bluuebunny/crossref_metadata_2025 huggingface dataset:
Iron regulatory proteins 1 and 2 have opposing roles in regulating inflammation in bacterial orchitis
Authors: Ghatpande N. , Harrer A. , Azouly B. , Guttmann-Raviv N. , Bhushan S. , Meinhardt A. , Meyron-Holtz E.G.
Published: August 2023

Acute bacterial orchitis (AO) is a prevalent cause of intra-scrotal inflammation, often resulting in sub-or infertility. A frequent cause eliciting AO is uropathogenicEscherichia coli(UPEC), a gram negative pathovar, characterized by the expression of various iron acquisition systems to survive in a low-iron environment. On the host side, iron is tightly regulated by iron regulatory proteins (IRP) 1 and 2 and these factors have been reported to play a role in testicular and immune cell function, however, their precise role remains unclear. Here, we show in a mouse model of UPEC-induced orchitis that the absence of IRP1 results in reduced immune response and testicular damage. Compared to infected wild-type (WT)-mice, testis of UPEC-infectedIrp1-/-mice showed impaired ERK signalling. Conversely, IRP2 deletion led to a stronger inflammatory response. Notably, differences in immune cell infiltrations were observed among the different genotypes. In contrast to WT andIrp2-/-mice, no increase in monocytes and neutrophils was detected in testis ofIrp1-/-mice upon UPEC-infection. Interestingly, inIrp1-/-UPEC-infected testis, we observed an increase in a subpopulation of macrophages (F4/80+ CD206+) associated with anti-inflammatory and wound-healing activities compared to WT. These findings suggest that IRP1 deletion may protect against UPEC-induced inflammation by modulating ERK signalling and dampening the immune response.
Assembly of SARS-CoV-2 ribonucleosomes by truncated N* variant of the nucleocapsid protein
Authors: Adly Armin N. , Bi Maxine , Carlson Christopher R. , Syed Abdullah M. , Ciling Alison , Doudna Jennifer A. , Cheng Yifan , Morgan David O.
Published: August 2023

The Nucleocapsid (N) protein of SARS-CoV-2 compacts the RNA genome into viral ribonucleoprotein (vRNP) complexes within virions. Assembly of vRNPs is inhibited by phosphorylation of the N protein SR region. Several SARS-CoV-2 variants of concern carry N protein mutations that reduce phosphorylation and enhance the efficiency of viral packaging. Variants of the dominant B.1.1 viral lineage also encode a truncated N protein, termed N* or Δ(1–209), that mediates genome packaging despite lacking the N-terminal RNA-binding domain and SR region. Here, we show that Δ(1–209) and viral RNA assemble into vRNPs that are remarkably similar in size and shape to those formed with full-length N protein. We show that assembly of Δ(1–209) vRNPs requires the leucine-rich helix (LH) of the central disordered region, and that the LH promotes N protein oligomerization. We also find that fusion of a phosphomimetic SR region to Δ(1–209) inhibits RNA binding and vRNP assembly. Our results provide new insights into the mechanisms by which RNA binding promotes N protein self-association and vRNP assembly, and how this process is modulated by SR phosphorylation.
Piezo regulates epithelial topology and promotes precision in organ size control
Authors: Kumar Nilay , Mim Mayesha Sahir , Levis Megan , Unger Maria , Miranda Gabriel , Robinett Trent , Zartman Jeremiah
Published: August 2023

Mechanosensitive Piezo channels regulate cell division through calcium-mediated activation of ERK signaling or activate Rho signaling to mediate cell extrusion and cell death. However, systems-level functions of Piezo in regulating organogenesis remain poorly understood. Here, we demonstrate that Piezo controls epithelial cell topology to ensure precise organ growth through the integration of live imaging experiments with pharmacological and genetic perturbations and computational modeling. Notably, knockout or knockdown ofPiezoled to bilateral asymmetry in wing phenotypes. While pharmacological activation of Piezo stimulated an increase in the frequency of spikes in cytosolic Ca2+, we discovered thatPiezooverexpression counterintuitively reduces Ca2+signaling dynamics. Knockdown ofPiezoinhibited proliferation and decreased apoptosis, resulting in an overall increase in epithelial overcrowding. In contrast, either genetic overexpression or pharmacological activation of Piezo increased cell proliferation and cell removal through basal extrusion. Surprisingly,Piezooverexpression increased the hexagonality of cellular topology. To test whether Piezo regulates cell topology, we formulated computational simulations to investigate how expression levels of Piezo protein regulate cell proliferation and apoptosis through modulation of the cut-off tension required for Piezo channel activation. Quantitative analysis validated computational simulation predictions of how perturbations toPiezoimpacted epithelial topology. Overall, our findings demonstrate that Piezo promotes robustness in regulating epithelial topology and is necessary for precise organ size control.
Warming alters cascading effects of a dominant arthropod predator on microbial community composition in the Arctic
Authors: Koltz Amanda M. , Koyama Akihiro , Wallenstein Matthew
Published: August 2023

Warming is expected to increase abundances of wolf spider, the top predator in soil communities in the Arctic, but we have little understanding on how increased wolf spider density under warmer conditions affects soil microbial structure through trophic cascades. We tested the effects of wolf spider density and warming on bacterial and fungal community structure in litter through a fully factorial mesocosm experiment in Arctic tundra over two summers. Replicated litter bags were deployed at the soil surface and underground in the organic soil profile and collected at 2- and 14-month incubation. The litter samples were analyzed for community structure of bacteria and fungi and mass weight loss. After 2-month incubation, bacterial and fungal community compositions were already structured interactively by the spider density and warming treatments. Such interaction effect was also found in litter microbial community structure as well as litter mass loss rates after 14-month incubation. Our results show that wolf spiders have indirect, cascading effects on microbial community structure but that warming can alter these effects. The non-linear responses of microbial communities and litter decomposition to warming and increased spider density cast uncertainty in predicting structure and function of Arctic terrestrial ecosystem under warmer conditions in the future.

IMPORTANCE

This is one of the first studies demonstrating that predator abundances and increased temperature interactively structure litter microbial communities in the Arctic. The Arctic is one of the fastest warming regions due to climate change and contains disproportionately large amounts of soil organic matter, including thick litter which accumulated over the long time because of slow decomposition. The accelerated soil organic matter decomposition due to the rapid warming can cause positive feedback where resulting greenhouse gas emission contribute to further global warming. Since microbial structure can affect decomposition rates of litter, the observed non-linear responses of soil microbial community compositions and litter decomposition rates indicate challenges in predicting Arctic ecosystem responses in the future.
A Spiking Neural Network with Continuous Local Learning for Robust Online Brain Machine Interface
Authors: Taeckens Elijah A. , Shah Sahil
Published: August 2023

Objective

Spiking neural networks (SNNs) are powerful tools that are well suited for brain machine interfaces (BMI) due to their similarity to biological neural systems and computational efficiency. They have shown comparable accuracy to state-of-the-art methods, but current training methods require large amounts of memory, and they cannot be trained on a continuous input stream without pausing periodically to perform backpropagation. An ideal BMI should be capable training continuously without interruption to minimize disruption to the user and adapt to changing neural environments.

Approach

We propose a continuous SNN weight update algorithm that can be trained to perform regression learning with no need for storing past spiking events in memory. As a result, the amount of memory needed for training is constant regardless of the input duration. We evaluate the accuracy of the network on recordings of neural data taken from the premotor cortex of a primate performing reaching tasks. Additionally, we evaluate the SNN in a simulated closed loop environment and observe its ability to adapt to sudden changes in the input neural structure.

Main results

The continuous learning SNN achieves the same peak correlation (ρ= 0.7) as existing SNN training methods when trained offline on real neural data while reducing the total memory usage by 92%. Additionally, it matches state-of-the-art accuracy in a closed loop environment, demonstrates adaptability when subjected to multiple types of neural input disruptions, and is capable of being trained online without any prior offline training.

Significance

This work presents a neural decoding algorithm that can be trained rapidly in a closed loop setting. The algorithm increases the speed of acclimating a new user to the system and also can adapt to sudden changes in neural behavior with minimal disruption to the user.
Temporal association activates projections from the perirhinal cortex and ventral CA1 to the prelimbic cortex and from the prelimbic cortex to the basolateral amygdala
Authors: Santos Thays Brenner dos , Kramer-Soares Juliana Carlota , Coelho Cesar Augusto de Oliveira , Oliveira Maria Gabriela Menezes
Published: August 2023

In temporal associations, the prelimbic cortex (PL) has persistent activity during the interval between the conditioned stimulus (CS) and the unconditioned stimulus (US), which maintains a CS representation. Regions cooperating for this function or encoding the CS before the interval could neuroanatomically connect to the PL, supporting learning. The basolateral amygdala (BLA) has CS- and US-responsive neurons, convergently activated. The PL could directly project to the BLA to associate the transient CS memory with the US. We investigated the neural circuit supporting temporal associations using the CFC-5s task, in which a 5-second interval separates the contextual CS from the US. Injecting retrobeads, we quantified c-Fos in PL- or BLA-projecting neurons from 9 regions after CFC-5s or contextual fear conditioning (CFC), in which CS/US overlap. The CFC-5s activated ventral CA1 (vCA1) and perirhinal cortex (PER) neurons projecting to the PL, and PL neurons projecting to BLA. Both CFC-5s and CFC activated vCA1 and lateral entorhinal (LEC) neurons projecting to BLA, and BLA neurons projecting to PL. Both conditioning activated the PER, LEC, cingulate and infralimbic cortices, nucleus reuniens, and ventral subiculum. Results added new relevance to the PER→PL projection and showed that the PL/BLA are reciprocally functionally connected in CFC-5s.
Broadening the scope: Multiple functional connectivity networks underlying threat and safety signaling
Authors: Cushing Cody A. , Peng Yujia , Anderson Zachary , Young Katherine S. , Bookheimer Susan Y. , Zinbarg Richard E. , Nusslock Robin , Craske Michelle G.
Published: August 2023

Introduction

Threat learning and extinction processes are thought to be foundational to anxiety and fear-related disorders. However, the study of these processes in the human brain has largely focused on a priori regions of interest, owing partly to the ease of translating between these regions in human and non-human animals. Moving beyond analyzing focal regions of interest to whole-brain dynamics during threat learning is essential for understanding the neuropathology of fear-related disorders in humans.

Methods

223 participants completed a 2-day Pavlovian threat conditioning paradigm while undergoing fMRI. Participants completed threat acquisition and extinction. Extinction recall was assessed 48 hours later. Using a data-driven group independent component analysis (ICA), we examined large-scale functional connectivity networks during each phase of threat conditioning. Connectivity networks were tested to see how they responded to conditional stimuli during early and late phases of threat acquisition and extinction and during early trials of extinction recall.

Results

A network overlapping with the default mode network involving hippocampus, vmPFC, and posterior cingulate was implicated in threat acquisition and extinction. Another network overlapping with the salience network involving dACC, mPFC, and inferior frontal gyrus was implicated in threat acquisition and extinction recall. Other networks overlapping with parts of the salience, somatomotor, visual, and fronto-parietal networks were involved in the acquisition or extinction of learned threat responses.

Conclusions

These findings help confirm previous investigations of specific brain regions in a model-free fashion and introduce new findings of spatially independent networks during threat and safety learning. Rather than being a single process in a core network of regions, threat learning involves multiple brain networks operating in parallel coordinating different functions at different timescales. Understanding the nature and interplay of these dynamics will be critical for comprehensive understanding of the multiple processes that may be at play in the neuropathology of anxiety and fear-related disorders.
Protein Structure Refinement via DeepTracer and AlphaFold2
Authors: Chen Jason , Zia Ayisha , Wang Fengbin , Hou Jie , Cao Renzhi , Si Dong
Published: August 2023

Understanding the structures of proteins has numerous applications, such as vaccine development. It is a slow and labor-intensive task to manually build protein structures from experimental electron density maps, therefore, machine learning approaches have been proposed to automate this process. However, most of the experimental maps are not atomic resolution, so they are insufficient for computer vision-based machine learning methods to precisely determine the protein structure. On the other hand, methods that utilize evolutionary information from protein sequences to predict structures, like AlphaFold2, have recently achieved groundbreaking accuracy but often require manual effort to refine the results. We propose DeepTracer-Refine, an automated method to refine AlphaFold structures by aligning them to DeepTracer’s predicted structure. We tested our method on 39 multi-domain proteins and we improved the average residue coverage from 78.2% to 90.0% and average lDDT score from 0.67 to 0.71. We also compared DeepTracer-Refine against another method, Phenix’s AlphaFold refinement, to demonstrate that our method not only performs better when the initial AlphaFold model is less precise but also exceeds Phenix in run-time performance.
Continuous quasi-attractors dissolve with too much – or too little – variability
Authors: Schönsberg Francesca , Monasson Rémi , Treves Alessandro
Published: August 2023

Hippocampal place cells in bats flying in a 200m tunnel have been shown to be active at multiple locations, with considerable variability in place field size and peak rate. We ask whether such disorderly representation of one’s own position in a large environment could be stored in memory through Hebbian plasticity, and be later retrieved from a partial cue. Simulating an autoassociative network in which similarly variable place fields are encoded with a covariance rule, we find that it may serve spatial memory only within a certain variability range, in particular of field width. The working range is flanked by two dysfunctional regions, accessed through apparent phase transitions. For a large network, phase boundaries can be estimated analytically to depend only on the number of fields per cell in one case, and to be a pure number in the other, implying a maximal size of the environment that can be stored in memory.
Triaging of ⍺-helical proteins to the mitochondrial outer membrane by distinct chaperone machinery based on substrate topology
Authors: Muthukumar Gayathri , Stevens Taylor A. , Inglis Alison J. , Esantsi Theodore K. , Saunders Reuben A. , Schulte Fabian , Voorhees Rebecca M. , Guna Alina , Weissman Jonathan S.
Published: August 2023

Mitochondrial outer membrane ⍺-helical proteins play critical roles in mitochondrial-cytoplasmic communication, but the rules governing the targeting and insertion of these biophysically diverse substrates remain unknown. Here, we first defined the complement of required mammalian biogenesis machinery through genome-wide CRISPRi screens using topologically distinct membrane proteins. Systematic analysis of nine identified factors across 21 diverse ⍺-helical substrates reveals that these components are organized into distinct targeting pathways which act on substrates based on their topology. NAC is required for efficient targeting of polytopic proteins whereas signal-anchored proteins require TTC1, a novel cytosolic chaperone which physically engages substrates. Biochemical and mutational studies reveal that TTC1 employs a conserved TPR domain and a hydrophobic groove in its C-terminal domain to support substrate solubilization and insertion into mitochondria. Thus, targeting of diverse mitochondrial membrane proteins is achieved through topological triaging in the cytosol using principles with similarities to ER membrane protein biogenesis systems.
The D-mannose/L-galactose pathway plays a predominant role in ascorbate biosynthesis in the liverwortMarchantia polymorphabut is not regulated by light and oxidative stress
Authors: Ishida Tetsuya , Tanaka Yasuhiro , Maruta Takanori , Ishikawa Takahiro
Published: August 2023

Ascorbate plays an indispensable role in plants, functioning as both an antioxidant and a cellular redox buffer. It is widely acknowledged that the ascorbate biosynthesis in the photosynthetic tissues of land plants is governed by light-mediated regulation of the D-mannose/L-galactose (D-Man/L-Gal) pathway. At the core of this light-dependent regulation lies theVTC2gene, encoding the rate-limiting enzyme GDP-L-Gal phosphorylase. TheVTC2expression is regulated by signalsviathe photosynthetic electron transport system. In this study, we directed our attention to the liverwortMarchantia polymorpha, representing one of the basal land plants, enabling us to conduct an in-depth analysis of its ascorbate biosynthesis. TheM. polymorphagenome harbors a solitary gene for each enzyme involved in the D-Man/L-Gal pathway, includingVTC2, along with three lactonase orthologs, which may be involved in the alternative ascorbate biosynthesis pathway. Through supplementation experiments with potential precursors, we observed that only L-Gal exhibited effectiveness in ascorbate biosynthesis. Furthermore, the generation ofVTC2-deficient mutants through genome editing unveiled the inability of thallus regeneration in the absence of L-Gal supplementation, thereby revealing the importance of the D-Man/L-Gal pathway in ascorbate biosynthesis withinM. polymorpha. Interestingly, gene expression analyses unveiled a distinct characteristic ofM. polymorpha, where none of the genes associated with the D-Man/L-Gal pathway, includingVTC2, showed upregulation in response to light, unlike other known land plants. This study sheds light on the exceptional nature ofM. polymorphaas a land plant that has evolved distinctive mechanisms concerning ascorbate biosynthesis and its regulation.
Mosaic of local adaptation between white clover and rhizobia along an urbanization gradient
Authors: Murray-Stoker David , Johnson Marc T. J.
Published: August 2023

Urbanization frequently alters the biotic and abiotic environmental context. Variation in both the biotic and abiotic environment can result in selection mosaics that lead to locally adapted phenotypes. Ecological changes to urban environments have been found to result in evolutionary responses across a diverse array of plants and animals, but the effects of urbanization on local adaptation and coevolution between species remains largely unstudied.

Using a common garden experiment of 30 populations and 1080 plants, we tested for local adaptation in the mutualism between white clover (Trifolium repens) and rhizobia (Rhizobium leguminosarumsymbiovartrifolii) along an urbanization gradient. We asked: (Q1) are white clover and rhizobia locally adapted? (Q2) Does nitrogen (N) addition mediate the strength of local adaptation? (Q3) Is the strength of local adaptation in host plants related to the strength of local adaptation in rhizobia, as expected if white clover and rhizobia are co-adapting? And (Q4) How does the degree of local adaptation vary with urbanization?

We found evidence for local adaptation for both white clover and rhizobia, with stronger signatures of local adaptation for rhizobia than white clover (Q1). While N addition positively affected plant biomass and negatively affected nodule density, N addition did not consistently mediate patterns of local adaptation (Q2). The strength of local adaptation was positively related between white clover and rhizobia under N addition, suggesting that soil N mediates co-adaptation between white clover and rhizobia (Q3). We did not find a consistent relationship between measures of urbanization and local adaptation (Q4). Additionally, fitness responses for white clover and rhizobia were unrelated toRhizobiumabundance and local adaptation was unrelated to the broader bacterial microbiome in the soil inoculants or root endosphere.

Synthesis. Our results show a spatial mosaic in local adaptation, with stronger local adaptation for rhizobia than white clover. While urbanization does influence the ecology of plant-microbe interactions, our study suggests urbanization does not disrupt local adaptation and coevolution among mutualists.
Real-time assessment of the impacts of polystyrene and silver nanoparticles on hatching process and early-stage development ofArtemiausing a microfluidic platform
Authors: Dey Preyojon , Bradley Terence M. , Boymelgreen Alicia
Published: August 2023

The development of real-time in-situ monitoring techniques is key to advancing a mechanistic understanding of the impacts of marine pollution, which is challenging to acquire through traditional end-point toxicity testing. We investigated the impacts of different nanopollutants on the hatching process and early-stage development of marine organisms, a vulnerable life stage, by observing oxygen consumption in real-time and morphological changes at regular intervals using a microfluidic platform. Here, two common and distinct nanoparticle (NP) types - polystyrene (PS) nanoplastic and silver (Ag) nanometal, were examined to assess and compare impacts on the hatching process and nauplius stage (first larval stage) ofArtemia, a widely used zooplankton model in ecotoxicological studies. The study was conducted over a wide range of doses that are relevant to different environmental conditions, ranging from 0-1 mg/L, over a period of 24 hours. The hatching process ofArtemiais comprised of four distinct stages which can be differentiated by metabolism and morphology: hydration, differentiation, emergence, and hatching. During hatching, NP exposure altered the time needed for the resumption of dormantArtemiacysts (hydration duration) at the lowest dose, dramatically prolonged the differentiation stage, and slowed embryo emergence from the cysts. The remaining time for the hatching stage during the experimental timeframe was also shortened. Overall, the presence of NPs led to increased oxygen consumption in multiple stages of the hatching process. Hatchability increased significantly with NP concentration although mortality showed an inverse pattern. This may be attributed to the increased aggregation of NPs in saltwater with increasing concentration which limits bioavailability during hatching but may be more readily consumed post-hatch. Ag NPs had a greater effect on hatching and mortality in comparison to PS NPs. A significant impact of NPs on swimming speed was observed, with a decrease observed in the presence of PS NPs and an increase observed in the presence of Ag NPs.

Graphical abstract

Highlights

Utilization of oxygen sensor integrated microfluidic chip and microscopy for ecotoxicological study.

Bioaccumulation of NPs affected hatching stages and respiration leading to inhibition of hatchability, with greater toxicity of silver NPs.

NPs caused significant mortality and alteration in swimming performance.
Herpes zoster mRNA vaccine induces superior vaccine immunity over licensed vaccine in mice and rhesus macaques
Authors: Huang Lulu , Zhao Tongyi , Zhao Weijun , Shao Andong , Zhao Huajun , Ma Wenxuan , Gong Yingfei , Zeng Xianhuan , Weng Changzhen , Bu Lingling , Di Zhenhua , Sun Shiyu , Dai Qinsheng , Sun Minhui , Wang Limei , Liu Zhenguang , Shi Leilei , Hu Jiesen , Fang Shentong , Zhang Cheng , Zhang Jian , Wang Guan , Loré Karin , Yang Yong , Lin Ang
Published: August 2023

Herpes zoster remains an important global health issue and mainly occurs in aged and immunocompromised individuals with an early exposure history to Varicella Zoster Virus (VZV). Although the licensed vaccine Shingrix has a remarkably high efficacy, undesired reactogenicity and increasing global demand causing vaccine shortage urged the development of improved or novel VZV vaccines. In this study, we developed a novel VZV mRNA vaccine candidate (named as ZOSAL) containing sequence-optimized mRNAs encoding full-length glycoprotein E encapsulated in an ionizable lipid nanoparticle. In mice and rhesus macaques, ZOSAL demonstrated superior immunogenicity and safety in multiple aspects over Shingrix, especially in the induction of strong T cell immunity. Transcriptomic analysis revealed that both ZOSAL and Shingrix could robustly activate innate immune compartments, especially Type-I IFN signaling and antigen processing/presentation. Multivariate correlation analysis further identified several early factors of innate compartments that can predict the magnitude of T cell responses, which further increased our understanding of the mode of action of two different VZV vaccine modalities. Collectively, our data demonstrated the superiority of VZV mRNA vaccine over licensed subunit vaccine. The mRNA platform therefore holds prospects for further investigations in next-generation VZV vaccine development.
ESAT-6 undergoes self-association at phagosomal pH and an ESAT-6 specific nanobody restricts M. tuberculosis growth in macrophages
Authors: Bates Timothy A , Trank-Greene Mila , Nguyenla Xammy , Anastas Aidan , Gurmessa Sintayehu , Merutka Ilaria R , Dixon Shandee D , Shumate Anthony , Groncki Abigail R , Parson Matthew AH , Ingram Jessica R , Barklis Eric , Burke John E , Shinde Ujwal , Ploegh Hidde L , Tafesse Fikadu G
Published: August 2023

Mycobacterium tuberculosis (Mtb) is known to survive within macrophages by compromising the integrity of the phagosomal compartment in which it resides. This activity primarily relies on the ESX-1 secretion system, predominantly involving the protein duo ESAT-6 and CFP-10. CFP-10 likely acts as a chaperone, while ESAT-6 likely disrupts phagosomal membrane stability via a largely unknown mechanism. we employ a series of biochemical analyses, protein modeling techniques, and a novel ESAT-6-specific nanobody to gain insight into the ESAT-6's mode of action. First, we measure the binding kinetics of the tight 1:1 complex formed by ESAT-6 and CFP-10 at neutral pH. Subsequently, we demonstrate a rapid self-association of ESAT-6 into large complexes under acidic conditions, leading to the identification of a stable tetrameric ESAT-6 species. Using molecular dynamics simulations, we pinpoint the most probable interaction interface. Furthermore, we show that cytoplasmic expression of an anti-ESAT-6 nanobody blocks Mtb replication, thereby underlining the pivotal role of ESAT-6 in intracellular survival. Together, these data suggest that ESAT-6 acts by a pH dependent mechanism to establish two-way communication between the cytoplasm and the Mtb-containing phagosome.
Epstein-Barr virus BRRF1 induces butyrophilin 2A1 in nasopharyngeal carcinoma cells via the IL-22/JAK3-STAT3 pathway
Authors: Liu Yue , Ye Zuodong , Chen Luo , Cheung Allen Ka Loon
Published: August 2023

Epstein-Barr virus is highly associated with nasopharyngeal carcinoma (NPC) with genes expressed for tumor transformation or maintenance of viral latency, but there are certain genes that can modulate immune molecules. Butyrophilin 2A1 (BTN2A1) is an important activating protein for presenting phosphoantigen presentation for recognition by Vγ9Vδ2 T cells to achieve anti-tumor activities. We have previously shown that Vγ9Vδ2 T cells achieve efficacy against NPC when BTN2A1 and BTN3A1 are upregulated by stimulating EBV gene expression, particularly LMP1. Whilst BTN3A1 can be induced by LMP1 mediated IFN-γ/JNK/NLRC5 pathway, the viral gene that can regulate BTN2A1 remains elusive. Here, we showed that BTN2A1 expression is directly mediated by EBV BRRF1, which can trigger BTN2A1 promoter and downstream JAK3-STAT3 pathway in NPC43 cells as enlightened by RNA-seq data and verified by inhibitor experiments. Further, BRRF1 downregulated IL-22 binding protein (IL-22RA2) to complement the EBNA1-targeting probe (P4) induced IL-22 expression. These functions act in concordance to enhance the expression of BTN2A1, which likely lead to increased tumor cell killing by Vγ9Vδ2 T cells. Overall, this study elucidated a new mechanism of stimulating BTN2A1 expression in nasopharyngeal carcinoma cells by the EBV gene BRRF1.

Summary statement

This study demonstrated a new function Epstein-Barr Virus BRRF1 to induce BTN2A1 in nasopharyngeal carcinoma via the IL-22/JAK3-STAT3 pathway, which potentiates Vγ9Vδ2 T cells against NPC.
Refining the pool of RNA-binding domains advances the classification and prediction of RNA-binding proteins
Authors: Wassmer Elsa , Koppàny Gergely , Hermes Malte , Diederichs Sven , Caudron-Herger Maïwen
Published: August 2023

Key Points

Comprehensive analysis of RNA-related protein domains and families enriched in RNA-binding proteins (RBPs)

Pan-species prediction of new RBPs, and prediction and validation of new RNA-binding domains

Online resource with complete dataset including high-confidence human RBPs according to a new scoring system

From transcription to decay, RNA-binding proteins (RBPs) influence RNA metabolism. Using the RBP2GO database that combines proteome-wide RBP screens from 13 species, we investigated the RNA-binding features of 176896 proteins. By compiling published lists of RNA-binding domains (RBDs) and RNA-related protein family (Rfam) IDs with lists from the InterPro database, we analyzed the distribution of the RBDs and Rfam IDs in RBPs and non-RBPs to select RBDs and Rfam IDs that were enriched in RBPs. We also explored proteins for their content in intrinsically disordered regions (IDRs) and low complexity regions (LCRs). We found a strong positive correlation between IDRs and RBDs and a co-occurrence of specific LCRs. Our bioinformatic analysis indicated that RBDs/Rfam IDs were strong indicators of the RNA-binding potential of proteins and helped predicting new RBP candidates, especially in less investigated species. By further analyzing RBPs without RBD, we predicted new RBDs that were validated by RNA-bound peptides. Finally, we created the RBP2GO composite score by combining the RBP2GO score with new quality factors linked to RBDs and Rfam IDs. Based on the RBP2GO composite score, we compiled a list of 2018 high-confidence human RBPs. The knowledge collected here was integrated into the RBP2GO database athttps://RBP2GO-2-Beta.dkfz.de.

GRAPHICAL ABSTRACT
Stability of Ecologically Scaffolded Traits During Evolutionary Transitions in Individuality
Authors: Doulcier Guilhem , Takacs Peter , Hammerschmidt Katrin , Bourrat Pierrick
Published: August 2023

Evolutionary transitions in individuality (ETIs), such as the emergence of multicellularity, are events in the history of life during which entities at one level of organisation (particles) form collective-level entities that subsequently become individuals in their own right. Recent empirical and theoretical studies advocate the importance of an externally imposed meta-population structure or “ecological scaffold” for the emergence of new levels of individuality. Such a scaffold enables survival and reproduction at the collective level and thus the possibility of selection for beneficial traits on that level. However, a long-standing difficulty for the ecological scaffolding approach has been its inability to adequately explain how collective-level trait values that evolved under scaffolding conditions can be retained once these conditions are lifted. We call this difficulty “the problem of endogenisation.” Here, we derive general conditions for the possibility of endogenisation. Key to endogenisation is the existence of a fitness valley that can be circumvented when scaffolding occurs. Using a stochastic meta-population model, we implement two versions of ecological scaffolding (one temporal and one spatial) and study subsequent evolutionary trajectories using the modelling techniques of adaptive dynamics. Our analysis yields several important results. The temporal model reveals that only collective traits based on particle-particle interactions can be endogenised when a temporary scaffold is applied to the entire population. The spatial model shows that, given the presence of an environmental gradient of externally imposed meta-population structure, ecological scaffolding can only occur in a limited “Goldilocks” zone of the environment. Further, if endogenisation conditions are also fulfilled, scaffolded collectives can colonise non-scaffolding areas of the environment. We conjecture that Goldilocks zones could act as initiators of ETIs and help explain the near ubiquity of collective-level individuality even if the conditions that promote it prove to be rare.
Altering the substitution and crosslinking of glucuronoarabinoxylans affects cell wall porosity and assembly inBrachypodium distachyon
Authors: Tryfona Theodora , Pankratova Yanina , Petrik Deborah , Rebaque Moran Diego , Wightman Raymond , Echevarria Poza Alberto , Yu Xiaolan , Deralia Parveen Kumar , Vilaplana Francisco , Anderson Charles T. , Hong Mei , Dupree Paul
Published: August 2023

The Poaceae family of plants provides cereal crops that are critical for human and animal nutrition and also they are an important source of biomass. Interacting plant cell wall components give rise to recalcitrance to digestion, thus understanding the wall molecular architecture is important to improve biomass properties. Xylan is the main hemicellulose in grass cell walls. Recently, we reported structural variation in grass xylans, suggesting functional specialisation and distinct interactions with cellulose and lignin. Here, we investigated the functions of these xylans by perturbing the biosynthesis of specific xylan types.

We generated CRISPR/Cas9 knockout mutants inBrachypodium distachyon XAX1andGUX2genes involved in xylan biosynthesis. Using carbohydrate gel electrophoresis we identified biochemical changes in different xylan types. Saccharification, cryo-SEM, subcritical water extraction and ssNMR were used to study wall architecture.

BdXAX1A andBdGUX2 enzymes modify different types of grass xylan.Brachypodiummutant walls are more porous, suggesting the xylan substitutions directed by bothBdXAX1A andGUX2 enzymes influence xylan-xylan and/or xylan-lignin interactions.

Since xylan substitutions influence wall architecture and digestibility, our findings open new avenues to improve cereals for food and to use grass biomass for feed and the production of bioenergy and biomaterials.
Structural Basis for Hyperpolarization-dependent Opening of the Human HCN1 Channel
Authors: Burtscher Verena , Mount Jonathan , Cowgill John , Chang Yongchang , Bickel Kathleen , Yuan Peng , Chanda Baron
Published: August 2023

Hyperpolarization and cyclic-nucleotide (HCN) activated ion channels play a critical role in generating self-propagating action potentials in pacemaking and rhythmic electrical circuits in the human body. Unlike most voltage-gated ion channels, the HCN channels activate upon membrane hyperpolarization, but the structural mechanisms underlying this gating behavior remain unclear. Here, we present cryo-electron microscopy structures of human HCN1 in Closed, Intermediate, and Open states. Our structures reveal that the inward motion of two gating charges past the charge transfer center (CTC) and concomitant tilting of the S5 helix drives the opening of the central pore. In the intermediate state structure, a single gating charge is positioned below the CTC and the pore appears closed, whereas in the open state structure, both charges move past CTC and the pore is fully open. Remarkably, the downward motion of the voltage sensor is accompanied by progressive unwinding of the inner end of S4 and S5 helices disrupting the tight gating interface that stabilizes the Closed state structure. This “melting” transition at the intracellular gating interface leads to a concerted iris-like displacement of S5 and S6 helices, resulting in pore opening. These findings reveal key structural features that are likely to underlie reversed voltage-dependence of HCN channels.
The interplay between lumen pressure and cell proliferation determines organoid morphology in a multicellular phase field model
Authors: Tanida Sakurako , Fuji Kana , Lu Linjie , Guyomar Tristan , Lee Byung Ho , Honigmann Alf , Grapin-Botton Anne , Riveline Daniel , Hiraiwa Tetsuya , Nonomura Makiko , Sano Masaki
Published: August 2023

Organoids are ideal systems to predict the phenotypes of organs. However, there is currently a lack of understanding regarding the generalized rules that enable use of simple cellular principles to make morphological predictions of entire organoids. Therefore, we employed a phase field model with the following basic components: the minimum conditions for the timing and volume of cell division, lumen nucleation rules, and lumenal pressure. Through our model, we could compute and generate a myriad of organoid phenotypes observed till date. We propose morphological indices necessary to characterize the shapes and construct phase diagrams and show their dependencies on proliferation time and lumen pressure. Additionally, we introduced the lumen-index parameter, which helped in examining the criteria to maintain organoids as spherical structures comprising a single layer of cells and enclosing an intact lumen. Finally, we predict a star-like organoid phenotype that did not undergo differentiation, suggesting that the volume constraint during cell division may determine the final phenotype. In summary, our approach provides researchers with guidelines to test the mechanisms of self-organization and predict the shape of organoid.

Author summary

In nature, a wide variety of organ morphologies are observed. Owing to the complexity of the process underlying the acquisition of organs’ morphology, it is challenging to investigate the mechanisms that lead to such variations. A promising approach to study these variations is the use of “computational organoid” study, which is the computational-based study of self-organizing shapes in multicellular assemblies and fluid-filled cavities called lumens that develop from a few proliferating cells. This study explores general mechanisms that dictate how various mechanical factors affect the growing self-organized multicellular assembly. We relied on computer simulations of the mathematical model called multicellular phase-field model with lumens and explored the mechanical factor effects, such as the lumen pressure while considering the time and volume conditions required for cell division. These simulations generated and categorized a wide range of organoid phenotypes based on the varying lumen pressure and cell division conditions. These phenotypes were characterized into seven distinct classes, based on the morphological index sets, including a cellular monolayer/multilayer surrounding single or multiple lumens and branch formation. These phenotypes were obtained without the assumption of differentiation. Our study elucidates the mechanisms underlying the organoid and organ formation with different shapes, thereby highlighting the significance of mechanical forces in shaping these complex biological structures.
Mouse model of atypical DAT deficiency syndrome uncovers dopamine dysfunction associated with parkinsonism and psychiatric disease
Authors: Herborg Freja , Konrad Lisa K. , Pugh Ciara , Delignat-Lavaud Benoît , Ratner Cecilia Friis , Awadallah Nora , Pino Jose A. , Berlin Frida , Rickhag Mathias , Holst Birgitte , Woldbye David , Torres Gonzalo , Trudeau Louis-Eric , Gether Ulrik
Published: August 2023

The dopamine transporter (DAT) plays a crucial role in regulating the brain’s dopamine (DA) homeostasis. Atypical DAT deficiency syndrome (DTSD) is a disease characterized by early-onset parkinsonism and comorbid psychiatric symptoms, but the pathobiological processes that link DAT dysfunction to both parkinsonism and psychiatric symptoms are unknown. Here, we present a genetic mouse model of atypical DTDS that expresses two coding DAT variants, DAT-I312F and DAT-D421N, derived from a patient diagnosed with ADHD and parkinsonism. Phenotypic characterization of the mutant mice revealed impaired DAT function and major homeostatic changes including increased ambient extracellular DA levels, decreased evoked DA release, and reduced expression of both tyrosine hydroxylase (TH) and of DA D1/D2 receptors. This was accompanied by diminished striatal dopaminergic axonal density and a psychomotor phenotype characterized by hyperactivity, enhanced exploratory activity, and pronounced clasping. Importantly, both amphetamine and anticholinergic treatment ameliorated aberrant hyperlocomotion in the mice. Summarized, by replicating core aspects of the patient’s phenotype, the mouse model not only provides insights into the mechanisms underlying atypical DTDS but also underlines the broad relevance of DA deficits for understanding the co-morbidity between neuropsychiatric diseases and parkinsonism.

ONE SENTENCE SUMMARY

In a new mouse disease model, we explore the behavioral consequences and dopaminergic dysfunction that arise from patient-derived mutations in the dopamine transporter associated with parkinsonism and co-morbid neuropsychiatric disease
Small molecule inhibitors of transcriptional Cyclin Dependent Kinases impose HIV-1 latency, presenting “block and lock” treatment strategies
Authors: Horvath Riley M. , Brumme Zabrina L. , Sadowski Ivan
Published: August 2023

Antiretroviral therapy is not a cure for HIV-1 as viral rebound ensues immediately following discontinuation. The block and lock therapeutic strategy seeks to enforce proviral latency and durably suppress viremic reemergence in the absence of antiretroviral therapy. Transcriptional Cyclin Dependent Kinase activity regulates LTR transcription, however, the effect and therapeutic potential of inhibiting these kinases for enforcing HIV-1 latency remains unrecognized. Using newly developed small molecule inhibitors that are highly selective for either CDK7 (YKL-5-124), CDK9 (LDC000067), or CDK8/19 (Senexin A), we found that targeting any one of these kinases prevented HIV-1 expression at concentrations that showed no toxicity. Furthermore, although CDK7 inhibition induced cell cycle arrest, inhibition of CDK9 and/or CDK8/19 did not. Of particular interest, proviral latency as induced by CDK8/19 inhibition was maintained following drug removal while CDK9 inhibitor induced latency rebounded within 24 hrs of discontinuation. Our results indicate that the Mediator complex kinases, CDK8/CDK19, are attractive block and lock targets while sole disruption of P-TEFb is unlikely to be efficacious.
TAX1BP1 recruits ATG9 vesicles through SCAMP3 binding
Authors: Hama Yutaro , Kurikawa Yoshitaka , Matsui Takahide , Mizushima Noboru , Yamamoto Hayashi
Published: August 2023

Macroautophagy is a cellular process that delivers cytoplasmic material to lysosomes for degradation via autophagosomes. It often involves the selective degradation of ubiquitinated proteins. During selective macroautophagy, five ubiquitin-binding adaptors, p62, NBR1, OPTN, NDP52, and TAX1BP1, form biomolecular condensates with ubiquitinated proteins and recruit ATG9 vesicles, which serve as the initial membrane source required for autophagosome formation. However, the molecular details underlying the cargo/adaptor-dependent recruitment of ATG9 vesicles remain unclear. Here, we show that ATG9 vesicles are recruited by three cargo adaptors: TAX1BP1, NBR1, and OPTN. We also find that ATG9A itself is not the determinant for recruitment by these cargo adaptors, and that TAX1BP1-dependent ATG9 vesicle recruitment is mediated by SCAMP3, a transmembrane protein on the ATG9 vesicles, through binding to the coiled-coil 1 domain of TAX1BP1. These findings provide mechanistic insights into the cargo/adaptor-dependent assembly of ATG9 vesicles in mammals.
Foothold selection during locomotion in uneven terrain: Results from the integration of eye tracking, motion capture, and photogrammetry
Authors: Muller Karl S , Panfili Dan , Shields Stephanie , Matthis Jonathan S , Bonnen Kathryn , Hayhoe Mary M
Published: August 2023

Relatively little is known about the way vision is used to guide locomotion in the natural world. What visual features are used to choose paths in natural complex terrain? To answer this question, we measured eye and body movements while participants walked in natural outdoor environments. We incorporated measurements of the 3D terrain structure into our analyses and reconstructed the terrain along the walker’s path, applying photogrammetry techniques to the eyetracker’s scene camera videos. Combining these reconstructions with the walker’s body movements, we demonstrate that walkers take terrain structure into account when selecting paths through an environment. We find that they change direction to avoid taking steeper steps that involve large height changes, instead of choosing more circuitous, relatively flat paths. Our data suggest walkers plan the location of individual footholds and plan ahead to select flatter paths. These results provide evidence that locomotor behavior in natural environments is controlled by decision mechanisms that account for multiple factors, including sensory and motor information, costs, and path planning.
Simple bacterial growth model for the formation of spontaneous and triggered dormant subpopulations
Authors: Svenningsen Mikkel Skjoldan , Mitarai Namiko
Published: August 2023

Bacterial persistence is a phenomenon where a subpopulation of cells can survive antibiotic treatment, and it is often linked to extremely slow growth or a dormant state. However, the mechanisms and factors that govern dormancy are not well understood. We propose a simplified growth model that treats the main cellular components as discrete variables and allocates resources among them according to different strategies. The model can reproduce some of the observed features of bacterial persistence, such as wide distribution in division times, long division times after a nutrient down-shift, and the existence of different dormant phenotypes. We also show how the growth structure, i.e., whether cells grow in a lineage or a branch, affects the dormant cells’ occurrence and distribution due to the growth states’ mother-daughter correlation. Our model provides a framework to explore the complex interactions between cellular processes and environmental conditions that lead to bacterial persistence.