Biology subjects

Matthews, B. J.

Publications and source records attributed to Matthews, B. J..

15 recordsLinked to original sources

bioRxiv2026

A molecular and cellular mechanism for bitter taste in the mosquito Aedes aegypti

The yellow fever mosquito, Aedes aegypti, is a vector of Zika, Dengue, Chikungunya and yellow fever, disease-causing viruses impacting millions of people annually across the globe. Female mosquitoes transmit pathogens through serial blood-feeding, while both male and female mosquitoes feed on plant resources. Contact chemosensation (taste) guides these two feeding modes in both positive ways, feeding readily on sugar in nectar or ATP in blood, and negative ways, demonstrating aversion to chemically diverse bitter compounds in blood or sugar meals. Here, we identify a receptor, AaegGr14, that is expressed in neurons in the labellum and cibarium of the mosquito. Activation of Gr14-expressing neurons causes reduced feeding, while Gr14 and Gr14-expressing GRNs are required for aversion to bitter compounds during nectar- but not blood-feeding. This work provides a molecular and cellular on-ramp to understand bitter taste in mosquitoes and establishes that there are feeding context-dependent differences in how taste mechanisms influence blood- and nectar-feeding. Understanding the molecular and cellular basis of bitter taste in mosquitoes during nectar- and blood-feeding will help inform vector control strategies and elucidate shared principles and unique aspects of insect taste systems.

neuroscience↗

bioRxiv2026

Profiling and Targeting of Regulatory RNAs to Upregulate Gene Expression

Transcription of long noncoding RNAs (lncRNAs), including enhancer RNAs (eRNAs) and promoter-associated RNAs (paRNAs), collectively termed regulatory RNAs (regRNAs), is a hallmark of active gene expression, yet it remains unknown whether regRNAs can be targeted to selectively enhance transcription in cis. We developed regRNA Capture-seq, a high-throughput method to profile regRNAs, and applied it to primary human hepatocytes, annotating thousands of regRNAs at [~]2,000 enhancers and promoters. Using this approach, we interrogated a genetically validated enhancer of the ornithine transcarbamylase (OTC) gene, mutations of which cause OTC deficiency (OTCD), the most common urea cycle disorder. Antisense oligonucleotides (ASOs) targeting enhancer-derived regRNAs led to dose-dependent upregulation of OTC in hepatocytes. Mechanistically, ASOs altered regRNA structure, elevated regRNA levels, displaced transcriptional repressors, and increased H3K27 acetylation at the targeted enhancer. This work establishes a potential therapeutic strategy for addressing haploinsufficiency and highlights regRNAs as actionable targets for ASO-mediated upregulation of gene expression.

genomics↗

bioRxiv2026

Living by the sea: chromosome-scale genome assembly and salt gland transcriptomes provide insights into ion regulatory mechanisms in the saline-tolerant mosquito Aedes togoi

The coastal rock pool mosquito, Aedes togoi, is among the few saline-tolerant mosquito species who lay their eggs in seawater pools where their larvae develop in water that spans dilute freshwater to hypersaline conditions. Ae. togoi is found in a relatively restricted range spanning the North Pacific coast of North America and coastal regions of Asia from subtropical to subarctic latitudes. Here, we present a de-novo chromosome-scale genome assembly and gene annotation for Ae. togoi, highlighting its relatively small genome size and novel chromosomal arrangements compared to other available genomes of Aedine mosquitoes. As part of the annotation process, we detail repeat content and distribution and curate several key multi-gene families, focusing on ion-transport proteins enriched in the larval salt-secreting gland that are candidates for facilitating hyperosmotic urine formation during development in saline water. Using these new resources, we gain mechanistic insight into the ion regulatory capabilities that power the remarkable saline tolerance of the larvae of Ae. togoi. Altogether, we have contributed to the growing body of genomic and transcriptomic resources for diverse mosquito species and provided mechanistic insights into the molecular adaptations required for an insect to thrive in highly dynamic environments such as coastal rock pools.

genomics↗

bioRxiv2026

Surface texture guides egg-laying decisions in Aedes aegypti mosquitoes

Mosquitoes undergo development as aquatic larvae and pupae before emerging as terrestrial adults. Accordingly, blood-fed and mated female mosquitoes must select an appropriate egg-laying site to maximize the fitness of their offspring. Female yellow fever mosquitoes (Aedes aegypti) lay their eggs above the waterline of small containers or natural bodies of water, where they can remain dormant for many months until they are submerged and hatch. Here, we show that female mosquitoes use surface texture as a powerful cue to guide egg-laying decisions, selecting rougher textures over smooth when choosing among containers and when selecting specific sites within a given substrate. In addition, we identify an interaction between substrate texture and water salinity with respect to egg-laying decisions, demonstrating that female mosquitoes integrate competing cues to determine the ultimate suitability of an egg-laying site. Finally, we explore the dynamics of local egg-laying search behaviour, demonstrating that texture modulates traversal speed while mosquitoes search for appropriate egg-laying sites.

animal behavior and cognition↗

bioRxiv2023

Cross-modal sensory compensation increases mosquito attraction to humans

Sensory compensation is a process that allows individuals with a loss of one sense, for instance hearing or vision, to adapt to changes in their sensory abilities. Where this phenomenon has been observed, there is enhanced perception by another sense to compensate for deficiency of the lost sense. Such compensation is important for humans and non-human animals that use multisensory integration for effective navigation and the execution of vital tasks. Among these, female mosquitoes are sensory specialists that rely heavily on integrating multiple human-emitted cues in their quest for a suitable host to obtain a blood meal. Here, we identify a previously undescribed mechanism of sensory compensation in female Aedes aegypti mosquitoes. Mutant mosquitoes lacking the odorant receptor co-receptor Orco show specific enhancement in heat-seeking behavior. This s compensation does not require the antenna, which was previously assumed to be the primary mosquito thermosensitive organ. Instead, we found that the tips of the forelegs are required to detect heat, and that the heightened sensitivity in heat detection is mediated by increased neuronal activity in foreleg sensory neurons, which are distant from the head appendage neurons that express Orco. By comparative gene expression analysis in wildtype and Orco mutant legs, we identify Ir140, a foreleg-enriched member of the Ionotropic Receptor (IR) superfamily of sensory receptors, as strongly upregulated in Orco mutant legs. Emphasizing the important role of IRs in thermosensation, we find that mutant mosquitoes lacking the IR co-receptor, Ir25a, lose all responses to heat, and Ir140 mutants show strong deficits in responding to human skin temperatures. We generated an Ir140, Orco double mutant and show that these animals lose the remarkable sensory compensation seen in Orco mutants. This strongly suggests that upregulation of Ir140 in the foreleg is the mechanism of sensory compensation in Orco mutants. Odorant receptor expression is sparse in legs, suggesting an indirect, long-range mechanism of sensory compensation. Our findings reveal a novel compensatory mechanism in which loss of one sensory modality in female Aedes aegypti mosquitoes results in greater sensitivity in another to maintain the overall effectiveness of their host-seeking behavior, further enhancing their status as the most dangerous predator of humans.

neuroscience↗

bioRxiv2021

Molecular evidence of intertidal habitats selecting for repeated ice-binding protein evolution in invertebrates

Ice-binding proteins (IBPs) have evolved independently in multiple taxonomic groups to improve their survival of sub-zero temperatures. Intertidal invertebrates in temperate and polar regions frequently encounter sub-zero temperatures, yet there is little information on IBPs in these organisms. We hypothesized that there are far more ice-binding proteins than are currently known and that the occurrence of freezing in the intertidal zone selects for these proteins. We compiled a list of genome-sequenced invertebrates across multiple habitats and a list of known IBP sequences and used BLAST to identify a wide array of putative IBPs in those invertebrates. We found that the probability of an invertebrate species having an ice-binding protein was significantly greater in intertidal species as compared to those primarily found in open ocean or freshwater habitats. These intertidal IBPs had high sequence similarity to fish and tick antifreeze glycoproteins and fish type II antifreeze proteins. Previously established classifiers based on machine learning techniques further predicted ice-binding activity in the majority of our newly identified putative IBPs. We investigated the potential evolutionary origin of one putative IBP from the hard-shelled mussel Mytilus coruscus and suggest that it arose through gene duplication and neofunctionalization. We show that IBPs likely readily evolve in response to freezing risk, that there is an array of uncharacterized ice binding proteins and highlight the need for broader laboratory-based surveys of the diversity of ice binding activity across diverse taxonomic and ecological groups. Summary statementIntertidal invertebrates have a disproportionate number of putative ice-binding proteins relative to other habitats. These putative proteins are highly similar to antifreeze glycoproteins and type II antifreeze proteins from fish.

biochemistry↗

bioRxiv2021

Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model

Sex differences in gene expression are widespread in the liver, where a large number of autosomal factors act in tandem with growth hormone signaling to regulate individual variability of sex differences in liver metabolism and disease. Here, we compare hepatic transcriptomic and epigenetic profiles of mouse strains C57Bl/6J and CAST/EiJ, representing two subspecies separated by 0.5-1 million years of evolution, to elucidate the actions of genetic factors regulating liver sex differences. We identify 144 protein coding genes and 78 lncRNAs showing strain-conserved sex bias; many have gene ontologies relevant to liver function, are more highly liver-specific and show greater sex bias, and are more proximally regulated than genes whose sex bias is strain-dependent. The strain-conserved genes include key growth hormone-dependent transcriptional regulators of liver sex bias; however, three other transcription factors, Trim24, Tox, and Zfp809, lose sex-biased expression in CAST/EiJ mouse liver. To elucidate these strain specificities in expression, we characterized the strain-dependence of sex-biased chromatin opening and enhancer marks at cis regulatory elements (CREs) within expression quantitative trait loci (eQTL) regulating liver sex-biased genes. Strikingly, 208 of 286 eQTLs with strain-specific, sex-differential effects on expression were associated with a complete gain, loss, or reversal of expression sex differences between strains. Moreover, 166 of the 286 eQTLs were linked to the strain-specific gain or loss of localized sex-biased CREs. Remarkably, a subset of these CREs lacked strain-specific genetic variants yet showed coordinated, strain-dependent sex-biased epigenetic regulation. Thus, we directly link hundreds of strain-specific genetic variants to the high variability in CRE activity and expression of sex-biased genes, and uncover underlying genetically-determined epigenetic states controlling liver sex bias in genetically diverse mouse populations. Author summaryMale-female differences in liver gene expression confer sex differences in diverse biological processes relevant to human health and disease, but are difficult to model in inbred mice given their identical genetic backgrounds. Outbred mice provide some variability, but cross-strain studies of sex bias in rodents have not been well studied. Here we elucidate the actions of genetic factors regulating liver sex differences in two Diversity Outbred mouse founder mouse strains, C57Bl/6 and CAST/EiJ. We find that many of the strain differences in sex-biased gene expression can be linked to the gain or loss of a cis regulatory element associated with one or more strain-specific sequence variants. Strikingly, in many cases, the associated cis regulatory element lacked strain-specific variants, yet was subject to coordinated, strain-dependent epigenetic regulation. Thus, harnessing the power of naturally occurring genetic diversity of Diversity Outbred mice, we integrated biological data at the genetic, epigenetic, and transcriptomic levels across evolutionary divergent mouse strains to discover hundreds of localized genomic regions that control phenotypic sex differences in the liver. These findings may serve as a model for studies of human genetic variation and the effect of population-wide variation on sex differences in health and disease.

genetics↗

bioRxiv2020

Non-canonical odor coding ensures unbreakable mosquito attraction to humans

Female Aedes aegypti mosquitoes are a persistent human foe, transmitting arboviruses including dengue and yellow fever when they bite us to obtain a blood meal. Mosquitoes are intensely attracted to human-emitted body odor, heat, and carbon dioxide, which they detect using three different large multi-gene families encoding odor-gated ion channels. Genetic mutations that cause profound disruptions to the olfactory system have modest effects on human attraction, suggesting significant redundancy in odor coding. The canonical view is that olfactory sensory neurons each express a single chemosensory receptor that defines its ligand selectivity. Using immunostaining, RNA in situ hybridization, and single nucleus RNA sequencing, we discovered that Aedes aegypti uses an entirely different organizational principle, with many neurons co-expressing multiple chemosensory receptor genes. In vivo electrophysiology demonstrates that the broad ligand-sensitivity of mosquito olfactory neurons is due to this non-canonical co-expression. The redundancy afforded by an olfactory system in which many neurons co-express multiple receptors with different chemical sensitivity may greatly increase the robustness of the mosquito olfactory system and explain our longstanding inability to engineer new compounds that disrupt the detection of human body odor by mosquitoes.

neuroscience↗

bioRxiv2020

Chemical signatures of human odour generate a unique neural code in the brain of Aedes aegypti mosquitoes

A globally invasive form of the mosquito Aedes aegypti specializes in biting humans, making it an efficient vector of dengue, yellow fever, Zika, and chikungunya viruses. Host-seeking females strongly prefer human odour over the odour of non-human animals, but exactly how they distinguish the two is not known. Vertebrate odours are complex blends of volatile chemicals with many shared components, making discrimination an interesting sensory coding challenge. Here we show that human and animal odour blends evoke activity in unique combinations of olfactory glomeruli within the Aedes aegypti antennal lobe. Human blends consistently activate a universal glomerulus, which is equally responsive to diverse animal and nectar-related blends, and a more selective human-sensitive glomerulus. This dual signal robustly distinguishes humans from animals across concentrations, individual humans, and diverse animal species. Remarkably, the human-sensitive glomerulus is narrowly tuned to the long-chain aldehydes decanal and undecanal, which we show are consistently enriched in (though not specific to) human odour and which likely originate from unique human skin lipids. We propose a model of host-odour coding wherein normalization of activity in the human-sensitive glomerulus by that in the broadly-tuned universal glomerulus generates a robust discriminatory signal of the relative concentration of long-chain aldehydes in a host odour blend. Our work demonstrates how animal brains may distil complex odour stimuli of innate biological relevance into simple neural codes and reveals novel targets for the design of next-generation mosquito-control strategies.

neuroscience↗

bioRxiv2020

Modelling the Putative Ancient Distribution of the Costal Rock Pool Mosquito Aedes togoi

The coastal rock pool mosquito, Aedes togoi, is found in coastal east Asia in climates ranging from subtropical to subarctic. However, a disjunct population in the Pacific Northwest of North America has an ambiguous heritage. Two potential models explain the presence of Ae. togoi in North America: ancient Beringian dispersal or modern anthropogenic introduction. Genetic studies have thus far proved inconclusive. Here we described the putative ancient distribution of Ae. togoi habitat in east Asia and examined the climatic feasibility of a Beringian introduction into North America using modern distribution records and ecological niche modeling of bioclimatic data from the last interglacial period (~120,000 BP), the last glacial maximum (~21,000 BP), and the mid-Holocene (~6000 BP). Our results suggest that suitable climatic conditions existed for Ae. togoi to arrive in North America through natural dispersal as well as to persist there until present times. Furthermore, we find that ancient distributions of suitable Ae. togoi habitat in east Asia may explain the genetic relationships between Ae. togoi populations identified in other studies. These findings indicate the utility of ecological niche modeling as a complementary tool for studying insect phylogeography.

zoology↗

bioRxiv2019

CTCF and Cohesin link sex-biased distal regulatory elements to sex-biased gene expression in mouse liver

BackgroundSex differences in the transcriptome and epigenome are widespread in mouse liver and are associated with sex-bias in liver disease. Several thousand sex-differential distal enhancers have been identified; however, their links to sex-biased genes and the impact of any sex-differences in nuclear organization, DNA looping, and chromatin interactions are unknown. ResultsTo address these issues, we first characterized 1,847 mouse liver genomic regions showing significant sex differential occupancy by cohesin and CTCF, two key 3D nuclear organizing factors. These sex-differential binding sites were largely distal to sex-biased genes, but rarely generated sex-differential TAD (topologically associating domain) or intra-TAD loop anchors. A substantial subset of the sex-biased cohesin-non-CTCF binding sites, but not the sex-biased cohesin-and-CTCF binding sites, overlapped sex-biased enhancers. Cohesin depletion reduced the expression of male-biased genes with distal, but not proximal, sex-biased enhancers by >10-fold, implicating cohesin in long-range enhancer interactions regulating sex-biased genes. Using circularized chromosome conformation capture-based sequencing (4C-seq), we showed that sex differences in distal sex-biased enhancer-promoter interactions are common. Sex-differential chromatin interactions involving sex-biased gene promoters, enhancers, and lncRNAs were associated with sex-biased binding of cohesin and/or CTCF. Furthermore, intra-TAD loops with sex-independent cohesin-and-CTCF anchors conferred sex specificity to chromatin interactions indirectly, by insulating sex-biased enhancer-promoter contacts and by bringing sex-biased genes into closer proximity to sex-biased enhancers. ConclusionsThese findings elucidate how 3-dimensional genome organization contributes to sex differences in gene expression in a non-reproductive tissue through both direct and indirect effects of cohesin and CTCF looping on distal enhancer interactions with sex-differentially expressed genes.

genomics↗

bioRxiv2018

The ion channel ppk301 controls freshwater egg-laying in the mosquito Aedes aegypti

Aedes aegypti mosquitoes are deadly vectors of arboviral pathogens including Zika, dengue, and yellow fever, and breed in containers of freshwater associated with human habitation1,2. Female Ae. aegypti lay eggs near freshwater because larval and pupal stages are aquatic3. They use volatile cues to locate water at a distance4, while at close-range they contact water to evaluate its suitability for egg-laying4-7. High salinity is lethal to mosquito offspring and therefore correctly laying eggs in freshwater is a crucial parenting decision made by female mosquitoes. Here we show that the DEG/ENaC channel8-10 ppk301 is required for mosquitoes to exploit freshwater egg-laying substrates. When ppk301 mutant females contact water, they do not lay eggs as readily as wild-type animals and are more likely to make aberrant decisions between freshwater and saltwater at concentrations that impair offspring survival. We used a CRISPR-Cas9-based genetic knock-in strategy combined with the Q-binary transactivator system11 to build genetic tools for labelling and imaging neurons in the mosquito. We found that ppk301 is expressed in sensory neurons in legs and proboscis, appendages that directly contact water, and that ppk301-expressing neurons project to central taste centres. Using in vivo calcium imaging with the genetically-encoded calcium sensor GCaMP6s12, we found that ppk301-expressing cells respond to water but, unexpectedly, also to salt. This suggests that ppk301 is instructive for egg-laying at low salt concentrations but that a ppk301-independent pathway is responsible for inhibiting egg-laying at high salt concentrations. Water is a key resource for insect survival and understanding how mosquitoes interact with water to control different behaviours is an opportunity to study the evolution of chemosensory systems. The new genetic tools described here will enable direct study of not only egg-laying, but also other behaviours in mosquitoes that influence disease transmission and enable comparative studies of insect biology more broadly.

neuroscience↗

bioRxiv2018

Insulation of gene expression by CTCF and cohesin-based subTADs (ubiquitous intra-TAD loop structures) in mouse liver

CTCF and cohesin are key drivers of 3D-nuclear organization, anchoring the megabase-scale Topologically Associating Domains (TADs) that segment the genome. Here, we present a computational method to identify cohesin-and-CTCF binding sites that form intra-TAD DNA loops (subTADs). We show that predicted subTAD anchors are structurally indistinguishable from those of TADs regarding their binding partners, sequence conservation, and resistance to cohesin knockdown; further, the subTAD loops retain key functional features of TADs, including insulation of chromatin contacts, blockage of repressive histone mark spread, and ubiquity across tissues. We propose that subTADs form by the same loop extrusion mechanism as larger loops, and that their shorter length enables finer regulatory control over gene expression. 4C-seq analysis using an Alb promoter viewpoint illustrates the role of subTADs in restricting enhancer-promoter interactions. These findings elucidate the role of intra-TAD cohesin-and-CTCF binding in nuclear organization, and demonstrate that distal enhancer insulation by subTADs is widespread.

genomics↗

bioRxiv2017

Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control

Female Aedes aegypti mosquitoes infect hundreds of millions of people each year with dangerous viral pathogens including dengue, yellow fever, Zika, and chikungunya. Progress in understanding the biology of this insect, and developing tools to fight it, has been slowed by the lack of a high-quality genome assembly. Here we combine diverse genome technologies to produce AaegL5, a dramatically improved and annotated assembly, and demonstrate how it accelerates mosquito science and control. We anchored the physical and cytogenetic maps, resolved the size and composition of the elusive sex-determining \"M locus\", significantly increased the known members of the glutathione-S-transferase genes important for insecticide resistance, and doubled the number of chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites. Using high-resolution QTL and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. We predict that AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly arboviral vector.

genomics↗

bioRxiv2017

orco mutagenesis causes loss of antennal lobe glomeruli and impaired social behavior in ants

Life inside ant colonies is orchestrated with a diverse set of pheromones, but it is not clear how ants perceive these social cues. It has been proposed that pheromone perception in ants evolved via expansions in the numbers of odorant receptors (ORs) and antennal lobe glomeruli. Here we generate the first mutant lines in ants by disrupting orco, a gene required for the function of all ORs. We find that orco mutants exhibit severe deficiencies in social behavior and fitness, suggesting that they are unable to perceive pheromones. Surprisingly, unlike in Drosophila melanogaster, orco mutant ants also lack most of the approximately 500 antennal lobe glomeruli found in wild-types. These results illustrate that ORs are essential for ant social organization, and raise the possibility that, similar to mammals, receptor function is required for the development and/or maintenance of the highly complex olfactory processing areas in the ant brain.

evolutionary biology↗