Biology subjects

Finch, G.

Publications and source records attributed to Finch, G..

6 recordsLinked to original sources

bioRxiv2024

Species Tree Topology Impacts the Inference of Ancient Whole-Genome Duplications Across the Angiosperm Phylogeny

PremiseThe history of angiosperms is marked by repeated rounds of ancient whole-genome duplications (WGDs). Here we use state of the art methods to provide an up-to-date view of the distribution of WGDs in the history of angiosperms that considers both the uncertainty introduced by inference methods and alternative phylogenetic hypotheses. MethodsTranscriptomic and genomic data were used to infer and place WGDs across two hypothesized angiosperm phylogenies. Initial WGD hypotheses were made using rate corrections to the distribution of synonymous divergences (Ks) of paralogs and orthologs. WGD hypotheses were tested using syntenic inferences and Bayesian models of duplicate gene gain and loss across the phylogeny. Key resultsThe number of ancient WGDs in the history of angiosperms ([~]170) is largely similar across different inference methods, but there is often variation in the precise placement of WGDs on the phylogeny. Ks based methods often yield alternative hypothesized WGD placements largely due to variation in substitution rates among lineages. Phylogenetic models of duplicate gene gain and loss are more robust to topological variation, allowing for post hoc testing of WGD hypotheses. However, errors in species tree inference can still produce spurious WGD hypotheses regardless of method used. ConclusionsHere we show that different WGD inference methods largely agree on an average of 3.5 WGD in the history of angiosperm species. However, the precise placement of WGDs on the phylogeny is subject to the inference method and tree topology. As researchers continue to test hypotheses regarding the impacts ancient WGDs have on angiosperm evolution, it is important to consider the uncertainty of the phylogeny as well as WGD inference methods.

evolutionary biology↗

bioRxiv2023

Global Pannexin 1-deletion increases tumor-infiltrating lymphocytes in the BRAF/Pten mouse melanoma model.

Immunotherapies for malignant melanoma seek to boost the anti-tumoral response of CD8+ T cells but have a limited patient response rate, in part due to limited tumoral immune cell infiltration. Genetic or pharmacological inhibition of Pannexin 1 (PANX1) channel-forming protein is known to decrease melanoma cell tumorigenic properties in vitro and ex vivo. Here, we crossed Panx1 knockout (Panx1-/-) mice with the inducible melanoma model: BrafCA, PtenloxP, Tyr::CreERT2 (BPC). We found that deleting the Panx1 gene in mice does not reduce BRAF(V600E)/Pten-driven primary tumor formation or improve survival. However, BPC-Panx1-/- mice tumors exhibited a significant increase in infiltration of CD8+ T lymphocytes with no changes in the expression of early T cell activation marker CD69, LAG-3 checkpoint receptor or PD-L1 in tumors when compared to BPC-Panx1+/+ genotype. Our results suggest that although a Panx1 deletion does not overturn the aggressive BRAF/Pten-driven melanoma progression in vivo, it does increase the infiltration of effector immune T cell populations in the tumor microenvironment. We propose that PANX1-targeted therapy could be explored as a strategy to increase tumor-infiltrating lymphocytes to boost anti-tumor immunity.

cancer biology↗

bioRxiv2023

Reduced male fertility of an Antarctic mite following extreme heat stress could prompt localized population declines

Climate change is leading to substantial global thermal changes, which are particularly pronounced in polar regions. Few studies have examined the impact of heat stress on reproduction in Antarctic terrestrial arthropods, specifically how brief, extreme events may alter survival. We observed that sublethal heat stress reduces male fecundity in an Antarctic mite, yielding females that produced fewer viable eggs. Females and males collected from microhabitats with high temperatures showed a similar reduction in fertility. This impact is temporary, as indicated by recovery of male fecundity following return to cooler, stable conditions. The diminished fecundity is likely due to a drastic reduction in the expression of male-associated factors that occur in tandem with a substantial increase in the expression of heat shock proteins. Cross mating between mites from different sites confirmed that heat-exposed populations have impaired male fertility. However, the impact on fertility declines with time when the mites are allowed to recover under less stressful conditions, suggesting that the negative effects are transient. Modeling indicated that heat stress is likely to reduce population growth and that short bouts of non-lethal heat stress could have substantial effects on local populations of Antarctic arthropods.

physiology↗

bioRxiv2022

Egg hatching success is significantly influenced by the time of thermal stress in multiple hard tick species

Ticks are blood-feeding arthropods responsible for the transmission of disease-causing pathogens to a wide range of vertebrate hosts, including livestock and humans. Tick-borne diseases have been implicated in significant economic losses to livestock production, and this threat will increase as these obligate parasites widen their geographical ranges. Just like in other ectotherms, thermal stress due to changing global temperatures has been shown to influence tick survival and distribution. However, studies on the influence of extreme temperatures in ticks have focused on advanced, mobile stages, ignoring stages that are immobile and cannot move to more favorable microhabitats. In this study, low- and high-temperature regimens were assessed in relation to egg viability for hard tick species - Amblyomma maculatum (Gulf Coast tick), Ixodes scapularis (black-legged tick), Dermacentor variabilis (American dog tick), and Rhipicephalus sanguineus (Brown dog tick). Tick eggs exposed early in development were significantly more susceptible to thermal stress when compared with those exposed later in development. In our tested models, treatment was more important for egg hatching than species differences. Lastly, there was evidence of extreme thermal exposure significantly altering the hatching times of tick eggs for specific treatments. These results provide insights into the critical period for tick egg viability and potential tick control strategies as the globe continues to experience climate change.

ecology↗

bioRxiv2021

Rapid stress hardening in the Antarctic midge improves male fertility by increasing courtship success and preventing the decline of accessory gland proteins following cold exposure

Rapid hardening is a process that quickly improves an animals performance following exposure to a potentially damaging stress. Features of reproduction can be improved by rapid hardening, but little is known about how rapid hardening may contribute to physiological responses in the cold environment of Antarctica. In this study of the Antarctic midge, Belgica antarctica (Diptera, Chironomidae), we examine how rapid hardening in response to dehydration (RDH) or cold (RCH) improves male pre- and post-copulatory function related to fertility when the insects are subsequently subjected to a damaging cold exposure. Neither RDH nor RCH improved survival in response to lethal cold stress, but male activity following sublethal cold exposure was enhanced. Both RCH and RDH improved mating success of males compared to those subjected directly to a sublethal bout of cold. Egg viability decreased following direct exposure to sublethal cold, but improved following RCH and RDH. Sublethal cold exposure reduced expression of four accessory gland proteins, while expression remained high in males exposed to RCH. Though rapid hardening may be cryptic in males, this study shows that it can be revealed by pre- and post-copulatory interactions with females.

physiology↗

bioRxiv2019

Multi-level analysis of reproduction in an Antarctic midge identifies female and male accessory gland products that are altered by larval stress and impact progeny viability

The Antarctic midge, Belgica antarctica, is a wingless, non-biting midge endemic to Antarctica. Larval development requires at least two years, but adult life lasts only two weeks. The nonfeeding adults mate in swarms and females die shortly after oviposition. Eggs are suspended in a gel of unknown composition that is expressed from the female accessory gland. This project characterizes molecular mechanisms underlying reproduction in this midge by examining differential gene expression in whole males, females, and larvae, as well as in male and female accessory glands. Functional studies were used to assess the role of the gel encasing the eggs, as well as the impact of stress on reproductive biology. RNA-seq analyses revealed sex- and development-specific gene sets along with those associated with the accessory glands. Proteomic analyses were used to define the composition of the egg-containing gel, which is generated during multiple developmental stages and derived from both the accessory gland and other female organs. Functional studies indicate the gel provides a larval food source and thermal and dehydration buffer, all of which are critical for viability. Larval dehydration stress directly reduces production of storage proteins and key accessory gland components, a feature that impacts adult reproductive success. Modeling reveals that bouts of dehydration may significantly impact population growth. This work lays a foundation for further examination of reproduction in midges and provides new information related to general reproduction in dipterans. A key aspect is that reproduction and stress dynamics, currently understudied in polar organisms, are likely to prove critical for determining how climate change will alter survivability.

genomics↗