Biology subjects

Yang, Y.

Publications and source records attributed to Yang, Y..

At least 595 records · Page 33Linked to original sources

bioRxiv2024

An organoid co-culture model for probing systemic anti-tumor immunity in lung cancer

Deciphering the interactions between tumor micro- and systemic immune macro-environment is essential for developing more effective cancer diagnosis and treatment strategies. Here, we established a gel-liquid interface (GLI) co-culture of lung cancer organoids (LCOs) and paired peripheral blood mononuclear cells (PBMCs), featuring with enhanced interactions of immune cells and tumor organoids, to mimic the in vivo systemic anti-tumor immunity induced by immune checkpoint inhibitors (ICI). The co-culture model recapitulates the in vivo ICI-induced T cell recruitment and subsequent tumor regression, predicting the clinical results precisely. We demonstrated that circulating tumor-reactive T cells, which are effector memory-like with high expression levels of GNLY, CD44 and CD9, can serve as an indicator of the immunotherapy efficacy. Interestingly, enhanced inflammatory signaling in blood T cells is accompanied with prompted exhaustion and compromised anti-tumor function, when encountering with organoids. Our findings suggest that the GLI co-culture can be used for developing diagnostic strategies for precision immunotherapies as well as understanding the underlying mechanisms. Summary figure O_FIG O_LINKSMALLFIG WIDTH=178 HEIGHT=200 SRC="FIGDIR/small/597327v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@a0829dorg.highwire.dtl.DTLVardef@1df3083org.highwire.dtl.DTLVardef@1ea1065org.highwire.dtl.DTLVardef@1da9464_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

CellFM: a large-scale foundation model pre-trained on transcriptomics of 100 million human cells

The rapid evolution of single-cell sequencing technologies has facilitated precise transcriptomics profiling at the single-cell level, shedding light on the intricate heterogeneity within cellular populations. Despite these advances, the inherent diversity of cells and data challenges such as noise, batch effects, and sparsity, underscores the pressing need for a unified model to learn and represent cellular states effectively. Single-cell Large Language Models (LLMs) have been crafted to bridge this gap yet exhibit limited performance on human cells. This short-fall may stem from the confounding effects of training data from diverse species, partly because of limited cells for the single species. Here, we have compiled a dataset of approximately 100 million human cells sequenced by multiple technolo-gies from human single-cell datasets with various file types deposited in public databases and websites. Leveraging these extensive data cohorts, we developed CellFM, a robust single-cell foundation model with an impressive 800 million parameters, marking an eight-fold increase over the current largest single-species model. To ensure the training of CellFM on the MindSpore AI framework from Huawei, we have integrated RetNet, a Transformer architecture variant with lin-ear complexity for a balance between efficiency and performance, serving as the backbone of our model. Our comprehensive experiments have shown that CellFM outperforms existing models across diverse applications, such as cell annotation, perturbation prediction, and gene function prediction.

bioinformatics↗

bioRxiv2024

Electrochemically controlled switching of dyes for enhanced super-resolution optical fluctuation imaging (SOFI)

In super-resolution optical fluctuation imaging (SOFI), the locations of molecules spaced closer than the diffraction limit of light can be identified through spatial and temporal correlation analysis of the fluorescence intensity fluctuation. Using organic dyes as fluorophore probes, the fast but stochastic switching of the individual dyes is favourable for improving SOFI imaging resolution and speed, especially in the case of high-order cumulant analysis. While in practice, fluorophore switching can be non-uniform, with some fluorophores remaining in ON or OFF state for extended periods. Furthermore, in some cases the overall rate of switching of the fluorophores can be too slow, presenting practical limitations for high-resolution and fast SOFI imaging. In this work, we demonstrate how to overcome these challenges using electrochemical controlled fluorophore switching. The oscillating electrochemical potential setting with high frequency increases the switching rate and reduces the switching heterogeneity of fluorophores. The dye Alexa Fluor 647, applied here as an example, exhibits over 3-fold decrease in average ON time and over 2-fold decrease in switching variance, resulting in significantly improved SOFI image resolution with fewer frames. We demonstrated that this new electrochemically controlled SOFI imaging modality can achieve a SOFI image with [~]130 nm resolution in 2 seconds of acquisition time, and 80 nm resolution in 6 seconds. This advancement enables fast, large area tile-scan super-resolution imaging, which opens the full potential of SOFI imaging.

biophysics↗

bioRxiv2024

Structures of PSI-FCPI from Thalassiosira pseudonana in high light provide convergent evolution and light-adaptive strategies in diatom FCPIs

Diatoms achieve great survival success in the fluctuating oceanic environment, rely on fucoxanthin chlorophyll a/c-binding proteins (FCPs) to complete light harvesting and quenching, which provide about 20% primary productivity on earth. We report two cryo-electron microscopic structures of photosystem I (PSI) with 13 or 5 FCPIs respectively at 2.78 [A] and 3.20 [A] resolution from Thalassiosira pseudonana under high light conditions. 8 Lhcr FCPIs are found detached from the PSI-13FCPI supercomplex under high light conditions, remaining 5 FCPIs are stably combined with the PSI core including Lhcr3, RedCAP, Lhcq8, Lhcf10, and FCP3 subunits. The specific pigment network in this centric diatom T. pseudonana demonstrates a higher proportion of Chlorophylls a, diadinoxanthins, and diatoxanthins but fewer fucoxanthins compared with the huge PSI-FCPI from another centric diatom Chaetoceros gracilis, thus exhibiting more efficiency in energy transfer and dissipation among FCPI antennas. These results reveal the assembly mechanism of several types of peripheral FCPIs and corresponding light-adaptive strategies in T. pseudonana, as well as the convergent evolution of the diatoms PSI-FCPI structures.

plant biology↗

bioRxiv2024

Human sensorimotor cortex reactivates recent visuomotor experience during awake rest

Previous studies have suggested that awake rest after training is helpful in improving motor performance and memory consolidation in visuomotor learning. Re-emergence of task-related activation patterns during awake rest has been reported, which play a role in memory consolidation or perceptual learning. This study aimed to test whether such reactivation occurs after visuomotor learning in the primary sensorimotor cortex. During fMRI scanning, 42 normal participants learned visuomotor tracking, while a rotational perturbation was introduced between a cursor position and a joystick angle. This visuomotor learning block was interleaved with the control block, during which the participants passively viewed a replay of previously performed cursor movements of their own. Half of the participants used their right hand, and the other half used their left hand to control the joystick. The resting-state scans were measured before and after the visuomotor learning sessions. A multivariate pattern classifier was trained to classify task and control blocks and then tested with resting scans before and after learning. Results revealed a significant increase in the number of volumes classified as the task in the post-learning rest compared with the pre-learning, indicating a re-emergence of task-related activities. Representational similarity analysis also showed a more similar pattern of activity with the task during the post-learning rest period. Furthermore, this effect is specific to the primary sensorimotor cortex contralateral to the hand used and significantly correlated with motor improvement after rest. Our finding revealed the reactivation of task-related patterns in the primary sensorimotor cortex for offline visuomotor learning. Significance StatementPrevious research suggests that awake rest after learning promotes memory consolidation, which is subserved by the re-emergence of task-specific activity patterns. We aimed to determine whether such reactivation occurs in the primary sensorimotor cortex following visuomotor learning for offline memory consolidation. Our results showed a significant increase in task-classified brain volumes during the post-learning rest period compared to the pre-learning period, indicating a re-emergence of task-related activity. Furthermore, this effect was specific to the primary sensorimotor cortex contralateral to the hand used for the task and significantly correlated with the motor performance following the rest period. These findings provide evidence for the reactivation of task-related patterns during offline visuomotor learning, which may underlie memory consolidation processes.

neuroscience↗

bioRxiv2024

Effects of Ca2+ on the Structure and Dynamics of PIP3 in Model Membranes Containing PC and PS

Phosphatidylinositol phosphates (PIPs) are a family of seven different eukaryotic membrane lipids that have a large role in cell viability, despite their minor concentration in eukaryotic cellular membranes. PIPs tightly regulate cellular processes such as cellular growth, metabolism, immunity, and development through direct interactions with partner proteins. Understanding the biophysical properties of PIPs in the complex membrane environment is important to understand how PIPs selectively regulate a partner protein. Here we investigate the structure and dynamics of PIP3 in lipid bilayers that are simplified models of the natural membrane environment. We probe the effects of the anionic lipid phosphatidylserine (PS) and the divalent cation Ca2+. We use solution and solid-state 1H, 31P, and 13C NMR all at natural abundance combined with MD simulations to characterize the structure and dynamics of PIPs. 1H and 31P 1D spectra show good resolution at high temperatures with isolated peaks in the headgroup, interfacial, and bilayer regions. Site specific assignment of these 1D reporters were made and used to measure the effects of Ca2+ and PS. In particular, the resolved 31P signals of the PIP3 headgroup allowed for extremely well localized information about PIP3 phosphate dynamics, which the MD simulations were able to help explain. Cross polarization kinetics provided additional site-specific dynamics measurements for the PIP3 headgroups.

biochemistry↗

bioRxiv2024

The intestinal microbiome and Cetobacterium somerae inhibit viral infection through TLR2-type I IFN signaling axis in zebrafish

Accumulated evidences demonstrate that intestinal microbiome can inhibit viral infection. However, our knowledge of the signaling pathways and specific commensal microbes that mediate the antiviral response is limited. Here, a rhabdoviral infection model in zebrafish allows us to investigate the modes of action of microbiome-mediated antiviral effect. We observed that antibiotics-treated and germ-free zebrafish exhibited greater viral infection. Mechanistically, depletion of the intestinal microbiome alters TLR2-Myd88 signaling, and blunts neutrophil response and type I interferon (IFN) production. Moreover, a single commensal bacterium, Cetobacterium somerae, recapitulated TLR2- and type I IFN-dependent antiviral effect of the microbiome in gnotobiotic zebrafish, and C. somerae exopolysaccharides (CsEPS) was the effector molecule that engaged TLR2 to mediate antiviral function. Together, our results suggest a conserved role of intestinal microbiome in regulating type I IFN response among vertebrates, and reveal that the intestinal microbiome inhibits viral infection through a CsEPS-TLR2-type I IFN signaling axis in zebrafish.

microbiology↗

bioRxiv2024

FADS and semi-rational design modified T7 RNA polymerase reduced dsRNA production, with lower terminal transferase and RDRP activities

T7 RNA polymerase (T7 RNAP) is the preferred tool for in vitro transcription (IVT), it synthesizes mRNA while accompanied by the generation of dsRNA by-products. This undesirable dsRNA triggers immune stress responses, compromises therapeutic efficacy, and raises safety concerns. To evolve T7 RNAP for reduced dsRNA, we pursued two complementary strategies. Firstly, the FADS (fluorescence-activated droplet sorting) based on molecular beacons was used to screen random libraries with diversity exceeding 105. Secondly, we constructed several single-site saturated libraries to facilitate the transition of T7 RNAP from the initiation to the elongation conformation. These libraries were screened using the traditional microplate-based dual-probe screening technique. Both approaches identified two dominant variants: Mut1 (V214A) and Mut7 (F162S/A247T) from FADS, Mut11 (K180E) and Mut14 (A70Q) from saturated libraries. Furthermore, the combinatorial mutant Mut17 (A70Q/F162S/K180E), generated via DNA shuffling, exhibited significantly reduced dsRNA production compared to the wild-type under various conditions, ranging from 0.18% to 1.80%, with a minimum value of 0.5 pg/g. Cell experiments confirmed that variants generated capped-mRNA with similar quality and quantity to the wild-type, while significantly reducing immune stress response in cells. These results indicate the compatibility and broad potential applications of these mutations. We then observed a close correlation between the production of dsRNA and the activities of T7 RNAP in terminal transferase and RDRP. Particularly, the terminal transferase activity appears to play a critical role in dsRNA generation. These findings align with the mechanism of dsRNA formation during IVT and provide new screening criteria for further evolution of T7 RNAP.

molecular biology↗

bioRxiv2024

Deletion of adipocyte Sine Oculis Homeobox Homolog 1 prevents lipolysis and attenuates skin fibrosis.

Dermal fibrosis is a cardinal feature of systemic sclerosis (SSc) for which there are limited treatment strategies. This is in part due to our fragmented understanding of how dermal white adipose tissue (DWAT) contributes to skin fibrosis. We identified elevated sine oculis homeobox homolog 1 (SIX1) expression in SSc skin samples from the GENISOS and PRESS cohorts, the expression of which correlated with adipose-associated genes and molecular pathways. SIX1 localization studies identified increased signals in the DWAT area in SSc and in experimental models of skin fibrosis. Global and adipocyte specific Six1 deletion abrogated end-stage fibrotic gene expression and dermal adipocyte shrinkage induced by SQ bleomycin treatment. Further studies revealed a link between elevated SIX1 and increased expression of SERPINE1 and its protein PAI-1 which are known pro-fibrotic mediators. However, SIX1 deletion did not appear to affect cellular trans differentiation. Taken together these results point at SIX1 as a potential target for dermal fibrosis in SSc. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSSkin thickening and tightening are leading causes of morbidity in systemic sclerosis (SSc). The authors previously reported that the aberrantly expressed developmental transcription factor sine oculis homeobox homology 1 (SIX1) drives pulmonary fibrosis. However, the contribution of SIX1 to skin fibrosis and associated dermal fat loss remains unknown. Added value of this studyThe role of dermal fat loss in skin fibrosis is not fully understood. Studies have shown that adipocytes can transition to mesenchymal cells promoting fibrosis, consistent with loss of the dermal white adipose layer. Our research provides insight into a novel molecular mechanism of lipodystrophy important for skin fibrosis in SSc. We identified the upregulation of SIX1 in adipocytes in skin from patients with SSc which was associated with the progression of skin fibrosis. We found elevated Six1 in mouse dermal adipocytes of early fibrotic skin. Ubiquitous and adipose-specific loss of Six1 decreased markers of experimental skin fibrosis in mice which recapitulate cardinal features of SSc dermal fibrosis. Increased SIX1 expression is linked with elevated levels of Serpine1 the gene that codes for the protein plasminogen activator inhibitor (PAI)-1. This is important since PAI-1 is a known pro-fibrotic agent in the skin that contributes to the deposition of extracellular matrix (ECM) products. Implications of all the available evidenceFat atrophy may represent a targetable contributor to early systemic sclerosis manifestations. This is as it precedes skin fibrosis and the use of topical agent which are usually lipophilic can help us target dermal adipocytes. Our results show that SIX1 could be an important early marker for skin fibrosis in SSc that can also be targeted therapeutically.

molecular biology↗

bioRxiv2024

Ultra-stable insulin-glucagon fusion protein exploits an endogenous hepatic switch to mitigate hypoglycemic risk

The risk of hypoglycemia and its serious medical sequelae restrict insulin replacement therapy for diabetes mellitus. Such adverse clinical impact has motivated development of diverse glucose-responsive technologies, including algorithm-controlled insulin pumps linked to continuous glucose monitors ("closed-loop systems") and glucose-sensing ("smart") insulins. These technologies seek to optimize glycemic control while minimizing hypoglycemic risk. Here, we describe an alternative approach that exploits an endogenous glucose-dependent switch in hepatic physiology: preferential insulin signaling (under hyperglycemic conditions) versus preferential counter-regulatory glucagon signaling (during hypoglycemia). Motivated by prior reports of glucagon-insulin co-infusion, we designed and tested an ultra-stable glucagon-insulin fusion protein whose relative hormonal activities were calibrated by respective modifications; physical stability was concurrently augmented to facilitate formulation, enhance shelf life and expand access. An N-terminal glucagon moiety was stabilized by an -helix-compatible Lys13-Glu17 lactam bridge; A C-terminal insulin moiety was stabilized as a single chain with foreshortened C domain. Studies in vitro demonstrated (a) resistance to fibrillation on prolonged agitation at 37 {degrees}C and (b) dual hormonal signaling activities with appropriate balance. Glucodynamic responses were monitored in rats relative to control fusion proteins lacking one or the other hormonal activity, and continuous intravenous infusion emulated basal subcutaneous therapy. Whereas efficacy in mitigating hyperglycemia was unaffected by the glucagon moiety, the fusion protein enhanced endogenous glucose production under hypoglycemic conditions. Together, these findings provide proof of principle toward a basal glucose-responsive insulin biotechnology of striking simplicity. The fusion proteins augmented stability promises to circumvent the costly cold chain presently constraining global insulin access. Significance StatementThe therapeutic goal of insulin replacement therapy in diabetes is normalization of blood-glucose concentration, which prevents or delays long-term complications. A critical barrier is posed by recurrent hypoglycemic events that results in short- and long-term morbidities. An innovative approach envisions co-injection of glucagon (a counter-regulatory hormone) to exploit a glycemia-dependent hepatic switch in relative hormone responsiveness. To provide an enabling technology, we describe an ultra-stable fusion protein containing insulin- and glucagon moieties. Proof of principle was obtained in rats. A single-chain insulin moiety provides glycemic control whereas a lactam-stabilized glucagon extension mitigates hypoglycemia. This dual-hormone fusion protein promises to provide a basal formulation with reduced risk of hypoglycemia. Resistance to fibrillation may circumvent the cold chain required for global access.

bioengineering↗

bioRxiv2024

The variability of multidimensional diffusion-relaxation MRI estimates in the human brain

Diffusion-relaxation correlation multidimensional MRI (MD-MRI) replaces voxel-averaged diffusion tensor quantities and R1 and R2 relaxation rates with their multidimensional distributions, enabling the selective extraction and mapping of specific diffusion-relaxation spectral ranges that correspond to different cellular features. This approach has the potential of achieving high sensitivity and specificity in detecting subtle changes that would otherwise be averaged out. Here, the whole brain characterization of MD-MRI distributions and derived parameters is presented and the intrascanner test-retest reliability, repeatability, and reproducibility are evaluated to promote the further development of these quantities as neuroimaging biomarkers. We compared white matter tracts and cortical and subcortical gray matter regions, revealing notable variations in their diffusion-relaxation profiles, indicative of unique microscopic morphological characteristics. We found that the reliability and repeatability of MD-MRI-derived diffusion and relaxation mean parameters were comparable to values expected in conventional diffusion tensor imaging and relaxometry studies. Importantly, the estimated signal fractions of intra-voxel spectral components in the MD-MRI distribution, corresponding to white matter, gray matter, and cerebrospinal fluid, were found to be reproducible. This underscores the viability of employing a spectral analysis approach to MD-MRI data. Our results show that a clinically feasible MD-MRI protocol can reliably deliver information of the rich structural and chemical variety that exists within each imaging voxel, creating potential for new MRI biomarkers with enhanced sensitivity and specificity.

neuroscience↗

bioRxiv2024

CLEAN-Contact: Contrastive Learning-enabled Enzyme Functional Annotation Prediction with Structural Inference

Recent years have witnessed the remarkable progress of deep learning within the realm of scientific disciplines, yielding a wealth of promising outcomes. A prominent challenge within this domain has been the task of predicting enzyme function, a complex problem that has seen the development of numerous computational methods, particularly those rooted in deep learning techniques. However, the majority of these methods have primarily focused on either amino acid sequence data or protein structure data, neglecting the potential synergy of combining of both modalities. To address this gap, we propose a novel Contrastive Learning framework for Enzyme functional ANnotation prediction combined with protein amino acid sequences and Contact maps (CLEAN-Contact). We rigorously evaluated the performance of our CLEAN-Contact framework against the state-of-the-art enzyme function prediction model using multiple benchmark datasets. Using CLEAN-Contact, we predicted novel enzyme functions within the proteome of Prochlorococcus marinus MED4. Our findings convincingly demonstrate the substantial superiority of our CLEAN-Contact framework, marking a significant step forward in enzyme function prediction accuracy.

bioinformatics↗

bioRxiv2024

Interleukin-1 prevents SARS-CoV-2-induced membrane fusion to restrict viral transmission via induction of actin bundles

Innate immune responses triggered by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection play pivotal roles in the pathogenesis of COVID-19, while host factors including pro-inflammatory cytokines are critical for viral containment. By utilizing quantitative and qualitative models, we discovered that soluble factors secreted by human monocytes potently inhibit SARS-CoV-2-induced cell-cell fusion in viral-infected cells. Through cytokine screening, we identified that interleukin-1{beta} (IL-1{beta}), a key mediator of inflammation, inhibits syncytia formation mediated by various SARS-CoV-2 strains. Mechanistically, IL-1{beta} activates RhoA/ROCK signaling through a non-canonical IL-1 receptor-dependent pathway, which drives the enrichment of actin bundles at the cell-cell junctions, thus prevents syncytia formation. Notably, in vivo infection experiments in mice confirms that IL-1{beta} significantly restricted SARS-CoV-2 spreading in the lung epithelia. Together, by revealing the function and underlying mechanism of IL-1{beta} on SARS-CoV-2-induced cell-cell fusion, our study highlights an unprecedented antiviral function for cytokines during viral infection.

immunology↗

bioRxiv2024

Epigenetic delineation of the earliest cardiac lineage segregation by single-cell multi-omics

The mammalian heart is formed from multiple mesoderm-derived cell lineages. However, it remains largely unknown when and how the specification of mesoderm towards cardiac lineages is determined. Here, we systematically depict the transcriptional trajectories toward cardiomyocyte in early mouse embryo, and characterize the epigenetic landscapes underlying the early mesodermal lineage specification by single-cell multi-omics analyses. The analyses also reveal distinct core regulatory networks (CRN) in controlling specification of mesodermal lineages. We further demonstrate the essential role HAND1 and FOXF1 in driving the earliest cardiac progenitors specification. These key transcription factors occupy at distinct enhancers, but function synergistically and hierarchically to regulate the expression of cardiac-specific genes. In addition, HAND1 is required for exiting from the nascent mesoderm program, while FOXF1 is essential for driving cardiac differentiation during juxta-cardiac field (JCF) specification. Our findings establish transcriptional and epigenetic determinants specifying the early cardiac lineage, providing insights for the investigation of congenital heart defects.

molecular biology↗

bioRxiv2024

Brain-wide functional connectome analysis of 40,000 individuals reveals brain networks that show aging effects in older adults

The functional connectome changes with aging. We systematically evaluated aging related alterations in the functional connectome using a whole-brain connectome network analysis in 39,675 participants in UK Biobank project. We used adaptive dense network discovery tools to identify networks directly associated with aging from resting-state fMRI data. We replicated our findings in 499 participants from the Lifespan Human Connectome Project in Aging study. The results consistently revealed two motor-related subnetworks (both permutation test p-values <0.001) that showed a decline in resting-state functional connectivity (rsFC) with increasing age. The first network primarily comprises sensorimotor and dorsal/ventral attention regions from precentral gyrus, postcentral gyrus, superior temporal gyrus, and insular gyrus, while the second network is exclusively composed of basal ganglia regions, namely the caudate, putamen, and globus pallidus. Path analysis indicates that white matter fractional anisotropy mediates 19.6% (p<0.001, 95% CI [7.6% 36.0%]) and 11.5% (p<0.001, 95% CI [6.3% 17.0%]) of the age-related decrease in both networks, respectively. The total volume of white matter hyperintensity mediates 32.1% (p<0.001, 95% CI [16.8% 53.0%]) of the aging-related effect on rsFC in the first subnetwork.

neuroscience↗

bioRxiv2024

Bivariate multilevel meta-analysis of log response ratio and standardized mean difference for robust and reproducible environmental and biological sciences

Meta-analytic modelling plays a pivotal role in synthesizing research and informing relevant policies. Yet researchers face many analytical challenges. In environmental and biological sciences, one of the most common yet unrecognised issues is the selection between two common effect size metrics, log response ratio (lnRR) and standardized mean difference (SMD); these two are the most popular and alternative effect sizes. Having to choose between them creates room for analytical flexibility, which is susceptible to researcher degrees of freedom. Another common issue is failure to deal with statistical dependence between effect sizes, resulting in invalid inferences on evidence. We propose addressing these two issues through the joint synthesis (dual use) of lnRR and SMD. Using 75 meta-analyses, including 3,887 environmental/biological primary studies ([~]20,000 effect sizes), we show a high false positive rate (40%) in conventional meta-analytic practices (random-effects model) compared to the proposed bivariate multilevel meta-analysis of lnRR and SMD along with robust variance estimation. Relying solely on either lnRR or SMD results in non-trivial discrepancies in detecting statistically significant effects (18%) and occasional inconsistencies in sign (9%). Discrepancies in interpreting effect size, heterogeneity, and publication bias are prevalent between models using lnRR and SMD (e.g., 52% for publication bias). In contrast, bivariate synthesis of lnRR and SMD yields substantial information gain, reducing standard error in effect size estimates by 29%, equivalent to adding 40 additional effect sizes. We present a user-friendly website with a step-by-step implementation guide. Our proposed robust approach aspires to improve meta-analytic modelling using lnRR and SMD in environmental and biological evidence synthesis, amplifying their reproducibility and credibility.

ecology↗

bioRxiv2024

Opto-chemogenetic inhibition of L-type CaV1 channels in neurons through a membrane-assisted molecular linkage

Acute, specific, and robust inhibition of L-type Ca2+ (CaV1) channels has been sought after for both research and therapeutic applications. Compared to other available CaV1 antagonists, genetically-encoded modulators, such as CMI (C-terminus mediated inhibition) peptides encoded by CaV1 DCT (distal C-terminus), hold great potentials due to its affirmative mechanisms of action on both gating and signaling. Here, we find that membrane-anchoring with a Ras tag could essentially help form a type of intramolecular-equivalent linkage, by which the tag anchored-peptide appears to dimerize with another protein or peptide on the membrane, supported by the evidence from patch-clamp electrophysiology and FRET imaging. We then design and implement the constitutive and inducible CMI modules, with appropriate dynamic ranges targeting the short and long variants of CaV1.3, both naturally occurring in neurons. Upon optical (infrared-responsive nanoparticles) and/or chemical (rapamycin) induction of FRB/FKBP binding, DCT peptides with no CMI in the cytosol acutely translocate onto the membrane via FRB-Ras, where the physical linkage requirement could be fulfilled. The peptides robustly produce acute and potent inhibitions on both recombinant CaV1.3 channels and neuronal CaV1 activities, and thus the Ca2+ influx-neuritogenesis coupling. Validated through opto-chemogenetic induction, this prototype demonstrates channel modulation via membrane-assisted molecular linkage, promising broad applicability to diverse membrane proteins.

bioengineering↗

bioRxiv2024

Laminar fMRI in the locked-in stage of amyotrophic lateral sclerosis shows preserved activity in layer Vb of primary motor cortex

Amyotrophic lateral sclerosis (ALS) affects the cerebral cortex layer-dependently, most notably by the foremost targeting of upper motor neurons (UMNs) sited in layer Vb. Previous studies have shown a retained ability of paralysed patients to activate residual cortical motor networks, even in late-stage ALS. However, it is currently unknown whether such activation reflects a retained capacity to process sensorimotor inputs or if it is a result of actual motor output. Given the distinct function of individual cortical layers, layer-specific functional measurements may provide insight to this question. In this study, using submillimetre resolution laminar fMRI, we assessed the layer-dependent activation associated with attempted (motor) and passive (somatosensory) movements in a locked-in stage ALS patient. We found robust activation in both superficial and deep layers of primary motor cortex. The peak activation in deep layers was localised to layer Vb. These findings demonstrate preserved activity in deep output layers of M1, possibly reflecting a retained ability to engage residual UMNs despite years of paralysis. Our study underscores the capacity of laminar fMRI to discern subtle cortical activity and elucidates a promising pathway for probing in vivo human ALS pathology with unprecedented resolution.

neuroscience↗