Biology subjects

Lin, J.

Publications and source records attributed to Lin, J..

At least 199 records · Page 11Linked to original sources

bioRxiv2024

Mechanically Sheared Axially Swept Light-Sheet Microscopy

We present a mechanically sheared image acquisition format for upright and open-top light-sheet microscopes that automatically places data in its proper spatial context. This approach, which reduces computational post-processing and eliminates unnecessary interpolation or duplication of the data, is demonstrated on an upright variant of Axially Swept Light-Sheet Microscopy (ASLM) that achieves a field of view, measuring 774 x 435 microns, that is 3.2-fold larger than previous models and a raw and isotropic resolution of [~]420 nm. Combined, we demonstrate the power of this approach by imaging sub-diffraction beads, cleared biological tissues, and expanded specimens.

biophysics↗

bioRxiv2024

Corticospinal and corticoreticulospinal projections benefit motor behaviors in chronic stroke

After corticospinal tract (CST) stroke, several motor deficits in the upper extremity (UE) emerge, including diminished muscle strength, motor control, and muscle individuation. Both the ipsilesional CST and contralesional corticoreticulospinal tract (CReST) innervate the paretic UE and may have different innervation patterns for the proximal and distal UE segments. These patterns may underpin distinct pathway relationships to separable motor behaviors. In this cross-sectional study of 15 chronic stroke patients and 28 healthy subjects, we examined two key questions: (1) whether segmental motor behaviors differentially relate to ipsilesional CST and contralesional CReST projection strengths, and (2) whether motor behaviors segmentally differ in the paretic UE. We measured strength, motor control, and muscle individuation in a proximal (biceps, BIC) and distal muscle (first dorsal interosseous, FDI) of the paretic UE. We measured the projection strengths of the ipsilesional CST and contralesional CReST to these muscles using transcranial magnetic stimulation (TMS). Stroke subjects had abnormal motor control and muscle individuation despite strength comparable to healthy subjects. In stroke subjects, stronger ipsilesional CST projections were linked to superior motor control in both UE segments, whereas stronger contralesional CReST projections were linked to superior muscle strength and individuation in both UE segments. Notably, both pathways also shared associations with behaviors in the proximal segment. Motor control deficits were segmentally comparable, but muscle individuation was worse for distal motor performance. These results suggest that each pathway has specialized contributions to chronic motor behaviors but also work together, with varying levels of success in supporting chronic deficits. Key points summaryO_LIIndividuals with chronic stroke typically have deficits in strength, motor control, and muscle individuation in their paretic upper extremity (UE). It remains unclear how these altered behaviors relate to descending motor pathways and whether they differ by proximal and distal UE segment. C_LIO_LIIn this study, we used transcranial magnetic stimulation (TMS) to examine projection strengths of the ipsilesional corticospinal tract (CST) and contralesional corticoreticulospinal tract (CReST) with respect to quantitated motor behaviors in chronic stroke. C_LIO_LIWe found that stronger ipsilesional CST projections were associated with better motor control in both UE segments, whereas stronger contralesional CReST projections were associated with better strength and individuation in both UE segments. In addition, projections of both pathways shared associations with motor behaviors in the proximal UE segment. C_LIO_LIWe also found that deficits in strength and motor control were comparable across UE segments, but muscle individuation was worse with controlled movement in the distal UE segment. C_LIO_LIThese results suggest that the CST and CReST have specialized contributions to chronic motor behaviors and also work together, although with different degrees of efficacy. C_LI

neuroscience↗

bioRxiv2024

Acute and sub-chronic toxicity of 6PPD-quinone to early-life stage lake trout (Salvelinus namaycush)

N-(1,3-Dimethylbutyl)-N-phenyl-p-phenylenediamine-quinone (6PPD-q) is a rubber-tire derivative which leaches into surface waters from roadway runoff, from tire particles and has been identified as a possible driver of urban runoff mortality syndrome in coho salmon. Sensitivity to this toxicant is highly variable across fish species and life stages. With environmental concentrations meeting or exceeding toxicity thresholds in sensitive fishes, the potential for ecologically relevant effects is significant. There is currently no data regarding the sensitivity of lake trout (Salvelinus namaycush) to 6PPD-q. As early-life stages of fishes are typically more sensitive than adults, the goal of these studies was to evaluate the acute and sub-chronic toxicity of 6PPD-q to early-life stage lake trout. Alevins exposed from hatch until 45 days post hatch (dph) to time-weighted average 6PPD-q concentrations ranging from 0.22-13.5 g/L exhibited a 45-day median lethal dose (LC50) of 0.39 g/L. Deformities throughout growth were observed, with a unique pooling of blood observed in the caudal fin and eye. A subsequent acute study with exogenously feeding lake trout fry determined a 96-hr LC50 of 0.50 g/L. From these studies we can conclude that lake trout alevins and exogenously feeding fry are sensitive to 6PPD-q, which underscores the relevance of this chemical to inland freshwater ecosystems.

physiology↗

bioRxiv2024

Structures of transcription-translation coupling complexes at each stage of the translation cycle

In the bacterium Escherichia coli, efficient expression of protein-coding genes is achieved through physical coupling of RNA polymerase (RNAP) synthesizing an mRNA and the first ribosome translating the mRNA, with transcription elongation factors NusG and NusA bridging RNAP and ribosome in a transcription-translation complex (TTC). Recent structural studies suggest that the flexibility in NusG and NusA accommodates the changes in ribosome conformation that occur during the translation cycle, but details have been unclear. Here, we report cryo-EM structures of TTCs at each stage of the translation cycle as an actively translating ribosome approaches to a halted transcription complex. We observe sequential conversion of a loosely coupled TTC (TTC-LC) to a tightly coupled TTC (TTC-B) to a collided TTC (TTC-A) as the ribosome approaches the transcription complex. We show that flexibility of the NusG linker and NusA "pantograph" enable TTC-LC and TTC-B to accommodate ribosome conformation at each stage of the translation cycle. We show that, in TTC-A, steric clash between ribosome and RNAP upon ribosome 30S head swiveling inhibits 30S head swiveling, consistent with translation slowdown, and applies mechanical force to the trailing edge of RNAP, causing transcription termination. Our results define the structures and properties of loosely coupled, tightly coupled, and collided TTCs at each stage of the translation cycle.

molecular biology↗

bioRxiv2024

Astrocytes control quiescent NSC reactivation via GPCR signaling-mediated F-actin remodeling

The transitioning of neural stem cells (NSCs) between quiescent and proliferative states is fundamental for brain development and homeostasis. Defects in NSC reactivation are associated with neurodevelopmental disorders. Drosophila quiescent NSCs extend an actin-rich primary protrusion toward the neuropil. However, the function of the actin cytoskeleton during NSC reactivation is unknown. Here, we reveal the fine F-actin structures in the protrusions of quiescent NSCs by expansion and super-resolution microscopy. We show that F-actin polymerization promotes the nuclear translocation of Mrtf, a microcephaly-associated transcription factor, for NSC reactivation and brain development. F-actin polymerization is regulated by a signaling cascade composed of G-protein-coupled receptor (GPCR) Smog, G-protein q subunit, Rho1 GTPase, and Diaphanous (Dia)/Formin during NSC reactivation. Further, astrocytes secrete a Smog ligand Fog to regulate Gq-Rho1-Dia-mediated NSC reactivation. Together, we establish that the Smog-Gq-Rho1 signaling axis derived from astrocytes, a NSC niche, regulates Dia-mediated F-actin dynamics in NSC reactivation.

developmental biology↗

bioRxiv2024

Intrinsically linked lineage-specificity of transposable elements and lncRNAs reshapes transcriptional regulation species- and tissue-specifically

Unlike protein-coding genes, many mammalian lncRNAs are lineage-specific (LS), but which human and mouse reference lncRNAs are lineage-specific, how they are generated, and whether their regulatory elements are lineage-specific remain unclear. To resolve their origins, properties, and impacts, we systematically classified primate-, simian-, rodent-, human-, and mouse-specific lncRNAs in GENCODE-annotated human and mouse genomes using structure-aware covariance modeling. We predicted their DNA-binding domains (DBDs) and genomic binding sites (DBSs) and traced the origins of embedded transposable elements (TEs). LS TEs contribute to over 84% (human) and 98% (mouse) of LS lncRNAs, 61% and 95% of their DBDs, and 46% and 73% of their DBSs. Analyses of multi-omics data and a developmental process suggest that LS TE-linked lineage-specificity substantially rewires transcriptional regulation and that many evolutionary novelties may be structurally predisposed. These findings bridge the gap between human diseases and mouse models, providing valuable resources for identifying human-specific therapeutic lncRNA targets.

genomics↗

bioRxiv2024

Does What You Eat Affect How You Mate? Disentangling the Interactions Between Diet-Induced Phenotypic Plasticity and Adult Reproductive Strategies in Black Soldier Flies.

Phenotypic plasticity enables organisms to response to environmental variations by generating a range of phenotypes from a single genotype. In holometabolous insects, traits that influence larval plasticity may hold relevance for adult life history strategies. We present a comprehensive investigation into phenotypic plasticity in black soldier flies, a species known for its efficient waste-to-biomass conversion in the larval stage. Here, we document adult sex-specific plastic responses and reproductive strategies shaped by larval diets. We examined traits including adult body size, reproductive organ development, sperm length, mating behaviours, egg production and other life history parameters across different treatments. Our findings reveal notable sex-specific differences in phenotypic plasticity, with females showing increased plasticity in reproductive investment. Furthermore, males and females differed starkly in allometric growth and weight ratio of reproductive organs. Diets that facilitated longer male lifespans also prompted earlier male emergence suggesting an interplay between lifespan and degree of protandry. This maximizes the overlap of male and female lifespans, thereby enhancing mating success in diverse environmental conditions. Our results reveal plastic responses in mating behaviours, where diets producing smaller adults, smaller reproductive organs, and shorter sperm correlated with significantly enhanced mating effort and performance. This study highlights the complex interactions between nutrition, development, and reproductive strategies, and has significant implications for the insect bioconversion industries.

evolutionary biology↗

bioRxiv2024

Gene Therapy Mediates Therapeutic Improvement in Cardiac Hypertrophy and Survival in a Murine Model of MYBPC3-Associated Cardiomyopathy

BackgroundHypertrophic cardiomyopathy (HCM) affects an estimated 600,000 people in the U.S. and is the leading cause of sudden cardiac arrest in those under 18. Loss-of-function mutations in Myosin Binding Protein C3, MYBPC3, are the most common genetic cause of HCM. The majority of MYBPC3 mutations causative for HCM result in truncations. The sarcomeric pathophysiology of the majority of HCM patients with MYBPC3 mutations appears to be due to haploinsufficiency, as the total amount of MYBPC3 protein incorporated into sarcomeres falls significantly below normal. MethodsA clear path for the treatment of haploinsufficiency is the restoration of the insufficient gene product; in this case wild-type MYBPC3. To achieve this, we engineered an AAV vector (TN-201) with superior properties for mediating cardiomyocyte-selective expression of MYBPC3 after systemic delivery. ResultsWe have demonstrated for the first time with AAV gene therapy the ability of both a mouse surrogate and TN-201, which encodes human MYBPC3 to reverse cardiac hypertrophy and systolic dysfunction and to improve diastolic dysfunction and survival in a symptomatic MYBPC3-deficient murine model of disease. Dose-ranging efficacy studies exhibited restoration of wild-type MYBPC3 protein levels and saturation of cardiac improvement at the clinically relevant dose of 3E13 vg/kg, outperforming a previously published construct. Further, we have established stable cardiac benefit for greater than one year post-injection, as well as reversal of cardiac dysfunction even in late-stage models of disease. ConclusionsOur data suggest that by restoring MYBPC3 to the sarcomere, TN-201 has the potential to slow and even reverse the course of the disease in patients with MYBPC3-associated HCM.

genetics↗

bioRxiv2024

Construction and Application of a Technical Platform for Determining Cell Cycle- and Autophagy-Associated Cellular Uptake of Lipid-Based Nanoparticles

Cellular accumulation of biomedical nanoparticles could be affected by cellular biological properties. However, little is known about the influence of cell cycle and autophagy on nanoparticle accumulation. Whats even more tough is that several long-lasting methodological barriers have hampered the experimental performance and restricted related research progress. Herein, a multi-functional platform was constructed for simultaneously overcoming existing obstacles by integrating several technical approaches, particularly mitotic shake-off, for thorough cell cycle phase separation. Strikingly, application of this platform revealed that G2-phase and M-phase cells, two cell populations previously muddled up together as G2/M-phase cells, respectively exhibited the maximum and minimum accumulation of lipid-based nanoparticles. Moreover, although further verification is needed, we have provided a novel line of evidence for enhanced nanoparticle accumulation by autophagy blockade. Besides providing a technical solution, this study discovered characteristic cell cycle- and autophagy-associated nanoparticle accumulations that may offer new insights for optimization and application of nanomedicines.

cell biology↗

bioRxiv2024

navigate: an open-source platform for smart light-sheet microscopy.

navigate is a turnkey, open-source software solution designed to enhance light-sheet fluorescence microscopy (LSFM) by integrating smart microscopy techniques into a user-friendly framework. It enables automated, intelligent imaging with a Python-based control system that supports GUI-reconfigurable acquisition routines and the integration of diverse hardware sets. As a comprehensive package, navigate democratizes access to advanced LSFM capabilities, facilitating the development and implementation of smart microscopy workflows without requiring deep programming knowledge or specialized expertise in light-sheet microscopy.

biophysics↗

bioRxiv2024

Daily vocalization patterns of the Saipan Reed Warbler (Acrocephalus hiwae)

We investigated how detectability and vocalization patterns of Saipan Reed Warblers (Acrocephalus hiwae) varied by time of day. We used long-duration sound recordings from eleven locations occupied by Saipan Reed Warblers to model the probability of detecting a vocalization in each hour of the day. We found that Saipan Reed Warblers sang during all daylight hours. We did not find evidence of a dawn or evening chorus in this species. These results are useful for determining what time of day surveys of Saipan Reed Warblers should be conducted, which is particularly relevant because Saipan Reed Warblers are protected by local and U.S. Federal laws.

zoology↗

bioRxiv2024

BRD4-mediated epigenetic regulation of endoplasmic reticulum-mitochondria contact sites is governed by the mitochondrial complex III

Inter-organellar communication is critical for cellular metabolic homeostasis. One of the most abundant inter-organellar interactions are those at the endoplasmic reticulum and mitochondria contact sites (ERMCS). However, a detailed understanding of the mechanisms governing ERMCS regulation and their roles in cellular metabolism are limited by a lack of tools that permit temporal induction and reversal. Through unbiased screening approaches, we identified fedratinib, an FDA-approved drug, that dramatically increases ERMCS abundance by inhibiting the epigenetic modifier BRD4. Fedratinib rapidly and reversibly modulates mitochondrial and ER morphology and alters metabolic homeostasis. Moreover, ERMCS modulation depends on mitochondria electron transport chain complex III function. Comparison of fedratinib activity to other reported inducers of ERMCS revealed common mechanisms of induction and function, providing clarity and union to a growing body of experimental observations. In total, our results uncovered a novel epigenetic signaling pathway and an endogenous metabolic regulator that connects ERMCS and cellular metabolism.

cell biology↗

bioRxiv2024

Deciphering the molecular mechanism of DNA-protein interactive co-condensates

Nucleic acid and protein co-condensates exhibit diverse morphologies crucial for fundamental cellular processes. Despite their significance, the molecular mechanisms governing morphology transitions remain poorly understood. To address this gap in knowledge, we investigated DNA and the human transcription factor p53 as a model system, specifically focusing on DNA-protein interactive co-condensates (DPICs)--a scenario where neither dsDNA nor the protein demonstrates phase-separation behavior individually. Through a combination of experimental assays and theoretical approaches, we elucidated: (i) the phase diagram of DPICs, identifying two distinct transition phenomena--a phase transition between viscoelastic fluid and viscoelastic solid states, and a morphology transition from droplet-like to "pearl chain"-like DPICs; (ii) the growth dynamics of DPICs. Droplet-like and "pearl chain"-like DPICs, although with dramatically distinct final morphologies and material properties, share a common initial critical microscopic cluster (CMC) size at the nanometer scale during the early stage of phase separation. These findings provide novel insights into the biophysical mechanisms underlying multi-component phase separations within cellular environments. Significance StatementNucleic acids and proteins have the capacity to form co-condensates, exhibiting various morphologies, including droplet-like and "pearl chains" formations. Despite this observation, the underlying biophysical mechanisms remain poorly understood. In this study, we employed DNA and the protein p53 as a model system. Our investigation revealed that the strength of the DNA-p53 interactions dictates the material properties of the co-condensates, leading to a transition from a viscoelastic fluid to a viscoelastic solid phase. This transition is accompanied by a morphological shift from droplet-like formations to structures resembling "pearl chains". Additionally, we explored the growth dynamics of these co-condensates and demonstrated that the strength of p53-DNA interactions influences the relaxation time of the co-condensates, thereby potentially determining their morphological features.

biophysics↗

bioRxiv2024

Arl2 Associates with Cdk5rap2 to Regulate Cortical Development via Microtubule Organization

ADP ribosylation factor-like GTPase 2 (Arl2) is crucial for controlling mitochondrial fusion and microtubule assembly in various organisms. Arl2 regulates the asymmetric division of neural stem cells in Drosophila via microtubule growth. However, the function of mammalian Arl2 during cortical development was unknown. Here, we demonstrate that mouse Arl2 plays a new role in corticogenesis via regulating microtubule growth, but not mitochondria functions. Arl2 knockdown leads to impaired proliferation of neural progenitor cells (NPCs) and neuronal migration. Arl2 knockdown in mouse NPCs significantly diminishes centrosomal microtubule growth and delocalization of centrosomal proteins Cdk5rap2 and {gamma}-tubulin. Moreover, Arl2 physically associates with Cdk5rap2 by in silico prediction using AlphaFold Multimer and in vitro binding assays. Remarkably, Cdk5rap2 overexpression significantly rescues the neurogenesis defects caused by Arl2 knockdown. Therefore, Arl2 plays an important role in mouse cortical development through microtubule growth via the centrosomal protein Cdk5rap2.

neuroscience↗

bioRxiv2024

Uncovering the Elusive Structures and Mechanisms of Prevalent Antidepressants

Most treatments to alleviate major depression work by either inhibiting human monoamine transporters, vital for the reuptake of monoamine neurotransmitters, or by inhibiting monoamine oxidases, which are vital for their degradation. The analysis of the experimental 3D structures of those antidepressants in their drug formulation state is key to precision drug design and development. In this study, we apply microcrystal electron diffraction (MicroED) to reveal the atomic 3D structures for the first time of five of the most prevalent antidepressants (reboxetine, pipofezine, ansofaxine, phenelzine, bifemelane) directly from the commercially available powder of the active ingredients. Their modes of binding are investigated by molecular docking, revealing the essential contacts and conformational changes into the biologically active state. This study underscores the combined use of MicroED and molecular docking to uncover elusive drug structures and mechanisms to aid in further drug development pipelines.

biochemistry↗

bioRxiv2023

A single-cell transposable element atlas of human cell identity

Single cell RNA sequencing (scRNA-seq) is revolutionizing the study of complex biological systems. However, most sequencing studies overlook the contribution of transposable element (TE) expression to the transcriptome. In both scRNA-seq and bulk tissue RNA sequencing (RNA-seq), quantification of TE expression is challenging due to repetitive sequence content and poorly characterized TE gene models. Here, we developed a tool and analysis pipeline for Single cell Transposable Element Locus Level Analysis of scRNA Sequencing (Stellarscope) that reassigns multi-mapped reads to specific genomic loci using an expectation-maximization algorithm. Using Stellarscope, we built an atlas of TE expression in human PBMCs. We found that locus-specific TEs delineate cell types and define new cell subsets not identified by standard mRNA expression profiles. Altogether, this study provides comprehensive insights into the influence of transposable elements in human biology.

genomics↗

bioRxiv2023

Ca2+ Oscillation in Vascular Smooth Muscle Cells Control Myogenic Spontaneous Vasomotion and Counteract Post-ischemic No-reflow

Ischemic stroke produces the highest adult disability. Despite successful recanalization, no-reflow, or the futile restoration of the cerebral perfusion after ischemia, is a major cause of brain lesion expansion. However, the vascular mechanism underlying this hypoperfusion is largely unknown, and no approach is available to actively promote optimal reperfusion to treat no-reflow. Here, by combining two-photon laser scanning microscopy (2PLSM) and a mouse middle cerebral arteriolar occlusion (MCAO) model, we found myogenic vasomotion deficits correlated with post-ischemic cerebral circulation interruptions and no-reflow. Transient occlusion-induced transient loss of mitochondrial membrane potential ({Delta}{Psi}m) permanently impaired mitochondria-endoplasmic reticulum (ER) contacts and abolished Ca2+ oscillation in smooth muscle cells (SMCs), the driving force of myogenic spontaneous vasomotion. Furthermore, tethering mitochondria and ER by specific overexpression of ME-Linker in SMCs restored cytosolic Ca2+ homeostasis, remotivated myogenic spontaneous vasomotion, achieved optimal reperfusion, and ameliorated neurological injury. Collectively, the maintaining of arteriolar myogenic vasomotion and mitochondria-ER contacts in SMCs, are of critical importance in preventing post-ischemic no-reflow.

neuroscience↗

bioRxiv2023

Computer simulation and mathematical modeling of the interactions between ecological and sexual selection to reveal the mechanism of sympatric speciation

In modern evolutionary theory, the mechanism of sympatric speciation is still an unsolved mystery. Ecological niche specialization and the subsequent premating reproductive isolation (RI) are the putative initial steps of sympatric speciation, even though the exact mechanism of how the former leads to the latter remains unclear. This study aims to develop a simple, intuitive, and realistic model ecosystem that uses the fewest variables possible but is still comprehensive enough to uncover the fundamental mechanisms of sympatric speciation. Applying the concept of an adaptive fitness landscape, the study used an individual-based computer simulation to investigate how ecological selection and sexual selection may interact to produce sympatric premating RI. Mathematical models were derived to describe the nonlinear adaptive dynamics of the system. A user-friendly computer application was able to solve, numerically, all the trajectories, fixed points, and bifurcation points of the models and display the solutions as phase portraits. The findings reveal that under favorable conditions, fixed points may emerge in the systems phase portraits to create stable mating-bias-allele polymorphisms and varying degrees of premating RI between niche ecotypes. Solving the nonlinear equations of the mathematical models establishes the precise parametric values required to produce such fixed points. It also specifies the conditions necessary for high-mating-bias mutant alleles to invade and produce, or enhance, premating RI. Restricting migration between niches impedes mutant invasion in parapatric and allopatric populations. Multi-locus mating traits may produce hybrids that prevent speciation. Simulation results of a gonochoric, multi-niche system demonstrate that linkage disequilibrium can emerge spontaneously among ecological, male-trait, and female-preference genotypes to produce premating RI. From these results, a five-stage mechanism of sympatric speciation is formulated: Initially, disruptive ecological selection creates selection pressure for high-mating-bias alleles to invade and rapidly establish premating RI. This then paves the way for the recruitment of late-stage mechanisms, such as adaptive coupling and post-zygotic isolation, to complete the speciation process. Applying nonlinear dynamics theories to model and analyze sympatric speciation has yielded novel findings that support and extend the results of prior studies. These new discoveries may help to overcome the theoretical objections to sympatric speciation and establish it as a prevalent mode of speciation in nature.

evolutionary biology↗