Biology subjects

Fan, Y.

Publications and source records attributed to Fan, Y..

At least 289 records · Page 16Linked to original sources

bioRxiv2019

Individual Variation in Control Network Topography Supports Executive Function in Youth

The spatial distribution of large-scale functional networks on the anatomic cortex differs between individuals, and is particularly variable in networks responsible for executive function. However, it remains unknown how this functional topography evolves in development and supports cognition. Capitalizing upon advances in machine learning and a large sample of youth (n=693, ages 8-23y) imaged with 27 minutes of high-quality fMRI data, we delineate how functional topography evolves during youth. We found that the functional topography of association networks is refined with age, allowing accurate prediction of an unseen individuals brain maturity. Furthermore, the cortical representation of executive networks predicts individual differences in executive function. Finally, variability of functional topography is associated with fundamental properties of brain organization including evolutionary expansion, cortical myelination, and cerebral blood flow. Our results emphasize the importance of considering both the plasticity and diversity of functional neuroanatomy during development, and suggest advances in personalized therapeutics.

neuroscience↗

bioRxiv2019

Tomato yellow leaf curl virus V2 protein plays a critical role in the nuclear export of V1 protein and viral systemic infection

Geminiviruses are an important group of circular, single-stranded DNA viruses that cause devastating diseases in crops. Geminiviruses replicate their genomic DNA in the nucleus. The newly-synthesized viral DNA is subsequently transported to the cytoplasm, moved to adjacent cells through plasmodesmata with the help of viral movement proteins, and, ultimately, moved long-distance to establish systemic infection. Thus, the nucleocytoplasmic transportation is crucial for a successful infection by geminiviruses. For Tomato yellow leaf curl virus (TYLCV), the V1 protein is known to bind and shuttle viral genomic DNA, but the role of V2 protein in this process is still unclear. Here, we report that the nucleus-localized V1 protein dramatically decreases when co-expressed with V2 protein, and that V2-facilitated nuclear export of V1 protein depends on host exportin- and a specific V1-V2 interaction. Chemical inhibition of exportin- or a substitutions at cysteine 85 of V2 protein, which abolishes the V1-V2 interaction, blocks the promoted redistribution of V1 protein to the perinuclear region and the cytoplasm. When the V2C85S mutation is incorporated into a TYLCV infectious clone, the TYLCV-C85S causes delayed onset of very mild symptoms compared to wild-type TYLCV, indicating that the V1-V2 interaction and, thus, V2-mediated nuclear export of V1 protein is crucial for viral spread and systemic infection. Our data point to a critical role of the V2 protein in promoting the nuclear export of the V1 protein, likely by promoting V1-mediated nucleocytoplasmic transportation of TYLCV genomic DNA, and in turn, promoting viral systemic infection.\n\nAuthor summaryAs both replication and the transcription of geminiviruses occur in the nucleus, transportation of the viral genomic DNA into and out of the nucleus of the infected cells is essential for a successful infection cycle. However, the nuclear export of geminiviruses is still little known and even less is known about the process for monopartite geminiviruses. We use TYLCV, a typical monopartite begomovirus in the family Geminiviridae, to examine the nucleocytoplasmic transportation. In this study, we found TYLCV V2 is able to redistribute the nucleus-localized V1 protein to the perinuclear region. Moreover, the nuclear export of V1 protein is dependent on the V1-V2 interaction and host exportin-. Blocking the V1-V2 interaction impeded the V2-mediated V1 protein redistribution and decrease TYLCV infection efficiency with delayed and mild symptoms. This report shows us a new explanation for the role of V2 in the nuclear export of V1 protein and TYLCV viral systemic infection.

pathology↗

bioRxiv2019

Aggregated and hyperstable damage-associated molecular patterns are released during ER stress to modulate immune function

Chronic ER stress occurs when protein misfolding in the ER lumen remains unresolved despite activation of the unfolded protein response. We have shown that traumatic injury such as a severe burn leads to chronic ER stress in vivo leading to systemic inflammation which can last for more than a year. The mechanisms linking chronic ER stress to systemic inflammatory responses is not clear. Here we show that induction of chronic ER stress leads to the release of known and novel damage-associated molecular patterns (DAMPs). The secreted DAMPs are aggregated and markedly protease resistant. ER stress-derived DAMPs activate dendritic cells which are then capable of polarizing naive T cells. Our findings indicate that induction of chronic ER stress may lead to the release of hyperstable DAMPs into the circulation resulting in persistent systemic inflammation and adverse outcomes.

cell biology↗

bioRxiv2019

Neurostructural Heterogeneity in Youth with Internalizing Symptoms

Internalizing disorders such as anxiety and depression are the most common psychiatric disorders, frequently begin in youth, and exhibit marked heterogeneity in treatment response and clinical course. It is increasingly recognized that symptom-based classification approaches to internalizing disorders do not align with underlying neurobiology. An alternative to classifying psychopathology based on clinical symptoms is to identify neurobiologically-informed subtypes based on brain imaging data. We used a recently developed semi-supervised machine learning method (HYDRA) to delineate patterns of neurobiological heterogeneity within youth with internalizing symptoms using structural imaging data collected at 3T from a large community-based sample of 1,141 youth. Using volume and cortical thickness, cross-validation methods indicated a highly stable solution (ARI=.66; permutation-based pfdr < .001) and identified two subtypes of internalizing youth. Subtype 1, defined by smaller brain volumes and reduced cortical thickness, was marked by impaired cognitive performance and higher levels of psychopathology than both Subtype 2 and typically developing youth. Using resting-state fMRI and diffusion images not considered during clustering, we found that Subtype 1 also showed reduced amplitudes of low-frequency fluctuations in fronto-limbic regions at rest, as well as reduced fractional anisotropy in white matter tracts such as the parahippocampal cingulum bundle and the uncinate fasciculus. In contrast, Subtype 2 showed intact cognitive performance, greater volume, cortical thickness, and amplitudes during rest compared to Subtype 1 and typically developing youth, despite still showing clinically significant levels of psychopathology. Identification of biologically-grounded subtypes of internalizing disorders may assist in targeting early interventions and assessing longitudinal prognosis.

neuroscience↗

bioRxiv2019

High-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis

Identifying genetic variants that are associated with methylation variation - an analysis commonly referred to as methylation quantitative trait locus (mQTL) mapping -- is important for understanding the epigenetic mechanisms underlying genotype-trait associations. Here, we develop a statistical method, IMAGE, for mQTL mapping in sequencing-based methylation studies. IMAGE properly accounts for the count nature of bisulfite sequencing data and incorporates allele-specific methylation patterns from heterozygous individuals to enable more powerful mQTL discovery. We compare IMAGE with existing approaches through extensive simulation. We also apply IMAGE to analyze two bisulfite sequencing studies, in which IMAGE identifies more mQTL than existing approaches.

genomics↗

bioRxiv2019

Prediction of antiviral drugs against African Swine Fever Viruses based on protein-protein interaction analysis

The African swine fever virus (ASFV) has severely influenced the swine industry of the world. Unfortunately, there is no effective antiviral drug or vaccine against the virus until now. Identification of new anti-ASFV drugs is urgently needed. Here, an up-to-date set of protein-protein interactions (PPIs) between ASFV and swine were curated by integration of PPIs from multiple sources. Thirty-two swine proteins were observed to interact with ASFVs and were defined as AIPs. They were found to play a central role in the swine PPI network, with significant larger degree, betweenness and smaller shortest path length than other swine proteins. Some of AIPs also interacted with several other viruses and could be taken as potential targets of drugs for broad-spectrum effect, such as HSP90AB1. Finally, the antiviral drugs which targeted AIPs and ASFV proteins were predicted. Several drugs with either broad-spectrum effect or high specificity on AIPs were identified, such as Polaprezinc. This work could not only deepen our understanding towards the ASFV-swine interactions, but also help for the development of effective antiviral drugs against the ASFVs.

bioinformatics↗

bioRxiv2019

A parallel cell-cycle entry pathway with inverted G1 signaling and alternate point of no return

Cell-cycle entry relies on an orderly progression of signaling events. To start, cells first activate the kinase cyclin D-CDK4/6, which leads to eventual inactivation of the retinoblastoma protein Rb. Hours later, cells inactivate APC/CCDH1 and cross the final commitment point. However, many cells with genetically deleted cyclin Ds, which activate and confer specificity to CDK4/6, can compensate and proliferate. Despite its importance in cancer, how this alternate pathway operates and whether wild-type cells use this pathway remain unknown. Here, using single-cell microscopy, we demonstrate that cells with acutely inhibited CDK4/6 enter the cell cycle with slowed and fluctuating cyclin E-CDK2 activity. Surprisingly, in this alternate pathway, the order of APC/CCDH1 and Rb inactivation is inverted in both cell lines and wild-type mice. Finally, we show that as a consequence of the signaling inversion, Rb inactivation replaces APC/CCDH1 inactivation as the point of no return. Together, we provide molecular characterization of a parallel cell-cycle entry pathway, and reveal temporal plasticity that underlies the G1 regulatory circuit.

cell biology↗

bioRxiv2019

The caudate nucleus contributes causally to decisions that combine noisy visual evidence and reward context

Our decisions often need to balance what we observe and what we desire. However, our understanding of how and where in the brain such decisions are made remains limited. A prime candidate for integrating sensory observations and desired rewards, and a focus of many modeling studies, is the basal ganglia pathway, which is known to make separate contributions to perceptual decisions that require the interpretation of uncertain sensory evidence and value-based decisions that select among outcome options 1-16. Here we report direct evidence for a causal role for a major input station of the basal ganglia, the caudate nucleus, in incorporating reward context and uncertain visual evidence to guide adaptive decision-making. In monkeys making saccadic decisions based on visual motion evidence and asymmetric reward-choice associations 17, single caudate neurons encoded information about both the visual evidence and the asymmetric rewards. Electrical microstimulation at caudate sites with task-modulated activity during motion viewing affected how the visual and reward information was used to form the decision. The microstimulation effects included coordinated changes in multiple computational components of the decision process, mimicking the monkeys voluntary adjustments in response to the asymmetric reward contexts. These results imply that the caudate nucleus plays key roles in coordinating the deliberative decision process that balances external evidence and internal preferences to guide adaptive behavior.

neuroscience↗

bioRxiv2019

The anterior insula channels prefrontal expectancy signals during affective processing

Expectancy shapes our perception of impending events. Although such an interplay between cognitive and affective processes is often impaired in mental disorders, it is not well understood how top-down expectancy signals modulate future affect. We therefore track the information flow in the brain during cognitive and affective processing segregated in time using task-specific cross-correlations. Participants in two independent fMRI studies (N1 = 37 & N2 = 55) were instructed to imagine a situation with affective content as indicated by a cue, which was then followed by an emotional picture congruent with expectancy. To correct for intrinsic covariance of brain function, we calculate resting-state cross-correlations analogous to the task. First, using factorial modeling of delta cross-correlations (task-rest) of the first study, we find that the magnitude of expectancy signals in the anterior insula cortex (AIC) modulates the BOLD response to emotional pictures in the anterior cingulate and dorsomedial prefrontal cortex in opposite directions. Second, using hierarchical linear modeling of lagged connectivity, we demonstrate that expectancy signals in the AIC indeed foreshadow this opposing pattern in the prefrontal cortex. Third, we replicate the results in the second study using a higher temporal resolution, showing that our task-specific cross-correlation approach robustly uncovers the dynamics of information flow. We conclude that the AIC arbitrates the recruitment of distinct prefrontal networks during cued picture processing according to triggered expectations. Taken together, our study provides new insights into neuronal pathways channeling cognition and affect within well-defined brain networks. Better understanding of such dynamics could lead to new applications tracking aberrant information processing in mental disorders.

neuroscience↗

bioRxiv2019

MeshMonk: Open-source large-scale intensive 3D phenotyping

In the post-genomics era, an emphasis has been placed on disentangling genotype-phenotype connections so that the biological basis of complex phenotypes can be understood. However, our ability to efficiently and comprehensively characterize phenotypes lags behind our ability to characterize genomes. Here, we report a toolbox for fast and reproducible high-throughput dense phenotyping of 3D images. Given a target image, a rigid registration is first used to orient a template to the target surface, then the template is transformed further to fit the specific shape of the target using a non-rigid transformation model. As validation, we used N = 41 3D facial images registered with MeshMonk and manually landmarked at 19 locations. We demonstrate that the MeshMonk registration is accurate, with 0.62 mm as the average root mean squared error between the manual and automatic placements and no variation in landmark position or centroid size significantly attributable to landmarking method used. Though validated using 19 landmarks for comparison with traditional methods, MeshMonk allows for automatic dense phenotyping, thus facilitating more comprehensive investigations of 3D shape variation. This expansion opens up an exciting avenue of study in assessing genomic and phenomic data to better understand the genetic contributions to complex morphological traits.

evolutionary biology↗

bioRxiv2018

Phase Transitions in Mutualistic Communities under Invasion

Predicting the outcome of species invasion in ecosystems is a challenge of both theoretical and practical significance. Progress so far has been limited by the intractability of the far-from-equilibrium nature of the transitions that occur during invasion events. Here, we address this limitation by solving for the transition dynamics of a cross-feeding community along an analytically tractable manifold defined by the system carrying capacity. We find that species invasion induces discontinuous transitions in the community composition, resembling phase transitions in physical systems. These sharp transitions are emergent properties of species-resource interactions and relate directly to the extent of niche overlap between invasive and native species. The high susceptibility of community structure to small variations in species phenotype and resource conditions near the phase boundaries can explain empirically observed stochasticity and the emergence of tipping points in ecosystems. Moreover, we demonstrate that these phase transitions can be modulated by environmental variations to construct nonlinear organization of species both in space and time.

ecology↗

bioRxiv2018

TSD: A computational tool to study the complex structural variants using PacBio targeted sequencing data

The PacBio sequencing is a powerful approach to study the DNA or RNA sequences in a longer scope. It is especially useful in exploring the complex structural variants generated by random integration or multiple rearrangement of internal or external sequences. However, there is still no tool designed to uncover their structural organization in the host genome. Here, we present a tool, TSD, for complex structural variant discovery using PacBio targeted sequencing data. It allows researchers to identify and visualize the genomic structures of targeted sequences by unlimited splitting, alignment and assembly of long PacBio reads. Application to the sequencing data derived from an HBV integrated human cell line(PLC/PRF/5) indicated that TSD could recover the full profile of HBV integration events, especially for the regions with the complex human-HBV genome integrations and multiple HBV rearrangements. Compared to other long read analysis tools, TSD showed a better performance for detecting complex genomic structural variants. TSD is publicly available at: https://github.com/menggf/tsd

bioinformatics↗

bioRxiv2018

Homologous recombination shapes the genetic diversity and drives the evolution of African swine fever viruses

Recent outbreaks of African swine fever virus (ASFV) in China severely influenced the swine industry of the country. Currently, there is no effective vaccine or drugs against ASFVs. How to effectively control the virus is challenging. In this study, we have analyzed all the publicly available ASFV genomes and demonstrated that there was a large genetic diversity of ASFV genomes. Interestingly, the genetic diversity was mainly caused by extensive genomic insertions and/or deletions (indels) instead of the point mutations. The genomic diversity of the virus resulted in proteome diversity. Over 250 types of proteins were inferred from the ASFV genomes, among which only 144 were observed in all analyzed viruses. Further analyses showed that the homologous recombination may contribute much to the indels, as supported by significant associations between the occurrence of extensive recombination events and the indels in the ASFV genomes. Repeated elements of dozens of nucleotides in length were observed to widely distribute and cluster in the adjacent positions of ASFV genomes, which may facilitate the occurrence of homologous recombination. Moreover, two enzymes, which were possibly related to the homologous recombination, i.e., a Lambda-like exonuclease with a YqaJ-like viral recombinase domain, and a DNA topoisomerase II, were found to be conservative in all the analyzed ASFVs. This work highlighted the importance of the homologous recombination in the evolution of the ASFVs, and helped with the strategy development of the prevention and control of the virus.

microbiology↗

bioRxiv2018

A novel core genome approach to enable prospective and dynamic monitoring of infectious outbreaks

Whole-genome sequencing is increasingly adopted in clinical settings to identify pathogen transmissions. Currently, such studies are performed largely retrospectively, but to be actionable they need to be carried out prospectively, in which samples are continuously added and compared to previous samples. To enable prospective pathogen comparison, genomic relatedness metrics based on single nucleotide differences must be consistent across time, efficient to compute and reliable for a large variety of samples. The choice of genomic regions to compare, i.e., the core genome, is critical to obtain a good metric.\n\nWe propose a novel core genome method that selects conserved sequences in the reference genome by comparing its k-mer content to that of publicly available genome assemblies. The conserved-sequence genome is sample set-independent, which enables prospective pathogen monitoring. Based on clinical data sets of 3436 S. aureus, 1362 K. pneumoniae and 348 E. faecium samples, we show that the conserved-sequence genome disambiguates same-patient samples better than a core genome consisting of conserved genes. The conserved-sequence genome confirms outbreak samples with high accuracy: in a set of 2335 S. aureus samples, it correctly identifies 44 out of 45 outbreak samples, whereas the conserved gene method confirms 38 out of 45 outbreak samples.

bioinformatics↗

bioRxiv2018

Marker-based watershed transform method for fully automatic mandibular segmentation from low-dose CBCT images

Introduction Introduction Methods and materials Results Discussion Conclusions Funding References Three-dimensional mandibular models are useful for planning maxillofacial surgery and orthodontic treatment.1,2 In studies of growth, mandibular models are important for assessing morphological changes over time.3,4 Such models are typically obtained from conventional computed tomography (CT), using high radiation dose to capture fine detail of the bony structure. Cone beam computed tomography (CBCT) shows promise for oral and craniofacial imaging applications due to lower radiation dose, lower cost and shorter acquisition time compared to CT. However, CBCT images have lower contrast and higher levels of ...

bioinformatics↗

bioRxiv2018

MYCN Amplification and ATRX Mutations are Incompatible in Neuroblastoma

Aggressive cancers often have activating mutations in growth-controlling oncogenes and inactivating mutations in tumor-suppressor genes. In neuroblastoma, amplification of the MYCN oncogene and inactivation of the ATRX tumor-suppressor gene correlate with high-risk disease and poor prognosis. Here we show that ATRX mutations and MYCN amplification are mutually exclusive across all ages and stages in neuroblastoma. Using human cell lines and mouse models, we found that elevated MYCN expression and ATRX mutations are incompatible. Elevated MYCN levels promote metabolic reprogramming, mitochondrial dysfunction, reactive-oxygen species generation, and DNA-replicative stress. The combination of replicative stress caused by defects in the ATRX-histone chaperone complex and that induced by MYCN-mediated metabolic reprogramming leads to synthetic lethality. Therefore, ATRX and MYCN represent an unusual example, where inactivation of a tumor-suppressor gene and activation of an oncogene are incompatible. This synthetic lethality may eventually be exploited to improve outcomes for patients with high-risk neuroblastoma.

cancer biology↗

bioRxiv2018

Portraits of genetic intra-tumour heterogeneity and subclonal selection across cancer types

Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin and drivers of ITH across cancer types are poorly understood. To address this question, we extensively characterize ITH across whole-genome sequences of 2,658 cancer samples, spanning 38 cancer types. Nearly all informative samples (95.1%) contain evidence of distinct subclonal expansions, with frequent branching relationships between subclones. We observe positive selection of subclonal driver mutations across most cancer types, and identify cancer type specific subclonal patterns of driver gene mutations, fusions, structural variants and copy-number alterations, as well as dynamic changes in mutational processes between subclonal expansions. Our results underline the importance of ITH and its drivers in tumor evolution, and provide an unprecedented pan-cancer resource of comprehensively annotated subclonal events from whole-genome sequencing data.

cancer biology↗

bioRxiv2018

Baculovirus utilizes cholesterol transporter Niemann-Pick C1 for host cell entry

The dual roles of baculovirus for the control of natural insect populations as an insecticide, and for foreign gene expression and delivery, have called for a comprehensive understanding of the molecular mechanisms governing viral infection. Here, we demonstrate that the Bombyx mori Niemann-Pick C1 (BmNPC1) is essential for baculovirus infection in insect cells. Both pretreatment of Bombyx mori embryonic cells (BmE) with NPC1 antagonists (imipramine or U18666A) and down-regulation of NPC1 expression resulted in a significant reduction in baculovirus BmNPV (Bombyx mori nuclear polyhedrosis virus) infectivity. Furthermore, we show that the major glycoprotein gp64 of BmNPV, responsible for both receptor binding and fusion, is able to interact predominantly with the BmNPC1 C domain, with an enhanced binding capacity at low pH conditions, indicating that NPC1 most likely plays a role during viral fusion in endosomal compartments. Our results, combined with previous studies identifying an essential role of hNPC1 in filovirus infection, suggest that the glycoprotein of several enveloped viruses possess a shared strategy of exploiting host NPC1 proteins during virus intracellular entry events.\n\nIMPORTANCEBmNPV is one of the most important members of the Baculoviridae; many viruses in this family have been frequently employed as viral vectors for foreign gene delivery or expression and as biopesticides, but their host receptors still remain unclear. Here, we describe that the intracellular cholesterol transporter BmNPC1 is indispensable for BmNPV infection in insect cells, and it interacts with the major viral glycoprotein gp64. Our study on the role of BmNPC1 in baculovirus infection has further expanded the list of the enveloped viruses that require host NPC1 proteins for entry, and will ultimately help us to uncover the molecular mechanism of the involvement of NPC1 proteins in the entry process of many enveloped viruses.

microbiology↗