss of ben-1 was found to confer an almost complete rescue of animal development in the presence of 30 {micro}M ABZ, likely explaining why no additive effects caused by the loss of a second beta-tubulin were observed. We demonstrate that ben-1 is the only beta-tubulin gene in C. elegans where loss confers substantial BZ resistance. Highlights- Loss of ben-1 provides almost complete rescue of development in albendazole (ABZ) - Loss of different beta-tubulin genes does not confer ABZ resistance - Loss of ben-1 and a second beta-tubulin does not enhance the ben-1 level of ABZ resistance

molecular biology↗

bioRxiv2024

Compensatory mutations potentiate constructive neutral evolution by gene duplication

Protein functions generally depend on their assembly into complexes. During evolution, some complexes have transitioned from homomers encoded by a single gene to heteromers encoded by duplicate genes. This transition could occur without adaptive evolution through intermolecular compensatory mutations. Here, we experimentally duplicate and evolve an homodimeric enzyme to examine if and how this could happen. We identify hundreds of deleterious mutations that inactivate individual homodimers but produce functional enzymes when co-expressed as duplicated proteins that heterodimerize. The structure of one such heteromer reveals how both losses of function are buffered through the introduction of asymmetry in the complex that allows them to subfunctionalize. Constructive neutral evolution can thus occur by gene duplication followed by only one deleterious mutation per duplicate. One sentence summaryCompensatory deleterious mutations entangle gene duplicates

evolutionary biology↗

bioRxiv2024

MR-SPLIT: a novel method to address selection and weak instrument bias in one-sample Mendelian randomization studies

Mendelian Randomization (MR) is a widely embraced approach to assess causality in epidemiological studies. Two-stage least squares (2SLS) method is a predominant technique in MR analysis. However, it can lead to biased estimates when instrumental variables (IVs) are weak. Moreover, the issue of the winners curse could emerge when utilizing the same dataset for both IV selection and causal effect estimation, leading to biased estimates of causal effects and high false positives. Focusing on one-sample MR analysis, this paper introduces a novel method termed as Mendelian Randomization with adaptive Sample-sPLitting with cross-fitting InstrumenTs (MR-SPLIT), designed to address bias issues due to IV selection and weak IVs, under the 2SLS IV regression framework. We show that the MR-SPLIT estimator is more efficient than its counterpart cross-fitting MR (CFMR) estimator. Additionally, we introduce a multiple sample-splitting technique to enhance the robustness of the method. We conduct extensive simulation studies to compare the performance of our method with its counterparts. The results underscored its superiority in bias reduction, effective type I error control, and increased power. We further demonstrate its utility through the application of a real-world dataset. Our study underscores the importance of addressing bias issues due to IV selection in high dimensions and weak IVs in one-sample MR analyses and provides a robust solution to the challenge.

genetics↗

bioRxiv2023

Dairy practices select for thermostable endolysins in phages

Endolysins are phage lytic enzymes that degrade the bacterial cell wall to release phage progeny. We found that the diversity of endolysins is unsuspectedly low and dominated by a single structural type in distinct phages that infect Streptococcus thermophilus. Through X-ray crystallography, we discovered that this type of endolysin contains a highly conserved calcium-binding motif in its cell wall binding domain. Inactivation of the motif in the purified endolysin or in the phage genome revealed its key role in stabilizing the enzyme under conditions that mimic the cheesemaking process, including at elevated temperatures. Fermented dairy products such as yogurt and cheeses are incubated or cooked at higher temperatures and require the addition of thermophilic lactic acid bacteria such as S. thermophilus to drive milk fermentation. It appears that dairy practices have influenced the genetic signatures of streptococcal phages by selecting for thermostable endolysins, which in turn have limited their diversity.

microbiology↗

bioRxiv2023

High-throughput and genome-scale targeted mutagenesis using CRISPR in a non-model multicellular organism, Bombyx mori

Large-scale genetic mutant libraries are powerful approaches to interrogating genotype-phenotype correlations and identifying genes responsible for certain environmental stimuli, both of which are the central goal of life science study. We produced the first large-scale CRISPR/Cas9-induced library in a non-model multicellular organism, Bombyx mori. We developed a piggyBac-delivered binary genome editing strategy, which can simultaneously meet the requirements of mixed microinjection, efficient multi-purpose genetic operation, and preservation of growth-defect lines. We constructed a single-guide RNA (sgRNA) plasmid library containing 92,917 sgRNAs targeting promoters and exons of 14,645 protein-coding genes, established 1726 transgenic sgRNA lines following microinjection of 66,650 embryos, and generated 300 mutant lines with diverse phenotypic changes. Phenomic characterization of mutant lines identified a large set of genes responsible for visual phenotypic or economically valuable trait changes. Next, we performed pooled context-specific positive screens for tolerance to environmental pollute cadmium exposure, and identified KWMTBOMO12902 as a strong candidate gene for breeding applications in sericulture industry. Collectively, our results provide a novel and versatile approach for functional B. mori genomics, and a powerful resource for identifying key candidate genes potential for improving various economic traits. This study also demonstrates the effectiveness, practicality, and convenience of large-scale mutant libraries in other non-model organisms.

genomics↗

bioRxiv2023

Neuropathy target esterase activity predicts retinopathy among PNPLA6 disorders

Biallelic pathogenic variants in the PNPLA6 gene cause a broad spectrum of disorders leading to gait disturbance, visual impairment, anterior hypopituitarism, and hair anomalies. PNPLA6 encodes Neuropathy target esterase (NTE), yet the role of NTE dysfunction on affected tissues in the large spectrum of associated disease remains unclear. We present a clinical meta-analysis of a novel cohort of 23 new patients along with 95 reported individuals with PNPLA6 variants that implicate missense variants as a driver of disease pathogenesis. Measuring esterase activity of 46 disease-associated and 20 common variants observed across PNPLA6-associated clinical diagnoses unambiguously reclassified 10 variants as likely pathogenic and 36 variants as pathogenic, establishing a robust functional assay for classifying PNPLA6 variants of unknown significance. Estimating the overall NTE activity of affected individuals revealed a striking inverse relationship between NTE activity and the presence of retinopathy and endocrinopathy. This phenomenon was recaptured in vivo in an allelic mouse series, where a similar NTE threshold for retinopathy exists. Thus, PNPLA6 disorders, previously considered allelic, are a continuous spectrum of pleiotropic phenotypes defined by an NTE genotype:activity:phenotype relationship. This relationship and the generation of a preclinical animal model pave the way for therapeutic trials, using NTE as a biomarker.

neuroscience↗

bioRxiv2023

Single-cell transcriptome analysis on the anatomic positional heterogeneity of pig skin

Different anatomic locations of the body skin dermis come from different origins, and its positional hereditary information can be maintained in adults, while highly resolvable cellular specialization is less well characterized in different anatomical regions. Pig is regarded as excellent model for human research in view of its similar physiology to human. In this study, we performed single-cell RNA sequencing of six different anatomical skin regions from the Chenghua pig with superior skin thickness trait. We obtained 215,274 cells, representing seven cell types, among which we primarily characterized the heterogeneity of smooth muscle cells, endothelial cells and fibroblasts. We identified several phenotypes of smooth muscle cell and endothelial cell and presented genes expression of pathways such as the immune response in different skin regions. By comparing differentially expressed fibroblast genes among different skin regions, we considered TNN, COL11A1, and INHBA as candidate genes for facilitating ECM accumulation. These findings of heterogeneity in the main three cell types from different anatomic skin sites will contribute to a better understanding of hereditary information and places the potential focus on skin generation, transmission and transplantation, paving the foundation for human skin priming.

cell biology↗

bioRxiv2023

Behavioral pattern separation and cognitive flexibility are enhanced in a mouse model of increased lateral entorhinal cortex-dentate gyrus circuit activity

Behavioral pattern separation and cognitive flexibility are essential cognitive abilities which are disrupted in many brain disorders. Better understanding of the neural circuitry involved in these abilities will open paths to treatment. In humans and mice, discrimination and adaptation rely on integrity of the hippocampal dentate gyrus (DG) which both receive glutamatergic input from the entorhinal cortex (EC), including the lateral EC (LEC). Inducible increase of EC-DG circuit activity improves simple hippocampal-dependent associative learning and increases DG neurogenesis. Here we asked if the activity of LEC fan cells that directly project to the DG (LECDG neurons) regulates behavioral pattern separation or cognitive flexibility. C57BL6/J male mice received bilateral LEC infusions of a virus expressing shRNA TRIP8b, an auxiliary protein of an HCN channel or a control virus (SCR shRNA); this approach increases the activity of LECDG neurons. Four weeks later, mice underwent testing for behavioral pattern separation and reversal learning (touchscreen-based Location Discrimination Reversal [LDR] task) and innate fear of open spaces (elevated plus maze [EPM]) followed by counting of new DG neurons (doublecortin-immunoreactive cells [DCX+] cells). TRIP8b and SCR shRNA mice performed similarly in general touchscreen training and LDR training. However, in late LDR testing, TRIP8b shRNA mice reached the first reversal more quickly and had more accurate discrimination vs. SCR shRNA mice, specifically when pattern separation was challenging (lit squares close together or "small separation"). Also, TRIP8b shRNA mice achieved more reversals in late LDR testing vs. SCR shRNA mice. Supporting a specific influence on cognitive behavior, SCR shRNA and TRIP8b shRNA mice did not differ in total distance traveled or in time spent in the closed arms of the EPM. Supporting an inducible increase in LEC-DG activity, DG neurogenesis was increased. These data indicate TRIP8b shRNA mice had better pattern separation and reversal learning and more neurogenesis vs. SCR shRNA mice. This work advances fundamental and translational neuroscience knowledge relevant to two cognitive functions critical for adaptation and survival -- behavioral pattern separation and cognitive flexibility -- and suggests the activity of LECDG neurons merits exploration as a therapeutic target to normalize dysfunctional DG behavioral output.

animal behavior and cognition↗

bioRxiv2022

Shape-shifting microgel automata controlled by DNA sequence instructions

Controlling material shapes using information-bearing molecular signals is central to the creation of autonomous, reconfigurable soft devices. While physical and chemical stimuli can direct simple material swelling, bending, or folding, it has been challenging to direct multi-step shape-change programs crucial for complex, robotic tasks. Here, we demonstrate gel automata-- sub-millimeter, photopatterned, highly swellable DNA gels--whose parts grow or shrink in response to easily designed DNA activator sequences, allowing for precisely controlled device articulation. We design and fabricate gel automata that reversibly transform between different letter shapes, and use neural networks to design automata that transform into every even or every odd numeral via designed reconfiguration programs. This sequential and repetitive metamorphosis of materials via chemical reorganization could dramatically advance our ability to manipulate micro-particles, cells, and tissues. One-Sentence SummaryPhotopatterned microgels follow sequences of DNA instructions to transform between complex, meaningful shapes such as letters and numerals.

bioengineering↗