bluuebunny/crossref_metadata_2025 huggingface dataset:
A hierarchical pathway for assembly of the distal appendages that organize primary cilia
Authors: Kanie Tomoharu , Love Julia F. , Fisher Saxton D. , Gustavsson Anna-Karin , Jackson Peter K.
Published: January 2023

Distal appendages are nine-fold symmetric blade-like structures attached to the distal end of the mother centriole. These structures are critical for formation of the primary cilium, by regulating at least four critical steps: ciliary vesicle recruitment, recruitment and initiation of intraflagellar transport (IFT), and removal of CP110. While specific proteins that localize to the distal appendages have been identified, how exactly each protein functions to achieve the multiple roles of the distal appendages is poorly understood. Here we comprehensively analyze known and newly discovered distal appendage proteins (CEP83, SCLT1, CEP164, TTBK2, FBF1, CEP89, KIZ, ANKRD26, PIDD1, LRRC45, NCS1, C3ORF14) for their precise localization, order of recruitment, and their roles in each step of cilia formation. Using CRISPR-Cas9 knockouts, we show that the order of the recruitment of the distal appendage proteins is highly interconnected and a more complex hierarchy. Our analysis highlights two protein modules, CEP83-SCLT1 and CEP164-TTBK2, as critical for structural assembly of distal appendages. Functional assay revealed that CEP89 selectively functions in RAB34+ciliary vesicle recruitment, while deletion of the integral components, CEP83-SCLT1-CEP164-TTBK2, severely compromised all four steps of cilium formation. Collectively, our analyses provide a more comprehensive view of the organization and the function of the distal appendage, paving the way for molecular understanding of ciliary assembly.
The assembly of cancer-specific ribosomes by the lncRNALISRRsuppresses melanoma anti-tumour immunity
Authors: Cinque Sonia , Verheyden Yvessa , Adnane Sara , Marino Alessandro , Katopodi Vicky , Demesmaeker Ewout , Knezevic Zorica , Hanache Sarah , Vendramin Roberto , Cuomo Alessandro , Pozniak Joanna , Calabuig Alvaro Cortes , Baldewijns Marcella , Tabruyn Sébastien , Bechter Oliver , Baietti Maria Francesca , Groaz Elisabetta , Bonaldi Tiziana , Leucci Eleonora
Published: January 2023

Although immune checkpoint blockade (ICB) has revolutionized cancer treatment, resistance mechanisms limit its clinical benefit. Here we characteriseLISRR, a cancer-specific lncRNA highly expressed in melanoma patients refractory to ICB. In cells undergoing (therapeutic) stress,LISRRrecruits DAZAP1 (Deleted in AZoospermia Associated Protein 1) to polysomes and drives the assembly of a subset of ribosomes at the endoplasmic reticulum, directing the synthesis of an immunosuppressive translatome. This includes the immune checkpoint PD-L1 and the enzymes necessary for building the glycocalyx, the sugar coat surrounding the cells. Notably, proper glycocalyx assembly is required for spermatozoa immune evasion during fertilization. Accordingly, targetingLISRRactivates immune responses and re-sensitizes to ICB in co-culture models,ex vivoin patient explants, andin vivoin humanized patient-derived models. Our study reveals the contribution of lncRNAs to the generation of cancer-specific ribosomes and identifies an RNA-based cancer-specific strategy to overcome intrinsic resistance to ICB.
Developing hippocampal spheroids model ictogenesis and epileptogenesis
Authors: Ephraim John Wesley , Caron Davide , Canal-Alonso Angel , Corchado Juan Manuel , Palazzolo Gemma , Panuccio Gabriella
Published: January 2023

Three-dimensional (3D) neural cell cultures inherently lend themselves to high-throughput network electrophysiology studies addressing brain function in health and disease in a more realistic architectural complexity than two-dimensional neural networks. Epilepsy is the emblem of brain network disorders, as it reflects aberrant circuit reorganization and hyper-synchronization, resulting in sudden and uncontrolled electrical discharges (seizures). Modeling the features of epilepsy has so far relied on pharmacological, ionic or genetic manipulation of cells, ex-vivo brain tissue or intact animals, failing to recapitulate most of the epilepsies, which are triggered by unknown causes. Here, we report the spontaneous emergence of epileptiform patterns in spheroids of rodent primary hippocampal cells cultured in physiological condition, i.e., in the absence of a known initiating insult, detected by microelectrode array electrophysiology. Three distinct electrical phenotypes, i.e. interictal (between seizures), ictal (seizure) or mixed, arise from DIV10 to DIV35. In particular, the tonic-clonic ictal discharges become the most prominent at DIV28-35. These patterns exhibit electrographic and spectral features that strikingly resemble those observed in the hippocampus of in vitro and in vivo rodent epilepsy models, as well as of drug-resistant epileptic humans. Remarkably, not all spheroids exhibit full-blown ictal activity, bringing parallelism with the yet unanswered question of why a brain becomes epileptic and a seizure is generated. This evidence warrants caution against hippocampal cell-based therapies for regenerative purposes, as they may initiate epileptogenesis; at the same time, hippocampal spheroids lend themselves as reductionist model supporting high-throughput pre-clinical research on epileptic syndromes involving the hippocampus.
Genomes of the human filarial parasitesMansonella perstansandMansonella ozzardi
Authors: Sinha Amit , Li Zhiru , Poole Catherine B. , Morgan Richard D. , Ettwiller Laurence , Lima Nathália F. , Ferreira Marcelo U. , Fombad Fanny F. , Wanji Samuel , Carlow Clotilde K. S.
Published: January 2023

The filarial parasitesMansonella ozzardiandMansonella perstans, causative agents of mansonellosis, infect hundreds of millions of people worldwide, yet remain among the most understudied of the human filarial pathogens.M. ozzardiis highly prevalent in Latin American countries and Caribbean Islands, whileM. perstansis predominantly found in sub-Saharan Africa as well as in a few areas in South America. In addition to the differences in their geographical distribution, the two parasites are transmitted by different insect vectors, as well as exhibit differences in their responses to commonly used anthelminthic drugs. The lack of genome information has hindered investigations into the biology and evolution ofMansonellaparasites and understanding the molecular basis of the clinical differences between species. In the current study, high quality genomes of two independent clinical isolates ofM. perstansfrom Cameroon and twoM. ozzardiisolates one from Brazil and one from Venezuela are reported. The genomes are approximately 76 Mb in size, encode about 10,000 genes each, and are largely complete based on BUSCO scores of about 90%, similar to other completed filarial genomes. These sequences represent the first genomes fromMansonellaparasites and enabled a comparative genomic analysis of the similarities and differences betweenMansonellaand other filarial parasites. Horizontal DNA transfers (HDT) from mitochondria (nuMTs) as well as transfers from genomes of endosymbioticWolbachiabacteria (nuWTs) to the host nuclear genome were identified and analyzed. Sequence comparisons and phylogenetic analysis of known targets of anti-filarial drugs diethylcarbamazine (DEC), ivermectin and mebendazole revealed that all known target genes were present in both species, except for the DEC target encoded bygon-2gene, which is fragmented in genome assemblies from bothM. ozzardiisolates. These new reference genome sequences will provide a valuable resource for further studies on biology, symbiosis, evolution and drug discovery.
Contrast Sensitivity Function in Deep Networks
Authors: Akbarinia Arash , Morgenstern Yaniv , Gegenfurtner Karl R.
Published: January 2023

The contrast sensitivity function (CSF) is a fundamental signature of the visual system that has been measured extensively in several species. It is defined by the visibility threshold for sinusoidal gratings at all spatial fre-quencies. Here, we investigated the CSF in deep neural networks using the same 2AFC contrast detection paradigm as in human psychophysics. We examined 240 networks pretrained on several tasks. To obtain their corre-sponding CSFs, we trained a linear classifier on top of the extracted features from frozen pretrained networks. The linear classifier is exclusively trained on a contrast discrimination task with natural images. It has to find which of the two input images has higher contrast. The network’s CSF is measured by detecting which one of two images contains a sinusoidal grating of varying orientation and spatial frequency. Our results demonstrate char-acteristics of the human CSF are manifested in deep networks both in the luminance channel (a band-limited inverted U-shaped function) and in the chromatic channels (two low-pass functions of similar properties). The exact shape of the networks’ CSF appears to be task-dependent. The human CSF is better captured by networks trained on low-level visual tasks such as image-denoising or autoencoding. However, human-like CSF also emerges in mid- and high-level tasks such as edge detection and object recognition. Our analysis shows that human-like CSF appears in all architectures but at different depths of processing, some at early layers, while others in intermediate and final layers. Overall, these results suggest that (i) deep networks model the human CSF faithfully, making them suitable candidates for applications of image quality and compression, (ii) efficient/purposeful processing of the natural world drives the CSF shape, and (iii) visual representation from all levels of visual hierarchy contribute to the tuning curve of the CSF, in turn implying a function which we intuitively think of as modulated by low-level visual features may arise as a consequence of pooling from a larger set of neurons at all levels of the visual system.
Myristoylated Neuronal Calcium Sensor-1 captures the ciliary vesicle at distal appendages
Authors: Kanie Tomoharu , Ng Roy , Abbott Keene L. , Pongs Olaf , Jackson Peter K.
Published: January 2023

The primary cilium is a microtubule-based organelle that cycles through assembly and disassembly. In many cell types, formation of the cilium is initiated by recruitment of ciliary vesicles to the distal appendage of the mother centriole. However, the distal appendage mechanism that directly captures ciliary vesicles is yet to be identified. In an accompanying paper, we show that the distal appendage protein, CEP89, is important for thef ciliary vesicle recruitment, but not for other steps of cilium formation (Tomoharu Kanie, Love, Fisher, Gustavsson, & Jackson, 2023). The lack of a membrane binding motif in CEP89 suggests that it may indirectly recruit ciliary vesicles via another binding partner. Here, we identify Neuronal Calcium Sensor-1 (NCS1) as a stoichiometric interactor of CEP89. NCS1 localizes to the position between CEP89 and a ciliary vesicle marker, RAB34, at the distal appendage. This localization was completely abolished in CEP89 knockouts, suggesting that CEP89 recruits NCS1 to the distal appendage. Similarly to CEP89 knockouts, ciliary vesicle recruitment as well as subsequent cilium formation was perturbed in NCS1 knockout cells. The ability of NCS1 to recruit the ciliary vesicle is dependent on its myristoylation motif and NCS1 knockout cells expressing myristoylation defective mutant failed to rescue the vesicle recruitment defect despite localizing proper localization to the centriole. In sum, our analysis reveals the first known mechanism for how the distal appendage recruits the ciliary vesicles.
NMDA Receptors Control Activity Hierarchy in Neural Network: Loss of Control in Hierarchy Leads to Learning Impairments, Dissociation, and Psychosis
Authors: Zhou Yuxin , Wang Jenn Lingshu , Qiu Liyan , Torpey Jordan , Wixson Jemma Glenn , Lyon Mark , Chen Xuanmao
Published: January 2023

While it is known that associative memory is preferentially encoded by memory-eligible “primed” neurons,in vivoneural activity hierarchy has not been quantified and little is known about how such a hierarchy is established. Leveragingin vivocalcium imaging of hippocampal neurons on freely behaving mice, we developed the first method to quantify real-time neural activity hierarchy in the CA1 region. Neurons at the top of activity hierarchy are identified as primed neurons. In cilia knockout mice that exhibit severe learning deficits, the percentage of primed neurons is drastically reduced. We developed a simplified neural network model that incorporates simulations of linear and non-linear weighted components, modeling the synaptic ionic conductance of AMPA and NMDA receptors, respectively. We found that moderate non-linear to linear conductance ratios naturally leads a small fraction of neurons to be primed in the simulated neural network. Removal of the non-linear component eliminates the existing activity hierarchy and reinstate it to the network stochastically primes a new pool of neurons. Blockade of NMDA receptors by ketamine not only decreases general neuronal activity causing learning impairments, but also disrupts neural activity hierarchy. Additionally, ketamine-induced super-synchronized slow oscillation during anesthesia can be simulated if the non-linear NMDAR component is removed to flatten activity hierarchy. Together, this study develops a unique method to measure neural activity hierarchy and identifies NMDA receptors as a key factor that controls the hierarchy. It presents the first evidence suggesting that hierarchy disruption by NMDAR blockade causes dissociation and psychosis.
Convergent behavior of extended stalk regions from staphylococcal surface proteins with widely divergent sequence patterns
Authors: Yarawsky Alexander E. , Ori Andrea L. , English Lance R. , Whitten Steven T. , Herr Andrew B.
Published: January 2023

Staphylococcus epidermidisandS. aureusare highly problematic bacteria in hospital settings. This stems, at least in part, from strong abilities to form biofilms on abiotic or biotic surfaces. Biofilms are well-organized multicellular aggregates of bacteria, which, when formed on indwelling medical devices, lead to infections that are difficult to treat. Cell wall-anchored (CWA) proteins are known to be important players in biofilm formation and infection. Many of these proteins have putative stalk-like regions or regions of low complexity near the cell wall-anchoring motif. Recent work demonstrated the strong propensity of the stalk region of theS. epidermidisaccumulation-associated protein (Aap) to remain highly extended under solution conditions that typically induce compaction or other significant conformational changes. This behavior is consistent with the expected function of a stalk-like region that is covalently attached to the cell wall peptidoglycan and projects the adhesive domains of Aap away from the cell surface. In this study, we evaluate whether the ability to resist compaction is a common theme among stalk regions from various staphylococcal CWA proteins. Circular dichroism spectroscopy was used to examine secondary structure changes as a function of temperature and cosolvents along with sedimentation velocity analytical ultracentrifugation and SAXS to characterize structural characteristics in solution. All stalk regions tested are intrinsically disordered, lacking secondary structure beyond random coil and polyproline type II helix, and they all sample highly extended conformations. Remarkably, the Ser-Asp dipeptide repeat region of SdrC exhibited nearly identical behavior in solution when compared to the Aap Pro/Gly-rich region, despite highly divergent sequence patterns, indicating conservation of function by various distinct staphylococcal CWA protein stalk regions.
Anaerobe isolation from denitrifying benzene-degrading enrichment culture and their capacity to mineralize benzene
Authors: Eziuzor Samuel C , Vogt Carsten
Published: January 2023

Only a few benzene-mineralizing anaerobes have been isolated to date. In an attempt using classical isolation techniques to isolate benzene-mineralizing pure cultures from a benzene-mineralizing nitrate-reducing microbial community, two putative isolates were gained under nitrate-reducing conditions spiked separately with acetate and benzene as sole sources of carbon and energy with media containing ammonium or without ammonium. Both putative isolates; Bz4 (with ammonium) and Bz7 (without ammonium) - mineralized13C-labelled acetate under anoxic conditions at 3.3 and 2.7 μM day-1, respectively, revealed by analysis of evolved13CO2. However, only Bz4 mineralized [13C6]-labelled benzene (0.298 μM benzene mineralized day-1) generated up to 960.2 ± 0.3 ‰ δ13C-CO2during 184 days while producing only slight amounts of nitrite (4.60 ± 0.004 μM); no benzene was mineralized by Bz7 during 184 d, and no nitrite was detected. The 16S rRNA gene amplicon sequencing of the acetate-grown bacteria revealed consortia enriched inNocardioides(8.9%),Pseudomonas(18.2%),Rhizobiaceae(21.0%),Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium(51.4%) for Bz4 and Simplicispira(96.7%) for Bz7. The gained Bz4 consortium that mineralized benzene under anoxic condition can be further purified and explored for their metabolic potentials.
Habitat amount, temperature and biotic interactions drive community structure, life-history traits, and performance traits of cavity-nesting bees and wasps and their natural enemies in cities
Authors: Casanelles-Abella Joan , Pellissier Loïc , Aleixo Cristiana , Orti Marta Alós , Chiron François , Deguines Nicolas , Laanisto Lauri , Myczko Łukasz , Niinemets Ülo , Pinho Pedro , Samson Roeland , Tryjanowski Piotr , Villarroya-Villalba Lucía , Moretti Marco
Published: January 2023

Urban ecosystems are associated with socio-ecological conditions that can filter and promote taxa. However, the strength of the effect of ecological filtering on biodiversity could vary among biotic and abiotic factors. Here, we investigate the effects of habitat amount, temperature, and host-enemy biotic interactions in shaping communities of cavity-nesting bees and wasps (CNBW) and their natural enemies.

We installed trap-nests in 80 sites distributed along urban intensity gradients in 5 European cities (Antwerp, Paris, Poznan, Tartu and Zurich). We quantified the species richness and abundance of CNBW hosts and their natural enemies, as well as two performance traits (survival and parasitism) and two life-history traits (sex ratio and number of offspring per nest for the hosts). We analysed the importance of the abiotic and biotic variables using generalized linear models and multi-model inference.

We found that habitat amount and temperature were the main drivers of CNBW host responses, with larger habitat amounts resulting in higher species richness and abundance, and a larger total number of brood cells per nest for both bees and wasps, as well as a larger probability of survival for bees. Conversely, higher local temperatures decreased species richness, abundance, survival rate, number of brood cells per nest, and proportion of females in CNBW hosts.

Biotic interactions with natural enemies shaped wasp species richness, with higher levels of parasitism resulting in more wasp species. Similarly, our results showed direct density-dependence between CNBW hosts and their natural enemies.

Overall, our study highlights the importance of habitat amount and temperature in shaping urban food webs, through direct effects on hosts responses and the subsequent consequences for their natural enemies. As cities prepare to tackle the future consequences of global change, strategies that make it possible to maintain available habitat and mitigate urban overheating emerge as a key urban adaptation for biodiversity conservation.
Marine heatwaves threaten cryptic coral diversity and erode associations amongst coevolving partners
Authors: Starko Samuel , Fifer James , Claar Danielle C. , Davies Sarah W. , Cunning Ross , Baker Andrew C. , Baum Julia K.
Published: January 2023

Climate change-amplified heatwaves are known to drive extensive mortality in marine foundation species. However, a paucity of longitudinal genomic datasets has impeded understanding of how these rapid selection events alter species’ genetic structure. Impacts of these events may be exacerbated in species with obligate symbioses, where the genetics of multiple co-evolving species may be affected. Here, we tracked the symbiotic associations and fate of reef-building corals for six years through a prolonged heatwave. Coral genetics strongly predicted survival of the common coralPoritesthrough the event, with strong differential survival (15 to 64%) apparent across morphologically identical -but genetically distinct- lineages. The event also disrupted strong associations between coral lineages and their symbiotic partners, homogenizing symbiotic assemblages across lineages and reducing the specificity of coral-algal symbioses. These results highlight that marine heatwaves threaten cryptic genetic diversity of foundation species and have the potential to decouple tight relationships between co-evolving host-symbiont pairs.
Immune response modulation byPseudomonas aeruginosapersister cells
Authors: Hastings Cody James , Himmler Grace Elizabeth , Patel Arpeet , Marques Cláudia Nogueira Hora
Published: January 2023

Bacterial persister cells – a metabolically dormant subpopulation tolerant to antimicrobials – contribute to chronic infections and are thought to evade host immunity. In this work, we studied the ability ofPseudomonas aeruginosapersister cells to withstand host innate immunity. We found that persister cells resist MAC-mediated killing by the complement system despite being bound by complement protein C3b at levels similar to regular vegetative cells, in part due to reduced bound C5b - and are engulfed at a lower rate (10-100 fold), even following opsonization. Once engulfed, persister cells resist killing and, contrary to regular vegetative cells which induce a M1 favored (CD80+/CD86+/CD206-, high levels of CXCL-8, IL-6, and TNF-α) macrophage polarization, they initially induce a M2 favored macrophage polarization (CD80+/CD86+/CD206+, high levels of IL-10, and intermediate levels of CXCL-8, IL-6, and TNF-α), which is skewed towards M1 favored polarization (high levels of CXCL-8 and IL-6, lower levels of IL-10) by 24 hours of infection, once persister cells awaken. Overall, our findings further establish the ability of persister cells to evade the innate host response and to contribute chronic infections.
A converged ubiquitin-proteasome pathway for the degradation of TOC and TOM tail-anchored receptors
Authors: Yang Meijing , Chen Shuai , Lim Shey-Li , Yang Lang , Zhong Jia Yi , Chan Koon Chuen , Zhao Zhizhu , Wong Kam-Bo , Wang Junqi , Lim Boon Leong
Published: January 2023

In plants, thousands of nucleus-encoded proteins translated in the cytosol are sorted to chloroplasts and mitochondria by binding to specific receptors of the TOC (translocon at the outer membranes of chloroplasts) and the TOM (translocon at the outer membranes of mitochondria) complexes for import into those organelles. The degradation pathways for these receptors are unclear. Here, we discovered a converged ubiquitin-proteasome pathway for the degradation ofArabidopsis thalianaTOC and TOM tail-anchored receptors. The receptors are ubiquitinated by E3 ligase(s) and pulled from the outer membranes by the AAA+ATPase CDC48, after which a previously characterized cytosolic protein, TTOP, binds to the exposed transmembrane domains (TMDs) at the C termini of the receptors and CDC48, and delivers these complexes to the 26S proteasome.
If it’s real, could it be an eel?
Authors: Foxon Floe
Published: January 2023

Previous studies have estimated the size, mass, and population of hypothetical unknown animals in a large, oligotrophic freshwater loch in Scotland based on biomass and other observational considerations. The ‘eel hypothesis’ proposes that the anthrozoological phenomenon at Loch Ness can be explained in part by observations of large specimens of European eel (Anguilla anguilla), as these animals are most compatible with morphological, behavioural, and environmental considerations. The present study expands upon the ‘eel hypothesis’ and related literature by estimating the probability of observing eels at least as large as have been proposed, using catch data from Loch Ness and other freshwater bodies in Europe. Skew normal and generalized extreme value distributions were fitted to eel body length distributions in order to estimate cumulative distribution functions from which probabilities were obtained. The chances of finding a large eel in Loch Ness are around 1 in 50, 000 for a 1-meter specimen, which is reasonable given the loch’s fish stock and suggests some sightings of smaller ‘unknown’ animals may be accounted for by large eels. However, the probability of finding a specimen upwards of 6 meters is essentially zero, therefore eels probably do not account for ‘sightings’ of larger animals. The existence of exceedingly large eels in the loch is not likely based on purely statistical considerations.
In VivoBiocompatibility of ZIF-8 for Slow Release via Intranasal Administration
Authors: Kumari Sneha , Howlett Thomas S. , Ehrman Ryanne N. , Koirala Shailendra , Trashi Orikeda , Trashi Ikeda , Wijesundara Yalini H. , Gassensmith Jeremiah J.
Published: January 2023

Zeolitic Imidazolate Framework-8 (ZIF-8) is becoming popular in research for its potential in antigen protection and for providing a thermally stable, slow-release platform. While papers applying these materials for immunological applications are aplenty in literature, studies that explore the biosafety of ZIF-8 in mammals—especially when administered intranasally—are not well represented. We checked the body clearance of uncoated and ZIF-coated liposomes and observed that the release slowed as ZIF-8 is easily degraded by mucosal fluid in the nasal cavity. We delivered varying doses of ZIF-8, checked their short- and long-term effects on diagnostic proteins found in blood serum, and found no noticeable differences from the saline control group. We also studied their lung diffusing capacity and tissue morphology; neither showed significant changes in morphology or function.

Abstract Figure

Graphical Abstract:

General overview of the investigation
Comparative plant growth responses in a crop-weed mix – a case study ofZea mays(L.) andEleusine indica(L.) Gaertn
Authors: Ikhajiagbe Beckley , Musa Saheed Ibrahim , Ekhator Efuwa Famous
Published: January 2023

The comparative plant growth responses ofZea maysandEleusine indicawere monitored in this studyunder an open field experiment.Both crop and weed were grown separately on the bowls and also in a crop-weed mix. Crop-weed mix were studied in different proportions. The experiment started first by acclimatizing theE. indicaon the soil for a period of three days before sowing the maize. Forty (40) days after plant interactions, results showed significant decreases in plant heights and of both maize andE. indicadepending on the ratio of both plants in the crop-weed mix.comparative to individual height. Similarly, significant decreases in leaf area was reported inE. indica(p=0.015) owing to the interaction. In the control, leaf area was 11.4cm2, but this decreased significantly to 5.94cm2in the 2e3m mix. Similar decreases in maize leaf area have been reported with leaf area values being low (4.32cm2)in the 5e3m mix compared to 19.9cm2in the control (1m). Changes in prominent root length showed a significant decrease between the controlE. indicaand the crop-weed mix. Similar result was observed for maize plant. Although shoot – root ratio was 1.0 in the control weed (1e), a higher value (4.5) was observed in 1m1e followed by 3.5 in the 1m3e and 2m3e mix respectively. For maize plant however, the shoot-root ratio was 4.5 in the control (1m), but reduced to 1.5 in the 1e3m mix. The maize plant was also observed to release allelochemicals, which further indicate its competitive strength.
Temperature and food chain length, but not latitude, explain region-specific kelp forest responses to an unprecedented heatwave
Authors: Starko Samuel , Timmer Brian , Reshitnyk Luba , Csordas Matthew , McHenry Jennifer , Schroeder Sarah , Hessing-Lewis Margot , Costa Maycira , Zielinksi Amanda , Zielinksi Rob , Cook Sarah , Underhill Rob , Boyer Leanna , Fretwell Christopher , Yakimishyn Jennifer , Heath William A. , Gruman Christine , Baum Julia K. , Neufeld Christopher J.
Published: January 2023

Kelp forests are among the most abundant coastal marine habitats but are vulnerable to the impacts of climate change. Between 2014 and 2016, an unprecedented heatwave and associated changes in trophic dynamics threatened kelp forests across the Northeast Pacific, with impacts documented from Mexico to Alaska. However, responses have varied substantially and remain poorly characterized across large stretches of coast, especially British Columbia (B.C.), which represents a significant percentage of the range of floating kelp species in the Northeast Pacific. Here, we explore variation in floating kelp (Macrocystis, Nereocystis) persistence pre- and post-heatwave across a >675 km latitudinal gradient, asking whether B.C. kelp forests are of conservation concern. We assembled and analyzed available quantitative kelp data, comparing snapshots of kelp extent before (1994 – 2007) and after (2018 – 2021) the heatwave in 11 regions spanning a range of temperature and sea otter-occupancy statuses, and contextualizing these with time series analyses, where available (n = 7 regions). We provide strong evidence that kelp forests have declined in many regions but with evidence of refugia at both local and regional scales. Kelp forest persistence was negatively correlated with summer sea temperatures in southern B.C., where temperatures varied by ~6°C across sites, at times exceeding species’ thermal tolerances. Kelp dynamics in northern regions appeared instead to be modulated by top-down control by urchins and sea otters. Our results demonstrate that B.C.’s kelp forest have been substantially reduced in recent years but that regional and local-scale factors influence the resilience of forests to large-scale perturbations.
Secretion encoded single-cell sequencing (SEC-seq) uncovers gene expression signatures associated with high VEGF-A secretion in mesenchymal stromal cells
Authors: Udani Shreya , Langerman Justin , Koo Doyeon , Baghdasarian Sevana , Cheng Brian , Kang Simran , Soemardy Citradewi , de Rutte Joseph , Plath Kathrin , Di Carlo Dino
Published: January 2023

Cells secrete numerous bioactive molecules essential for the function of healthy organisms. However, there are no scalable methods to link individual cell secretions to their transcriptional state. By developing and using secretion encoded single-cell sequencing (SEC-seq), which exploits hydrogel nanovials to capture individual cells and their secretions, we simultaneously measured the secretion of vascular endothelial growth factor A (VEGF-A) and the transcriptome for thousands of individual mesenchymal stromal cells (MSCs). We found that VEGF-A secretion is heterogeneous across the cell population and lowly correlated with theVEGFAtranscript level. While there is a modest population-wide increase in VEGF-A secretion by hypoxic induction, highest VEGF-A secretion across normoxic and hypoxic culture conditions occurs in a subpopulation of MSCs characterized by a unique gene expression signature. Taken together, SEC-seq enables the identification of specific genes involved in the control of secretory states, which may be exploited for developing means to modulate cellular secretion for disease treatment.
Enkurin: A novel marker for myeloproliferative neoplasms from platelet, megakaryocyte, and whole blood specimens
Authors: Seetharam Sumanth Mosale , Liu Yi , Wu Jason , Fechter Lenn , Murugesan Kanagavel , Maecker Holden , Gotlib Jason , Zehnder James , Paulmurugan Ramasamy , Krishnan Anandi
Published: January 2023

Impaired protein homeostasis, though well established in age-related disorders, has been linked in recent research with the pathogenesis of myeloproliferative neoplasms (MPNs). As yet, however, little is known about MPN-specific modulators of proteostasis, thus impeding our ability for increased mechanistic understanding and discovery of additional therapeutic targets. Loss of proteostasis, in itself, is traced to dysregulated mechanisms in protein folding and intracellular calcium signaling at the endoplasmic reticulum (ER). Here, usingex vivoandin vitrosystems (includingCD34+cultures from patient bone marrow, and healthy cord/peripheral blood specimens), we extend our prior data from MPN patient platelet RNA sequencing, and discover select proteostasis-associated markers at RNA and/or protein levels in each of platelets, parent megakaryocytes, and whole blood specimens. Importantly, we identify a novel role in MPNs for enkurin (ENKUR), a calcium mediator protein, implicated originally only in spermatogenesis. Our data reveal consistentENKURdownregulation at both RNA and protein levels across MPN patient specimens and experimental models, with a concomitant upregulation of a cell cycle marker,CDC20. Silencing ofENKURby shRNA in CD34+derived megakaryocytes further confirm this association withCDC20at both RNA and protein levels; and indicate a likely role for thePI3K/Aktpathway. The inverse association ofENKURandCDC20expression was further confirmed upon treatment with thapsigargin (an agent that causes protein misfolding in the ER by selective loss of calcium) in both megakaryocyte and platelet fractions at RNA and protein levels. Together, our work sheds light on enkurin as a novel marker of MPN pathogenesis beyond the genetic alterations; and indicates further mechanistic investigation into a role for dysregulated calcium homeostasis, and ER and protein folding stress in MPN transformation.

VISUAL ABSTRACT

Key Points

Enkurin, a calcium adaptor protein, is identified as a novel marker of pathogenesis in MPNs.

MPN megakaryocyte and platelet expression of enkurin at RNA and protein levels is inversely associated with a cell differentiation cycle gene, CDC20.

Likely role for dysregulated calcium homeostasis, and ER and protein folding stress in MPN transformation.
Adaptive evolution of carnivory inNepenthespitcher plants: a comparative transcriptomics and proteomics perspective
Authors: Scharmann M , Metali F , Grafe T U , Widmer A
Published: January 2023

While trait diversity associated with evolutionary radiations is easily recognized, their function and adaptive relevance often remain elusive. Here we study the evolution of carnivory genes inNepenthes, an iconic radiation of carnivorous pitcher plants. We investigate 13 species chosen to represent the diversity of nutrient acquisition strategies, geography and climates covered by the genus. Using a combination of proteomics and transcriptomics, we discovered thatNepenthessecrete hundreds of enzymes and antimicrobial proteins into their digestive fluids. Further genes related to plant carnivory were uncovered by analyses of gene expression changes induced by experimental feeding of starvedNepenthestraps. Feeding status appears to affect the relative abundance of nearly 35% of all expressed genes, and may be accompanied by a strong physiological shift away from photosynthesis towards heterotrophy, proteolysis, and protein synthesis. Among the many thousand genes showing signatures of adaptive evolution in sequence or expression level within theNepenthesradiation, the secreted pitcher fluid proteins and the carnivory-related genes were over-represented. A bias towards carnivory genes, and towards trap-expressed genes versus leaf-expressed genes, was also observed among the genes differing in expression in a young pair of sister species. Together, our results suggest that the molecular basis of the carnivorous syndrome was disproportionally targeted by positive selection during theNepenthesradiation. This study demonstrates how the evolutionary relevance of putative key traits can be tested at the level of underlying genes.
Viral and bacterial ecogenomics in globally expanding red snow blooms
Authors: Barno Adam R. , Green Kevin , Rohwer Forest , Silveira Cynthia B.
Published: January 2023

Chlamydomonasalgal blooms give snowmelt a red color, reducing snow albedo and creating a runaway effect that accelerates snow melting. The occurrence of red snow is predicted to grow in polar and subpolar regions with increasing global temperatures. Here, a global metaanalysis of microbial abundances showed that red snow had higher microbial abundances than white snow. We hypothesize that the increased microbial densities affect virus-bacteria interactions in snow, with potential effects on snowmelt dynamics. A genomic analysis of viral and bacterial communities in red and white snow from the Whistler region of British Columbia, Canada, identified 792 putative viruses infecting bacteria. The most abundant putative snow viruses displayed low genomic similarity with known viruses. We recovered the complete circular genomes of nine putative viruses, two of which were classified as temperate. Genomes of putative snow viruses encoded genes involved in energy metabolisms, such as NAD+synthesis and salvage pathways. In model phages, these genes facilitate increased viral particle production and lysis rates. Yet, the frequency of temperate phages was positively correlated with microbial abundance in the snow samples. These results suggest the increased significance of temperate virus-bacteria interactions as microbial densities increase during snowmelt. We propose that this virus-bacteria dynamic may facilitate the red snow algae growth stimulated by bacteria, representing a potential biological feedback on snowmelt rates.
Theory and practice of using cell strainers to sortCaenorhabditis elegansby size
Authors: Lanier Vincent J. , White Amanda M. , Faumont Serge , Lockery Shawn R.
Published: January 2023

The nematodeCaenorhabditis elegansis a model organism widely used in basic, translational, and industrial research.C. elegansdevelopment is characterized by five morphologically distinct stages, including four larval stages and the adult stage. Stages differ in a variety of aspects including size, gene expression, physiology, and behavior. Enrichment for a particular developmental stage is often the first step in experimental design. When many hundreds of worms are required, the standard methods of enrichment are to grow a synchronized population of hatchlings for a fixed time, or to sort a mixed population of worms according to size. Current size-sorting methods have higher throughput than synchronization and avoid its use of harsh chemicals. However, these size-sorting methods currently require expensive instrumentation or custom microfluidic devices, both of which are unavailable to the majorityC. eleganslaboratories. Accordingly, there is a need for inexpensive, accessible sorting strategies. We investigated the use of low-cost, commercially available cell strainers to filterC. elegansby size. We found that the probability of recovery after filtration as a function of body size for cell strainers of three different mesh sizes is well described by logistic functions. Application of these functions to predict filtration outcomes revealed non-ideal properties of filtration of worms by cell strainers that nevertheless enhanced filtration outcomes. Further, we found that serial filtration using a pair of strainers that have different mesh sizes can be used to enrich for particular larval stages with a purity close to that of synchronization, the most widely used enrichment method. Throughput of the cell strainer method, up to 14,000 worms per minute, greatly exceeds that of other enrichment methods. We conclude that size sorting by cell strainers is a useful addition to the array of existing methods for enrichment of particular developmental stages inC. elegans.
TCDD dysregulation of lncRNA expression, liver zonation and intercellular communication across the liver lobule
Authors: Karri Kritika , Waxman David J.
Published: January 2023

The persistent environmental aryl hydrocarbon receptor agonist and hepatotoxin TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) induces hepatic lipid accumulation (steatosis), inflammation (steatohepatitis) and fibrosis. Thousands of liver-expressed, nuclear-localized lncRNAs with regulatory potential have been identified; however, their roles in TCDD-induced hepatoxicity and liver disease are unknown. We analyzed single nucleus (sn)RNA-seq data from control and chronic TCDD-exposed mouse liver to determine liver cell-type specificity, zonation and differential expression profiles for thousands of IncRNAs. TCDD dysregulated >4,000 of these lncRNAs in one or more liver cell types, including 684 lncRNAs specifically dysregulated in liver non-parenchymal cells. Trajectory inference analysis revealed major disruption by TCDD of hepatocyte zonation, affecting >800 genes, including 121 IncRNAs, with strong enrichment for lipid metabolism genes. TCDD also dysregulated expression of >200 transcription factors, including 19 Nuclear Receptors, most notably in hepatocytes and Kupffer cells. TCDD-induced changes in cell–cell communication patterns included marked decreases in EGF signaling from hepatocytes to non-parenchymal cells and increases in extracellular matrix-receptor interactions central to liver fibrosis. Gene regulatory networks constructed from the snRNA-seq data identified TCDD-exposed liver network-essential lncRNA regulators linked to functions such as fatty acid metabolic process, peroxisome and xenobiotic metabolic. Networks were validated by the striking enrichments that predicted regulatory IncRNAs showed for specific biological pathways. These findings highlight the power of snRNA-seq to discover functional roles for many xenobiotic-responsive lncRNAs in both hepatocytes and liver non-parenchymal cells and to elucidate novel aspects of foreign chemical-induced hepatotoxicity and liver disease, including dysregulation of intercellular communication within the liver lobule.
Protein language model embedded geometric graphs power inter-protein contact prediction
Authors: Si Yunda , Yan Chengfei
Published: January 2023

Accurate prediction of contacting residue pairs between interacting proteins is very useful for structural characterization of protein-protein interactions (PPIs). Although significant improvement has been made in inter-protein contact prediction recently, there is still large room for improving the prediction accuracy. Here we present a new deep learning method referred to as PLMGraph-Inter for inter-protein contact prediction. Specifically, we employ rotationally and translationally invariant geometric graphs obtained from structures of interacting proteins to integrate multiple protein language models, which are successively transformed by graph encoders formed by geometric vector perceptrons and residual networks formed by dimensional hybrid residual blocks to predict inter-protein contacts. Extensive evaluation on multiple test sets illustrates that PLMGraph-Inter outperforms five top inter-protein contact prediction methods, including DeepHomo, GLINTER, CDPred, DeepHomo2 and DRN-1D2D_Inter by large margins. In addition, we also show that the prediction of PLMGraph-Inter can complement the result of AlphaFold-Multimer. Finally, we show leveraging the contacts predicted by PLMGraph-Inter as constraints for protein-protein docking can dramatically improve its performance for protein complex structure prediction.
Innate immunity can distinguish beneficial from pathogenic rhizosphere microbiota
Authors: Thoms David , Chen Melissa Y. , Liu Yang , Moreira Zayda Morales , Luo Youqing , Song Siyu , Wang Nicole R. , Haney Cara H.
Published: January 2023

For optimal growth and development, hosts depend on their ability to promote healthy symbiotic interactions while restricting pathogen growth. To ask whether hosts can distinguish phylogenetically similar pathogens and beneficial bacteria, we used two closely related plant-associated strains ofPseudomonas fluorescenswhere one is beneficial and the other exhibits toxin-dependent virulence. We show that while the two strains co-existin vitro, the beneficial outcompetes that pathogenin planta. Using several readouts for plant innate immunity, we found that the beneficial and pathogenic strains elicit mechanistically distinct immune responses that occur in distinct root compartments. We show that while both the pathogenic and beneficial bacterial have plant recognizable MAMPs, the pathogen uniquely induces MAMP-independent immune responses. We found that the pathogen induces both a toxin-independent and a unique toxin-dependent defense response that remains intact in immune signaling mutants includingbak1/bkk1andnpr1/4D. We conclude that hosts can distinguish between phylogenetically similar microbes.
Mechanism underlying delayed rectifying in human voltage-mediated activation Eag2 channel
Authors: Zhang Mingfeng , Shan Yuanyue , Pei Duanqing
Published: January 2023

Voltage gradient is a general physical cue that regulates diverse biological function through voltage-gated ion channels. How voltage sensing mediates ion flows remains unknown at the molecular level. Here, we report six conformations of the human Eag2 (hEag2) ranging from closed, pre-open, open, and pore dilation but non-conducting states captured by cryo-electron microscopy (cryo-EM). These multiple states illuminate dynamics of selectivity filter and ion permeating pathway with delayed rectifier property and Cole-Moore effect at the atomic level. Mechanistically, a short S4-S5 linker is coupled with the constrict sites to mediate voltage transducing in a non-domain-swapped configuration, resulting transitions for constrict sites of F464s and Q472s from gating to open state stabilizing for voltage energy transduction. Meanwhile, an additional ion occupied at positions S6 potassium ion confers the delayed rectifier property and Cole-Moore effects. These results provide novel insight into voltage transducing and potassium current across membrane, and shed light on the long-sought Cole-Moore effects.
Sugar signaling modulates SHOOT MERISTEMLESS expression and meristem function in Arabidopsis
Authors: Lopes Filipa L. , Formosa-Jordan Pau , Malivert Alice , Margalha Leonor , Confraria Ana , Feil Regina , Lunn John E. , Jönsson Henrik , Landrein Benoît , Baena-González Elena
Published: January 2023

In plants, development of all above-ground tissues is controlled by the shoot apical meristem (SAM) which balances cell proliferation and differentiation to allow life-long growth. To maximize fitness and survival, meristem activity is adjusted to the prevailing conditions through a poorly understood integration of developmental signals with environmental and nutritional information. Here, we show that sugar signals influence SAM function by altering the protein levels of SHOOT MERISTEMLESS (STM), a key regulator of meristem maintenance. STM is less abundant in the inflorescence meristems of plants grown or treated under limiting light conditions, with lower STM levels correlating with lower sugar content in these meristems. Additionally, sucrose but not light is sufficient to sustain STM accumulation in excised inflorescences. Plants overexpressing the α1-subunit of SUCROSE-NON-FERMENTING1-RELATED KINASE 1 (SnRK1) accumulate less STM protein under optimal light conditions, despite higher sugar accumulation in the meristem. Furthermore, SnRK1α1 interacts physically with STM, suggesting a direct local repression. Surprisingly, silencingSnRK1αin the meristem leads to reducedSTMexpression and severe developmental phenotypes previously associated with STM loss-of-function. Altogether, we demonstrate that sugars promote STM accumulation and that the SnRK1 sugar sensor plays a dual role in the SAM, limiting STM abundance under unfavorable conditions but being required for overall meristem organization and integrity. This highlights the importance of sugars and SnRK1 signaling for the proper coordination of meristem activities.