Biology subjects

Fong, D.

Publications and source records attributed to Fong, D..

6 recordsLinked to original sources

bioRxiv2025

Aedes aegypti midgut chymotrypsin has no significant role in blood meal protein digestion or fecundity

The Aedes aegypti mosquito is a vector of dengue, Zika, and chikungunya. The mosquitos reliance on blood facilitates the transmission of these viral pathogens to humans. Digestion of blood proteins depends on the biphasic expression of serine proteases, with trypsin-like activity contributing to most of the activity in the midgut. Other proteases found (serine collagenase- and chymotrypsin-like) are thought to contribute to digestion, but their roles are largely understudied. Thus, elucidating the activity and specific roles of all midgut proteases will help understand the complexity of the digestion process and help validate them as potential targets for the development of a new vector control strategy. Herein, we focused on characterizing the activity profile and role of Ae. aegypti chymotrypsin (AaCHYMO). Knockdown studies resulted in elimination and significant reduction of chymotrypsin-like activity in blood fed midgut extracts, while in vitro fluorescent and blood protein digestion assays revealed important substrate specificity differences. Interestingly, knockdown of AaCHYMO did not impact fecundity, indicating the presence of an intricate network of proteases working collectively to degrade blood proteins. Further, knockdown of the ecdysone receptor (EcR) led to a decrease in overall AaCHYMO expression and activity in the mosquito, which may play an important regulatory role.

biochemistry↗

bioRxiv2024

Comprehensive proteolytic profiling of Aedes aegypti mosquito midgut extracts: Unraveling the blood meal protein digestion system

To sustain the gonotrophic cycle, the Aedes aegypti mosquito must acquire a blood meal from a human or other vertebrate host. However, in the process of blood feeding, the mosquito may facilitate the transmission of several bloodborne viral pathogens (e.g., dengue, Zika, and chikungunya). The blood meal is essential as it contains proteins that are digested into polypeptides and amino acid nutrients that are eventually used for egg production. These proteins are digested by several midgut proteolytic enzymes. As such, the female mosquitos reliance on blood may serve as a potential target for vector and viral transmission control. However, this strategy may prove to be challenging since midgut proteolytic activity is a complex process dependent on several exo- and endo-proteases. Therefore, to understand the complexity of Ae. aegypti blood meal digestion, we used Multiplex Substrate Profiling by Mass Spectrometry (MSP-MS) to generate global proteolytic profiles of sugar- and blood-fed midgut tissue extracts, along with substrate profiles of recombinantly expressed midgut proteases. Our results reveal a shift from high exoproteolytic activity in sugar-fed mosquitoes to an expressive increase in endoproteolytic activity in blood-fed mosquitoes. This approach allowed for the identification of 146 cleaved peptide bonds (by the combined 6 h and 24 h blood-fed samples) in the MSP-MS substrate library, and of these 146, 99 (68%) were cleaved by the five recombinant proteases evaluated. These reveal the individual contribution of each recombinant midgut protease to the overall blood meal digestion process of the Ae. aegypti mosquito. Further, our molecular docking simulations support the substrate specificity of each recombinant protease. Therefore, the present study provides key information of midgut proteases and the blood meal digestion process in mosquitoes, which may be exploited for the development of potential inhibitor targets for vector and viral transmission control strategies. Author SummaryThe Aedes aegypti mosquito is a vector of viral pathogens that can be transmitted directly to humans. For instance, the transmission of dengue, Zika, or chikungunya viruses may happen during the Ae. aegypti acquisition of an infected blood meal. This blood meal is important for the anautogenous mosquito because without the digestion of blood proteins the mosquito will not obtain the necessary nutrients needed for egg production. After imbibing a blood meal, midgut digestive enzymes (proteases) are expressed and secreted into the lumen. To fully understand their roles in blood meal digestion, we used a special technique called Multiplex Substrate Profiling by Mass Spectrometry (MSP-MS). This method allows us to generate global proteolytic activity profiles of Ae. aegypti midgut tissue extracts that were fed with sugar or blood. In addition, we generated substrate cleavage profiles of recombinantly expressed midgut proteases allowing us to understand the enzyme preferences for blood proteins. Therefore, utilizing this approach, we found the contribution of each individual recombinant protease tested relative to the global activity profile of blood-fed midgut tissue extracts. This may be a starting point for the validation of midgut protease inhibition and the development of a new potential vector control strategy.

biochemistry↗

bioRxiv2022

NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange

MotivationThe investigation of sets of genes using biological pathways is a common task for researchers and is supported by a wide variety of software tools. This type of analysis generates hypotheses about the biological processes active or modulated in a specific experimental context. ResultsThe NDEx Integrated Query (IQuery) is a new tool for network and pathway-based gene set interpretation that complements or extends existing resources. It combines novel sources of pathways, integration with Cytoscape, and the ability to store and share analysis results. The IQuery web application performs multiple gene set analyses based on diverse pathways and networks stored in NDEx. These include curated pathways from WikiPathways and SIGNOR, published pathway figures from the last 27 years, machine-assembled networks using the INDRA system, and the new NCI-PID v2.0, an updated version of the popular NCI Pathway Interaction Database. IQuerys integration with MSigDB and cBioPortal now provides pathway analysis in the context of these two resources. Availability and ImplementationIQuery is available at https://www.ndexbio.org/iquery and is implemented in Javascript and Java. ContactDexter Pratt (depratt@health.ucsd.edu)

bioinformatics↗

bioRxiv2021

Capturing scientific knowledge in computable form

Technological advances in computing provide major opportunities to accelerate scientific discovery. The wide availability of structured knowledge would allow us to take full advantage of these by enabling efficient human-computer interaction. Traditionally, biological knowledge is captured in publications and knowledge bases, however, the information in articles is not directly accessible to computers, and knowledge bases are constrained by finite resources available for manual curation. To accelerate knowledge capture and communication and to keep pace with the rapid growth of scientific reports, we developed the Biofactoid (biofactoid.org) software suite, which crowdsources structured knowledge in articles from authors. Biofactoid is a web-based system that lets scientists draw a network of interactions between genes, their products, and chemical compounds and employs smart-automation to translate user input into a structured language using the expressive power of a formal ontology. The resulting data is shared via public information resources, enabling author-curated knowledge to be appreciated in the context of all existing computable knowledge. Authors of recently published papers across a range of journals have already contributed their pathway information, much of which is novel and extends existing pathway databases into new biological areas. We envision the adoption of Biofactoid for crowdsourced curation by scientists and publishers as part of an ecosystem of tools that accelerate scientific communication and discovery. AvailabilityBiofactoid server at https://biofactoid.org

bioinformatics↗

bioRxiv2019

Astrocyte-selective AAV-ADAMTS4 gene therapy combined with hindlimb rehabilitation promotes functional recovery after spinal cord injury

Chondroitin sulphate proteoglycans (CSPGs) are inhibitors to axon regeneration and plasticity. Bacterial chondroitinase ABC degrades CSPGs and has been extensively reported to be therapeutic after SCI but there remain concerns for its clinical translation. A disintegrin and metalloproteinase with thrombospondin motifs-4 (ADAMTS4) is a human enzyme that catalyses the proteolysis of CSPG protein cores. Infusion of ADAMTS4 into the damaged spinal cord was previously shown to improve functional recovery after SCI, however, this therapy is limited in its enzyme form. Adeno-associated viral (AAV) vector gene therapy has emerged as the vector of choice for safe, robust and long-term transgene expression in the central nervous system. Here, an AAV expression cassette containing ADAMTS4 under the control of the astrocytic GfaABC1D promoter was packaged into an AAV5 vector. Sustained expression of ADAMTS4 was achieved in vitro and in vivo, leading to widespread degradation of CSPGs. AAV-ADAMTS4 resulted in significantly decreased lesion size, increased sprouting of hindlimb corticospinal tract axons, increased serotonergic fiber density caudal to the injury, and improved functional recovery after moderate contusive SCI. Hindlimb-specific exercise rehabilitation was used to drive neuroplasticity towards improving functional connections. The combination of hindlimb rehabilitation with AAV-ADAMTS4 led to enhanced functional recovery after SCI. Thus, widespread and long-term degradation of CSPGs through AAV-ADAMTS4 gene therapy in a combinational approach with rehabilitation represents a promising candidate for further preclinical development.

neuroscience↗

bioRxiv2019

Pathway Commons: 2019 Update

Pathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules (e.g., metabolites and drug compounds). Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange (BioPAX) language and the Proteomics Standards Initiative Molecular Interactions format, and then integrated. Pathway Commons provides biologists with (1) tools to search this comprehensive resource, (2) a download site offering integrated bulk sets of pathway data (e.g., tables of interactions and gene sets), (3) reusable software libraries for working with pathway information in several programming languages (Java, R, Python, and Javascript), and (4) a web service for programmatically querying the entire dataset. Visualization of pathways is supported using the Systems Biological Graphical Notation (SBGN). Pathway Commons currently contains data from 22 databases with 4,794 detailed human biochemical processes (i.e., pathways) and [~]2.3 million interactions. To enhance the usability of this large resource for end-users, we develop and maintain interactive web applications and training materials that enable pathway exploration and advanced analysis.

bioinformatics↗