Optimization of Protein-Protein Interaction Measurements for Drug Discovery Using AFM Force Spectroscopy

Increasingly targeted in drug discovery, protein-protein interactions challenge current high throughput screening technologies in the pharmaceutical industry. Developing an effective and efficient method for screening small molecules or compounds is critical to accelerate the discovery of ligands for enzymes, receptors and other pharmaceutical targets. Here, we report developments of methods to increase the signal-to-noise ratio (SNR) for screening protein-protein interactions using atomic force microscopy (AFM) force spectroscopy. We have demonstrated the effectiveness of these developments on detecting the binding process between focal adhesion kinases (FAK) with protein kinase B (Akt1), which is a target for potential cancer drugs. These developments include optimized probe and substrate functionalization processes and redesigned probe-substrate contact regimes. Furthermore, a statistical-based data processing method was developed to enhance the contrast of the experimental data. Collectively, these results demonstrate the potential of the AFM force spectroscopy in automating drug screening with high throughput

Genome-wide analysis of the interaction between the endosymbiotic bacterium Wolbachia and its Drosophila host

BACKGROUND: Intracellular Wolbachia bacteria are obligate, maternally-inherited, endosymbionts found frequently in insects and other invertebrates. The success of Wolbachia can be attributed in part to an ability to alter host reproduction via mechanisms including cytoplasmic incompatibility (CI), parthenogenesis, feminization and male killing. Despite substantial scientific effort, the molecular mechanisms underlying the Wolbachia/host interaction are unknown. RESULTS: Here, an in vitro Wolbachia infection was generated in the Drosophila S2 cell line, and transcription profiles of infected and uninfected cells were compared by microarray. Differentially-expressed patterns related to reproduction, immune response and heat stress response are observed, including multiple genes that have been previously reported to be involved in the Wolbachia/host interaction. Subsequent in vivo characterization of differentially-expressed products in gonads demonstrates that Angiotensin Converting Enzyme (Ance) varies between Wolbachia infected and uninfected flies and that the variation occurs in a sex-specific manner. Consistent with expectations for the conserved CI mechanism, the observed Ance expression pattern is repeatable in different Drosophila species and with different Wolbachia types. To examine Ance involvement in the CI phenotype, compatible and incompatible crosses of Ance mutant flies were conducted. Significant differences are observed in the egg hatch rate resulting from incompatible crosses, providing support for additional experiments examining for an interaction of Ance with the CI mechanism. CONCLUSION: Wolbachia infection is shown to affect the expression of multiple host genes, including Ance. Evidence for potential Ance involvement in the CI mechanism is described, including the prior report of Ance in spermatid differentiation, Wolbachia-induced sex-specific effects on Ance expression and an Ance mutation effect on CI levels. The results support the use of Wolbachia infected cell cultures as an appropriate model for predicting in vivo host/Wolbachia interactions

Anopheles gambiae Immune Responses to Human and Rodent Plasmodium Parasite Species

Transmission of malaria is dependent on the successful completion of the Plasmodium lifecycle in the Anopheles vector. Major obstacles are encountered in the midgut tissue, where most parasites are killed by the mosquito's immune system. In the present study, DNA microarray analyses have been used to compare Anopheles gambiae responses to invasion of the midgut epithelium by the ookinete stage of the human pathogen Plasmodium falciparum and the rodent experimental model pathogen P. berghei. Invasion by P. berghei had a more profound impact on the mosquito transcriptome, including a variety of functional gene classes, while P. falciparum elicited a broader immune response at the gene transcript level. Ingestion of human malaria-infected blood lacking invasive ookinetes also induced a variety of immune genes, including several anti-Plasmodium factors. Twelve selected genes were assessed for effect on infection with both parasite species and bacteria using RNAi gene silencing assays, and seven of these genes were found to influence mosquito resistance to both parasite species. An MD2-like receptor, AgMDL1, and an immunolectin, FBN39, showed specificity in regulating only resistance to P. falciparum, while the antimicrobial peptide gambicin and a novel putative short secreted peptide, IRSP5, were more specific for defense against the rodent parasite P. berghei. While all the genes that affected Plasmodium development also influenced mosquito resistance to bacterial infection, four of the antimicrobial genes had no effect on Plasmodium development. Our study shows that the impact of P. falciparum and P. berghei infection on A. gambiae biology at the gene transcript level is quite diverse, and the defense against the two Plasmodium species is mediated by antimicrobial factors with both universal and Plasmodium-species specific activities. Furthermore, our data indicate that the mosquito is capable of sensing infected blood constituents in the absence of invading ookinetes, thereby inducing anti-Plasmodium immune responses

Response of the mosquito protein interaction network to dengue infection

<p>Abstract</p> <p>Background</p> <p>Two fifths of the world's population is at risk from dengue. The absence of effective drugs and vaccines leaves vector control as the primary intervention tool. Understanding dengue virus (DENV) host interactions is essential for the development of novel control strategies. The availability of genome sequences for both human and mosquito host greatly facilitates genome-wide studies of DENV-host interactions.</p> <p>Results</p> <p>We developed the first draft of the mosquito protein interaction network using a computational approach. The weighted network includes 4,214 <it>Aedes aegypti </it>proteins with 10,209 interactions, among which 3,500 proteins are connected into an interconnected scale-free network. We demonstrated the application of this network for the further annotation of mosquito proteins and dissection of pathway crosstalk. Using three datasets based on physical interaction assays, genome-wide RNA interference (RNAi) screens and microarray assays, we identified 714 putative DENV-associated mosquito proteins. An integrated analysis of these proteins in the network highlighted four regions consisting of highly interconnected proteins with closely related functions in each of replication/transcription/translation (RTT), immunity, transport and metabolism. Putative DENV-associated proteins were further selected for validation by RNAi-mediated gene silencing, and dengue viral titer in mosquito midguts was significantly reduced for five out of ten (50.0%) randomly selected genes.</p> <p>Conclusions</p> <p>Our results indicate the presence of common host requirements for DENV in mosquitoes and humans. We discuss the significance of our findings for pharmacological intervention and genetic modification of mosquitoes for blocking dengue transmission.</p

StyleSpeech: Self-supervised Style Enhancing with VQ-VAE-based Pre-training for Expressive Audiobook Speech Synthesis

The expressive quality of synthesized speech for audiobooks is limited by generalized model architecture and unbalanced style distribution in the training data. To address these issues, in this paper, we propose a self-supervised style enhancing method with VQ-VAE-based pre-training for expressive audiobook speech synthesis. Firstly, a text style encoder is pre-trained with a large amount of unlabeled text-only data. Secondly, a spectrogram style extractor based on VQ-VAE is pre-trained in a self-supervised manner, with plenty of audio data that covers complex style variations. Then a novel architecture with two encoder-decoder paths is specially designed to model the pronunciation and high-level style expressiveness respectively, with the guidance of the style extractor. Both objective and subjective evaluations demonstrate that our proposed method can effectively improve the naturalness and expressiveness of the synthesized speech in audiobook synthesis especially for the role and out-of-domain scenarios.Comment: Accepted to ICASSP 202

Deep Learning Based Multi-Node ISAC 4D Environmental Reconstruction with Uplink- Downlink Cooperation

Utilizing widely distributed communication nodes to achieve environmental reconstruction is one of the significant scenarios for Integrated Sensing and Communication (ISAC) and a crucial technology for 6G. To achieve this crucial functionality, we propose a deep learning based multi-node ISAC 4D environment reconstruction method with Uplink-Downlink (UL-DL) cooperation, which employs virtual aperture technology, Constant False Alarm Rate (CFAR) detection, and Mutiple Signal Classification (MUSIC) algorithm to maximize the sensing capabilities of single sensing nodes. Simultaneously, it introduces a cooperative environmental reconstruction scheme involving multi-node cooperation and Uplink-Downlink (UL-DL) cooperation to overcome the limitations of single-node sensing caused by occlusion and limited viewpoints. Furthermore, the deep learning models Attention Gate Gridding Residual Neural Network (AGGRNN) and Multi-View Sensing Fusion Network (MVSFNet) to enhance the density of sparsely reconstructed point clouds are proposed, aiming to restore as many original environmental details as possible while preserving the spatial structure of the point cloud. Additionally, we propose a multi-level fusion strategy incorporating both data-level and feature-level fusion to fully leverage the advantages of multi-node cooperation. Experimental results demonstrate that the environmental reconstruction performance of this method significantly outperforms other comparative method, enabling high-precision environmental reconstruction using ISAC system.Comment: 13 pages,21 figures,4 table

Gene discovery in an invasive tephritid model pest species, the Mediterranean fruit fly, Ceratitis capitata

<p>Abstract</p> <p>Background</p> <p>The medfly, <it>Ceratitis capitata</it>, is a highly invasive agricultural pest that has become a model insect for the development of biological control programs. Despite research into the behavior and classical and population genetics of this organism, the quantity of sequence data available is limited. We have utilized an expressed sequence tag (EST) approach to obtain detailed information on transcriptome signatures that relate to a variety of physiological systems in the medfly; this information emphasizes on reproduction, sex determination, and chemosensory perception, since the study was based on normalized cDNA libraries from embryos and adult heads.</p> <p>Results</p> <p>A total of 21,253 high-quality ESTs were obtained from the embryo and head libraries. Clustering analyses performed separately for each library resulted in 5201 embryo and 6684 head transcripts. Considering an estimated 19% overlap in the transcriptomes of the two libraries, they represent about 9614 unique transcripts involved in a wide range of biological processes and molecular functions. Of particular interest are the sequences that share homology with <it>Drosophila </it>genes involved in sex determination, olfaction, and reproductive behavior. The medfly <it>transformer2 </it>(<it>tra2</it>) homolog was identified among the embryonic sequences, and its genomic organization and expression were characterized.</p> <p>Conclusion</p> <p>The sequences obtained in this study represent the first major dataset of expressed genes in a tephritid species of agricultural importance. This resource provides essential information to support the investigation of numerous questions regarding the biology of the medfly and other related species and also constitutes an invaluable tool for the annotation of complete genome sequences. Our study has revealed intriguing findings regarding the transcript regulation of <it>tra2 </it>and other sex determination genes, as well as insights into the comparative genomics of genes implicated in chemosensory reception and reproduction.</p