Biology subjects

Yao, L.

Publications and source records attributed to Yao, L..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

VHL Mutation Drives Human Clear Cell Renal Cell Carcinoma Progression Through PI3K/AKT-Dependent Cholesteryl Ester Accumulation

BackgroundCholesteryl ester (CE) accumulation in intracellular lipid droplets (LDs) is an essential signature of clear cell renal cell carcinoma (ccRCC), but its molecular mechanism and pathological significance remain elusive. MethodsEnabled by the label-free Raman spectromicroscopy, which integrated stimulated Raman scattering microscopy with confocal Raman spectroscopy on the same platform, we quantitatively analyzed LD distribution and composition at the single cell level in intact ccRCC cell and tissue specimens in situ without any processing or exogenous labeling. Since we found that commonly used ccRCC cell lines actually did not show the CE-rich signature, primary cancer cells were isolated from human tissues to retain the lipid signature of ccRCC with CE level as high as the original tissue, which offers a preferable cell model for the study of cholesterol metabolism in ccRCC. Moreover, we established a patient-derived xenograft (PDX) mouse model that retained the CE-rich phenotype of human ccRCC. FindingsSurprisingly, our results revealed that CE accumulation was induced by tumor suppressor VHL mutation, the most common mutation of ccRCC. Moreover, VHL mutation was found to promote CE accumulation by upregulating HIF and subsequent PI3K/AKT/mTOR/SREBPs pathway. Inspiringly, inhibition of cholesterol esterification remarkably suppressed ccRCC aggressiveness in vitro and in vivo with negligible toxicity, through the reduced membrane cholesterol-mediated downregulations of integrin and MAPK signaling pathways. InterpretationCollectively, our study improves current understanding of the role of CE accumulation in ccRCC and opens up new opportunities for treatment. FundingThis work was supported by National Natural Science Foundation of China (No. U23B2046 and No. 62027824), National Key R&D Program of China (No. 2023YFC2415500), Fundamental Research Funds for the Central Universities (No. YWF-22-L-547), PKU-Baidu Fund (No. 2020BD033), Peking University First Hospital Scientific and Technological Achievement Transformation Incubation Guidance Fund (No.2022CX02), and Beijing Municipal Health Commission (No. 2020-2Z-40713).

cancer biology↗

bioRxiv2022

Evaluation of a scalable approach to generate cell-type specific transcriptomic profiles of mesenchymal lineage cells

Genome-wide association studies (GWASs) have revolutionized our understanding of the genetics of complex diseases, such as osteoporosis; however, the challenge has been converting associations to causal genes. Studies have demonstrated the utility of transcriptomics data in linking disease-associated variants to genes; though for osteoporosis, few population transcriptomics datasets have been generated on bone or bone cells, and an even smaller number have profiled individual cell-types. To begin to evaluate approaches to address this challenge, we profiled the transcriptomes of bone marrow-derived stromal cells (BMSCs) cultured under osteogenic conditions, a popular model of osteoblast differentiation and activity, from five Diversity Outbred (DO) mice using single-cell RNA-seq (scRNA-seq). The goal of the study was to determine if BMSCs could serve as a model for the generation of cell-type specific transcriptomic profiles of mesenchymal lineage cells derived from large populations of mice to inform genetic studies. We demonstrate that dissociation of BMSCs from a heavily mineralized matrix had little effect on viability or their transcriptomic signatures. Furthermore, we show that BMSCs cultured under osteogenic conditions are diverse and consist of cells with characteristics of mesenchymal progenitors, marrow adipogenic lineage precursors (MALPs), osteoblasts, osteocyte-like cells, and immune cells. Importantly, all cells were nearly identical from a transcriptomic perspective to cells isolated directly from bone. We also demonstrated the ability to multiplex single cells and subsequently assign cells to their "mouse-of-origin" using demultiplexing approaches based on genotypes inferred from coding SNPs. We employed scRNA-seq analytical tools to confirm the biological identity of profiled cell-types. SCENIC was used to reconstruct gene regulatory networks (GRNs) and we showed that identified cell-types show GRNs expected of osteogenic and pre-adipogenic lineage cells. Further, CELLECT analysis showed that osteoblasts, osteocyte-like cells, and MALPs captured a significant component of BMD heritability. Together, these data suggest that BMSCs cultured under osteogenic conditions coupled with scRNA-seq can be used as a scalable and biologically informative model to generate cell-type specific transcriptomic profiles of mesenchymal lineage cells in large mouse, and potentially human, populations.

bioinformatics↗

bioRxiv2022

Genome charaterization based on the Spike-614 and NS8-84 loci of SARS-CoV-2 reveals two major onsets of the COVID-19 pandemic

The global COVID-19 pandemic has lasted for three years since its outbreak, however its origin is still unknown. Here, we analyzed the genotypes of 3.14 million SARS-CoV-2 genomes based on the amino acid 614 of the Spke (S) and the amino acid 48 of NS8 (nonstructural protein 8), and identified 16 linkage haplotypes. The GL haplotype (S_614G and NS8_48L) was the major haplotype driving the global pandemic and accounted for 99.2% of the sequenced genomes, while the DL haplotype (S_614D and NS8_48L) caused the pandemic in China in the spring of 2020 and accounted for approximately 60% of the genomes in China and 0.45% of the global genomes. The GS (S_614G and NS8_48S), DS (S_614D and NS8_48S) and NS (S_614N and NS8_48S) haplotypes accounted for 0.26%, 0.06%, and 0.0067% of the genomes, respectively. The main evolutionary trajectory of SARS-CoV-2 is DS[->]DL[->]GL, whereas the other haplotypes are minor byproducts in the evolution. Surprisingly, the newest haplotype GL had the oldest time of most recent common ancestor (tMRCA), which was May 1 2019 by mean, while the oldest haplotype had the newest tMRCA with a mean of October 17, indicating that the ancestral strains that gave birth to GL had been extinct and replaced by the more adapted newcomer at the place of its origin, just like the sequential rise and fall of the delta and omicron variants. However, they arrived and evolved into toxic strains and ignited a pandemic in China where the GL strains did not exist at the end of 2019. The GL strains had spread all over the world before they were discovered, and ignited the global pandemic, which had not been noticed until the pandemic was declared in China. However, the GL haplotype had little influence in China during the early phase of the pandemic due to its late arrival as well as the strict transmission controls in China. Therefore, we propose two major onsets of the COVID-19 pandemic, one was mainly driven by the haplotype DL in China, the other was driven by the haplotype GL globally.

bioinformatics↗

bioRxiv2022

Ring-finger protein 34 facilitates nervous necrosis virus evading antiviral innate immunity by targeting TBK1 and IRF3 for ubiquitination and degradation

Ubiquitination, as one of the most prevalent posttranslational modifications of proteins, enables a tight control on host immune responses. Many viruses hijack the host ubiquitin system to regulate host antiviral responses for their survival. Here, we found that fish pathogen nervous necrosis virus (NNV) recruited an E3 ubiquitin ligase ring finger protein 34 (RNF34) to inhibit RLRs-mediated interferons (IFN) response via ubiquitinating TBK1 and IRF3. Ectopic expression of RNF34 greatly enhances NNV replication and prevents IFN production, while deficiency of RNF34 led to the opposite effect. Furthermore, RNF34 targets TBK1 and IRF3 via its RING domain. Of note, the interactions between RNF34 and TBK1 or IRF3 were conserved in different fish species. Mechanically, RNF34 promote K27-linked ubiquitination and degradation of TBK1 and IRF3, which in turn diminishing TBK1-induced translocation of IRF3 from cytoplasm to nucleus. Ultimately, NNV capsid protein (CP) was found directly bind with RNF34 and this interaction was conserved in different fishes, and CP induced TBK1 and IRF3 degradation and IFN suppression was depended on RNF34. Our finding demonstrated a novel mechanism by which NNV CP evaded host innate immunity via RNF34, and provided a potential drug target for the control of NNV infection. Author SummaryUbiquitination plays an essential role in the regulation of innate immune responses to pathogens. NNV, a kind of RNA virus, is the causal agent of a highly destructive disease in a variety of marine and freshwater fish. Previous study reported NNV could hijack the ubiquitin system to manipulate the hosts immune responses, however, how NNV utilizes ubiquitination to facilitate its own replication is not well understood. Here, we identified a novel distinct role of E3 ubiquitin ligase RNF34 as an IFN antagonist to promote NNV infection. Nervous necrosis virus capsid protein utilized RNF34 to target TBK1 and IRF3 for K27 and K48-linked ubiquitination degradation. Importantly, the interactions between RNF34 and CP, TBK1 or IRF3 are conserved in different fishes, suggesting it is a general immune evasion strategy exploited by NNV to target the IFN response via RNF34.

immunology↗

bioRxiv2022

KBPRNA: A novel method integrating bulk RNA-seq data and LINCS-L1000 gene signatures to predict kinase activity based on machine learning

BackgroundKinases are a type of enzymes which can transfer phosphate groups from high-energy and phosphate-donating molecules to specific substrates. Kinase activities could be utilized to be represented as specific biomarkers of specific cancer types. Nowadays novel algorithms have already been developed to compute kinase activities from phosphorylated proteomics data. However, phosphorylated proteomics sequencing could be costly expensive and need valuable samples. Moreover,not methods which could achieve kinase activities from bulk RNA-sequence data have been developed. Here we propose KBPRNA, a general computational framework for extracting specific kinase activities from bulk RNA-sequencing data in cancer samples. KBPRNA also achieves better performance in predicting kinase activities from bulk RNA-sequence data under cancer conditions benchmarking against other models. ResultsIn this study, we used LINCS-L1000 dataset which was used to be reported as efficient gene signatures in defining bulk RNA-seq data as input dataset of KBPRNA. Also, we utilized eXtreme Gradient Boosting (XGboost) as the main algorithm to extract valuable information to predict kinase activities. This model outperforms other methods such as linear regression and random forest in predicting kinase activities from bulk RNA-seq data. KBPRNA integrated tissue samples coming from breast invasive carcinoma, hepatocellular carcinoma, lung squamous cell carcinoma, Glioblastoma multiforme and Uterine Corpus Endometrial Carcinoma. It was found that KBPRNA achieved good performance with an average R score above threshold of 0.5 in kinase activity prediction. ConclusionsModel training and testing process showed that KBPRNA outperformed other machine learning methods in predicting kinase activities coming from various cancer types tissue samples. This model could be utilized to approximate basic kinase activities and link it with specific biological functions, which in further promoted the progress of cancer identification and prognosis.

bioinformatics↗

bioRxiv2022

Glucocerebrosidase activity and lipid levels are related to protein pathologies in Parkinson's disease

Parkinsons disease (PD) and dementia with Lewy bodies (DLB) are progressive neurodegenerative diseases characterized by the accumulation of misfolded -synuclein in the form of Lewy pathology. While most cases are sporadic, there are rare genetic mutations that cause disease and more common variants that increase incidence of disease. The most prominent genetic mutations for PD and DLB are in the GBA1 and LRRK2 genes. GBA1 mutations are associated with decreased glucocerebrosidase activity and lysosomal accumulation of its lipid substrates, glucosylceramide and glucosylsphingosine. Previous studies have shown a link between this enzyme and lipids even in sporadic PD. However, it is unclear how the protein pathologies of disease are related to enzyme activity and glycosphingolipid levels. To address this gap in knowledge, we examined quantitative protein pathology, glucocerebrosidase activity and lipid substrates in parallel from 4 regions of 91 brains with no neurological disease, idiopathic, GBA1-linked, or LRRK2-linked PD and DLB. We find that several biomarkers are altered with respect to mutation and disease severity. We found mild association of glucocerebrosidase activity with disease, but a strong association of glucosylsphingosine with -synuclein pathology, irrespective of genetic mutation. This association suggests that Lewy pathology precipitates changes in lipid levels related to disease severity.

neuroscience↗

bioRxiv2022

High air humidity dampens salicylic acid pathway and plant resistance via targeting of NPR1

The occurrence of plant disease is determined by interactions among host, pathogen and climate conditions. Air humidity has long been recognized to profoundly influence diseases in the phyllosphere and high air humidity (e.g., after rain falls) is known as a prerequisite for numerous disease outbreaks in the field1-3. However, the molecular basis of how high humidity interferes with plant resistance mechanisms to favor disease remained elusive. Here we show that high humidity is associated with an "immune-compromised" status of plants, revealed by lower expression of defense genes during bacterial infection of Arabidopsis plants. Examination of humiditys effect on individual immune pathways showed that the accumulation and signaling of salicylic acid (SA), an essential hormone conferring plant resistance against infectious microbes4,5, are significantly inhibited under high humidity. Surprisingly, NPR1 protein, an SA receptor and central transcriptional co-activator of SA-responsive genes6-9, accumulated to a significantly higher level in the nucleus under high humidity. Further investigation indicated a decreased binding affinity of NPR1 protein to the target gene promoter, suggestive of an "inactive" nature of NPR1, under high humidity and an impaired ubiquitination and degradation of NPR1 protein, likely due to down-regulation of Cullin 3-mediated cellular ubiquitination pathway and 26S proteasome pathway under high humidity. Our study uncovers disruption of NPR1 protein turnover as a major mechanism, by which high humidity dampens plant immune strength against pathogens, and provides new insights into the long-observed air humidity influence on diseases in nature.

plant biology↗

bioRxiv2022

Chinese fir genome and the evolution of gymnosperms

Seed plants comprise angiosperms and gymnosperms. The latter includes gnetophytes, cycads, Ginkgo, and conifers. Conifers are distributed worldwide, with 630 species distributed across eight families and 70 genera. Their distinctiveness has triggered much debate on their origin, evolution, and phylogenetic placement among seed plants. To better understand the evolution of gymnosperms and their relation to other seed plants, we report here a high-quality genome sequence for a tree species, Chinese fir (Cunninghamia lanceolata), which has excellent timber quality and high aluminum adaptability and is a member of Cupressaceae with high levels of heterozygosity. We assembled an 11.24 Gb genome with a contig N50 value of 2.15 Mb and anchored the 10.89 Gb sequence to 11 chromosomes. Phylogenomic analyses showed that cycads sister to Ginkgo, which place to sister in all gymnosperm lineages, and Gnetales within conifers sister to Pinaceae. Whole-genome duplication (WGD) analysis showed that the ancestor of seed plants has differentiated into angiosperms and gymnosperms after having experienced a WGD event. The ancestor of extant gymnosperm has experienced a gymnosperm-specific WGD event and the extant angiosperms do not share a common WGD before their most recent common ancestor diverged into existing angiosperms lineages. Analysis of the MADS-box gene family of C. lanceolata revealed the developmental mechanism of the reproductive organs in C. lanceolata, which supported the (A)B(C) model of the development of gymnosperms reproductive organs. In addition, astringent seeds and shedding of whole branches (with withered leaves) might be a strategy of C. lanceolata that evolved during long-term adaptation to an aluminum-rich environment. The findings also reveal the molecular regulation mechanism of shade tolerance in C. lanceolata seedlings. Our results improve the resolution of ancestral genomic features within seed plants and the knowledge of genome evolution and diversification of gymnosperms.

genomics↗

bioRxiv2022

Genomic data support Betula halophila and Betula microphylla as one species and reveal unidirectional introgression from Betula pendula to Betula microphylla

Conservation of rare species faces challenges arising from uncertainties in species recognition, interspecific gene flow and global climate change. Betula microphylla and Betula halophila are endangered species in Xinjiang province, Northwest China, where they occur with the abundant Betula pendula. The species status of B. halophila remains dubious. The extent of gene flow between B. microphylla and B. pendula remain unexplored. Here, we first resolve the identity of B. halophila and then assess the extent of gene flow between B. microphylla and B. pendula using restriction-site associated DNA sequencing (RADseq). We sequenced 40 B. pendula individuals, 40 B. microphylla individuals, one B. halophila individual and seven B. tianshanica individuals. Our molecular analyses show that B. halophila and B. microphylla refer to the same species. STRUCTURE analyses show unidirectional genetic admixture from B. pendula to B. microphylla. The ABBA-BABA test indicates that the genetic admixture reflects introgression rather than incomplete lineage sorting. Furthermore, we identified 233 functional genes within the introgressed regions with eight genes related to salt-tolerance, suggesting the possibility of potential adaptive introgression. Our study shows an urgent need to conserve the genetically pure populations of B. microphylla and to shift conservation efforts from B. halophila to B. microphylla. In addition, ex-situ conservation of B. microphylla and conservation strategies to avoid genetic swamping by B. pendula and B. tianshanica should be implemented.

evolutionary biology↗

bioRxiv2022

Activin A promotes bone fracture repair and acts through a novel myofibroblastic cell population in callus

Insufficient bone fracture repair represents a significant clinical burden, and identification of novel therapeutics enhancing repair would have substantial clinical and societal impact. Activin A is a TGF-{beta} protein superfamily member known to stimulate ectopic bone formation, but its roles in fracture repair and its therapeutic potentials remain unclear. Using two mouse tibia fracture repair models, here we mapped activin A expression at the tissue and single cell levels, tested its requirement for normal repair and evaluated its ability to enhance repair when provided exogenously. Activin A was minimally expressed in periosteum of intact bones but was markedly upregulated in developing callus soon after fracture. Single cell RNA-sequencing revealed that the activin A-encoding gene Inhba marked a unique, highly proliferative progenitor cell (PPC) population with a myofibroblast character which emerged over repair time and lay at the center of a developmental trajectory bifurcation producing cartilage and bone cells within callus. Systemic administration of a neutralizing activin A antibody impaired fracture repair and its endochondral and intramembranous phases, whereas local delivery of recombinant activin A enhanced repair. Activin A delivery also induced SMAD2 phosphorylation in vivo and increased the fraction of SMA+ myofibroblasts within fracture callus. Gain- and loss-of-function experiments in vitro showed that activin A directly stimulated myofibroblast differentiation, chondrogenesis and osteogenesis in periosteal progenitor cells. Together, these data identify a unique population of Inhba-expressing proliferative progenitor cells that give rise to chondrocytes and osteoblasts during fracture healing and establish activin A as a potential new therapeutic tool to enhance it. One Sentence SummaryDeficits in bone fracture repair remain a clinical challenge and the present study provides evidence for the therapeutic potentials of activin A

pathology↗

bioRxiv2022

Analysis of sex differential genes at whole genome level reveals their organ- and chromosome-dependent expressions, regulations, and interactions

Males and females possess genomes that are almost identical but differ in morbidity, prevalence, severity, response to therapies and mortality of many diseases. We comprehensively analyzed gene expression data in seven tissues from BXD recombinant inbred (RI) mouse strains. We found that there were considerable differences in the numbers and functions among different tissues and between autosomal and sex chromosomes. Among sex differential genes, those on autosomal chromosomes mainly function to regulate metabolic pathways related to their host organs, while those on sex chromosomes mainly regulate nuclear proteins required for DNA replication or transcription during early development. Kidney possessed the fewest sex differential genes on sex chromosomes. The sexually dimorphic genes expressed on X chromosomes were all related to perception, while genes on the autosomal chromosomes were related to metabolism. These patterns of gene expression do not translate into similarity of protein structures, rather they are grouping with function.

cell biology↗

bioRxiv2022

More than 90% of nacre matrix proteins are composed of silk-like proteins

A proteome is a powerful tool to study nacre biomineralization that occurs in an ordered microenvironment composed mainly of proteins and polysaccharides. As more and more proteins are detected, new questions arise about which proteins are responsible for forming this microenvironment. In this study, shell matrix proteins (SMPs) of nacre were analyzed using label-free quantitative proteome. A total of 99.89% of the insoluble nacre SMPs were composed of silk-like proteins, chitin-binding proteins, and cysteine-rich SMPs, which were responsible for organic framework assembly. A total of 99.34% of the soluble nacre SMPs were composed of silk-like proteins and chitin-binding proteins, which were responsible for forming protein gel filling in organic frameworks. The content of silk-like proteins was more than 90% in both insoluble and soluble nacre SMPs. As organic frameworks and protein gel together constructed a microenvironment for calcium carbonate biomineralization, these results provided a novel understanding of nacre formation.

biochemistry↗

bioRxiv2022

Engineering of NEMO as calcium indicators with ultra-high dynamics and sensitivity

Genetically-encoded calcium indicators (GECI) are indispensable tools for real-time monitoring of intracellular calcium signals and cellular activities in living organisms. Current GECIs face the challenge of sub-optimal peak signal-to-baseline-ratio (SBR) with limited resolution for reporting subtle calcium transients. We report herein the development of a suite of calcium sensors, designated NEMO, with fast kinetics and wide dynamic ranges (>100-fold). NEMO indicators report Ca2+ transients with peak SBRs ~20-fold larger than the top-of-the-range GCaMP series. NEMO sensors further enable the quantification of absolution calcium concentration with ratiometric or photochromic imaging. Compared to GCaMPs, NEMOs could detect single action potentials in neurons with a peak SBR two times higher and a median peak SBR four times larger in vivo, thereby outperforming most existing state-of-the-art GECIs. Given their high sensitivity and resolution to report intracellular Ca2+ signals, NEMO sensors may find broad applications in monitoring neuronal activities and other Ca2+-modulated physiological processes in both mammals and plants.

synthetic biology↗

bioRxiv2022

Csf1 from marrow adipogenic precursors is required for osteoclast formation and hematopoiesis in bone

Colony stimulating factor 1 (Csf1) is an essential growth factor for osteoclast progenitors and thus an important regulator for bone resorption. It remains elusive which mesenchymal cells synthesize Csf1 stimulating osteoclastogenesis. We recently identified a novel mesenchymal cell population, marrow adipogenic lineage precursors (MALPs), in bone. Single cell RNA- sequencing indicated specific expression of Csf1 in MALPs, which is further increased during aging. To investigate its role, we constructed Csf1 CKO mice using Adipoq-Cre. These mice showed increased femoral trabecular bone over time, but their cortical bone appeared normal. In comparison, depletion of Csf1 in the entire mesenchymal lineage using Prx1-Cre led to a more striking high bone mass phenotype, suggesting that additional mesenchymal subpopulations secrete Csf1. TRAP staining revealed diminished osteoclasts in the femoral secondary spongiosa region of Csf1 CKOAdipoq mice, but not at the chondral-osseous junction nor at the endosteal surface of cortical bone. Moreover, Csf1 CKOAdipoq mice were resistant to LPS-induced calvarial osteolysis. Bone marrow cellularity, hematopoietic progenitors, and macrophages were also reduced in these mice. Taken together, our studies demonstrate that MALPs are a critical player in controlling bone remodeling and hematopoiesis.

cell biology↗

bioRxiv2022

Insights from Incorporating Quantum Computing into Drug Design Workflows

While many quantum computing (QC) methods promise theoretical advantages over classical counterparts, quantum hardware remains limited. Exploiting near-term QC in computer-aided drug design (CADD) thus requires judicious partitioning between classical and quantum calculations. We present HypaCADD, a hybrid classical-quantum workflow for finding ligands binding to proteins, while accounting for genetic mutations. We explicitly identify modules of our drug design workflow currently amenable to replacement by QC: non-intuitively, we identify the mutation-impact predictor as the best candidate. HypaCADD thus combines classical docking and molecular dynamics with quantum machine learning (QML) to infer the impact of mutations. We present a case study with the SARS-CoV-2 protease and associated mutants. We map a classical machine-learning module onto QC, using a neural network constructed from qubit-rotation gates. We have implemented this in simulation and on two commercial quantum computers. We find that the QML models can perform on par with, if not better than, classical baselines. In summary, HypaCADD offers a successful strategy for leveraging QC for CADD.

bioinformatics↗

bioRxiv2022

A Multi-scale, Multiomic Atlas of Human Normal and Follicular Lymphoma Lymph Nodes

Reference atlases, molecular and spatial maps of mammalian tissues, are critical resources for discovery efforts and translational research. Their utility is dependent on operationalizing the resulting data by identifying cell types, histological patterns, and predictive biomarkers underlying health and disease. The human lymph node (LN) offers a compelling use case because of its importance in immunity, structural and cellular diversity, and neoplastic involvement. One hematological malignancy, follicular lymphoma (FL), evolves from developmentally blocked germinal center B cells residing in and trafficking through these tissues. To promote survival and immune escape, tumor B cells undergo significant genetic changes and extensively remodel the lymphoid microenvironment. Here, we present an integrated portrait of healthy and FL LNs using multiple genomic and advanced imaging technologies. By leveraging the strengths of each platform, we identified several tumor-specific features and microenvironmental patterns enriched in individuals who experience early relapse, the most high-risk of FL patients.

cancer biology↗

bioRxiv2022

Robust and Versatile Arrayed Libraries for Human Genome-Wide CRISPR Activation, Deletion and Silencing

Arrayed CRISPR libraries extend the scope of gene-perturbation screens but require large numbers of efficacious sgRNA-expressing vectors. Using a newly invented liquid-phase plasmid cloning methodology, we constructed genome-wide arrayed libraries for human gene ablation (19,936 plasmids), activation, and epigenetic silencing (22,442 plasmids). At least 76% of each plasmid preparation encoded an intact array of 4 non-overlapping sgRNAs designed to tolerate most human DNA polymorphisms. We achieved perturbation efficacies of 75-99%, 76-92% and up to 10,000x in deletion, silencing and activation experiments, respectively. Upon conversion into massively parallel lentiviral vectors, an arrayed activation screen of 1,634 human transcription factors yielded 11 novel regulators of the cellular prion protein PrPC. Furthermore, a screen using a pooled version of the ablation library identified 5 novel modifiers of autophagy that went undetected with either of two 1sgRNA libraries. The CRISPR libraries described here represent a powerful resource for the targeted perturbation of human protein-coding genes.

genomics↗

bioRxiv2022

Semi-field evaluation of the space spray efficacy of Fludora Co-Max EW against wild insecticide-resistant Aedes aegypti and Culex quinquefasciatus mosquito populations from Abidjan, Cote d'Ivoire

BackgroundSpace spraying of insecticides is still an important mean of controlling Aedes and Culex mosquitoes and arboviral diseases. This study evaluated the space spray efficacy of Fludora Co-Max EW (a combination of flupyradifurone and transfluthrin, with Film Forming Aqueous Spray Technology (FFAST)) against wild, insecticide-resistant Aedes aegypti and Culex quinquefasciatus populations from Abidjan, Cote dIvoire, against K-Othrine EC (deltamethrin-only product), through small-scale field trials. MethodologyWild Ae. aegypti and Cx. quinquefasciatus mosquito larvae were collected in Abidjan, Cote dIvoire from August to December 2020. Mosquito larvae were reared until adult stage. Emerged adult females were tested against Fludora Co-Max EW and K-Othrine EC using ultra-low volume cold fogging (ULV) and thermal fogging (TF) both outdoors and indoors in Agboville, Cote dIvoire. Cages containing 20 mosquitoes each were placed at 10, 25, 50, 75 and 100 m from the spraying line for outdoor spraying, and at ceiling, mid-height and floor levels for indoor house spraying. Knockdown and mortality were recorded at each checkpoint and compared by treatments. Principal findingsOverall, Fludora Co-Max EW induced significantly higher knockdown and mortality effects in the wild insecticide-resistant Ae. aegypti and Cx. quinquefasciatus compared with K-Othrine EC. With both species, Fludora Co-Max EW mortality rates were above 80% (up to 100%) for outdoor ULV spray at each distance checkpoint (i.e. 10 to 100 m), and 100% for indoor ULV and TF sprays at all level checkpoints (i.e. ceiling, mid-height and floor). K-Othrine EC induced high mortality indoors (97.9-100%), whereas outdoor mortality rapidly declined in Ae. aegypti from 96.7% to 36.7% with ULV, and 85.0% to 38.3% with TF, from 10 to 100 m. For outdoor Fludora Co-Max EW spray, ULV showed both higher knockdown and killing performance Ae. aegypti and Cx. quinquefasciatus compared with TF. Fludora Co-Max EW performed better against Cx. quinquefasciatus compared with Ae. aegypti. Conclusion/significanceFludora Co-Max EW induced high mortality and knockdown effects against wild insecticide-resistant Ae. aegypti and Cx. quinquefasciatus Abidjan strains and performed better than K-Othrine EC. The presence of flupyradifurone and transfluthrin (with new and independent modes of action) and FFAST technology in the current Fludora Co-Max EW formulation appears to have broadened its killing capacity. Fludora Co-Max EW is thus an effective adulticide and may be a useful tool for Aedes and Culex mosquito and arbovirus control in endemic areas. Author SummarySpace spraying of insecticides is an important tool to control Aedes and Culex mosquitoes and prevent the viral diseases (i.e. dengue, yellow fever, etc.) that they transmit. We studied the efficacy of the product Fludora Co-Max EW (a new space spray insecticide) against adult wild insecticide-resistant populations of Aedes aegypti and Culex quinquefasciatus mosquitoes from Abidjan, Cote dIvoire. We compared Fludora Co-Max EW knockdown and mortality effects in these mosquitoes with the local insecticide K-Othrine EC using ultra-low volume (ULV) and thermal fogging (TF) spraying outdoors and indoors. The product Fludora Co-Max EW induced high rates of knockdown and mortality (i.e. 80-100%) in these wild insecticide-resistant mosquitoes and performed better than the product K-Othrine EC. Additionally, ULV sprays of Fludora Co-Max EW demonstrated higher knockdown and killing efficacy at larger distances (i.e. up to 100 m) compared with TF. The higher efficacy of Fludora Co-Max EW may be due to the interaction of two unrelated insecticides, flupyradifurone and transfluthrin, in combination with Film Forming Aqueous Spray Technology (FFAST). Fludora Co-Max EW therefore appears to be an effective and useful tool to control adult populations of wild insecticide-resistant Aedes and Culex mosquitoes and may be recommended for preventing related mosquito-transmitted viral diseases.

ecology↗