Biology subjects

Cai, S.

Publications and source records attributed to Cai, S..

At least 73 records · Page 4Linked to original sources

bioRxiv2021

Auditory attention detection with EEG channel attention

Auditory attention detection (AAD) seeks to detect the attended speech from EEG signals in a multi-talker scenario, i.e. cocktail party. As the EEG channels reflect the activities of different brain areas, a task-oriented channel selection technique improves the performance of brain-computer interface applications. In this study, we propose a soft channel attention mechanism, instead of hard channel selection, that derives an EEG channel mask by optimizing the auditory attention detection task. The neural AAD system consists of a neural channel attention mechanism and a convolutional neural network (CNN) classifier. We evaluate the proposed framework on a publicly available database. We achieve 88.3% and 77.2% for 2-second and 0.1-second decision windows with 64-channel EEG; and 86.1% and 83.9% for 2-second decision windows with 32-channel and 16-channel EEG, respectively. The proposed framework outperforms other competitive models by a large margin in all test cases.

neuroscience↗

bioRxiv2021

Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ

Nuclear processes depend on the organization of chromatin, whose basic units are cylinder-shaped complexes called nucleosomes. A subset of mammalian nucleosomes in situ (inside cells) resembles the canonical structure determined in vitro 25 years ago. Nucleosome structure in situ is otherwise poorly understood. Using cryo-ET and 3-D classification analysis of budding yeast cells, here we find that canonical nucleosomes account for less than 10% of total nucleosomes expected in situ. In a strain in which H2A-GFP is the sole source of histone H2A, class averages that resemble canonical nucleosomes both with and without GFP densities are found ex vivo (in nuclear lysates), but not in situ. These data suggest that the budding yeast intranuclear environment favors multiple non-canonical nucleosome conformations. Using the structural observations here and the results of previous genomics and biochemical studies, we propose a model in which the average budding yeast nucleosomes DNA is partially detached in situ.

cell biology↗

bioRxiv2020

The neural circuitry underlying the "rhythm effect" in stuttering

PurposeStuttering is characterized by intermittent speech disfluencies which are dramatically reduced when speakers synchronize their speech with a steady beat. The goal of this study was to characterize the neural underpinnings of this phenomenon using functional magnetic resonance imaging. MethodData were collected from 17 adults who stutter and 17 adults who do not stutter while they read sentences aloud either in a normal, self-paced fashion or paced by the beat of a series of isochronous tones ("rhythmic"). Task activation and task-based functional connectivity analyses were carried out to compare neural responses between speaking conditions and groups. ResultsAdults who stutter produced fewer disfluent trials in the rhythmic condition than in the normal condition. While adults who do not stutter had greater activation in the rhythmic condition compared to the normal condition in regions associated with speech planning, auditory feedback control, and timing perception, adults who stutter did not have any significant changes. However, adults who stutter demonstrated increased functional connectivity between bilateral inferior cerebellum and bilateral orbitofrontal cortex as well as increased connectivity among cerebellar regions during rhythmic speech as compared to normal speech. ConclusionModulation of connectivity in the cerebellum and prefrontal cortex during rhythmic speech suggests that this fluency-inducing technique activates a compensatory timing system in the cerebellum and potentially modulates top-down motor control and attentional systems. These findings corroborate previous work associating the cerebellum with fluency in adults who stutter and indicate that the cerebellum may be targeted to enhance future therapeutic interventions.

neuroscience↗

bioRxiv2020

Through-scalp deep-brain stimulation in tether-free, naturally-behaving mice with widefield NIR-II illumination

Neural modulation techniques with electricity, light and other forms of energy have enabled the deconstruction of neural circuitry. One major challenge of existing neural modulation techniques is the invasive brain implants and the permanent skull attachment of an optical fiber for modulating neural activity in the deep brain. Here we report an implant-free and tether-free optical neuromodulation technique in deep-brain regions through the intact scalp with brain-penetrant second near-infrared (NIR-II) illumination. Macromolecular infrared nanotransducers for deep-brain stimulation (MINDS) demonstrate exceptional photothermal conversion efficiency of 71% at 1064 nm, the wavelength that minimizes light attenuation by the brain in the entire 400-1700 nm spectrum. Upon widefield 1064-nm illumination >50 cm above the mouse head at a low incident power density of 10 mW/mm2, deep-brain neurons are activated by MINDS-sensitized TRPV1 channels with minimal thermal damage. Our approach could open opportunities for simultaneous neuromodulation of multiple socially interacting animals by remotely irradiating NIR-II light to stimulate each subject individually.

neuroscience↗

bioRxiv2020

Genetically Determined Strength of Natural Killer Cells is Enhanced by Adaptive HLA class I Admixture in East Asians

Human natural killer (NK) cells are essential for controlling infection, cancer and fetal development. NK cell functions are modulated by interactions between polymorphic inhibitory killer cell immunoglobulin-like receptors (KIR) and polymorphic HLA-A, -B and -C ligands expressed on tissue cells. All HLA-C alleles encode a KIR ligand and contribute to reproduction and immunity. In contrast, only some HLA-A and -B alleles encode KIR ligands and they focus on immunity. By high-resolution analysis of KIR and HLA-A, -B and -C genes, we show that the Chinese Southern Han are significantly enriched for interactions between inhibitory KIR and HLA-A and -B. This enrichment has had substantial input through population admixture with neighboring populations, who contributed HLA class I haplotypes expressing the KIR ligands B*46:01 and B*58:01, which subsequently rose to high frequency by natural selection. Consequently, over 80% of Southern Han HLA haplotypes encode more than one KIR ligand. Complementing the high number of KIR ligands, the Chinese Southern Han KIR locus combines a high frequency of genes expressing potent inhibitory KIR, with a low frequency of those expressing activating KIR. The Southern Han centromeric KIR region encodes strong, conserved, inhibitory HLA-C specific receptors, and the telomeric region provides a high number and diversity of inhibitory HLA-A and -B specific receptors. In all these characteristics, the Southern Han represent other East Asians, whose NK cell repertoires are thus enhanced in quantity, diversity and effector strength, likely through natural selection for resistance to endemic viral infections.

immunology↗

bioRxiv2020

An endogenous scaling mechanism in zebrafish appendages that controls two-pore potassium-leak channel activity to regulate morphogen and growth factor transcription.

The increase in activity of the two-pore potassium-leak channel Kcnk5b maintains allometric juvenile growth of adult zebrafish appendages. However, it remains unknown how this channel maintains allometric growth and how its bioelectric activity is regulated to scale these anatomical structures. We show the activation of Kcnk5b is sufficient to activate several genes that are part of important development programs. We provide in vivo transplantation evidence that the activation of gene transcription is cell autonomous. We also show that Kcnk5b will induce the expression of different subsets of the tested developmental genes in different cultured mammalian cell lines, which may explain how one electrophysiological stimulus can coordinately regulate the allometric growth of diverse populations of cells in the fin that use different developmental signals. We also provide evidence that the post-translational modification of serine 345 in Kcnk5b by calcineurin regulates channel activity to scale the fin. Thus, we show how an endogenous bioelectric mechanism can be regulated to promote coordinated developmental signaling to generate and scale a vertebrate appendage.

developmental biology↗

bioRxiv2020

TAZ inhibits GR and coordinates hepatic glucose homeostasis in normal physiologic states

The elucidation of the mechanisms whereby the liver maintains glucose homeostasis is crucial for the understanding of physiologic and pathologic states. Here, we show a novel role of hepatic transcriptional co-activator with PDZ-binding motif (TAZ) in the inhibition of glucocorticoid receptor (GR). TAZ interacts via its WW domain with the ligand-binding domain of GR to limit the binding of GR to gluconeogenic gene promoters. Therefore, liver-specific TAZ knockout mice show increases in glucose production and blood glucose concentration. Conversely, the overexpression of TAZ in mouse liver reduces the binding of GR to gluconeogenic gene promoters and glucose production. Thus, our findings demonstrate distinct roles of the hippo pathway effector proteins yes-associated protein 1 (YAP) and TAZ in liver physiology: while deletion of hepatic YAP has little effect on glucose homeostasis, hepatic TAZ protein expression decreases upon fasting and coordinates gluconeogenesis in response to physiologic fasting and feeding.

biochemistry↗

bioRxiv2020

Studies on CRMP2 SUMOylation-deficient transgenic mice identify sex-specific NaV1.7 regulation in the pathogenesis of chronic neuropathic pain

The sodium channel NaV1.7 is a master regulator of nociceptive neuronal firing. Mutations in this channel can result in painful conditions as well as produce insensitivity to pain. Despite being recognized as a "poster child" for nociceptive signaling and human pain, targeting NaV1.7 has not yet produced a clinical drug. Recent work has illuminated the NaV1.7 interactome, offering insights into the regulation of these channels and identifying potentially new druggable targets. Amongst the regulators of NaV1.7 is the cytosolic collapsin response mediator protein 2 (CRMP2). CRMP2, modified at Lysine 374 (K374) by addition of a small ubiquitin-like modifier (SUMO), bound NaV1.7 to regulate its membrane localization and function. Corollary to this, preventing CRMP2 SUMOylation was sufficient to reverse mechanical allodynia in rats with neuropathic pain. Notably, loss of CRMP2 SUMOylation did not compromise other innate functions of CRMP2. To further elucidate the in vivo role of CRMP2 SUMOylation in pain, we generated CRMP2 K374A knock-in (CRMP2K374A/K374A) mice in which Lys374 was replaced with Ala. CRMP2K374A/K374A mice had reduced NaV1.7 membrane localization and function in female, but not male, sensory neurons. Behavioral appraisal of CRMP2K374A/K374A mice demonstrated no changes in depressive or repetitive, compulsive-like behaviors, and a decrease in noxious thermal sensitivity. No changes were observed in CRMP2K374A/K374A mice to inflammatory, acute, or visceral pain. In contrast, in a neuropathic model, CRMP2K374A/K374A mice failed to develop persistent mechanical allodynia. Our study suggests that CRMP2 SUMOylation-dependent control of peripheral NaV1.7 is a hallmark of chronic, but not physiological, neuropathic pain.

neuroscience↗

bioRxiv2020

Evaluating the transcriptional fidelity of cancer models

BackgroundCancer researchers use cell lines, patient derived xenografts, engineered mice, and tumoroids as models to investigate tumor biology and to identify therapies. The generalizability and power of a model derives from the fidelity with which it represents the tumor type under investigation, however, the extent to which this is true is often unclear. The preponderance of models and the ability to readily generate new ones has created a demand for tools that can measure the extent and ways in which cancer models resemble or diverge from native tumors. MethodsWe developed a machine learning based computational tool, CancerCellNet, that measures the similarity of cancer models to 22 naturally occurring tumor types and 36 subtypes, in a platform and species agnostic manner. We applied this tool to 657 cancer cell lines, 415 patient derived xenografts, 26 distinct genetically engineered mouse models, and 131 tumoroids. We validated CancerCellNet by application to independent data, and we tested several predictions with immunofluorescence. ResultsWe have documented the cancer models with the greatest transcriptional fidelity to natural tumors, we have identified cancers underserved by adequate models, and we have found models with annotations that do not match their classification. By comparing models across modalities, we report that, on average, genetically engineered mice and tumoroids have higher transcriptional fidelity than patient derived xenografts and cell lines in four out of five tumor types. However, several patient derived xenografts and tumoroids have classification scores that are on par with native tumors, highlighting both their potential as faithful model classes and their heterogeneity. ConclusionsCancerCellNet enables the rapid assessment of transcriptional fidelity of tumor models. We have made CancerCellNet available as freely downloadable software and as a web application that can be applied to new cancer models that allows for direct comparison to the cancer models evaluated here.

bioinformatics↗

bioRxiv2020

Macromolecular and biochemical changes of G0 fission yeast nuclei

When starved of nitrogen, fission yeast Schizosaccharomyces pombe cells enter a quiescent "G0" state with smaller nuclei and transcriptional repression. The genomics of S. pombe G0 cells has been well studied, but much of its nuclear cell biology remains unknown. Here we use confocal microscopy, immunoblots, and electron cryotomography to investigate the cytological, biochemical, and ultrastructural differences between S. pombe proliferating, G1-arrested, and G0 cell nuclei, with an emphasis on the histone acetylation, RNA polymerase II fates, and macromolecular complex packing. Compared to proliferating cells, G0 cells have lower levels of histone acetylation, nuclear RNA polymerase II, and active transcription. The G0 nucleus has similar macromolecular crowding yet fewer chromatin-associated multi-megadalton globular complexes. Induced histone hyperacetylation in G0 results in cells that have larger nuclei and therefore less compact chromatin. However, these histone-hyperacetylated G0 cells remain transcriptionally repressed with similar nuclear crowding. Canonical nucleosomes - those that resemble the crystal structure - are rare in proliferating, G1-arrested, and G0 cells. Our study therefore shows that extreme changes in nucleus physiology are possible without extreme reorganisation at the macromolecular level. SummaryWe use multiple cell-biological techniques to compare proliferating and quiescent G0 fission yeast cell nucleus transcription, histone acetylation, macromolecular packing.

cell biology↗

bioRxiv2019

Cryo-ET analysis of budding yeast synaptonemal complexes in situ

In meiosis, cells undergo two sequential rounds of cell division, termed meiosis I and meiosis II. Textbook models of the meiosis I substage called pachytene show that nuclei have conspicuous 100-nm-wide, ladder-like synaptonemal complexes (SC), which form between homologous chromosomes. It remains unknown if cells have any other large, meiosis-specific nuclear structures. Here we present cryo-ET analysis of frozen-hydrated budding yeast cells before, during, and after pachytene. We found no evidence for the dense ladder-like structures expected of the SC or the ordered chromatin loops expected to project from their sides. Instead, we found large quantities of 12-nm-wide triple-helices that pack into crystalline bundles. These structures are present in meiotic cells, but not in interphase cells, so we call them meiotic triple helices (MTHs). MTHs are enriched in the nucleus but not enriched in the cytoplasm. Bundles of MTHs form at the same time as SCs in wild-type cells and also in mutant cells that are unable to form SCs. These results suggest that in yeast, SCs are not crystalline and that they coexist with large, previously unreported meiotic machines.

cell biology↗

bioRxiv2019

Single-cell transcriptional diversity is a hallmark of developmental potential

Single-cell RNA-sequencing (scRNA-seq) is a powerful approach for reconstructing cellular differentiation trajectories. However, inferring both the state and direction of differentiation without prior knowledge has remained challenging. Here we describe a simple yet robust determinant of developmental potential--the number of detectably expressed genes per cell-- and leverage this measure of transcriptional diversity to develop a new framework for predicting ordered differentiation states from scRNA-seq data. When evaluated on ~150,000 single-cell transcriptomes spanning 53 lineages and five species, our approach, called CytoTRACE, outperformed previous methods and ~19,000 molecular signatures for resolving experimentally-confirmed developmental trajectories. In addition, it enabled unbiased identification of tissue-resident stem cells, including cells with long-term regenerative potential. When used to analyze human breast tumors, we discovered candidate genes associated with less-differentiated luminal progenitor cells and validated GULP1 as a novel gene involved in tumorigenesis. Our study establishes a key RNA-based correlate of developmental potential and provides a new platform for robust delineation of cellular hierarchies (https://cytotrace.stanford.edu).

genomics↗

bioRxiv2019

A collection of yeast cellular electron cryotomography data

BackgroundCells are powered by a large set of macromolecular complexes, which work together in a crowded environment. The in situ mechanisms of these complexes are unclear because their 3-D distribution, organization, and interactions are largely unknown. Electron cryotomography (cryo-ET) is a key tool to address these knowledge gaps because it produces cryotomograms -- 3-D images that reveal biological structure at approximately 4-nm resolution. Cryo-ET does not involve any fixation, dehydration, staining, or plastic embedment, meaning that cellular features are visualized in a life-like, frozen-hydrated state. To study chromatin and mitotic machinery in situ, we have subjected yeast cells to a variety of genetic and/or chemical perturbations, cryosectioned them, and then imaged the cells by cryo-ET.\n\nFindingsEvery study from our group has generated more cryo-ET data than needed. Only the small subset of data that contributed to figures in these studies have been publicly shared. Here we share more than 1,000 cryo-ET raw datasets of cryosectioned budding yeast S. cerevisiae. This data will be valuable to cell biologists who are interested in the nanoscale organization of yeasts and of eukaryotic cells in general. To facilitate access, all the unpublished tilt series and a subset of corresponding cryotomograms have been deposited in the EMPIAR resource for the cell-biology community to use freely. To improve tilt series discoverability, we have uploaded metadata and preliminary notes to publicly accessible google spreadsheets.\n\nConclusionsCellular cryo-ET data can be mined to obtain new cell-biological, structural, and 3-D statistical insights in situ. Because these data capture cells in a life-like state, they contain some structures that are either absent or not visible in traditional EM data. Template matching and subtomogram averaging of known macromolecular complexes can reveal their 3-D distributions and low-resolution structures. Furthermore, these data can serve as testbeds for high-throughput image-analysis pipelines, as training sets for feature-recognition software, for feasibility analysis when planning new structural cell-biology projects, and as practice data for students who are learning cellular cryo-ET.

cell biology↗

bioRxiv2019

Age-dependent characterization of the carotid and cerebral artery morphologies in a transgenic mouse model of sickle cell anemia using ultrasound and microcomputed tomography

Children with sickle cell anemia have elevated stroke risks as well as other arterial complications, but morphological changes to large arteries are not well defined, and the focus has been on the microcirculation where deoxygenation promotes sickling of red blood cells. The goal of this study was to define morphological changes in carotid and cerebral arteries in the Townes transgenic sickle cell mouse model, and to specifically determine anatomical measurement differences in mice homozygous for {beta}-globin S mutation (SS) compared to heterozygous (AS) littermate controls. We used a combination of live imaging with ultrasound and microcomputed tomography (micro-CT) imaging of corrosion casted vessels to quantify arterial dimensions and changes in mice 4, 12, and 24 weeks of age with or without sickle cell anemia. 12 week SS mice had significantly larger common carotid artery diameters than AS mice, and significantly larger diameters in the extracranial and intracranial portions of the internal carotid artery (ICA), determined by ultrasound and micro-CT, respectively. There were also side specific differences between the left and right vessels. There was significant narrowing along ICA length in 12-and 24-week SS mice, decreasing by as much as 70%, such that there was no difference in size between the anterior and middle cerebral arteries, where the ICA terminates, by genotype. Significant narrowing along the length was also measured in the anterior cerebral arteries of 12-and 24-week SS mice, but not AS. Collectively, these findings indicate that sickle cell anemia causes increased arterial dimensions in 12-and 24-week aged mice. We also provide these measurements for the common carotid, internal carotid, anterior cerebral, and middle cerebral arteries for left and right sides, for AS and SS genotypes as a reference for other investigators using in silico modeling of arterial complications caused by aging with sickle cell anemia.

pathology↗

bioRxiv2019

TooManyCells identifies and visualizes relationships of single-cell clades

Transcriptional programs contribute to phenotypic and functional cell states. While elucidation of cell state heterogeneity and its role in biology and pathobiology has been advanced by studying single cell level measurements, the underlying assumptions of current analytical methods limit the identification and exploration of cell clades. Unlike other methods, which produce a single uni-layer partition of cells ignoring echelons of cell states, we present TooManyCells, a software consisting of a suite of graph-based tools for efficient, global, and unbiased identification and visualization of cell clades while maintaining and presenting the relationship between cell states. TooManyCells provides a set of tools based on a matrix-free efficient divisive hierarchical spectral clustering algorithm wholly different from the prevalent Louvain-based methods. BirchBeer, the visualization component of TooManyCells, introduces a new approach for single cell analysis that is built on a concept intentionally orthogonal to the widely used dimensionality reduction methods. Together, this suite of tools provide a paradigm shift in the analysis and interpretation of single cell data by enabling simultaneous comparisons of cell states at context-and application-dependent scales. A byproduct of this shift is the immediate detection and visualization of rare populations that outperforms previous algorithms as demonstrated by applying these tools to existing single cell RNA-seq data sets from various mouse organs.

bioinformatics↗

bioRxiv2018

Sex-dependent differences in pain and sleep in a porcine model of Neurofibromatosis type 1

Neurofibromatosis Type 1 (NF1) is an autosomal dominant genetic disorder resulting from germline mutations in the NF1 gene, which encodes neurofibromin. Patients experience a variety of symptoms, but pain in the context of NF1 remains largely underrecognized. Here, we characterize nociceptive signaling and pain behaviors in a miniswine harboring a disruptive NF1 mutation (exon 42 deletion). We explore these phenotypes in relationship to collapsin response mediator protein 2 (CRMP2), a known interactor of neurofibromin. Mechanistically, we found two previously unknown phosphorylated residues of CRMP2 in NF1+/ex42del pig dorsal root ganglia (DRGs) and replicated increased voltage-gated calcium channel currents in NF1+/ex42del pig DRGs previously described in rodent models of NF1. We present the first characterization of pain-related behaviors in a pig model of NF1, identifying unchanged agitation scores, lower tactile thresholds (allodynia), and decreased response latencies to thermal laser stimulation (hyperalgesia) in the NF1 mutant animals; NF1+/ex42del pigs demonstrated sexually dimorphic behaviors. NF1+/ex42del pigs showed reduced sleep quality and increased resting, two health-related quality of life symptoms found to be comorbid in people with NF1 pain. Finally, we show decreased depolarization-evoked calcium influx in both wildtype and NF1+/ex42del pig DRGs treated with CRMP2 phosphorylation inhibitor (5)-lacosamide. Our data supports use of NF1+/ex42del pigs as an ideal model for studying NF1-associated pain and are a better model for understanding the pathophysiology of NF1 compared to rodents. Moreover, our findings demonstrate that interfering with CRMP2 phosphorylation might be a promising therapeutic strategy for NF1-related pain management.

neuroscience↗

bioRxiv2018

High stretchability, strength and toughness of living cells enabled by hyperelastic vimentin network

In many normal and abnormal physiological processes, including cellular migration during normal development and invasion in cancer metastasis, cells are required to withstand severe deformations. The structural integrity of eukaryotic cells under small deformations has been known to depend on the cytoskeleton including actin filaments (F-actin), microtubules and intermediate filaments (IFs). However, it remains unclear how cells resist severe deformations since both F-actin and microtubules fluidize or disassemble under moderate strains. Here, we demonstrate that vimentin intermediate filaments (VIFs), a marker of mesenchymal cells, dominate cytoplasmic mechanics at large deformations. Our results show that cytoskeletal VIFs form a stretchable, hyperelastic network. This network works synergistically with other dissipative cytoplasmic components, substantially enhancing the strength, stretchability, resilience and toughness of the living cytoplasm.

biophysics↗

bioRxiv2018

The in situ structures of mono-, di-, and tri-nucleosomes in human heterochromatin

The in situ 3-D organization of chromatin at the nucleosome and oligonucleosome levels is unknown. Here we use cryo-electron tomography (cryo-ET) to determine the in situ structures of HeLa nucleosomes, which have canonical core structures and asymmetric, flexible linker DNA. Subtomogram remapping suggests that sequential nucleosomes in heterochromatin follow irregular paths at the oligonucleosome level. This basic principle of higher-order repressive chromatin folding is compatible with the conformational variability of the two linker DNAs at the single-nucleosome level.

cell biology↗