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Zhao, F.

Publications and source records attributed to Zhao, F..

At least 145 records · Page 8Linked to original sources
bioRxiv2019

Mapping polyclonal antibody responses in non-human primates vaccinated with HIV Env trimer subunit vaccines

Rational immunogen design aims to focus antibody responses to vulnerable sites on the primary antigens. Given the size of these antigens there is however potential for eliciting unwanted, off-target responses. Here, we used our electron microscopy polyclonal epitope mapping approach to describe the antibody specificities elicited by immunization of non-human primates with soluble HIV envelope trimers and subsequent repeated viral challenge. An increased diversity of epitopes recognized, and the approach angle by which these antibodies bound, constituted a hallmark of the humoral response in most protected animals. We also show that fusion peptide-specific antibodies are responsible for some neutralization breadth. Moreover, cryoEM analysis of a fully-protected animal revealed a high degree of clonality within a subset of putatively neutralizing antibodies, enabling a detailed molecular description of the antibody paratope. Our results provide important insights into the immune response against a vaccine candidate that entered into clinical trials earlier this year.

immunology↗
bioRxiv2019

High Yield Monolayer Graphene Grids for Near-Atomic Resolution Cryo-Electron Microscopy

Cryogenic electron microscopy (cryo-EM) has become one of the most powerful techniques to reveal the atomic structures and working mechanisms of biological macromolecules. New designs of the cryo-EM grids--aimed at preserving thin, uniform vitrified ice and improving protein adsorption--have been considered a promising approach to achieving higher resolution with the minimal amount of materials and data. Here, we describe a method for preparing graphene cryo-EM grids with 99% monolayer graphene coverage that allows for more than 70% grid squares for effective data acquisition with improved image quality and protein density. Using our graphene grids, we have achieved 2.6 [A] resolution for streptavidin, with a molecular weight of 52 kDa, from 11,000 particles. Our graphene grids increase the density of examined soluble, membrane, and lipo-proteins by at least five times, affording the opportunity for structural investigation of challenging proteins which cannot be produced in large quantity. In addition, our method employs only simple tools that most structural biology laboratories can access. Moreover, our approach allows for customized grid designs targeting specific proteins, due to its broad compatibility with a variety of nanomaterials. Significance statementSingle particle cryogenic electron microscopy (cryo-EM) represents the cutting-edge technology to determine three-dimensional atomic structures of bio-macromolecules. However, issues of cryo-sample preparation limit the cryo-EM to achieve higher resolution. Here, we demonstrated a high yield, monolayer graphene supporting film to improve the cryo-sample quality. Using our approach, we have achieved so far, the highest resolution structure of the smallest protein by cryo-EM with the minimal number of datasets. Our technique paves the way for universal cryo-sample preparation for near-atomic resolution cryo-EM.

biophysics↗
bioRxiv2019

Single-cell analysis of human retina identifies evolutionarily conserved and species-specific mechanisms controlling development.

The development of single-cell RNA-Sequencing (scRNA-Seq) has allowed high resolution analysis of cell type diversity and transcriptional networks controlling cell fate specification. To identify the transcriptional networks governing human retinal development, we performed scRNA-Seq over retinal organoid and in vivo retinal development, across 20 timepoints. Using both pseudotemporal and cross-species analyses, we examined the conservation of gene expression across retinal progenitor maturation and specification of all seven major retinal cell types. Furthermore, we examined gene expression differences between developing macula and periphery and between two distinct populations of horizontal cells. We also identify both shared and species-specific patterns of gene expression during human and mouse retinal development. Finally, we identify an unexpected role for ATOH7 expression in regulation of photoreceptor specification during late retinogenesis. These results provide a roadmap to future studies of human retinal development, and may help guide the design of cell-based therapies for treating retinal dystrophies.

neuroscience↗
bioRxiv2019

MACF1 Facilitates SMAD7 Nuclear Translocation to Drive Bone Formation in Mice

MACF1 is a large crosslinker that contributes to cytoskeleton integrity and cell differentiation. Loss of MACF1 impairs multiple cellular functions in neuron development and epidermal migration, and is the molecular basis for many diseases such as heart failure and Parkinsons disease. MACF1 is highly abundant in bones, however, its involvements in osteogenic differentiation and bone formation are still unknown. In this study, by conditional gene targeting to delete the Macf1 gene specifically in MSCs, we observed ossification retardation and bone loss in MACF1 deficient mice in different developmental stages, which we traced to disorganized cytoskeleton and decreased osteogenic differentiation capability in MSCs. Further, we show that MACF1 interacts and facilitates SMAD7 nuclear translocation to initiate downstream transcription. These findings are hopefully to expand the biological scope of MACF1 in bones, and provide experimental basis for targeting MACF1 in degenerative bone diseases such as osteoporosis.

developmental biology↗
bioRxiv2019

Linking light-dependent life history traits with population dynamics for Prochlorococcus and cyanophage

Prochlorococcus grow in diurnal rhythms driven by diel cycles. Their ecology depends on light, nutrients, and top-down mortality processes including lysis by viruses. Cyanophage, viruses that infect cyanobacteria, are also impacted by light. For example, extracellular viability and intra-cell infection kinetics of some cyanophage vary between light and dark conditions. Nonetheless, it remains unclear if light-dependent viral life history traits scale-up to influence population-level dynamics. Here we examined the impact of diel-forcing on both cellular- and population-scale dynamics in multiple Prochlorococcus-phage systems. To do so, we developed a light-driven population model including both cellular growth and viral infection dynamics. We then tested the model against measurements of experimental infection dynamics with diel forcing to examine the extent to which population level changes in both viral and host abundances could be explained by light-dependent life history traits. Model-data integration reveals that light-dependent adsorption can improve fits to population dynamics for some virus-host pairs. However, light-dependent variation alone does not fully explain realized host and virus population dynamics. Instead, we show evidence of a previously unrecognized lysis saturation at relatively high virus to cell ratios. Altogether, our study represents a quantitative approach to integrate mechanistic models to reconcile Prochlorococcus-virus dynamics spanning cellular to population scales.

microbiology↗
bioRxiv2019

Biomechanical Analysis of Angular Motion in Association with Bilateral Semicircular Canal Function

The aim of this study was to develop a finite element (FE) model of bilateral human semicircular canals (SCCs) in order to simulate and analyze the complex fluid-structural interaction between the endolymph and cupulae by calculating the degree of cupular expansion and the cupular deflection. The results showed that cupular deflection responses were consistent with Ewalds II law, whereas each pair of bilateral cupulae simultaneously expanded or compressed to the same degree. In addition, both the degree of cupular expansion and cupular deflection can be expressed as the solution of forced oscillation during head sinusoidal rotation, and the amplitude of cupular expansion was approximately two times greater than that of cupular deflection. Regarding the amplitude-frequency and phase-frequency characteristics, the amplitude ratios among the horizontal semicircular canal (HC) cupular expansion, the anterior semicircular canal (AC) cupular expansion, and the posterior semicircular canal (PC) cupular expansion was constant at 1:0.82:1.62, and the phase differences among them were constant at 0 or 180 degrees at the frequencies of 0.5 to 6 Hz. However, both the amplitude ratio and the phase differencies of the cupular deflection incresed nonlinearly with the increase of frequency and tended to be constant at the frequency band between 2 and 6 Hz. The results indicate that the responses of cupular expansion might only be related to the mass and rigidity of three cupulae and the endolymph, but the responses of cupular deflection are related to the mass, rigidity, or damping of them, and these physical properties would be affected by vestibular dysfunction. Therefore, both the degree of cupular expansion and cupular deflection should be considered important mechanical variables for induced neural signals. Such a numerical model can be further built to provide a useful theoretical approach for exploring the biomechanical nature underlying vestibular dysfunction.\n\nStatement of significanceBy taking the advantage of the torsional pendulum model and the FE model, a healthy human vestibular SCCs was developed to investigate the angular motion in association with SCC function. As a result, the responses of cupular expansion and deflection during head horizontal sinusoidal rotation were analyzed for the first time, showing quantitative correlation to the eye movement due to the vestibular ocular reflex (VOR) pathway. These responses play important roles in the cupular mechano-electrical transduction process. The significant outcome derived from this study provides a useful theoretical approach for further exploring the biomechanical nature underlying vestibular dysfunction.

bioengineering↗
bioRxiv2019

Clinicopathological characteristics and survival of lymphoepithelial carcinoma of the oral cavity and pharynx: a population-based study

Lymphoepithelial carcinoma (LEC) of the oral cavity and pharynx is uncommon, and the characteristics and survival remains unclear. The present study aims to describe the clinicopathological characteristics and determine the factors associated with survival of this uncommon cancer. A population-based study was carried out to investigate clinical characteristics and prognosis of LEC of the oral cavity and pharynx using the data from Surveillance, Epidemiology and End Results (SEER) database between 1988 and 2013. The propensity-matched analysis was conducted for prognostic analysis, and a prognostic nomogram was also constructed. Totally, 1025 patients with LEC of the oral cavity and pharynx were identified, including 769 nasopharyngeal LEC patients and 256 non-nasopharyngeal LEC patients. The median OS of all LEC patients was 232.0m (95% CI 169.0-258.0). The 1-, 5-, 10- and 20-year survival rates were 92.9%, 72.9%, 59.3%, and 46.8%, respectively. Surgery could significantly prolong the survival time of LEC patients (P<0.01, mOS: 190m vs. 255m). Radiotherapy, as well as radiotherapy after surgery, could prolong the mOS (P<0.01 for both). The survival analysis demonstrated that old age (>60 years), lymph node (N3) and distant metastases were independent factors for poor survival, whereas radiotherapy and surgery were independent factors for favorable survival. No significant differences in survival time between nasopharyngeal LEC and non-nasopharyngeal LEC patients were observed. The prognostic nomogram was established base on five independent prognostic factors (C-index=0.70; 95% CI 0.66-0.74). In conclusion, LEC of the oral cavity and pharynx is a rare disease, and old age, lymph node and distant metastases, surgery and radiotherapy were significantly associated with prognosis. The prognostic nomogram could be used to make individual predictions of OS.

genetics↗
bioRxiv2019

Efficient and accurate prediction of transmembrane topology from amino acid sequence only

MotivationRapid and accurate identification of transmembrane (TM) topology is well suited for the annotation of the entire membrane proteome. It is the initial step of predicting the structure and function of membrane proteins. However, existing methods that utilize only amino acid sequence information suffer from low prediction accuracy, whereas methods that exploit sequence profile or consensus need too much computational time.\n\nMethodHere we propose a deep learning framework DeepCNF that predicts TM topology from amino acid sequence only. Compared to previous sequence-based approaches that use hidden Markov models or dynamic Bayesian networks, DeepCNF is able to incorporate much more contextual information by a hierarchical deep neural network, while simultaneously modeling the interdependency between adjacent topology labels.\n\nResultExperimental results show that PureseqTM not only outperforms existing sequence-based methods, but also reaches or even surpasses the profile/consensus methods. On the 39 newly released membrane proteins, our approach successfully identifies the correct TM segments and boundaries for at least 3 cases while all existing methods fail to do so. When applied to the entire human proteome, our method can identify the incorrect annotations of TM regions by UniProt and discover the membrane-related proteins that are not manually curated as membrane proteins.\n\nAvailabilityhttp://pureseqtm.predmp.com/

bioinformatics↗
bioRxiv2019

Xyloglucan homeostasis and microtubule dynamics synergistically maintain meristem geometry and robustness of phyllotaxis in Arabidopsis

The shoot apical meristem (SAM) gives rise to all aerial organs of the plant. The cell walls are supposed to play a central role in this process, translating molecular regulation into dynamic changes of growth rates and directions, although their precise role in morphogenesis during organ formation remains not well understood. Here we investigate the role of xyloglucans (XyGs), which form a major, yet functionally poorly characterized, wall component in the SAM. Using immunolabeling, biochemical analysis, genetic approaches, micro-indentation, laser ablations and live imaging, we show that XyGs are important for meristem shape and phyllotaxis, although no difference in cell wall stiffness could be observed when XyGs are perturbed. Mutations in enzymes required for XyG synthesis also affect other cell wall components such as cellulose content and the pectin methylation status. Interestingly, we show that the control of cortical microtubules dynamics by the severing enzyme KATANIN becomes vital when XyGs are perturbed or absent. This suggests an active role of the cytoskeleton in compensating for altered wall composition.

plant biology↗
bioRxiv2019

A microtubule-mediated mechanical feedback controls leaf blade development in three dimensions

Many plant species have thin leaf blades, which is an important adaptation that optimizes the exchanges with the environment. Here, we provide evidence that their three-dimensional geometry is governed by microtubule alignment along mechanical stress patterns in internal walls. Depending on the primary shape of the primordium, this process has the potential to amplify an initial degree of flatness, or promote the formation of nearly axisymmetric, mostly elongating organs, such as stems and roots. This mechanism may explain leaf evolution from branches, which is alternative to Zimmermanns influential, but widely questioned, telome theory.\n\nOne Sentence SummaryMechanical feedback controls leaf development in three dimensions

developmental biology↗
bioRxiv2019

Chromatin mapping and single-cell immune profiling define the temporal dynamics of ibrutinib drug response in chronic lymphocytic leukemia

Chronic lymphocytic leukemia (CLL) is a genetically, epigenetically, and clinically heterogeneous disease. Despite this heterogeneity, the Bruton tyrosine kinase (BTK) inhibitor ibrutinib provides effective treatment for the vast majority of CLL patients. To define the underlining regulatory program, we analyzed high-resolution time courses of ibrutinib treatment in closely monitored patients, combining cellular phenotyping (flow cytometry), single-cell transcriptome profiling (scRNA-seq), and chromatin mapping (ATAC-seq). We identified a consistent regulatory program shared across all patients, which was further validated by an independent CLL cohort. In CLL cells, this program starts with a sharp decrease of NF-{kappa}B binding, followed by reduced regulatory activity of lineage-defining transcription factors (including PAX5 and IRF4) and erosion of CLL cell identity, finally leading to the acquisition of a quiescence-like gene signature which was shared across several immune cell types. Nevertheless, we observed patient-to-patient variation in the speed of its execution, which we exploited to predict patient-specific dynamics in the response to ibrutinib based on pre-treatment samples. In aggregate, our study describes the cellular, molecular, and regulatory effects of therapeutic B cell receptor inhibition in CLL at high temporal resolution, and it establishes a broadly applicable method for epigenome/transcriptome-based treatment monitoring.

cancer biology↗
bioRxiv2018

Hypoxic Training Increases the Concentration of Serum Irisin and Reduces Weight in Diet-induced Obese Rats

Irisin promotes browning of white fat, improves energy metabolism, and-weight loss. In this study, we investigated the effects of different oxygen concentrations during hypoxic training on the serum irisin and the PGC-1(peroxisome proliferator-activated receptor gamma coactivator 1-alpha)-FNDC5(fibronectin type III domain containing 5)-UCPl(uncoupling protein 1) signaling pathway in the skeletal muscle of obese rats. Male Sprague-Dawley Obese rats (n=80) were randomly divided into 8 groups as follows: the control group (group A, n=10); the endurance exercise group (AE group, n=10), which involved animal treadmill training at slope 0{degrees}, 20 m/min, 40 min/d, and 5 d/w; the 16.3% hypoxia exposure group (group B, n=10), 13.3% hypoxia exposure group (group C, n=10), and 11.3% hypoxia exposure group (group D, n=10), which were exposed to a low oxygen environment with oxygen concentrations of 16.3%, 13.3%, and 11.3%, respectively, for 12 h/d; and the 16.3% hypoxic training group (BE group, n=10), 13.3% hypoxic training group (CE group, n=10), and 11.3% hypoxic training group (DE group, n=10) with animal treadmill training during hypoxia exposure. After 8 weeks, the serum irisin concentrations in the AE, BE, CE, and DE groups were significantly higher than that in the A group (p<0.05). Hypoxia exposure and hypoxic training at the three different concentrations significantly increased PGC-1 and FNDC5 gene expression in the skeletal muscle. The PGC-1 and FNDC5 protein contents were significantly higher in the skeletal muscle of the obese rats in the C, AE, and DE groups than those in group A (p<0.05). UCP1 protein expression was significantly higher in groups C, CE, D, and DE than in group A (p<0.05). To conclude, training at oxygen concentrations of 13.3% and 11.3% significantly increased the serum irisin level, and 11.3% hypoxic training enhanced the effects of the PGC-l-Irisin-UCP1 signaling pathway in skeletal muscle.

biochemistry↗
bioRxiv2018

Single-cell RNA-seq analysis maps the development of human fetal retina

Vision starts with image formation at the retina, which contains diverse neuronal cell types that extract, process, and relay visual information to higher order processing centers in the brain. Though there has been steady progress in defining retinal cell types, very little is known about retinal development in humans, which starts well before birth. In this study, we performed transcriptomic profiling of developing human fetal retina from gestational weeks 12 to 27 using single-cell RNA-seq (scRNA-seq) and used pseudotime analysis to reconstruct the developmental trajectories of retinogenesis. Our analysis reveals transcriptional programs driving differentiation down four different cell types and suggests that Muller glia (MG) can serve as embryonic progenitors in early retinal development. In addition, we also show that transcriptional differences separate retinal progenitor cells (RPCs) into distinct subtypes and use this information to reconstruct RPC developmental trajectories and cell fate. Our results support a hierarchical program of differentiation governing cell-type diversity in the developing human retina. In summary, our work details comprehensive molecular classification of retinal cells, reconstructs their relationships, and paves the way for future mechanistic studies on the impact of gene regulation upon human retinogenesis.

neuroscience↗
bioRxiv2018

LRScaf: Improving Draft Genomes Using Long Noisy Reads

BackgroundThe advent of Third Generation Sequencing (TGS) technologies opens the door to improve genome assembly. Long reads are promised to enhance the quality of fragmental draft assemblies constructed from Next Generation Sequencing (NGS) technologies. To date, a few of algorithms, i.e., SSPACE-LongRead, OPERA-LG, SMIS, npScarf, DBG2OLC, Unicycler, and LINKS, have been released that are capable of improving draft assemblies. However, hybrid assembly on large genomes is still challenging.\n\nResultsWe develop a scalable and computationally efficient scaffolder, Long Reads Scaffolder (LRScaf), that is capable of boosting assembly contiguity to a large extent using long reads. In our experiment, our method significantly improves the contiguity of human draft assemblies, increasing the NG50 value of CHM1 from 127.5 Kb to 10.4 Mb using 20-fold coverage PacBio dataset and the NG50 value of NA12878 from 115.7 Kb to 17.4 Mb using 35-fold coverage Nanopore dataset. The run time for the scaffolding procedure using LRScaf is the shortest in all cases of our experiment. Compared with the run time of SSPACE-LongRead, LRScaf is faster 300 times for S. cerevisiae and 2,300 times for D. melanogaster. The peak RAM of LRScaf, by contrast, is more efficient than LINKS in our test. For the rice case, the peak RAM of LINKS (877.72 Gb) is about 196 times higher than LRScaf. For the experiment of human assembly, the peak RAM of LINKS is beyond the capacity of system memory (1 Tb) whereas LRScaf takes 20.28 and 41.20 Gb on CHM1 and NA12878 datasets.\n\nConclusionsThe new method, LRScaf, yields the best or at least moderate contiguity and accuracy of scaffolds in the shortest run time compared with the state-of-the-art methods. Furthermore, it offers a new opportunity for the hybrid assembly of large genomes.

bioinformatics↗
bioRxiv2018

Heterogeneity of Long-History Migration Predicts Smiling, Laughter and Positive Emotion Across the Globe and Within the United States

Recent findings demonstrate that heterogeneity of long-history migration predicts present-day emotion behaviors and norms. Residents of countries characterized by high ancestral diversity display emotion expressions that are easier to decode by observers, endorse norms of higher emotion expressivity, and smile more in response to certain stimuli than residents of countries that lack ancestral diversity. We build on the extant findings and investigate historical heterogeneity as a predictor of daily smiling, laughter, and positive emotion across the worlds countries and the states of the United States. Study 1 finds that historical heterogeneity is positively associated with self-reports of smiling, laughter, and positive emotions in the Gallup World Poll when controlling for GDP and current present-day population diversity. Study 2 extends the findings to effects of long-history migration within the United States. We estimated the average percentage of foreign-born citizens in each state between 1850 and 2010 based on US Census information as an indicator of historical heterogeneity. Consistent with the world findings of Study 1, historical heterogeneity predicted smiling, laughter, and positive, but not negative, emotion. The relationships remained significant when controlling for per capita income and present-day diversity of population of each state. Together, the findings further demonstrate the important role of long-history migration in shaping emotion cultures of countries and states, which persist beyond the original socio-ecological conditions, and open promising avenues for cross-cultural research.

evolutionary biology↗
bioRxiv2017

Neural code uses self-information principle to organize the brain’s universal cell-assembly coding

The brain generates cognition and behavior through firing changes of its neurons, yet, with enormous firing variability, the organizing principle underlying real-time neural code remains unclear. Here, we test the Neural Self-Information Theory that neural code is constructed via the self-information principle under which each inter-spike-interval (ISI) is inherently self-tagged with discrete information based on its relation to ISI variability-probability distribution - higher-probability ISIs, which reflect the balanced excitation-inhibition ground state, convey minimal information, whereas lower-probability ISIs, which signify statistical surprisals, carry more information. Moreover, temporally coordinated ISI surprisals across neural cliques intrinsically give rise to real-time cell-assembly neural code. As a result, this self-information-based neural coding is uniquely intrinsic to the neurons themselves, with no need for outside observers to set any reference point to manually mark external or internal inputs. Applying this neural self-information concept, we devised an unbiased general decoding strategy and successfully uncovered 15 distinct cell-assembly patterns from multiple cortical and hippocampal circuits associated with different sleep cycles, earthquake, elevator-drop, foot-shock experiences, navigation or various actions in five-choice visual-discrimination operant-conditioning tasks. Detailed analyses of all 15 cell assemblies revealed that ~20% of the skewed ISI distribution tails were responsible for the emergence of robust cell-assembly codes, conforming to the Pareto Principle. These findings support the notion that neural coding is organized via the self-information principle to generate real-time information across brain regions, cognitive modalities, and behaviors.

neuroscience↗
bioRxiv2017

Peripherally-induced regulatory T cells contribute to the control of autoimmune diabetes

Type 1 diabetes (T1D) results from the autoimmune destruction of pancreatic beta cells and is partly caused by deficiencies in the Foxp3+ regulatory T cell (Treg) compartment. Conversely, therapies that increase Treg function can prevent autoimmune diabetes in animal models. The majority of Tregs develop in the thymus (tTregs), but a proportion of Foxp3+ Tregs is generated in the periphery (pTregs) from Foxp3-CD4+ T cell precursors. Whether pTregs play a distinct role in T1D has not yet been explored. We report here that pTregs are a key modifier of disease in the nonobesed diabetic (NOD) mouse model for T1D. We generated NOD mice deficient for the Foxp3 enhancer CNS1 involved in pTreg induction. We show that CNS1 knockout decreased the frequency of pTregs and increased the risk of diabetes. Our results show that pTregs fulfill an important non-redundant function in the prevention of beta cell autoimmunity that causes T1D.

immunology↗