Biology subjects

Parker, A.

Publications and source records attributed to Parker, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Single-probe, amplification-free multiplex mRNA PNA-FISH maps bacterial gene expression in intact three-dimensional biofilms

Biofilms are spatially structured communities in which local microenvironments drive physiological differentiation, yet mapping gene expression inside intact three-dimensional biofilms remains challenging. Bacterial spatial transcriptomics methods typically rely on tiled probe sets, sequential hybridization rounds, or signal amplification. Here, we show that a single short, directly labelled peptide nucleic acid (PNA) probe per target is sufficient to quantify bacterial mRNA in situ without amplification. With all probes designed for a common hybridization condition, a transcript panel is resolved in one hybridization on a standard confocal microscope, in unmodified cells while preserving biofilm architecture. Benchmarked against the biphasic cycle of Legionella pneumophila, multiplex mRNA PNA-FISH recovers the expected transcriptional switch and agrees quantitatively with RT-qPCR in planktonic and biofilm populations. In flow-cell biofilms, it shows that sessile populations do not recapitulate the planktonic program and that transcriptional differences follow cellular aggregation state rather than depth.

molecular biology↗

bioRxiv2026

SweepLink: Joint Inference of Demography and Linked~Selection from Time-series Data

Genome-wide time-series data, i.e. allele frequency trajectories tracked across multiple sampling times, are among the richest sources of information for inferring selection. Beyond a beneficial allele's own rise in frequency, such data capture how it drags nearby loci upward via linkage, an effect known as genetic hitch-hiking. Yet most existing tools are single-locus, treating loci independently: they infer site-specific selection coefficients in isolation, then rely on ad hoc window statistics to account for hitch-hiking. Many existing tools further require a predefined population size, or scale poorly when jointly inferring selection and demography, and their power is highly sensitive to a significance threshold. To address these shortcomings, we here present SweepLink, a two-layer Hidden Markov Model that overcomes these limitations by jointly inferring demography and linked selection genome-wide: a spatial layer captures correlations between neighboring selection coefficients, coupled with a temporal Wright-Fisher diffusion layer. As we show with extensive simulations, this setup pushes drift-driven false signals toward neutrality while reinforcing loci that receive support from neighbouring loci, thereby increasing the sensitivity for weak and moderate selection, while matching the power of existing tools to detect strong selection. These simulations further show that SweepLink yields confident posteriors that remain stable at maximal significance, removing the need for arbitrary thresholds. We applied SweepLink to ancient DNA time-series data from the British population, previously analysed with a single-locus tool. SweepLink recovers four of the previously reported signals (LCT, SLC45A2, DHCR7, HERC2), and partially recovers the MHC/HLA signal. It also identifies additional candidate regions, including DPYD, FADS1/2 and OAS1, missed by the prior scan but supported by independent studies.

evolutionary biology↗

bioRxiv2025

A novel transgenic reporter to study vertebrate epigenetics

Epigenetic reprogramming contributes to the generation of cellular diversity during vertebrate development but the mechanisms directing this are still not well understood. Large-scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies, but similar large-scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated "EpiTag" zebrafish transgenic reporter line that permits easy cellular-level visualization of epigenetic silencing or activation in living animals during development, gametogenesis, and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants, identifying relevant vertebrate tissue-specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction-associated fatty liver disease (MAFLD). The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue-specific epigenetic gene regulation in vertebrates. One Sentence SummaryEpiTag transgenic zebrafish provide a powerful new tool for visualizing and studying epigenetic regulation in living vertebrate animals.

genomics↗

bioRxiv2025

Synergistic interference with SARS-CoV-2 replication by Molnupiravir-derived N4 hydroxycytidine and inhibitors of CTP synthetase

N4-hydroxycytidine (NHC), the active metabolite of Molnupiravir, is incorporated into nascent RNA of SARS-CoV-2 and interferes with subsequent virus replication. We have previously described synergy between NHC and inhibitors of dehydroorotate dehydrogenase (DHODH), an enzyme required for pyrimidine synthesis. Upon DHODH inhibition, the lack of endogenous pyrimidines conceivably enhances NHC incorporation. However, the question remains whether preventing the synthesis of just one pyrimidine base, cytidine, might as well augment the antiviral efficacy of NHC. We tested this by inhibiting CTP synthetases (CTPSs), the cellular enzymes that directly catalyze the synthesis of a cytidine nucleotide. We observed that inhibitors of CTP synthetase (CTPSis), namely cyclopentenyl cytosine (CPEC) as well as STP938 and STP720, display a strong synergy with NHC for diminishing SARS-CoV-2 replication in cell culture, as shown earlier for DHODH inhibitors. NHC and CTPSis in combination prevented the cytopathic effect of SARS-CoV-2 and strongly reduced the release of viral RNA and infectious particles, as well as the synthesis of viral proteins. This combination was also active against an Omicron variant of SARS-CoV-2. Addition of cytidine, but not uridine, rescued virus growth under these conditions. Of note, treating SARS-CoV-2-infected hamsters with the CTPS1 inhibitor STP938 strongly diminished COVID pathology. We propose that CTPS inhibition has the potential to increase the efficacy of antiviral cytidine analogues and to treat coronavirus infections. HIGHLIGHTSO_LIThe efficacy of NHC against SARS-CoV-2 replication in cell culture models is intensified by several orders of magnitude through targeting cellular CTP-Synthetase. C_LIO_LIThe drug combination still displays its effect against SARS-CoV-2 replication in the presence of uridine, suggesting that serum uridine cannot counteract its efficacy. C_LIO_LICTPS inhibition diminishes COVID-19-like pathology in an established animal model. C_LI

microbiology↗

bioRxiv2024

Suppression of NRF2-dependent cancer growth by a covalent allosteric molecular glue

The NRF2 transcription factor is constitutively active in cancer where it functions to maintain oxidative homeostasis and reprogram cellular metabolism. NRF2-active tumors exhibit NRF2-dependency and resistance to chemo/radiotherapy. Here we characterize VVD-065, a first-in-class NRF2 inhibitor that acts via an unprecedented allosteric molecular glue mechanism. In the absence of stress or mutation, NRF2 is rapidly degraded by the KEAP1-CUL3 ubiquitin-ligase complex. VVD-065 specifically and covalently engages C151 on KEAP1, which in turn promotes KEAP1-CUL3 complex formation, leading to enhancement of NRF2 degradation. Previously reported C151-directed compounds decrease KEAP1-CUL3 interactions and stabilize NRF2, thus establishing KEAP1_C151 as a tunable regulator of the KEAP1-CUL3 complex and NRF2 stability. VVD-065 inhibited NRF2-dependent tumor growth and sensitized cancers to chemo/radiotherapy, supporting an open Phase I clinical trial (NCT05954312).

cancer biology↗

bioRxiv2024

DYRK1A kinase triplication is the major cause of Otitis Media in Down Syndrome

Down syndrome (DS), which arises from trisomy of the whole or part of chromosome 21 (Hsa21), is one of the most common genetic abnormalities in humans. DS manifests as a broad spectrum of phenotypic features, including hearing loss due to otitis media with effusion (OME), affecting around 50% of children with DS. We employed a panel of mouse models of DS comprising a nested series of duplications covering the regions of the mouse genome syntenic to Hsa21 in order to define the loci involved with OME in DS. We identified a major locus on mouse chromosome 16, containing only 12 genes, that causes OME. Within this region we demonstrate that normalizing the gene dosage of Dyrk1a restored the wild-type phenotype. Investigation of downstream pathways of DYRK1A uncovered a number of pathological mechanisms whereby DYRK1A triplication leads to middle ear inflammation and vascular leak. These include cross-talk of DYRK1A and TGF{beta} signaling and its impact on proinflammatory cytokines IL-6 and IL-17, as well as raised VEGF levels in the middle ear accompanied by increased Hif1a. We conclude that DYRK1A is a potential therapeutic target for OME in children with DS.

genetics↗

bioRxiv2024

Neuronal lipid droplets play a conserved and sex-biased role in maintaining whole-body energy homeostasis

ABSTRACTLipids are essential for neuron development and physiology. Yet, the central hubs that coordinate lipid supply and demand in neurons remain unclear. Here, we combine invertebrate and vertebrate models to establish the presence and functional significance of neuronal lipid droplets (LD) in vivo. We find that LD are normally present in neurons in a non-uniform distribution across the brain, and demonstrate triglyceride metabolism enzymes and lipid droplet-associated proteins control neuronal LD formation through both canonical and recently-discovered pathways. Appropriate LD regulation in neurons has conserved and male-biased effects on whole-body energy homeostasis across flies and mice, specifically neurons that couple environmental cues with energy homeostasis. Mechanistically, LD-derived lipids support neuron function by providing phospholipids to sustain mitochondrial and endoplasmic reticulum homeostasis. Together, our work identifies a conserved role for LD as the organelle that coordinates lipid management in neurons, with implications for our understanding of mechanisms that preserve neuronal lipid homeostasis and function in health and disease. HIGHLIGHTSO_LILipid droplets (LD) normally form in neurons across species Neuronal LD are regulated by a conserved gene network C_LIO_LINeuronal LD regulation plays a conserved and sex-biased role in maintaining energy homeostasis C_LIO_LILD regulation supports ER and mitochondrial function in hunger-activated neurons C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/613929v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@1936e92org.highwire.dtl.DTLVardef@40478aorg.highwire.dtl.DTLVardef@18d5faorg.highwire.dtl.DTLVardef@882ee9_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

CIB2 function is distinct from Whirlin in the development of cochlear stereocilia staircase pattern

Variations in genes coding for calcium and integrin binding protein 2 (CIB2) and whirlin cause deafness both in humans and mice. We previously reported that CIB2 binds to whirlin, and is essential for normal staircase architecture of auditory hair cells stereocilia. Here, we refine the interacting domains between these proteins and provide evidence that both proteins have distinct role in the development and organization of stereocilia bundles required for auditory transduction. Using a series of CIB2 and whirlin deletion constructs and nanoscale pulldown (NanoSPD) assays, we localized the regions of CIB2 that are critical for interaction with whirlin. AlphaFold 2 multimer, independently identified the same interacting regions between CIB2 and whirlin proteins, providing a detailed structural model of the interaction between the CIB2 EF2 domain and whirlin HHD2 domain. Next, we investigated genetic interaction between murine Cib2 and Whrn using genetic approaches. Hearing in mice double heterozygous for functionally null alleles (Cib2KO/+;Whrnwi/+) was similar to age-matched wild type mice, indicating that partial deficiency for both Cib2 and Whrn does not impair hearing. Double homozygous mutant mice (Cib2KO/KO;Whrnwi/wi) had profound hearing loss and cochlear stereocilia exhibited a predominant phenotype seen in single Whrnwi/wi mutants. Furthermore, over-expression of Whrn in Cib2KO/KOmice did not rescue the stereocilia morphology. These data suggest that, CIB2 is multifunctional, with key independent functions in development and/or maintenance of stereocilia staircase pattern in auditory hair cells.

neuroscience↗

bioRxiv2024

Impact of variants and vaccination on nasal immunity across three waves of SARS-CoV-2

SARS-CoV-2 infection and COVID-19 disease vary with respect to viral variant and host vaccination status. However, how vaccines, emergent variants, and their intersection shift host responses in the human nasal mucosa remains uncharacterized. We and others have shown during the first SARS-CoV-2 wave that a muted nasal epithelial interferon response at the site of infection underlies severe COVID-19. We sought to further understand how upper airway cell subsets and states associate with COVID-19 phenotypes across viral variants and vaccination. Here, we integrated new single-cell RNA-sequencing (scRNA-seq) data from nasopharyngeal swabs collected from 67 adult participants during the Delta and Omicron waves with data from 45 participants collected during the original (Ancestral) wave in our prior study. By characterizing detailed cellular states during infection, we identified changes in epithelial and immune cells that are both unique and shared across variants and vaccination status. By defining SARS-CoV-2 RNA+ cells for each variant, we found that Delta samples had a marked increase in the abundance of viral RNA+ cells. Despite this dramatic increase in viral RNA+ cells in Delta cases, the nasal cellular compositions of Delta and Omicron exhibit greater similarity, driven partly by myeloid subsets, than the Ancestral landscapes associated with specialized epithelial subsets. We found that vaccination prior to infection was surprisingly associated with nasal macrophage recruitment and activation rather than adaptive immune cell signatures. While patients with severe disease caused by Ancestral or Delta variants had muted interferon responses, Omicron-infected patients had equivalent interferon responses regardless of disease severity. Our study defines the evolution of cellular targets and signatures of disease severity in the upper respiratory tract across SARS-CoV-2 variants, and suggests that intramuscular vaccines shape myeloid responses in the nasal mucosa upon SARS-CoV-2 infection.

immunology↗

bioRxiv2024

An optogenetic assay for the dauer decision in Caenorhabditis elegans

The dauer decision in Caenorhabditis elegans is a critical developmental decision that ensures survival under harsh environmental conditions. Factors such as temperature, food availability, and pheromone strongly influence the decision to enter and exit dauer. Traditional assays that assess the dauer decision are often confounded by the influence of pheromones from the population, which are often dynamic and highly variable. To mitigate this issue, we developed a simple, single-housing assay for dauer quantification that is compatible with optogenetics. We show that insulin-like peptides (ILPs) from ASJ and other neurons strongly influence the decision to exit dauer, and that ASJ activity can be manipulated with optogenetics to influence the dauer decision in a temporally precise manner.

neuroscience↗

bioRxiv2023

Mimicking of tau hyperphosphorylation in GABAergic motoneurons of C. elegans induces severe peripheral and neuronal alterations

In several neurodegenerative diseases including Alzheimers disease (AD), tau, a microtubule-associated protein (MAP) enriched in the axon, becomes hyperphosphorylated, detaches from microtubules, redistributes to the somato-dendritic compartment and self-aggregates. The mechanisms leading to neuronal dysfunction and death by tau pathology remain to be fully elucidated. C. elegans has been successfully used by several groups including ours to identify mechanisms involved in neurodegeneration. We generated three strains, one overexpressing wild-type human tau (WT Tau), one a tau mutant mimicking hyperphosphorylation (hyperP Tau) and one preventing phosphorylation (hypoP Tau) in GABA motor neurons. A significant reduction of body size and egg laying was noted in these tau strains. Starting at day 1, we found that the worms overexpressing hyperP Tau were smaller than the N2 control strain and the worms either overexpressing WT Tau or hypoP Tau. Starting at day 5, the worms overexpressing WT Tau were smaller than control and the worms overexpressing hypoP Tau. Egg laying was reduced in both hyperP Tau and WT Tau worms. Survival was only decreased in WT Tau worms. Motility deficits were also observed. For age-dependent paralysis, a difference was noted between control and hyperP Tau. Swimming activity and speed were increased in hypoP Tau and decreased in hyperP Tau strains. Axonal integrity was altered in all tau strains. In the case of synaptic activity, at day 1, it was increased in the hypoP Tau strain and decreased in the hyperP Tau one. Collectively, our data revealed that overexpression of tau exerted neuronal and peripheral defects indicating that tau dysfunction could affect cell-cell communication.

neuroscience↗

bioRxiv2022

Homeostasis, injury and recovery dynamics at multiple scales in a self-organizing intestinal crypt

We have built a multi-scale agent-based model (ABM) that reproduces the self-organizing behaviour reported for the intestinal crypt. We demonstrate that a stable spatial organization emerges from the dynamic interaction of multiple signalling pathways, such as Wnt, Notch, BMP, RNF43/ZNRF3 and YAP-Hippo pathways, which regulate proliferation and differentiation, respond to environmental mechanical cues, form feedback mechanisms and modulate the dynamics of the cell cycle protein network. The model recapitulates the crypt phenotype reported after persistent stem cell ablation and after the inhibition of the CDK1 cycle protein. Moreover, we simulated 5-fluorouracil (5-FU)-induced toxicity at multiple scales starting from DNA and RNA damage, which disturbs the cell cycle, cell signalling, proliferation, differentiation and migration and leads to loss of barrier integrity. During recovery, our in-silico crypt regenerates its structure in a self-organizing, dynamic fashion driven by dedifferentiation and enhanced by negative feedback loops. Overall, we present a systems model able to simulate the disruption of molecular events and its impact across multiple levels of epithelial organization and demonstrate its application to epithelial research and drug discovery.

systems biology↗

bioRxiv2022

Multi-omics analysis reveals a crucial role for Retinoic Acid in promoting epigenetic and transcriptional competence of an in vitro model of human Pharyngeal Endoderm.

In vitro differentiation of human Pluripotent Stem Cells (hPSCs) into different cell types has enabled the study of developmental processes that are impossible to dissect in vivo. This innovation has allowed for the derivation of therapeutically relevant cell types that can be used for downstream applications and studies. The Pharyngeal Endoderm (PE) is considered an extremely relevant developmental tissue since it acts as a precursor to a plethora of organ systems such as Esophagus, Parathyroids, Thyroids, Lung, and Thymus. While several studies have highlighted the importance of these cells, an in vitro platform to generate human PE cells is still missing. Here we fill this knowledge gap, by providing a novel in vitro protocol for the derivation of bona fide PE cells from hPSCs. We demonstrated that our PE cells robustly express Pharyngeal Endoderm markers, they are transcriptionally similar to PE cells isolated from in vivo mouse development and represent a transcriptionally homogeneous population. Importantly, we elucidated the contribution of Retinoic Acid in promoting a transcriptional and epigenetic rewiring of PE cells. In addition, we defined the epigenetic landscape of PE cells by combining ATAC-Seq and ChIP-Seq of histone modifications. The integration of these data led to the identification of new putative regulatory regions and to the generation of a gene regulatory network orchestrating the development of PE cells. By combining hPSCs differentiation with computational genomics, our work reveals the epigenetic dynamics that occur during human PE differentiation, providing a solid resource and foundation for research focused on the development of PE derivatives and modeling of their developmental defects in genetic syndromes.

developmental biology↗

bioRxiv2022

Selective inhibitors of JAK1 targeting a subtype-restricted allosteric cysteine

The JAK family of non-receptor tyrosine kinases includes four subtypes (JAK1, JAK2, JAK3, and TYK2) and is responsible for signal transduction downstream of diverse cytokine receptors. JAK inhibitors have emerged as important therapies for immuno(onc)ological disorders, but their use is limited by undesirable side effects presumed to arise from poor subtype selectivity, a common challenge for inhibitors targeting the ATP-binding pocket of kinases. Here, we describe the chemical proteomic discovery of a druggable allosteric cysteine present in the non-catalytic pseudokinase domain of JAK1 (C817) and TYK2 (C838), but absent from JAK2 or JAK3. Electrophilic compounds selectively engaging this site block JAK1-dependent transphosphorylation and cytokine signaling, while appearing to act largely as "silent" ligands for TYK2. Importantly, the allosteric JAK1 inhibitors do not impair JAK2-dependent cytokine signaling and are inactive in cells expressing a C817A JAK1 mutant. Our findings thus reveal an allosteric approach for inhibiting JAK1 with unprecedented subtype selectivity.

pharmacology and toxicology↗

bioRxiv2021

Neuroplastin genetically interacts with Cadherin 23 and the encoded isoform Np55 is sufficient for cochlear hair cell function and hearing

Mammalian hearing involves the mechanoelectrical transduction (MET) of sound-induced fluid waves in the cochlea. Essential to this process are the specialised sensory cochlear cells, the inner (IHCs) and outer hair cells (OHCs). While genetic hearing loss is highly heterogeneous, understanding the requirement of each gene will lead to a better understanding of the molecular basis of hearing and also to therapeutic opportunities for deafness. The Neuroplastin (Nptn) gene, which encodes two protein isoforms Np55 and Np65, is required for hearing, and homozygous loss-of-function mutations that affect both isoforms lead to profound deafness in mice. Here we have utilised several distinct mouse models to elaborate upon the spatial, temporal, and functional requirement of Nptn for hearing. While we demonstrate that both Np55 and Np65 are present in cochlear cells, characterisation of a Np65-specific mouse knockout shows normal hearing thresholds indicating that Np65 is functionally redundant for hearing. In contrast, we find that Nptn-knockout mice have significantly reduced maximal MET currents and MET channel open probabilities in mature OHCs, with both OHCs and IHCs also failing to develop fully mature basolateral currents. Furthermore, comparing the hearing thresholds and IHC synapse structure of Nptn-knockout mice with those of mice that lack Nptn only in IHCs and OHCs shows that the majority of the auditory deficit is explained by hair cell dysfunction, with abnormal afferent synapses contributing only a small proportion of the hearing loss. Finally, we show that continued expression of NEUROPLASTIN in OHCs of adult mice is required for membrane localisation of Plasma Membrane Ca2+ ATPase 2 (PMCA2), which is essential for hearing function. Moreover, Nptn haploinsufficiency phenocopies Atp2b2 (encodes PMCA2) mutations, with heterozygous Nptn-knockout mice exhibiting hearing loss through genetic interaction with the Cdh23ahl allele. Together, our findings provide further insight to the functional requirement of Neuroplastin for mammalian hearing. Author SummarySensorineural hearing loss, caused by problems with sensory cells in the cochlea or the auditory nerve, is the most common type of hearing loss. Mutations in Neuroplastin have already been implicated in deafness in mice. We have used mutant mouse models to investigate where Neuroplastin is expressed in the cochlea and its function. When mice do not express a functioning copy of Neuroplastin they have disruptions to the primary sensory synapse. We show that although synaptic disruption contributes to the loss of hearing function it is not the primary cause. Instead, continued expression of Neuroplastin is needed to maintain the localisation of Plasma Membrane Ca2+ ATPase 2 channels which help regulate calcium flow. We have also shown that two types of NEUROPLASTIN protein (isoforms) are both expressed within the cochlea, although only one of these isoforms needs to be expressed for normal hearing. Finally, we also demonstrate that the hearing loss caused by the absence of Neuroplastin is made worse when combined with a common mutation within a gene called Cadherin 23 (Cdh23ahl). This is an important finding as although there are currently no human patients with an identified NEUROPLASTIN mutation, it may be involved in human deafness in combination with other mutations.

neuroscience↗

bioRxiv2021

Myosin-driven Nucleation of Actin Filaments Drives Stereocilia Development Critical for Hearing

The assembly and maintenance of actin-based mechanosensitive stereocilia in the cochlea is critical for lifelong hearing. Myosin-15 (MYO15) is hypothesized to modulate stereocilia height by trafficking actin regulatory proteins to their tip compartments, where actin polymerization must be precisely controlled during development. We identified a mutation (p.D1647G) in the MYO15 motor-domain that initially maintained trafficking, but caused progressive hearing loss by stunting stereocilia growth, revealing an additional function for MYO15. Consistent with its maintenance of tip trafficking in vivo, purified p.D1647G MYO15 modestly reduced actin-stimulated ATPase activity in vitro. Using ensemble and single-filament fluorescence in vitro assays, we demonstrated that wild-type MYO15 directly accelerated actin filament polymerization by driving nucleation, whilst p.D1647G MYO15 blocked this activity. Collectively, our studies suggest direct actin nucleation by MYO15 at the stereocilia tip is necessary for elongation in vivo, and that this is a primary mechanism disrupted in DFNB3 hereditary human hearing loss.

cell biology↗

bioRxiv2021

Elevated nest temperature has opposing effects on host species infested with parasitic nest flies

Environmental factors, such as elevated temperature, can have varying effects on hosts and their parasites, which can have consequences for disease outcomes. The individual direct effects of temperature must be disentangled to determine the net-effect in host-parasite relationships, yet few studies have determined the net-effects in a multi-host system. To address this gap, we experimentally manipulated temperature and parasite presence in the nests of two host species infested by parasitic blowflies (Protocalliphora sialia). We conducted a factorial experiment by increasing temperature (or not) and removing all parasites (or not) in the nests of eastern bluebirds (Sialia sialis) and tree swallows (Tachycineta bicolor). We then measured nestling morphometrics, blood loss, and survival and quantified parasite abundance. We predicted that if temperature had a direct effect on parasite fitness, then elevated temperature would cause similar directional effects on parasite abundance across host species. If temperature had a direct effect on hosts, and therefore an indirect effect on the parasite, parasite abundance would differ across host species. Heated swallow nests had fewer parasites compared to non-heated nests. In contrast, heated bluebird nests had more parasites compared to non-heated nests. The results of our study demonstrate that elevated temperature can have differential effects on host species, which can impact infestation susceptibility. Furthermore, changing climates could have complex net-effects on parasite fitness and host health across multi-host-parasite interactions.

ecology↗

bioRxiv2021

Improved methods for protein and single-molecule RNA detection in C. elegans embryos

Visualization of gene products in Caenorhabditis elegans has provided insights into the molecular and biological functions of many novel genes in their native contexts. Single-molecule Fluorescence In Situ Hybridization (smFISH) and Immunofluorescence (IF) visualize the abundance and localization of mRNAs and proteins, respectively, allowing researchers to elucidate the localization, dynamics, and functions of many genes. Here, we describe several improvements and optimizations to existing IF and smFISH approaches specifically for use in C. elegans embryos. We present 1) optimized fixation and permeabilization steps to preserve cellular morphology while maintaining probe and antibody accessibility, 2) a streamlined, in-tube approach that negates freeze-cracking, 3) the smiFISH (single molecule inexpensive FISH) adaptation that reduces cost, 4) an assessment of optimal anti-fade products, and 5) straightforward quantification and data analysis methods. Most importantly, published IF and smFISH protocols have predominantly been mutually exclusive, preventing exploration of relationships between an mRNA and a relevant protein in the same sample. Here, we present methods to combine IF and smFISH protocols in C. elegans embryos including an efficient method harnessing nanobodies. Finally, we discuss tricks and tips to help the reader optimize and troubleshoot individual steps in each protocol.

cell biology↗