Biology subjects

Han, C.

Publications and source records attributed to Han, C..

123 records · Page 7Linked to original sources

bioRxiv2020

Reconstruction of Bone Defect Based on the Fusion of Osteoblasts and MSM/HA/PLGA Porous Scaffolds

Reconstruction of bone defect is one of the difficult problems in orthopedic treatment, and bone tissue scaffold implantation is the most promising direction of bone defect reconstruction. In this study, we used the combination of HA (Hydroxyapatite) and PLGA [Poly (lactic-co-glycolic acid)] in the construction of polymer scaffolds, and introduced bioactive MSM (Methyl sulfonyl methane) into polymer scaffolds to prepare porous scaffolds. The osteoblasts, isolated and cultured in vitro, were seeded in the porous scaffolds to construct tissue-engineered scaffolds. Meanwhile, the model of rabbit radius defect was constructed to evaluate the biological aspects of five tissue-engineered scaffolds, which provided experimental basis for the application of the porous scaffolds in bone tissue engineering. The SEM characterization showed the pore size of porous scaffolds was uniform and the porosity was about 90%. The results of contact Angle testing suggested that the hydrophobic porous scaffold surface could effectively promote cell adhesion and cell proliferation, while mechanical property test showed good machinability. The results of drug loading and release efficiency of MSM showed that porous scaffolds could load MSM efficiently and prolong the release time of MSM. In vitro incubation of porous scaffolds and osteoblasts showed that the addition of a small quantity of MSM could promote the infiltration and proliferation of osteoblasts on the porous scaffolds. Similar results were obtained by implanting the tissue-engineered scaffolds, fused with the osteoblasts and MSM/HA/PLGA porous scaffolds, into the rabbit radius defect, which provided experimental basis for the application of the MSM/HA/PLGA porous scaffolds in bone tissue engineering.

bioengineering↗

bioRxiv2020

Quantitative LCMS for ceramides/dihydroceramides: pregnancy baseline biomarkers and potential metabolic messengers

Ceramides and dihydroceramides are sphingolipids that present in abundance at the cellular membrane of eukaryotes. Although their metabolic dysregulation has been implicated in many diseases, our knowledge about circulating ceramide changes during the pregnancy remains limited. In this study, we present the development and validation of a high-throughput liquid chromatography-tandem mass spectrometric (LC/MS/MS) method for simultaneous quantification of 16 ceramides and 10 dihydroceramides in human serum within 5 mins by using stable isotope-labeled ceramides as internal standards (ISs). This method employs a protein precipitation method for high throughput sample preparation, reverse phase isocratic elusion for chromatographic separation, and Multiple Reaction Monitoring (MRM) for mass spectrometric detection. To qualify for clinical applications, our assay was validated against the FDA guidelines: the Lower Limit of Quantitation (LLOQ as low as 1 nM), linearity (R2>0.99), precision (Coefficient of Variation<15%), accuracy (Percent Error<15%), extraction recovery (>90%), stability (>85%), and carryover (<0.1%). With enhanced sensitivity and specificity from this method, we have, for the first time, determined the serological levels of ceramides and dihydroceramides to reveal unique temporal gestational patterns. Our approach could have value in providing insights into disorders of pregnancy.

biochemistry↗

bioRxiv2020

Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation

BackgroundThe three-dimensional genome organization is critical for gene regulation and can malfunction in diseases like cancer. As a key regulator of genome organization, CCCTC-binding factor (CTCF) has been characterized as a DNA-binding protein with important functions in maintaining the topological structure of chromatin and inducing DNA looping. Among the prolific binding sites in the genome, several events with altered CTCF occupancy have been reported as associated with effects in physiology or disease. However, there is no hitherto a comprehensive survey of genome-wide CTCF binding patterns across different human cancers. ResultsTo dissect functions of CTCF binding, we systematically analyze over 700 CTCF ChIP-seq profiles across human tissues and cancers and identify cancer-specific CTCF binding patterns in six cancer types. We show that cancer-specific lost and gained CTCF binding events are associated with altered chromatin interactions in patient samples, but not always with DNA methylation changes or sequence mutations. While lost bindings primarily occur near gene promoters, most gained CTCF binding events are induced by oncogenic transcription factors and exhibit enhancer activities. We validate these findings in T-cell acute lymphoblastic leukemia and show that oncogenic NOTCH1 induces specific CTCF binding and they cooperatively activate expression of target genes, indicating transcriptional condensation phenomena. ConclusionsCancer-specific CTCF binding events are not always associated with DNA methylation changes or mutations, but can be induced by other transcription factors to regulate oncogenic gene expression. Our results substantiate CTCF binding alteration as a functional epigenomic signature of cancer.

genomics↗

bioRxiv2019

Evolution from total variation to nonlinear sparsifying transform for sparse-view CT image reconstruction

Sparse-view CT has been widely studied as an effective strategy for reducing radiation dose to patients. However, the conventional image reconstruction algorithms, such as filtered back-projection method and classical algebraic reconstruction techniques, can no longer be competent in the image reconstruction task of sparse-view CT. A new principle, called compressed sensing (CS), has been therefore developed to provide an effective solution for the ill-posed inverse problem of sparse-view CT image reconstruction. Total variation (TV) minimization, which is most extensively studied among the existing CS techniques, has been recognized as a powerful tool for dealing with this difficult problem in image reconstruction community. However, in recent years, the drawbacks of TV are being increasingly reported, which are appearance of patchy artifacts, depict of incorrect object boundaries, and loss in image textures or smooth intensity changes. These degradations appear especially in reconstructing actual CT images with complicated intensity changes. In order to address these drawbacks, a series of advanced algorithms using nonlinear sparsifying transform (NLST) have been proposed very recently. The NLST-based CS is based on a different framework from the TV, and it achieves an improvement in image quality. Since it is a relatively newly proposed idea, within the scope of our knowledge, there exist few literatures that discusses comprehensively how the image quality improvement occurs in comparison with the conventional TV method. In this study, we investigated the image quality differences between the conventional TV minimization and the NLST-based CS, as well as image quality differences among different kinds of NLST-based CS algorithms in the sparse-view CT image reconstruction. More specifically, image reconstructions of actual CT images of different body parts were carried out to demonstrate the image quality differences.

bioinformatics↗

bioRxiv2019

Gradual decrease in the inter-population diversity of HIV-1 Env among group M lineages worldwide

HIV-1 group M was transmitted to humans nearly one century ago. The virus has since diversified to form distinct clades, which spread to multiple regions worldwide. Of the different proteins encoded by HIV-1, the envelope glycoproteins (Envs) have diversified most rapidly in all infected populations. We compared the range of variants that emerged during the AIDS pandemic in diverse HIV-1 clades and distinct geographic regions. Our analyses focused on two components of Env that contain multiple epitopes of broadly-neutralizing antibodies: the glycan shield and apex domain. Interestingly, at each Env position, the amino acid in the inferred clade ancestor was replaced by a unique combination of emerging variants. Key antigenic sites and genetic signatures of vaccine protection have gradually evolved toward conserved frequency distributions (FDs) of all amino acids. FDs are specific for position and clade and are highly conserved in populations from different regions. Remarkably, founder effects of Env mutations in distinct clades and recently-infected regions were significantly reduced during the epidemic by evolution of each site toward the position-specific FD. These findings suggest that the selective pressures that guide evolution of Env are conserved in different populations. They are sufficiently strong to reduce founder effects at the clade and regional levels and have significantly altered the distribution of Env forms that circulate worldwide. Consequently, the intra-population diversity of the Env protein continues to increase whereas the inter-population diversity is gradually decreasing.\n\nImportanceThe Env protein of HIV-1 is the primary target in AIDS vaccine design. Due to frequent mutations, new Env variants continuously emerge in the population. The increasing number of Env forms and apparent randomness of the changes limit our ability to design broadly-effective vaccines. We examined the populations-level changes that occurred in Env during the AIDS epidemic. Each position of the molecule has evolved toward a specific combination of amino acids. Similar changes occurred in different HIV-1 subtypes and geographic regions toward the same sets of forms, often from distinct ancestral sequences. Such conserved patterns of evolution define a new framework for designing vaccines that are tailored to the unique combination of Env variants expected to circulate in each population.

evolutionary biology↗

bioRxiv2019

Low FoxO expression in Drosophila somatosensory neurons protects dendrite growth under nutrient restriction

During prolonged nutrient restriction, developing animals redistribute vital nutrients to favor brain growth at the expense of other organs. In Drosophila, such brain sparing relies on a glia-derived growth factor to sustain proliferation of neural stem cells. However, whether other aspects of neural development are also spared under nutrient restriction is unknown. Here we show that dynamically growing somatosensory neurons in the Drosophila peripheral nervous system exhibit organ sparing at the level of arbor growth: Under nutrient stress, sensory dendrites preferentially grow as compared to neighboring non-neural tissues, resulting in dendrite overgrowth. Underlying this neuronal nutrient-insensitivity is the lower expression of the stress sensor FoxO in neurons. Consequently, nutrient restriction suppresses Tor signaling less and does not induce autophagy in neurons. Preferential dendrite growth is functional desirable because it results in heightened animal responses to sensory stimuli, indicative of a potential survival advantage under environmental challenges.

neuroscience↗

bioRxiv2019

Computational modelling of the long-term effects of brain stimulation on the local and global structural connectivity of epileptic patients

In patients with drug resistant focal epilepsy, targeted weak stimulation of the affected brain regions has been proposed as an alternative to surgery. However, the effectiveness of stimulation as a treatment presents great variation from patient to patient. In this study, brain activity is simulated for a period of one day using a network of Wilson-Cowan oscillators coupled according to diffusion imaging based structural connectivity. We use this computational model to examine the potential long-term effects of stimulation on brain connectivity. Our findings indicate that the overall simulated effect of stimulation is heavily dependent on the excitability of the stimulated regions. Additionally, stimulation seems to lead to long-term effects in the connectivity of secondary (non-stimulated) regions in epileptic patients. These effects are correlated with a worse surgery outcome in some patients, which suggests that long-term simulations could be used as a tool to determine suitability for surgery/stimulation.

neuroscience↗

bioRxiv2019

Background free tracking of single RNA in living cells using catalytically inactive CasE

RNAs have important and diverse functions. Visualizing an isolated RNA in living cells provide us essential information of its roles. By now, there are two kinds of live RNA imaging systems invented, one is the MS2 system and the other is the Cas13a system. In this study, we show that when fused with split-Fp, CasE can be engineered into a live RNA tracking tool.

molecular biology↗

bioRxiv2019

Three-dimensional genome reorganization during mouse spermatogenesis

Three-dimensional genome organization plays an important role in many biological processes. Yet, how the genome is packaged at the molecular level during mammalian spermatogenesis remains unclear. Here, we performed Hi-C in seven sequential stages during mouse spermatogenesis. We found that topological associating domains (TADs) and chromatin loops underwent highly dynamic reorganization. They displayed clear existence in primitive type A spermatogonia, disappearance at pachytene stage, and reestablishment in spermatozoa. Surprisingly, even in the absence of TADs and chromatin loops at pachytene stage, CTCF remained bound at TAD boundary regions (identified in primitive type A spermatogonia). Additionally, many enhancers and promoters exhibited features of open chromatin and transcription remained active at pachytene stage. A/B compartmentalization and segmentation ratio were conserved in different stages of spermatogenesis in autosomes, although there were A/B compartment switching events correlated with gene activity changes. Intriguingly, A/B compartment structure on the X chromosome disappeared during pacSC, rST and eST stages. Together, our work uncovered a dynamic three-dimensional chromatin organization during mouse spermatogenesis and suggested that transcriptional regulation could be independent of TADs and chromatin loops at specific developmental stages.

genomics↗

bioRxiv2018

Alteration of Vascular Endothelial Cadherin in Alzheimer’s Disease Patient and Mouse Model

Alzheimers disease (AD) is characterized by amyloid plaques and pathologic cerebrovascular remodeling. Cerebrovascular abnormalities may contribute to the pathology of AD, but the molecular mechanisms are not fully understood. In this study, we evaluated blood-brain barrier (BBB) disruption and the role of VE-cadherin in the progression of amyloid pathology. Here, we determined that levels of VE-cadherin are decreased in brain vessels of AD patients and mouse model of AD. In vitro experiments showed that the disappearance of VE-cadherin by beta-amyloid at the endothelial cell surface was due to cleavage of VE-cadherin. VE-cadherin cleavage was inhibited by a {gamma}-secretase and ADAM10 inhibitor. The disappearance of VE-cadherin in brain vessels was also seen in amyloid precursor protein transgenic mice. In the postmortem brain of individuals with AD, furthermore, levels of VE-cadherin were significantly reduced in vessels. Dementia patients showed a distinct blood biochemical profile characterized by high soluble VE-cadherin (sVEC). There was a strong association between plasma sVEC (adjusted odds ratio = 3.41, P < 0.001) and dementia. These results suggest that measurements of plasma VE-cadherin could have the potential for predicting the risk of progressive AD.

neuroscience↗

bioRxiv2018

Nuclear export of chimeric mRNAs depends on an lncRNA-triggered autoregulatory loop

Aberrant chromosomal translocations leading to tumorigenesis have been ascribed to the heterogeneously oncogenic functions. However, how fusion transcripts exporting remains to be declared. Here, we showed that the nuclear speckle-specific long non coding RNA MALAT1 controls chimeric mRNA export processes and regulates myeloid progenitor cell differentiation in malignant hematopoiesis. We demonstrated that MALAT1 regulates chimeric mRNAs export in an m6A-dependent manner and thus controls hematopoietic cell differentiation. Specifically, reducing MALAT1 or m6A methyltransferases and the reader YTHDC1 result in the universal retention of distinct oncogenic gene mRNAs in nucleus. Mechanically, MALAT1 hijacks both the chimeric mRNAs and fusion proteins in nuclear speckles during chromosomal translocations and mediates the colocalization of oncogenic fusion proteins with METTL14. MALAT1 and fusion protein complexes serve as a functional loading bridge for the interaction of chimeric mRNA and METTL14. This study demonstrated a universal mechanism of chimeric mRNA transport that involves lncRNA-fusion protein-m6A autoregulatory loop for controlling myeloid cell differentiation. Targeting the lncRNA-triggered autoregulatory loop to disrupt chimeric mRNA transport might represent a new common paradigm for treating blood malignancies.

cancer biology↗

bioRxiv2018

Highly efficient CRISPR/Cas9-mediated tissue specific mutagenesis in Drosophila

Tissue-specific loss-of-function (LOF) analysis is an essential approach for characterizing gene function. Here we describe an efficient CRISPR-mediated tissue-restricted mutagenesis (CRISPR-TRiM) method for ablating gene function in Drosophila. This binary system consists of a tissue-specific Cas9 and a ubiquitously expressed multi-guide RNA (gRNA) transgene. To facilitate the construction of these components, we developed convenient tools for generating and evaluating enhancer-driven Cas9 lines, identified a multi-gRNA design that is highly efficient in mutagenizing somatic cells, and established an assay for testing the efficiency of multi-gRNAs in creating double-stranded breaks. We found that excision of genomic DNA induced by two gRNAs is infrequent in somatic cells, while indels more reliably cause tissue-specific LOF. Furthermore, we show that enhancer-driven Cas9 is less cytotoxic yet results in more complete gene removal than Gal4-driven Cas9 in larval neurons. Finally, we demonstrate that CRISPR-TRiM efficiently unmasks redundant gene functions in neuronal morphogenesis. Importantly, two Cas9 transgenes that turn on with different timings in the neuronal lineage revealed the extent to which gene products persist in cells after tissue-specific gene knockout. These CRISRPR tools can be applied to analyze tissue-specific gene function in many biological processes.

developmental biology↗

bioRxiv2017

No evidence for correlations between handgrip strength and sexually dimorphic acoustic properties of voices

ObjectivesRecent research on the signal value of masculine physical characteristics in men has focused on the possibility that such characteristics are valid cues of physical strength. However, evidence that sexually dimorphic vocal characteristics are correlated with physical strength is equivocal. Consequently, we undertook a further test for possible relationships between physical strength and masculine vocal characteristics.\n\nMethodsWe tested the putative relationships between White UK (N=115) and Chinese (N=106) participants handgrip strength (a widely used proxy for general upper-body strength) and five sexually dimorphic acoustic properties of voices: fundamental frequency (F0), fundamental frequencys standard deviation (F0-SD), formant dispersion (Df), formant position (Pf), and estimated vocal-tract length (VTL).\n\nResultsAnalyses revealed no clear evidence that stronger individuals had more masculine voices.\n\nConclusionsOur results do not support the hypothesis that masculine vocal characteristics are a valid cue of physical strength.

evolutionary biology↗

bioRxiv2017

Women’s preferences for facial masculinity are not related to their hormonal status

Although widely cited as strong evidence that sexual selection has shaped human facial attractiveness judgments, evidence that preferences for masculine characteristics in mens faces are related to womens hormonal status is equivocal and controversial. Consequently, we conducted the largest ever longitudinal study of the hormonal correlates of womens preferences for facial masculinity (N=584). Analyses showed no compelling evidence that preferences for facial masculinity were related to changes in womens salivary steroid hormone levels. Furthermore, both within-subject and between-subject comparisons showed no evidence that oral contraceptive use decreased masculinity preferences. However, women generally preferred masculinized over feminized versions of mens faces, particularly when assessing mens attractiveness for short-term, rather than long-term, relationships. Our results do not support the hypothesized link between womens preferences for facial masculinity and their hormonal status.

animal behavior and cognition↗

bioRxiv2017

Within-Woman Hormone-Attractiveness Correlations Are Not Simply Byproducts Of Between-Women Hormone-Attractiveness Correlations

Putative associations between sex hormones and attractive physical characteristics in women are central to many theories of human physical attractiveness and mate choice. Although such theories have become very influential, evidence that physically attractive and unattractive women have different hormonal profiles is equivocal. Consequently, we investigated hypothesized relationships between salivary estradiol and progesterone and two aspects of womens physical attractiveness that are commonly assumed to be correlated with levels of these hormones: facial attractiveness (N=249) and waist-to-hip ratio (N=247). Our analyses revealed no evidence that women with more attractive faces or lower (i.e., more attractive) waist-to-hip ratios had higher levels of estradiol or progesterone. These results do not support the influential hypothesis that between-woman differences in physical attractiveness are related to estradiol and/or progesterone.

animal behavior and cognition↗