Biology subjects

Yang, Z.

Publications and source records attributed to Yang, Z..

At least 541 records · Page 30Linked to original sources

bioRxiv2020

Tracing two causative SNPs reveals SARS-CoV-2 transmission in North America population

During the COVID-19 pandemic, precisely tracing the route of the SARS-CoV-2 transmission in human population remains challenging. Because this RNA virus can mutate massively without a specifically tracing maker. Herein, using a geographic stratified genome-wide association study (GWAS) of 2599 full-genome sequences, we identified that two SNPs (i.e., 1059.C>T and 25563.G>T) of linkage disequilibrium were presented in approximately half of North America SARS-CoV-2 population (p = 2.44 x 10-212 and p = 2.98 x 10-261), resulting two missense mutations (i.e., Thr 265 Ile and Gln 57 His) in ORF1ab and ORF3a, respectively. Interestingly, these two SNPs exclusively occurred in the North America dominated clade 1, accumulated during mid to late March, 2020. We did not find any of these two SNPs by retrospectively tracing the two SNPs in bat and pangolin related SARS-CoV-2 and human SARS-CoV-2 from the first epicenter Wuhan or other regions of China mainland. This suggested that the SARS-CoV-2 population of Chinese mainland were different from the prevalent strains of North America. Time-dependently, we found that these two SNPs first occurred in Europe SARS-CoV-2 (26-Feb-2020) which was 3 days early than the occurring date of North America isolates and 17 days early for Asia isolates (Taiwan China dominated). Collectively, this population genetic analysis highlights a well-confidential transmission route of the North America isolates and the two SNPs we newly identified are possibly novel diagnosable or druggable targets for surveillance and treatment.

microbiology↗

bioRxiv2020

Electron tomography visualization of HIV-1 fusion with target cells using fusion inhibitors to trap the pre-hairpin intermediate

Fusion of HIV-1 with the membrane of its target cell, an obligate first step in virus infectivity, is mediated by binding of the viral envelope (Env) spike protein to its receptors, CD4 and CCR5/CXCR4, on the cell surface. The process of viral fusion appears to be fast compared with viral egress and has not been visualized by electron microscopy (EM). To capture fusion events for EM, the process must be slowed or stopped by trapping Env-receptor binding at an intermediate stage. Here we describe using fusion inhibitors to trap HIV-1 virions attached to target cells by Envs in an extended pre-hairpin intermediate state. Electron tomography revealed HIV-1 virions bound to TZM-bl cells by 2-4 narrow spokes, with slightly more spokes present when evaluated with mutant virions that lacked the Env cytoplasmic tail. These results represent the first direct visualization of the hypothesized pre-hairpin intermediate and improve our understanding of Env-mediated HIV-1 fusion and infection of host cells.

cell biology↗

bioRxiv2020

SIRT1 ameliorates premature senescence-induced defenestration in hepatic sinusoidal endothelial cell

Premature senescence, linked to progerin, involves in endothelial dysfunction and liver diseases. Activating sirtuin 1 (SIRT1) ameliorates liver fibrosis. However, the potential mechanisms of premature senescence in defenestration in hepatic sinusoidal endothelial cells (HSECs) and how SIRT1 affects fenestrae remains elusive. Our study showed that in vivo, premature senescence occurred, with decrease of SIRT1, during CCl4-induced defenestration in HSECs and liver fibrogenesis; whereas overexpressing SIRT1 with adenovirus vector lessened progerin-associated premature senescence to relieve CCl4-induced defenestration and liver fibrosis. In vitro, fenestrae in HSECs disappeared, with progerin-associated premature senescence; these effects aggravated by H2O2-induced oxidative damage. Nevertheless, knockdown of NOX2 or overexpression of SIRT1 with adenovirus vector reduced progerin-associated premature senescence to maintain fenestrae through deacetylating p53. Furthermore, more Ac p53 K381 and progerin co-localized with accumulation of actin filament (F-actin) in the nuclear envelope of H2O2-treated HSECs; in contrast, these effects were rescued by overexpressing SIRT1. In conclusion, NOX2-dependent oxidative damage aggravates defenestration in HSECs via progerin-associated premature senescence; SIRT1-mediated deacetylation of p53 maintains fenestrae and attenuates liver fibrogenesis through inhibiting premature senescence.

cell biology↗

bioRxiv2020

Using single-cell entropy to describe the dynamics of reprogramming and differentiation of induced pluripotent stem cells

Induced pluripotent stem cells (iPSCs) provide a great model to study the process of stem cell reprogramming and differentiation. Single-cell RNA sequencing (scRNA-seq) enables us to investigate the reprogramming process at single-cell level. Here, we introduce single-cell entropy (scEntropy) as a macroscopic variable to quantify the cellular transcriptome from scRNA-seq data during reprogramming and differentiation of iPSCs. scEntropy measures the relative order parameter of genomic transcriptions at single cell level during the process of cell fate changes, which show increase tendency during differentiation, and decrease upon reprogramming. Hence, scEntropy provides an intrinsic measurement of the cell state, and can be served as a pseudo-time of the stem cell differentiation process. Moreover, based on the evolutionary dynamics of scEntropy, we construct a phenomenological Fokker-Planck equation model and the corresponding stochastic differential equation for the process of cell state transitions during pluripotent stem cell differentiation. These equations provide further insights to infer the processes of cell fates changes and stem cell differentiation. This study is the first to introduce the novel concept of scEntropy to quantify the biological process of iPSC, and suggests that the scEntropy can provide a suitable macroscopic variable for single cells to describe cell fate transition during differentiation and reprogramming of stem cells.

cell biology↗

bioRxiv2020

Role of short-chain fatty acids in the gut-brain axis in schizophrenia: contribution to immune activation and pathophysiology in humans and mice

ObjectiveGut microbiota dysbiosis and aberrant gut-brain functional modules including short-chain fatty acid (SCFA) production and long-lasting immune activation (IA) are presented in schizophrenia. Given the key roles of gut microbiota and SCFA in shaping immunity, we propose that dysbiosis-induced SCFA upregulation could contribute to IA and behavioral symptoms in schizophrenia. DesignGut microbiota, SCFA, and IA biomarkers were compared between schizophrenic patients and healthy controls. The roles of SCFA in schizophrenia-related IA were analyzed in cultured peripheral blood mononuclear cells (PBMCs) and a mouse model of schizophrenia. The effects of SCFAs on schizophrenia-related phenotypes were analyzed in both human and mouse. ResultsBoth microbial-derived SCFA and SCFA-producing bacteria were elevated in the guts of schizophrenic patients, and this increased SCFA production in gut was associated with IA in schizophrenia. The microbiome signature underpinning schizophrenia-related IA includes increased diversity and increased SCFA-producing bacteria and inflammation-associated bacteria. The impact of SCFAs on immune responses of cultured PBMC depend on the diagnosis and IA status of donors. Small-molecule serum filtrates from immune-activated schizophrenic patients increased the inflammatory response of PBMCs from healthy volunteers, which can be enhanced and attenuated by SCFAs supplementation and inhibition of SCFA signaling, respectively. Chronically elevated SCFAs in adolescence induced neuroinflammation and schizophrenia-like behaviors in adult mice. Moreover, chronically elevated SCFAs in adult mice prenatally exposed to IA potentiated their expression of schizophrenia-like behaviors. Conclusionmicrobiota-derived SCFAs are important mediators of dysregulated gut-brain axis and participant in pathogenesis via enhance IA in schizophrenia. SummaryO_ST_ABSSignificance of this studyC_ST_ABSO_LIWhat is already known about this subject? [tpltrtarr]Schizophrenia pathogenesis goes beyond the brain since increasing peripheral abnormalities are revealed including gut microbiota dysbiosis, GI dysfunction, and systemic immune activation (IA). [tpltrtarr]Systemic IA/inflammation contributes to the neuroinflammation and brain impairment underlying schizophrenia, and adjunctive immunotherapy can improve psychotic symptoms. [tpltrtarr]Short-chain fatty acids (SCFA) mediate the microbiota-gut-brain communication and modulate several pathways involved in schizophrenia, including pathways of immunity and neurotransmitters. C_LIO_LIWhat are the new findings? [tpltrtarr]Patients with schizophrenia displayed increased rates of IA and increased SCFA production compared with healthy controls, and increased SCFA is associated with IA in patients. [tpltrtarr]A unique microbiota signature including enriched SCFA-producing bacterial species can distinguish patients with IA from other patients and controls. [tpltrtarr]Small molecules in the serum of immune-activated patients with schizophrenia enhance LPS-induced immune response of cultured peripheral blood mononuclear cell (PBMCs), which is partially mediated by SCFA signaling. [tpltrtarr]SCFA intake upregulates both peripheral and brain inflammation and potentiates the expression of schizophrenia-like behaviors in mice prenatally exposed to IA. C_LIO_LIHow might it impact on clinical practice in the foreseeable future? [tpltrtarr]Interference of SCFA signaling or targeted destruction of SCFA-producing bacteria may provide a new approach for the prevention and treatment of schizophrenia. [tpltrtarr]Immune activation status of patients should be an important condition considered when selecting immunotherapy for future precision psychiatric therapy. C_LI

neuroscience↗

bioRxiv2020

Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders

BackgroundWith the reduce of cost and incomparable advantages, WGS is likely to change the way of clinical diagnosis of rare and undiagnosed diseases. However, the sensitivity and breadth of coverage of clinical WGS as a diagnostic test for genetic disorders has not been fully evaluated, especially for CNV detection. MethodsAll the samples underwent WGS using MGISEQ-2000. The performance of NA12878, YH cell line, and the Chinese trios were measured for sensitivity, PPV, depth and breadth of coverage. We also compared the performance of WES and WGS using NA12878. The sensitivity and PPV were tested using family-based trio design in the Chinese trios. We also developed a systematic WGS pipeline for the analysis of 8 clinical cases with known disease-causing variants. ResultsIn general, the sensitivity and PPV for SNV/indel detection increased with mean depth, and reached a plateau at a ~40X mean depth using down-sampling samples of NA12878. With a mean depth of 40X, the sensitivity of homozyous and heterozygous SNPs of NA12878 was >99.25% and >99.50% respectively, and PPVs were 99.97% and 98.96%. Homozygous and heterozygous indels showed lower sensitivity and PPV. The sensitivity and PPV is still not 100% even with a mean depth of ~150X. We also observed a substantial variation in the sensitivity of CNV detection across different tools, especially in CNVs with a size of less than 1kb. In general, the breadth of coverage for disease-associated genes and CNVs increased with mean depth. The sensitivity and coverage of WGS (~40X) is better than WES (~120X). Among the Chinese trios with ~40X mean depth, the sensitivity in the offspring was >99.48% and >96.36% for SNP and indel detection, and PPVs were 99.86% and 97.93%. All the 12 previously validated variants in the 8 clinical cases were successfully detected by our WGS pipeline. ConclusionsThe current standard of a mean depth of 40X may be sufficient for SNV/indel detection and identification of most CNVs. Clinical scientists should know the range of sensitivity and PPV for different classes of variants for a particular WGS pipeline, which would be useful when interpreting and delivering clinical reports.

genomics↗

bioRxiv2020

Characterization of Met25 as a Color Associated Genetic Market in Yarrowia lipolytica

Yarrowia lipolytica offers an ideal host for biosynthesis of high value natural products and oleochemicals through metabolic engineering despite being restricted to a limited number of selective markers, and counter-selection achieved primarily with URA3. In this work, we investigate MET25, a locus of sulfide housekeeping within the cell, to be exploited as a standard genetic marker. Divalent lead supplemented in media induces lead sulfide (PbS) aggregation in MET25-deficient cells such that deficient cells grow brown/black, and cells with functional copies of MET25 grow white. Loss of MET25 did not induce strict auxotrophic requirements for methionine in Y. lipolytica, indicating MET25 deficiency could be rescued by alternative pathways. Plasmid and chromosomal-based complementation of MET25 deficient cells on a double layer agar plate with nutrient gradients demonstrates delayed phenotype (white morphology) restoration, indicating post-transcriptional feedback regulation of methionine biosynthesis in this yeast. MET25 deficient Y. lipolytica could be used as an efficient whole-cell lead sensor with detection limit as low as 10 ppm of lead in drinking water. We further tested whether MET25 deficiency can be exploited to confer resistance to methyl-mercury through chemical neutralization and detoxification. Kinetic growth curves of wild type and MET25-deficient cells were obtained under varying concentrations of methylmercury and cellular toxicity to methyl mercury was calculated from the Hill equation. Our results indicate that methylmecury may not be used as the counter-selectable marker due to insignificant changes of growth fitness. This work demonstrates the utility of using MET25 as a sensitive lead sensor and the challenges of using MET25 as a counter-selectable genetic marker, as well as the complex regulation of methionine biosynthesis in Y. lipolyitca, which may shed lights for us to develop valuable biotechnological applications centering around the sulfur house-keeping metabolism of the nonconventional yeast.

microbiology↗

bioRxiv2020

A Comprehensive Multi-Center Cross-platform Benchmarking Study of Single-cell RNA Sequencing Using Reference Samples

Single-cell RNA sequencing (scRNA-seq) has become a very powerful technology for biomedical research and is becoming much more affordable as methods continue to evolve, but it is unknown how reproducible different platforms are using different bioinformatics pipelines, particularly the recently developed scRNA-seq batch correction algorithms. We carried out a comprehensive multi-center cross-platform comparison on different scRNA-seq platforms using standard reference samples. We compared six pre-processing pipelines, seven bioinformatics normalization procedures, and seven batch effect correction methods including CCA, MNN, Scanorama, BBKNN, Harmony, limma and ComBat to evaluate the performance and reproducibility of 20 scRNA-seq data sets derived from four different platforms and centers. We benchmarked scRNA-seq performance across different platforms and testing sites using global gene expression profiles as well as some cell-type specific marker genes. We showed that there were large batch effects; and the reproducibility of scRNA-seq across platforms was dictated both by the expression level of genes selected and the batch correction methods used. We found that CCA, MNN, and BBKNN all corrected the batch variations fairly well for the scRNA-seq data derived from biologically similar samples across platforms/sites. However, for the scRNA-seq data derived from or consisting of biologically distinct samples, limma and ComBat failed to correct batch effects, whereas CCA over-corrected the batch effect and misclassified the cell types and samples. In contrast, MNN, Harmony and BBKNN separated biologically different samples/cell types into correspondingly distinct dimensional subspaces; however, consistent with this algorithms logic, MNN required that the samples evaluated each contain a shared portion of highly similar cells. In summary, we found a great cross-platform consistency in separating two distinct samples when an appropriate batch correction method was used. We hope this large cross-platform/site scRNA-seq data set will provide a valuable resource, and that our findings will offer useful advice for the single-cell sequencing community.

genomics↗

bioRxiv2020

Scalable method for micro-CT analysis enables large scale quantitative characterization of brain lesions and implants

Anatomic evaluation is an important aspect of many studies in neuroscience; however, it often lacks information about the three-dimensional structure of the brain. Micro-CT imaging provides an excellent, nondestructive, method for the evaluation of brain structure, but current applications to neurophysiological or lesions studies require removal of the skull and hazardous chemicals, dehydration or embedding, limiting their scalability and utility. Here we present a protocol using eosin in combination with bone decalcification to enhance contrast in the tissue and then employ monochromatic and propagation phase-contrast micro-CT imaging to enable the imaging of brain structure with the preservation of the surrounding skull. Instead of relying on descriptive, time-consuming, or subjective methods, we develop simple quantitative analyses to map the locations of recording electrodes and to characterize the presence and extent of brain lesions.

neuroscience↗

bioRxiv2020

TagSeqTools: a flexible and comprehensive analysis pipeline for NAD tagSeq data

NAD tagSeq has recently been developed for the identification and characterization of NAD+-capped RNAs (NAD-RNAs). This method adopts a strategy of chemo-enzymatic reactions to label the NAD-RNAs with a synthetic RNA tag before subjecting to the Oxford Nanopore direct RNA sequencing. A computational tool designed for analyzing the sequencing data of tagged RNA will facilitate the broader application of this method. Hence, we introduce TagSeqTools as a flexible, general pipeline for the identification and quantification of tagged RNAs (i.e., NAD+-capped RNAs) using long-read transcriptome sequencing data generated by NAD tagSeq method. TagSeqTools comprises two major modules, TagSeek for differentiating tagged and untagged reads, and TagSeqQuant for the quantitative and further characterization analysis of genes and isoforms. Besides, the pipeline also integrates some advanced functions to identify antisense or splicing, and supports the data reformation for visualization. Therefore, TagSeqTools provides a convenient and comprehensive workflow for researchers to analyze the data produced by the NAD tagSeq method or other tagging-based experiments using Oxford nanopore direct RNA sequencing. The pipeline is available at https://github.com/dorothyzh/TagSeqTools, under Apache License 2.0.

bioinformatics↗

bioRxiv2020

TipQAD: an automated tool for quantifying apical fluorescence dynamics in tip-growing cells

Cell polarity is a fundamental property essential for the function and development of all cellular organisms. Tip growth is an extreme form of polar growth requiring spatiotemporally dynamic but highly coordinated cellular activities. Quantification of these dynamic activities is important for the systematic study of the mechanisms controlling cell polarity, but an automated and unbiased method for analyzing and quantification of tip-growing cells has been missing. In this paper, we developed a computational model and an associated tool called TipQAD for quantifying the spatiotemporal dynamics of fluorescence protein (FP) labeled molecules or structures in tip-growing cells. This tool robustly and accurately measured the spatial distribution and temporal dynamics of FP-labeled proteins in the cytoplasm or the plasma membrane at the tip region of several types of tip-growing cells. We also demonstrated its ability to analyze data from FRAP experiments. In conclusion, this tool showed great potential for automated measurements of the spatiotemporal dynamics of fluorescent-labeled cellular molecules and structures.

plant biology↗

bioRxiv2020

No evidence for intermolecular recombination in human fibroblast and blood mtDNA from individuals with biparental mtDNA transmission

Strictly maternal inheritance and lack of intermolecular recombination of the human mitochondrial genome (mtDNA) are the assumed preconditions for molecular evolution studies, phylogenetic reconstruction and population genetic analyses. This hypothesis, however, has been challenged by investigations providing evidence for genetic recombination of mtDNA, thus sparking controversy. Using single-molecule real-time (SMRT) sequencing technology, we sequenced the entire mtDNA from blood and fibroblast cells from five individuals with biparental mtDNA transmission in three separate, multiple-generation families. After phasing the single nucleotide polymorphism (SNP) genotypes of mtDNA, no intermolecular recombination between paternal and maternal mtDNA was found when the mtDNA was transmitted in either biparental or maternal mode. Our study provides support for the argument that intermolecular mtDNA recombination is absent or extremely rare in humans. As a consequence, these results support the feasibility of mtDNA-based molecular evolution studies and phylogenetic and population genetic analyses for humans, while also avoiding inaccurate phylogenetic inferences and incorrect rejection of the molecular clock.

genetics↗

bioRxiv2020

The intriguing dynamics of chromatin folding and assembly

We investigate the dynamics of chromatin folding based on the "strings and binders" (SBS) model with molecular dynamics simulation. SBS model is a coarse-grained model considering a self-avoiding chain interacting with diffusive binders. By introducing transition among different categories of beads with specific transition cycles and transition probabilities, our model is capable of introducing different dynamics quantitatively during the folding process, thus capturing variety of phenomena related to chromatin dynamics. Firstly, roles of dynamics in the process of chromatin folding were examined. We discovered that there is a minimum gyration of chromatin under varying characteristic times of transition which indicates neither dramatically dynamic nor static folding process is optimal for chromatin to reach stable states with relatively low free energy. Secondly, it is noticeable that when beads transit from or into others in distinct dynamics, the equilibrium concentrations are distinct as well. As a consequence, the distribution of chromatin loop length is relevant to the dynamics of binders which can be modified by complex such as Wings apart-like protein homolog (Wapl) and SCC2/SCC4 cohesin loader complex (SCC2/SCC4). Finally, our model is able to reproduce contact matrices of both wild type HAP1 cell and {Delta}WAPL HAP1 cell obtained from Hi-C technology with a relatively high accuracy. Our model recapitulate the accumulating contacts at the corners of TADs and vanishing short-range contacts along the diagonal, manifesting the difference of chromatin structures before and after eliminating WAPL. STATEMENT OF SIGNIFICANCEOur model includes reciprocal transition among beads in SBS model to introduce different dynamics in chromatin folding process. Our model is able to examine the roles of dynamics in chromatin folding, reveal the loop length variation due to the concentration imbalance caused by distinct dynamics and reproduce contact matrices of both wild type and WAPL-deficient cells. Our research work provides a model to investigate the dynamics of chromatin folding quantitatively and displays its significance of revealing multiple experimental results using computational tools.

biophysics↗

bioRxiv2020

Regulated unbinding of ZAP70 at the T cell receptor by kinetic avidity

Protein-protein binding domains are critical in signalling networks. Src homology 2 (SH2) domains are binding domains that interact with sequences containing phosphorylated tyrosines. A subset of SH2 domain-containing proteins have tandem domains, which are thought to enhance binding affinity and specificity. However, a trade-off exists between long-lived binding and the ability to rapidly reverse signalling, which is a critical requirement of noise filtering mechanisms such as kinetic proofreading. Here, we use modelling to show that the unbinding rate of tandem, but not single, SH2 domains can be accelerated by phosphatases when tandem domains bind by a kinetic, but not a static, avidity mode. We use surface plasmon resonance to show that ZAP70, a tandem SH2 domain-containing kinase, binds kinetically to biphosphorylated peptides from the T cell antigen receptor (TCR) and that the unbinding rate can be accelerated by the phosphatase CD45. An important functional prediction of regulated unbinding is that the intracellular ZAP70/TCR half-life in T cells will be correlated to the extracellular TCR/antigen half-life and we show that this is the case in both cell lines and primary T cells. The work highlights that binding by kinetic avidity breaks the trade-off between signal fidelity (requiring long half-life) and signal reversibility (requiring short half-life), which is a key requirement for T cell antigen discriminated mediated by kinetic proofreading.

immunology↗

bioRxiv2020

Large-scale Quantification of Vertebrate Biodiversity in Ailaoshan Nature Reserve from Leech iDNA

1Protected areas are central to meeting biodiversity conservation goals, but measuring their effectiveness is challenging. We address this challenge by using DNA from leech-ingested bloodmeals to estimate vertebrate occupancies across the 677 km2 Ailaoshan reserve in Yunnan, China. 163 park rangers collected 30,468 leeches from 172 patrol areas. We identified 86 vertebrate species, including amphibians, mammals, birds, and squamates. Multi-species occupancy modelling showed that species richness increased with elevation and distance to reserve edge, including the distributions of most of the large mammals (e.g. sambar, black bear, serow, tufted deer). The exceptions were the three domestic mammal species (cows, sheep, goats) and muntjak deer, which were more common at lower elevations. eDNA-estimated vertebrate occupancies are Granular, Repeatable, Auditable, Direct, Efficient, and Simple-to-understand measures that can be used to assess conservation effectiveness and thus to improve the contributions that protected areas make to achieving global biodiversity goals.

ecology↗

bioRxiv2020

Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody

The newly identified 2019 novel coronavirus (2019-nCoV) has caused more than 800 laboratory-confirmed human infections, including 25 deaths, posing a serious threat to human health. Currently, however, there is no specific antiviral treatment or vaccine. Considering the relatively high identity of receptor binding domain (RBD) in 2019-nCoV and SARS-CoV, it is urgent to assess the cross-reactivity of anti-SARS-CoV antibodies with 2019-nCoV spike protein, which could have important implications for rapid development of vaccines and therapeutic antibodies against 2019-nCoV. Here, we report for the first time that a SARS-CoV-specific human monoclonal antibody, CR3022, could bind potently with 2019-nCoV RBD (KD of 6.3 nM). The epitope of CR3022 does not overlap with the ACE2 binding site within 2019-nCoV RBD. Therefore, CR3022 has the potential to be developed as candidate therapeutics, alone or in combination with other neutralizing antibodies, for the prevention and treatment of 2019-nCoV infections. Interestingly, some of the most potent SARS-CoV-specific neutralizing antibodies (e.g., m396, CR3014) that target the ACE2 binding site of SARS-CoV failed to bind 2019-nCoV spike protein, indicating that the difference in the RBD of SARS-CoV and 2019-nCoV has a critical impact for the cross-reactivity of neutralizing antibodies, and that it is still necessary to develop novel monoclonal antibodies that could bind specifically to 2019-nCoV RBD.

microbiology↗

bioRxiv2020

Reliability of dynamic network reconfiguration: Impact of code implementation, parameter selection, scan duration, and task condition

Multilayer network models have been proposed as an effective means of capturing the dynamic configuration of distributed neural circuits and quantitatively describing how communities vary over time. Beyond general insights into brain function, a growing number of studies have begun to employ these methods for the study of individual differences. However, test-retest reliabilities for multilayer network measures have yet to be fully quantified or optimized, potentially limiting their utility for individual difference studies. Here, we systematically evaluated the impact of multilayer community detection algorithms, selection of network parameters, scan duration, and task condition on test-retest reliabilities of multilayer network measures (i.e., flexibility, integration, and recruitment). A key finding was that the default method used for community detection by the popular generalized Louvain algorithm can generate erroneous results. Although available, an updated algorithm addressing this issue is yet to be broadly adopted in the neuroimaging literature. Beyond the algorithm, the present work identified parameter selection as a key determinant of test-retest reliability; however, optimization of these parameters and expected reliabilities appeared to be dataset-specific. Once parameters were optimized, consistent with findings from the static functional connectivity literature, scan duration was a much stronger determinant of reliability than scan condition. When the parameters were optimized and scan duration was sufficient, both passive (i.e., resting state, Inscapes, and movie) and active (i.e., flanker) tasks were reliable, although reliability in the movie watching condition was significantly higher than in the other three tasks. The minimal data requirement for achieving reliable measures for the movie watching condition was 20 min, and 30 min for the other three tasks. Our results caution the field against the use of default parameters without optimization based on the specific datasets to be employed - a process likely to be limited for most due to the lack of test-retest samples to enable parameter optimization. HighlightsO_LIDynamic network reliability is highly dependent on many methodological decisions C_LIO_LIThe default multilayer community detection algorithm generates erroneous results C_LIO_LIReliability-optimized intra-/inter-layer coupling parameters are dataset-dependent C_LIO_LIScan duration is a much stronger determinant of reliability than scan condition C_LIO_LIMovies are the most reliable condition, requiring at least 20 min of data C_LI

neuroscience↗

bioRxiv2020

Construction, characterization, and immunization of nanoparticles that display a diverse array of influenza HA trimers

Current influenza vaccines do not elicit broadly protective immune responses against multiple strains. New strategies to focus the humoral immune response to conserved regions on influenza antigens are therefore required for recognition by broadly neutralizing antibodies. It has been suggested that B-cells with receptors that recognize conserved epitopes would be preferentially stimulated through avidity effects by mosaic particles presenting multiple forms of a variable antigen. We adapted SpyCatcher-based platforms, AP205 virus-like particles (VLPs) and mi3 nanoparticles (NPs), to covalently co-display SpyTagged hemagglutinin (HA) trimers from group 1 and group 2 influenza A strains. Here we show successful homotypic and heterotypic conjugation of up to 8 different HA trimers to both VLPs and NPs. We characterized the HA-VLPs and HA-NPs by cryo-electron tomography to derive the average number of conjugated HAs and their separation distances on particles, and compared immunizations of mosaic and homotypic particles in wild-type mice. Both types of HA particles elicited strong antibody responses, but the mosaic particles did not consistently elicit broader immune responses than mixtures of homotypic particles. We conclude that covalent attachment of HAs from currently-circulating influenza strains represents a viable alternative to current annual influenza vaccine strategies, but in the absence of further modifications, is unlikely to represent a method for making a universal influenza vaccine.

immunology↗