Biology subjects

Larson, K.

Publications and source records attributed to Larson, K..

9 recordsLinked to original sources

bioRxiv2025

Phenological turnover matters when making trait-based predictions of plant-pollinator interactions

1. Understanding the processes determining species interactions is key to predicting and safeguarding ecological networks under rapid environmental change. One approach to estimating interactions is to use morphologies of taxa interacting across trophic levels to reveal suites of traits they are more likely to interact with (i.e. a trait niche). 2. Previous work studying these morphological trait niches has typically used interactions between species that are pooled in space and time. However, species assemblages, and the traits of individuals within species, can change across even small landscapes over a season, leading to morphological trait space being dynamically reshaped. Therefore, it is unclear how morphological trait turnover affects our inferences of trait niches, and our ability to answer this is in part limited by a lack of individual-level trait data. 3. Here, we directly address this by studying a montane Arctic plant-pollinator community over five growing seasons (>1,300 hours of fieldwork). Specifically, we linked every recorded plant-bumblebee interaction with the traits of the bee individual involved (n = 1,150), to investigate 1) whether plant taxa (n = 10) exhibited bee trait niches by interacting with specific regions of multidimensional trait space of visiting bumblebees, and 2) how our inference of these trait niches was affected by considering bumblebee trait turnover and plant taxon turnover. 4. When not considering turnover (interactions in space and time are pooled), plant taxa demonstrated bee trait niches. However, next we considered how bee trait space is reshaped over the elevational and seasonal gradient (especially with the emergence of different castes), and how this reshaping co-occurs with different spatiotemporal ranges of the plant taxa. From this we found the degree to which plant taxa exhibited trait niches declined significantly, and that seasonal reshaping of bee trait space was the primary driver of this trend. 5. Overall, in highly dynamic systems, like the Arctic, overlooking community turnover could mask and even overestimate the ability of morphology to explain interactions. Hence, determining how morphological traits of individual interaction partners are in phenological synchrony at localised scales will be fundamental to understanding the role morphology plays in underpinning plant-pollinator interactions.

ecology↗

bioRxiv2024

PP1 PNUTS binds the restrictor and dephosphorylates RNA pol II CTD Ser5 to stimulate transcription termination

The restrictor, ZC3H4/WDR82, is the major termination factor for antisense transcription from bidirectional promoters, but its mechanism is poorly understood. We report that ZC3H4/WDR82 co-purifies with PP1 phosphatase and PP1 phosphatase nuclear targeting subunit, PNUTS, which binds directly to the WDR82 subunit of restrictor. AlphaFold predicts a quaternary complex, PPWZ, in which PP1-associated PNUTS and ZC3H4 both contact WDR82. To investigate the role of protein dephosphorylation in PPWZ activity, we expressed a substrate trap comprising inactive PP1H66K linked to the PNUTS C-terminus. PP1H66K-PNUTS binds pol II large subunit and nuclear exosome components. PP1H66K-PNUTS, but not PP1WT-PNUTS, functions as a dominant-negative inhibitor of antisense termination and CTD Ser5 dephosphorylation. Both these activities require the PNUTS WDR82 binding domain that interacts with restrictor. We show that CTD Ser5 hyperphosphorylation is associated with higher processivity and reduced pausing that would counteract termination, and propose that Ser5 dephosphorylation by PPWZ is coupled to termination. In summary, we identify the PP1 phosphatase activity of the PPWZ complex as essential for terminator function and propose that this heterotetramer is the physiologically relevant form of restrictor.

molecular biology↗

bioRxiv2024

MAIA: An open-source, modular, bioreactor for cities

This work presents the design and fabrication of MAIA, an open-source, modular, low-cost, and portable bioreactor for democratizing the development of synthetic biology based projects for urban settings. The integration of open-source synthetic biology (synbio) tools in a citys infrastructure planning and design is crucial for addressing the great challenges related to urbanization. Synbio tools have great potential to help us complement our current sensing and actuating urban infrastructure. The MAIA reactor controls bacterial growth variables, making it suitable for cell-based experiments while reducing the need for expensive laboratory equipment. Its low-cost and open-source design allow for easy replication and modification, making it accessible to a broader audience. Its portability makes it suitable for use outside of traditional laboratory settings. We qualitatively and quantitatively validated the reactors capability to support cell growth, stimulate gene expression, and act as a creative tool for students and users.

synthetic biology↗

bioRxiv2023

The drivers of dark diversity in the Scandinavian tundra are metric-dependent

AimDark diversity refers to the set of species that are not observed in an area but could potentially occur based on suitable local environmental conditions. In this paper, we applied both niche-based and co-occurrence-based methods to estimate the dark diversity of vascular plant species in the subarctic tundra. We then aimed to unravel the drivers explaining (1) why some locations were missing relatively more suitable species than others, and (2) why certain plant species were more often absent from suitable locations than others. LocationThe Scandinavian tundra around Abisko, northern Sweden. MethodsWe calculated the dark diversity in 107 plots spread out across four mountain trails using four different methods. Two niche-based (Beals index and hypergeometric method) and two co-occurrences-based (climatic niche model and climatic niche model followed by species-specific threshold) methods. This was then followed by multiple generalized linear mixed models and general linear models to determine which habitat characteristics and species traits contributed most to the dark diversity. ResultsThe study showed a notable divergence in the predicted drivers of dark diversity depending on the method used. Nevertheless, we can conclude that plot-level dark diversity was generally 18% higher in areas at low elevations and 30% and 10% higher in areas with a low species richness or low levels of habitat disturbance, respectively. ConclusionOur findings call for caution when interpreting statistical findings of dark diversity estimates. Even so, all analyses point towards an important role for natural processes such as competitive dominance as main driver of the spatial patterns found in dark diversity in the northern Scandes.

ecology↗

bioRxiv2022

SELECTIVE INHIBITION OF SOLUBLE TNF ATTENUATES HIPPOCAMPAL NEUROINFLAMMATION AND PSD-95 EXPRESSION TO IMPROVE NEUROLOGICAL FUNCTIONS IN A RAT MODEL OF GULF WAR ILLNESS

BACKGROUNDSystemic inflammation is a major contributor to poor brain pathology across many disease conditions. Specifically, the upregulation of the pro-inflammatory cytokine TNF in the hippocampus activates its receptor TNFR1, reducing AMPA receptor trafficking to impair LTP and associated behavioral outcomes. Studies using animal models of GWI have shown both a chronic upregulation of TNF and impaired neurological function. Therefore, this study aimed to investigate whether selectively inhibiting only the soluble form of TNF (solTNF) that preferentially activates TNFR1 can reverse neuroinflammation to improve neuroplasticity and neurological function. METHODSGWI was induced in rats by treating with DFP (or vehicle) for 5 consecutive days. Six months later, the rats were treated with XPro1595 (or vehicle) for 2 weeks to selectively inhibit solTNF, after which they were subjected to a battery of behavioral tests (cognition, anxiety-related, depressive-like behavior, and neuropathic pain). MRI brain scans were performed, and the animals were euthanized for brain pathological analysis. RESULTSThe hippocampus of the GWI rats had significantly increased neuroinflammatory levels, resulting in edema and reduced AMPA receptor trafficking to the post-synaptic membrane that collectively promoted impairments in memory, anxiety, depressive-like behavior, and neuropathic pain. However, treating the rats with XPro1595 in the chronic environment attenuated the neuroinflammatory response, that reduced edema and impaired AMPA receptor trafficking, allowing for improvements in all areas of neurological function. CONCLUSIONOverall findings suggest that selectively inhibiting solTNF using XPro1595 reduces neuroinflammation, synaptic plasticity, and overall function when administered in the chronic setting of a rat model of GWI. This data supports the use of XPro1595 in Veterans with GWI.

neuroscience↗

bioRxiv2021

Mapping trait versus species turnover reveals spatiotemporal variation in functional redundancy in a plant-pollinator network

Functional overlap between species (redundancy) shapes competitive and mutualistic interactions, determining community responses to perturbations. Most studies view functional redundancy as static, even though individuals within species vary in traits over seasonal or spatial gradients. Consequently, we lack knowledge on trait turnover within species, how functional redundancy spatiotemporally varies, and when and where interaction networks are vulnerable to functional loss. Studying an Arctic bumblebee community, we investigated how body-size turnover over elevation and season shapes their host-plant interactions, and test how sensitive networks are to sequentially losing body-size groups. With trait turnover being larger than species, we found: i) late-season networks were less specialised when nodes comprised functionally similar bumblebees; ii) removal of bumblebee-body-size groups over species accelerated coextinction of host plants, with the magnitude varying in space and time. We demonstrate functional redundancy can vary spatiotemporally, and functional loss impacts interaction partners more than expected from species loss alone.

ecology↗

bioRxiv2018

Aerodigestive sampling reveals altered microbial exchange between lung, oropharyngeal, and gastric microbiomes in children with impaired swallow function

11.1 BackgroundChildren with oropharyngeal dysphagia have impaired airway protection mechanisms and are at higher risk for pneumonia and other pulmonary complications. Aspiration of gastric contents is often implicated as a cause for these pulmonary complications, despite being supported by little evidence. The goal of this study is to determine the relative contribution of oropharyngeal and gastric microbial communities to perturbations in the lung microbiome of children with and without oropharyngeal dysphagia and aspiration.\n\n1.2 MethodsWe conducted a prospective cohort study of 222 patients consecutively recruited from a tertiary aerodigestive center undergoing simultaneous esophagogastroduodenoscopy and flexible bronchoscopy. Bronchoalveolar lavage, gastric and oropharyngeal samples were collected and 16S sequencing was performed. A subset of patients also underwent video fluoroscopic swallow studies to assess swallow function and were categorized as aspiration/no aspiration. Microbial communities across the aerodi-gestive tract were compared in patients with and without aspiration by calculating within-patient beta diversities and quantifying microbial exchange across sites.\n\n1.3 ResultsWithin all patients, lung, oropharyngeal and gastric microbiomes overlap. The degree of similarity is the lowest between the oropharynx and lungs (median Jensen-Shannon distance (JSD) = 0.90), and as high between the stomach and lungs as between the oropharynx and stomach (median JSD = 0.55 and 0.56, respectively; p = 0.6). Unlike the oropharyngeal microbiome, lung and gastric communities are highly variable across people and driven primarily by person rather than body site. In patients with aspiration, the lung microbiome more closely resembles oropharyngeal rather than gastric communities and there is greater prevalence of microbial exchange between the lung and oropharynx than between gastric and lung sites (p = 0.04 and 3x10-5, respectively).\n\n1.4 ConclusionsThe gastric and lung microbiomes display significant overlap in patients with intact airway protective mechanisms while the lung and oropharynx remain distinct. In patients with impaired swal-low function and aspiration, the lung microbiome shifts towards oropharyngeal rather than gastric communities. This finding may explain why antireflux surgeries fail to show benefit in pediatric pulmonary outcomes.

microbiology↗

bioRxiv2018

Detection of arterial wall abnormalities via Bayesian model selection

Patient-specific modeling of hemodynamics in arterial networks has so far relied on parameter estimation for inexpensive or small-scale models. We describe here a Bayesian uncertainty quantification framework which makes two major advances: an efficient parallel implementation, allowing parameter estimation for more complex forward models, and a system for practical model selection, allowing evidence-based comparison between distinct physical models. We demonstrate the proposed methodology by generating simulated noisy flow velocity data from a branching arterial tree model in which a structural defect is introduced at an unknown location; our approach is shown to accurately locate the abnormality and estimate its physical properties even in the presence of significant observational and systemic error. As the method readily admits real data, it shows great potential in patient-specific parameter fitting for hemodynamical flow models.

bioengineering↗

bioRxiv2018

Inversion frequencies and phenotypic effects are modulated by the environment

Understanding how environmental variation drives phenotypic diversification within species is a major objective in evolutionary biology. The seaweed fly Coelopa frigida provides an excellent model for the study of genetically driven phenotypes because it carries an /{beta} inversion polymorphism that affects body size. Coelopa frigida inhabits highly variable beds of decomposing seaweed on the coast in Scandinavia thus providing a suitable test ground to investigate the genetic effects of substrate on both the frequency of the inversion (directional selection) and on the phenotype (genotype x environment effects). Here we use a reciprocal transplant experiment to test the effect of the /{beta} inversion on body size traits and development time across four suitable natural breeding substrates from the clinal distribution. We show that while development time is unaffected by GxE effects, both the frequency of the inversion and the relative phenotypic effects of the inversion on body size differ between population x substrate combinations. This indicates that the environment modulates the fitness as well as the phenotypic effects of the inversion karyotypes. It further suggests that the inversion may have accumulated qualitatively different mutations in different populations that interact with the environment. Together our results are consistent with the idea that the inversion in C. frigida likely evolves via a combination of local mutation, GxE effects, and differential fitness of inversion karyotypes in heterogeneous environments.

evolutionary biology↗