Ectopic Expression of a Truncated Isoform of Hair Keratin 81 in Breast Cancer Alters Biophysical Characteristics to Promote Metastatic Propensity

Keratins are an integral part of cell structure and function. Here, it is shown that ectopic expression of a truncated isoform of keratin 81 (tKRT81) in breast cancer is upregulated in metastatic lesions compared to primary tumors and patient-derived circulating tumor cells, and is associated with more aggressive subtypes. tKRT81 physically interacts with keratin 18 (KRT18) and leads to changes in the cytosolic keratin intermediate filament network and desmosomal plaque formation. These structural changes are associated with a softer, more elastically deformable cancer cell with enhanced adhesion and clustering ability leading to greater in vivo lung metastatic burden. This work describes a novel biomechanical mechanism by which tKRT81 promotes metastasis, highlighting the importance of the biophysical characteristics of tumor cells.

Evidence of collective influence in innate sensing using fluidic force microscopy

The innate immune system initiates early response to infection by sensing molecular patterns of infection through pattern-recognition receptors (PRRs). Previous work on PRR stimulation of macrophages revealed significant heterogeneity in single cell responses, suggesting the importance of individual macrophage stimulation. Current methods either isolate individual macrophages or stimulate a whole culture and measure individual readouts. We probed single cell NF-κB responses to localized stimuli within a naïve culture with Fluidic Force Microscopy (FluidFM). Individual cells stimulated in naïve culture were more sensitive compared to individual cells in uniformly stimulated cultures. In cluster stimulation, NF-κB activation decreased with increased cell density or decreased stimulation time. Our results support the growing body of evidence for cell-to-cell communication in macrophage activation, and limit potential mechanisms. Such a mechanism might be manipulated to tune macrophage sensitivity, and the density-dependent modulation of sensitivity to PRR signals could have relevance to biological situations where macrophage density increases.

Protein target highlights in CASP15: Analysis of models by structure providers

We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.

Hidden Markov movement models reveal diverse seasonal movement patterns in two North American ungulates

Animal movement is the mechanism connecting landscapes to fitness, and understanding variation in seasonal animal movements has benefited from the analysis and categorization of animal displacement. However, seasonal movement patterns can defy classification when movements are highly variable. Hidden Markov movement models (HMMs) are a class of latent-state models well-suited to modeling movement data. Here, we used HMMs to assess seasonal patterns of variation in the movement of pronghorn (Antilocapra americana), a species known for variable seasonal movements that challenge analytical approaches, while using a population of mule deer (Odocoileus hemionus), for whom seasonal movements are well-documented, as a comparison. We used population-level HMMs in a Bayesian framework to estimate a seasonal trend in the daily probability of transitioning between a short-distance local movement state and a long-distance movement state. The estimated seasonal patterns of movements in mule deer closely aligned with prior work based on indices of animal displacement: a short period of long-distance movements in the fall season and again in the spring, consistent with migrations to and from seasonal ranges. We found seasonal movement patterns for pronghorn were more variable, as a period of long-distance movements in the fall was followed by a winter period in which pronghorn were much more likely to further initiate and remain in a long-distance movement pattern compared with the movement patterns of mule deer. Overall, pronghorn were simply more likely to be in a long-distance movement pattern throughout the year. Hidden Markov movement models provide inference on seasonal movements similar to other methods, while providing a robust framework to understand movement patterns on shorter timescales and for more challenging movement patterns. Hidden Markov movement models can allow a rigorous assessment of the drivers of changes in movement patterns such as extreme weather events and land development, important for management and conservation.

An open source plant kinase chemogenomics set

One hundred twenty-nine protein kinases, selected to represent the diversity of the rice (Oryza sativa) kinome, were cloned and tested for expression in Escherichia coli. Forty of these rice kinases were purified and screened using differential scanning fluorimetry (DSF) against 627 diverse kinase inhibitors, with a range of structures and activities targeting diverse human kinases. Thirty-seven active compounds were then tested for their ability to modify primary root development in Arabidopsis. Of these, 14 compounds caused a significant reduction of primary root length compared with control plants. Two of these inhibitory compounds bind to the predicted orthologue of Arabidopsis PSKR1, one of two receptors for PSK, a small sulfated peptide that positively controls root development. The reduced root length phenotype could not be rescued by the exogenous addition of the PSK peptide, suggesting that chemical treatment may inhibit both PSKR1 and its closely related receptor PSKR2. Six of the compounds acting as root growth inhibitors in Arabidopsis conferred the same effect in rice. Compound RAF265 (CHIR-265), previously shown to bind the human kinase BRAF (B-Raf proto-oncogene, serine/threonine kinase), also binds to nine highly conserved rice kinases tested. The binding of human and rice kinases to the same compound suggests that human kinase inhibitor sets will be useful for dissecting the function of plant kinases.

Advances in understanding interferon-mediated immune responses to enteric viruses in intestinal organoids

Interferons (IFN) are antiviral cytokines with critical roles in regulating pathogens at epithelial barriers, but their capacity to restrict human enteric viruses has been incompletely characterized in part due to challenges in cultivating some viruses in vitro, particularly human norovirus. Accordingly, advancements in the development of antiviral therapies and vaccine strategies for enteric viral infections have been similarly constrained. Currently emerging is the use of human intestinal enteroids (HIEs) to investigate mechanisms of human enteric viral pathogenesis. HIEs provide a unique opportunity to investigate host-virus interactions using an in vitro system that recapitulates the cellular complexity of the in vivo gastrointestinal epithelium. This approach permits the exploration of intestinal epithelial cell interactions with enteric viruses as well as the innate immune responses mediated by IFNs and IFN-stimulated genes. Here, we describe recent findings related to the production, signaling, and function of IFNs in the response to enteric viral infections, which will ultimately help to reveal important aspects of pathogenesis and facilitate the future development of therapeutics and vaccines.

Gabra5 plays a sexually dimorphic role in POMC neuron activity and glucose balance

Pro-opiomelanocortin (POMC) neurons are important for the regulation of body weight and glucose balance. The inhibitory tone to POMC neurons is mediated primarily by the GABA receptors. However, the detailed mechanisms and functions of GABA receptors are not well understood. The α5 subunit of GABA_A receptor, Gabra5, is reported to regulate feeding, and we found that Gabra5 is highly expressed in POMC neurons. To explore the function of Gabra5 in POMC neurons, we knocked down Gabra5 specifically from mature hypothalamic POMC neurons using the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 strategy. This POMC-specific knock-down of Gabra5 did not affect body weight or food intake in either male or female mice. Interestingly, the loss of Gabra5 caused significant increases in the firing frequency and resting membrane potential, and a decrease in the amplitude of the miniature inhibitory postsynaptic current (mIPSC) in male POMC neurons. However, the loss of Gabra5 only modestly decreased the frequency of mIPSC in female POMC neurons. Consistently, POMC-specific knock-down of Gabra5 significantly improved glucose tolerance in male mice but not in female mice. These results revealed a sexually dimorphic role of Gabra5 in POMC neuron activity and glucose balance, independent of body weight control.

Ice matters: Life-history strategies of two Antarctic seals dictate climate change eventualities in the Weddell Sea

The impacts of climate change in Antarctica and the Southern Ocean are not uniform and ice-obligate species with dissimilar life-history characteristics will likely respond differently to their changing ecosystems. We use a unique data set of Weddell Leptonychotes weddellii and crabeater seals' (CESs) Lobodon carcinophaga breeding season distribution in the Weddell Sea, determined from satellite imagery. We contrast the theoretical climate impacts on both ice-obligate predators who differ in life-history characteristics: CESs are highly specialized Antarctic krill Euphausia superba predators and breed in the seasonal pack ice; Weddell seals (WESs) are generalist predators and breed on comparatively stable fast ice. We used presence-absence data and a suite of remotely sensed environmental variables to build habitat models. Each of the environmental predictors is multiplied by a 'climate change score' based on known responses to climate change to create a 'change importance product'. Results show CESs are more sensitive to climate change than WESs. Crabeater seals prefer to breed close to krill, and the compounding effects of changing sea ice concentrations and sea surface temperatures, the proximity to krill and abundance of stable breeding ice, can influence their post-breeding foraging success and ultimately their future breeding success. But in contrast to the Ross Sea, here WESs prefer to breed closer to larger colonies of emperor penguins (Aptenodytes forsteri). This suggests that the Weddell Sea may currently be prey-abundant, allowing the only two air-breathing Antarctic silverfish predators (Pleuragramma antarctica) (WESs and emperor penguins) to breed closer to each other. This is the first basin-scale, region-specific comparison of breeding season habitat in these two key Antarctic predators based on real-world data to compare climate change responses. This work shows that broad-brush, basin-scale approaches to understanding species-specific responses to climate change are not always appropriate, and regional models are needed-especially when designing marine protected areas.

Direct and ancillary benefits of ecosystem-based fisheries management in forage fish fisheries

Natural resource management is evolving toward holistic, ecosystem-based approaches to decision making. The ecosystem science underpinning these approaches needs to account for the complexity of multiple interacting components within and across coupled natural-human systems. In this research, we investigate the potential economic and ecological gains from adopting ecosystem-based approaches for the sardine and anchovy fisheries off of the coast of California, USA. Research has shown that while predators in this system are likely substituting one forage species for another, the assemblage of sardine and anchovy can be a significant driver of predator populations. Currently, the harvest control rules for sardine and anchovy fisheries align more with traditional single species framework. We ask what are the economic and ecological gains when jointly determining the harvest control rules for both forage fish stocks and their predators relative to the status quo? What are the implications of synchronous and anti-synchronous environmental recruitment variation between the anchovy and sardine stocks on optimal food-web management? To investigate these questions, we develop an economic-ecological model for sardine, anchovy, a harvested predator (halibut), and an endangered predator (Brown Pelican) that includes recruitment variability over time driven by changing environmental conditions. Utilizing large-scale numerical optimal control methods, we investigate how the multiple variants of integrated management of sardine, anchovy, and halibut impact the overall economic condition of the fisheries and Brown Pelican populations over time. We find significant gains in moving to integrated catch control rules both in terms of the economic gains of the fished stocks, and in terms of the impacts on the Brown Pelican populations. We also compare the relative performance of current stylized catch control rules to optimal single species and optimal ecosystem-based fisheries management (EBFM) across ecological and economic dimensions, where the former trade-off considerable economic value for ecological goals. More generally, we demonstrate how EBFM approaches introduce and integrate additional management levers for policymakers to achieve non-fishery objectives at lowest costs to the fishing sectors.

Multiplex genome editing in Arabidopsis thaliana using Mb3Cas12a

The use of CRISPR-Cas proteins for the creation of multiplex genome engineering represents an important avenue for crop improvement, and further improvements for creation of knock-in plant lines via CRISPR-based technologies may enable the high-throughput creation of designer alleles. To circumvent limitations of the commonly used CRISPR-Cas9 system for multiplex genome engineering, we explored the use of Moraxella bovoculi 3 Cas12a (Mb3Cas12a) for multiplex genome editing in Arabidopsis thaliana. We identified optimized cis-regulatory sequences for driving expression of single-transcript multiplex crRNA arrays in A. thaliana, resulting in stable germline transmission of Mb3Cas12a-edited alleles at multiple target sites. By utilizing this system, we demonstrate single-transcript multiplexed genome engineering using of up to 13 crRNA targets. We further show high target specificity of Mb3Cas12a-based genome editing via whole-genome sequencing. Taken together, our method provides a simplified platform for efficient multiplex genome engineering in plant-based systems.

Independent evolution of rosmarinic acid biosynthesis in two sister families under the Lamiids clade of flowering plants

As a means to maintain their sessile lifestyle amid challenging environments, plants produce an enormous diversity of compounds as chemical defenses against biotic and abiotic insults. The underpinning metabolic pathways that support the biosynthesis of these specialized chemicals in divergent plant species provide a rich arena for understanding the molecular evolution of complex metabolic traits. Rosmarinic acid (RA) is a phenolic natural product first discovered in plants of the mint family (Lamiaceae) and is recognized for its wide range of medicinal properties and potential applications in human dietary and medical interventions. Interestingly, the RA chemotype is present sporadically in multiple taxa of flowering plants as well as some hornworts and ferns, prompting the question whether its biosynthesis arose independently across different lineages. Here we report the elucidation of the RA biosynthetic pathway in Phacelia campanularia (desert bells). This species represents the borage family (Boraginaceae), an RA-producing family closely related to the Lamiaceae within the Lamiids clade. Using a multi-omics approach in combination with functional characterization of candidate genes both in vitro and in vivo, we found that RA biosynthesis in P. campanularia involves specific activities of a BAHD acyltransferase and two cytochrome P450 hydroxylases. Further phylogenetic and comparative structure-function analyses of the P. campanularia RA biosynthetic enzymes clearly indicate that RA biosynthesis has evolved independently at least twice in the Lamiids, an exemplary case of chemotypic convergence through disparate evolutionary trajectories.