Killer whale (Orcinus orca)
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Kinship clustering within an ecologically diverse killer whale metapopulation
Metapopulation dynamics can be shaped by foraging ecology, and thus be sensitive to shifts in prey availability. Genotyping 204 North Atlantic killer whales at 1346 loci, we investigated whether spatio-temporal population structuring is linked to prey type and distribution. Using population-based methods (reflecting evolutionary means), we report a widespread metapopulation connected across ecological groups based upon nuclear genome SNPs, yet spatial structuring based upon mitogenome haplotypes. These contrasting patterns of markers with maternal and biparental inheritance are consistent with matrilineal site fidelity and philopatry, and male-mediated gene flow among demes. Connectivity between fish-eating and ‘mixed-diet’ (eating both fish and mammal prey) killer whales, marks a deviation within a species renowned for its marked structure associated with ecology. However, relatedness estimates suggest distinct spatial clusters, and heterogeneity in recent gene flow between them. The contrasting patterns between inference of structure and inference of relatedness suggest that gene flow has been partially restricted over the past two to three generations (50–70 years). This coincides with the collapse of North Atlantic herring stocks in the late 1960s and the subsequent cessation of their seasonal connectivity. Statistically significant association between diet types and assignment of Icelandic killer whales to relatedness-based clusters indicated limited gene flow was maintained through Icelandic ‘mixed-diet’ whales when herring-mediated connectivity was diminished. Thus, conservation of dietary variation within this metapopulation is critical to ensure genetic health. Our study highlights the role of resource dynamics and foraging ecology in shaping population structure and emphasises the need for transnational management of this widespread migratory species and its prey.
LolA and LolB are conserved in Bacteroidota and are crucial for gliding motility and Type IX secretion
Lipoproteins are key outer membrane (OM) components in Gram-negative bacteria, essential for functions like membrane biogenesis and virulence. Bacteroidota, a diverse and widespread phylum, produce numerous OM lipoproteins that play vital roles in nutrient acquisition, Type IX secretion system (T9SS), and gliding motility. In Escherichia coli, lipoprotein transport to the OM is mediated by the Lol system, where LolA shuttles lipoproteins to LolB, which anchors them in the OM. However, LolB homologs were previously thought to be limited to γ- and β-proteobacteria. This study uncovers the presence of LolB in Bacteroidota and demonstrates that multiple LolA and LolB proteins co-exist in various species. Specifically, in Flavobacterium johnsoniae, LolA1 and LolB1 transport gliding motility and T9SS lipoproteins to the OM. Notably, these proteins are not interchangeable with their E. coli counterparts, indicating functional specialization. Some lipoproteins still localize to the OM in the absence of LolA and LolB, suggesting the existence of alternative transport pathways in Bacteroidota. This points to a more complex lipoprotein transport system in Bacteroidota compared to other Gram-negative bacteria. These findings reveal previously unrecognized lipoprotein transport mechanisms in Bacteroidota and suggest that this phylum has evolved unique strategies to manage the essential task of lipoprotein localization.
Coding principles and mechanisms of serotonergic transmission modes
Serotonin-mediated intercellular communication has been implicated in myriad human behaviors and diseases, yet how serotonin communicates and how the communication is regulated remain unclear due to limitations of available monitoring tools. Here, we report a method multiplexing genetically encoded sensor-based imaging and fast-scan cyclic voltammetry, enabling simultaneous recordings of synaptic, perisynaptic, proximate and distal extrasynaptic serotonergic transmission. Employing this method alongside a genetically encoded sensor-based image analysis program (GESIAP), we discovered that heterogeneous firing patterns of serotonergic neurons create various transmission modes in the mouse raphe nucleus and amygdala, encoding information of firing pulse frequency, number, and synchrony using neurotransmitter quantity, releasing synapse count, and synaptic and/or volume transmission. During tonic and low-frequency phasic activities, serotonin is confined within synaptic clefts due to efficient retrieval by perisynaptic transporters, mediating synaptic transmission modes. Conversely, during high-frequency, especially synchronized phasic activities, or when transporter inhibition, serotonin may surpass transporter capacity, and escape synaptic clefts through 1‒3 outlet channels, leading to volume transmission modes. Our results elucidate a mechanism of how channeled synaptic enclosures, synaptic properties, and transporters collaborate to define the coding principles of activity pattern-dependent serotonergic transmission modes.
Oblique line scan illumination enables expansive, accurate and sensitive single-protein measurements in solution and in living cells
An ideal tool for the study of cellular biology would enable the measure of molecular activity nondestructively within living cells. Single-molecule localization microscopy (SMLM) techniques, such as single-molecule tracking (SMT), enable in situ measurements in cells but have historically been limited by a necessary tradeoff between spatiotemporal resolution and throughput. Here we address these limitations using oblique line scan (OLS), a robust single-objective light-sheet-based illumination and detection modality that achieves nanoscale spatial resolution and sub-millisecond temporal resolution across a large field of view. We show that OLS can be used to capture protein motion up to 14 μm2 s−1 in living cells. We further extend the utility of OLS with in-solution SMT for single-molecule measurement of ligand–protein interactions and disruption of protein–protein interactions using purified proteins. We illustrate the versatility of OLS by showcasing two-color SMT, STORM and single-molecule fluorescence recovery after photobleaching. OLS paves the way for robust, high-throughput, single-molecule investigations of protein function required for basic research, drug screening and systems biology studies.
Single-cell RNA transcriptomic analysis identifies Creb5 and CD11b-DCs as regulator of asthma exacerbations
Immune responses that result in asthma exacerbation are associated with allergen or viral exposure. Identification of common immune factors will be beneficial for the development of uniformed targeted therapy. We employed a House Dust Mite (HDM) mouse model of asthma and challenged allergic HDM mice with allergens (HDM, cockroach extract (CRE)) or respiratory syncytial virus (RSV). Purified lung immune cells underwent high-dimensional single-cell RNA deep sequencing (scRNA-seq) to generate an RNA transcriptome. Gene silencing with siRNA was employed to confirm the efficacy of scRNA-seq analysis. scRNA-seq UMAP analysis portrayed an array of cell markers within individual immune clusters. SCENIC R analysis showed an increase in regulon number and activity in CD11b– DC cells. Analysis of conserved regulon factors further identified Creb5 as a shared regulon between the exacerbation groups. Creb5 siRNAs attenuated HDM, CRE or RSV-induced asthma exacerbation. scRNA-seq multidimensional analysis of immune clusters identified gene pathways that were conserved between the exacerbation groups. We propose that these analyses provide a strong framework that could be used to identify specific therapeutic targets in multifaceted pathologies.
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