bluuebunny/crossref_metadata_2025 huggingface dataset:
Systematic mapping of MCU-mediated mitochondrial calcium signaling networks
Authors: Herran Hilda Delgado de la , Reane Denis Vecellio , Cheng Yiming , Katona Máté , Hosp Fabian , Greotti Elisa , Wettmarshausen Jennifer , Patron Maria , Mohr Hermine , Mello Natalia Prudente de , Chudenkova Margarita , Gorza Matteo , Walia Safal , Feng Michael Sheng-Fu , Leimpek Anja , Mielenz Dirk , Pellegata Natalia S. , Langer Thomas , Hajnóczky György , Mann Matthias , Murgia Marta , Perocchi Fabiana
Published: February 2024

The Mitochondrial Ca2+Uniporter Channel (MCUC) allows calcium entry into the mitochondrial matrix to regulate energy metabolism but also cell death. Although, several MCUC components have been identified, the molecular basis of mitochondrial Ca2+signaling networks and their remodeling upon changes in uniporter activity have not been systematically assessed. Using an unbiased and quantitative proteomic approach, we map the MCUC interactome in HEK293 cells under physiological conditions and upon chronic loss or gain of mitochondrial Ca2+uptake. Besides all previously known subunits of the uniporter, we identify 89 high-confidence interactors linking MCUC to several mitochondrial complexes and pathways, half of which are currently linked to metabolic, neurological, and immunological diseases. As a proof-of-concept, we validate EFHD1 as a binding partner of MCU, EMRE and MCUB with a MICU1-dependent inhibitory effect on Ca2+uptake. To investigate compensatory mechanisms and functional consequences of mitochondrial Ca2+dyshomeostasis, we systematically survey the MCU interactome upon silencing of EMRE, MCUB, MICU1 or MICU2. We observe profound changes in the MCU interconnectivity, whereby downregulation of EMRE reduces the number of MCU interactors of over 10-fold, while silencing of MCUB leads to a wider functional network linking MCU to mitochondrial stress response pathways and cell death. Altogether our study provides a comprehensive map of MCUC protein-protein interactions and a rich, high-confidence resource that can be explored to gain insights into the players and mechanisms involved in calcium signal transduction cascades and their relevance in human diseases.
De Novo Sensorimotor Learning Through Reuse of Movement Components
Authors: Gabriel G. A. , Mushtaq F. , Morehead J. R.
Published: February 2024

From tying one’s shoelaces to driving a car, complex skills involving the coordination of multiple muscles are common in everyday life; yet relatively little is known about how these skills are learned. Recent studies have shown that new sensorimotor skills involving re-mapping familiar body movements to unfamiliar outputs cannot be learned by adjusting pre-existing controllers, and that new task-specific controllers must instead be learned “de novo”. To date, however, few studies have investigated de novo learning in scenarios requiring continuous and coordinated control of relatively unpractised body movements. In this study, we used a myoelectric interface to investigate how a novel controller is learned when the task involves an unpractised combination of relatively untrained continuous muscle contractions. Over five sessions on five consecutive days, participants learned to trace a series of trajectories using a computer cursor controlled by the activation of two muscles. The timing of the generated cursor trajectory and its shape relative to the target improved for conditions trained with post-trial visual feedback. Improvements in timing transferred to all untrained conditions, but improvements in shape transferred only to untrained conditions requiring the trained order of muscle activation. All muscle outputs in the final session could already be generated during the first session, suggesting that participants learned the new task by improving the selection of existing motor commands. These results show that generating novel motor behaviours need not involve learning to generate new motor commands.

Significance Statement

Real-world skills often involve continuous coordination of multiple muscles. Such skills cannot be learned by adjusting an existing control policy, instead requiring a new controller to be learned “de novo”. It remains unclear how new controllers are learned for tasks involving unfamiliar combinations of body movements. In this study, we used a novel human-computer interface task to test this. Over five sessions, participants learned to trace a series of cursor trajectories by coordinating the activation of two muscles. We found that participants tended to reuse the same muscle contractions for trained and untrained variants of the task, and that performance improvements were attributable to improvements in the choice of muscle contractions from a pre-existing repertoire. Our results demonstrate that learning of new complex movements does not necessarily require learning to generate new patterns of muscle activity.
Generic comparison of lumen nucleation and fusion in epithelial organoids with and without hydrostatic pressure
Authors: Lu Linjie , Fuji Kana , Guyomar Tristan , Alcheikh Yara , Lieb Michele , Andre Marie , Tanida Sakurako , Nonomura Makiko , Hiraiwa Tetsuya , Yennek Siham , Petzold Heike , Martin-Lemaitre Cecilie , Grapin-Botton Anne , Honigmann Alf , Sano Masaki , Riveline Daniel
Published: February 2024

Many internal organs in the body harbor a fluid-filled lumen. The mechanisms of lumens initiation and fusion have been reported as dependent on organ-type during organogenesis. In contrast, the physics of lumen suggests that force balance between luminal pressure and cell mechanics could lead to conserved rules which may unify their self-organisation. However, this hypothesis lacks experimental evidence. Here we compare lumen dynamics for three different systems (MDCK cysts, pancreatic spheres, and epiblast cysts) by using quantitative cell biology, microfabrication and theory. We report that initial cell number determines the maximum number of lumens but does not impact the steady state which is a final single lumen. In addition, lumen numbers exhibit two phases over time, a nucleation phase followed by a fusion phase. In the nucleation phase, lumens form between two cells in pancreatic and MDCK cysts whereas they form at the rosette stage between ten cells in epiblasts. In the second phase, lumens fuse by an increase in lumen volume for pancreatic spheres and MDCK cysts, whereas cell convergent directional motion leads to lumens fusion in epiblasts. We show that these phenomena are associated to the luminal hydrostatic pressure. We support these results with theoretical arguments and numerical simulations. We finally use MDCK cysts to manipulate cell adhesion and lumen volume and we successfully reproduce the fusion dynamics of pancreatic spheres and epiblasts. Our results reveal self-organisation rules of lumens across systems with relevance for morphogenesis during development and for the design of synthetic organs.
The moon’s influence on the activity of tropical forest mammals
Authors: Bischof Richard , Vallejo-Vargas Andrea F. , Semper-Pascual Asunción , Schowanek Simon D. , Beaudrot Lydia , Turek Daniel , Jansen Patrick A. , Rovero Francesco , Johnson Steig E. , Lima Marcela Guimarães Moreira , Santos Fernanda , Uzabaho Eustrate , Espinosa Santiago , Ahumada Jorge A. , Bitariho Robert , Salvador Julia , Mugerwa Badru , Sainge Moses N. , Sheil Douglas
Published: February 2024

Changes in lunar illumination alter the balance of risks and opportunities for animals at night, influencing activity patterns and species interactions. Our knowledge about behavioral responses to moonlight is incomplete, yet it can serve to assess and predict how species respond to environmental changes such as light pollution or loss of canopy cover. As a baseline, we wish to examine if and how wildlife responds to the lunar cycle in some of the darkest places inhabited by terrestrial mammals: the floors of tropical forests.

We quantified the prevalence and direction of activity responses to the moon in tropical forest mammal communities. Using custom Bayesian multinomial logistic regression models, we analyzed long-term camera trapping data on 88 mammal species from 17 protected forests on three continents. We also tested the hypothesis that nocturnal species are more prone to avoiding moonlight, as well as quantified diel activity shifts in response to moonlight.

We found that, apparent avoidance of moonlight (lunar phobia, 16% of species) is more common than apparent attraction (lunar philia, 3% of species). The three species exhibiting lunar philia followed diurnal or diurnal-crepuscular activity patterns. Lunar phobia, detected in 14 species, is more pronounced with higher degree of nocturnality, and is disproportionately common among rodents. Strongly lunar phobic species were less active during moonlit nights, which in most cases also decreases their total daily activity.

Our findings indicate that moonlight influences animal behavior even beneath the forest canopy. This suggests that such impacts may be exacerbated in degraded and fragmented forests. Additionally, the effect of artificial light on wild communities is becoming increasingly apparent. Our study offers empirical data from protected tropical forests as a baseline for comparison with more disturbed areas, together with a robust approach for detecting activity shifts in response to environmental change.

Open Research statement:The data and code for performing the analyses described in this article are available athttps://github.com/richbi/TropicalMoon.
Psychological stress disturbs bone metabolism via miR-335-3p/Fos signaling in osteoclast
Authors: Zhang Jiayao , Li Juan , Huang Jiehong , Xiang Xuerui , Li Ruoyu , Zhai Yun , Lin Shuxian , Liu Weicai
Published: February 2024

It has been well-validated that chronic psychological stress leads to bone loss, but the underlying mechanism remains unclarified. In this study, we established and analyzed the chronic unpredictable mild stress (CUMS) mice to investigate the miRNA-related pathogenic mechanism involved in psychological stress induced osteoporosis. Our result found that these CUMS mice exhibited osteoporosis phenotype that mainly attributed to the abnormal activities of osteoclasts. Subsequently, miRNA sequencing and other analysis showed that miR-335-3p, which is normally highly expressed in the brain, was significantly down-regulated in the nucleus ambiguous (NAC), serum, and bone of the CUMS mice. Additionally,in vitrostudies detected that miR-335-3p is important for osteoclast differentiation, with its direct targeting site in FOS. Further studies demonstrated FOS was upregulated in CUMS osteoclast, and the inhibition of FOS suppressed the accelerated osteoclastic differentiation, as well as the expression of osteoclastic genes, such asNfatc1, Acp5, Mmp9, in miR-335-3p restrained osteoclasts. In conclusion, this work indicated that psychological stress may down-regulate the miR-335-3p expression, which resulted in the accumulation of FOS and the up-regulation of NFACT1 signaling pathway in osteoclasts, leading to its accelerated differentiation and abnormal activity. These results decipher a previously unrecognized paradigm that miRNA can act as a link between psychological stress and bone metabolism.

Impact statement

miR-335-3p, which targets FOS and inhibits its activation of NFATC1 signaling, is an important regulator for osteoclast function and responsible for the psychological stress induced osteoporosis
Regulated mRNA recruitment in dinoflagellates is reflected in hyper-variable mRNA spliced leaders and novel eIF4Es
Authors: Jones Grant D. , Williams Ernest P. , Haq Saddef , Bachvaroff Tsvetan R. , Sanchez M. Basanta , Place Allen R. , Jagus Rosemary
Published: February 2024

Dinoflagellates are eukaryotic algae with large genomes that rely heavily on post-transcriptional control for the regulation of gene expression. Dinoflagellate mRNAs aretrans-spliced with a conserved 22 base spliced leader sequence (SL) that includes the 5’-cap to which the translation initiation factor 4E (eIF4E) binds to facilitate ribosomal recruitment. The binding of an eIF4E to a specific mRNA SL is a potential regulatory point in controlling dinoflagellate gene expression. Here we show that m7G is the 5’-cap base of the 65 bp SL RNA with additional methylations throughout the SL to give a mixture of novel multi-methylated sequences inAmphidinium carterae(CCMP1314). There is also sequence variability in all four bases seen at the first position followed by a variety of polymorphisms. Three novel clades of eIF4E have been shown in dinoflagellates that are distinct from the three metazoan classes of eIF4E. Members of each clade differ significantly from each other, but all bear the distinctive features of a cap-binding protein. Here we show large differences in expression and activity in six of the eight eIF4E family members fromA. carterae. Transcripts of each are expressed throughout the diel cycle, but only eIF4E-1 family members and eIF4E-2a show discernable expression at the level of protein. Recombinant eIF4E-1 family members and eIF4E-3a, but not eIF4E-2a, are able to bind to m7GTP substratesin vitro. Overall, eIF4E-1a emerges with characteristics consistent with the role of a prototypical initiation factor; eIF4E-1a is the most conserved and highly expressed eIF4E family member, has the highest affinity for m7GpppG and m7GpppC by surface plasmon resonance, and is able to complement a yeast strain conditionally deficient in eIF4E. The large number of eIF4E family members along with the sequence and methylation state variability in the mRNA SLs underscore the unique nature of the translational machinery in the dinoflagellate lineage and suggest a wide range of possibilities for differential recruitment of mRNAs to the translation machinery.

Impact Statement

In the dinoflagellate,A. carterae, hyper-variable mRNA spliced leaders and novel eIF4Es reflect the reliance of dinoflagellates on variable mRNA recruitment for the regulation of gene expression.
Wider spread of excitatory neuron influence in association cortex than sensory cortex
Authors: Khoury Christine F. , Ferrone Michael , Runyan Caroline A.
Published: February 2024

The basic structure of local cortical circuits, including the composition of cell types, is highly conserved across the cortical processing hierarchy. However, computational roles and the spatial and temporal properties of population activity differ fundamentally in sensory-level and association-level areas. In primary sensory cortex, the timescale of population activity is shorter and pairwise correlations decay more rapidly over distance between neurons, supporting a population code that is suited to encoding rapidly fluctuating sensory stimuli. In association cortex, the timescale of population activity is longer, and pairwise correlations are stronger over wider distances, a code that is suited to holding information in memory and driving behavior. Here, we tested whether these differences in population codes could potentially be explained by intrinsic differences in local network structure. We targeted single excitatory neurons optogenetically, while monitoring the surrounding ongoing population activity in sensory (auditory cortex) and association (posterior parietal cortex) areas in mice. While the temporal impacts of these perturbations were similar across regions, the spatial spread of excitatory influence was wider in association cortex than in sensory cortex. Our findings suggest that differences in recurrent connectivity could contribute to the different properties of population codes in sensory and association cortex, and imply that circuit models of cortical function should be tailored to the properties specific to individual regions.

Significance statement

Cell-type-specific functional interactions and connectivity patterns have largely been studied in sensory cortex. Yet the properties of local network activity differ dramatically across the cortical hierarchy, possibly due to differences in intrinsic connectivity patterns. Here, we compared the functional impacts of individual excitatory neurons on local population activity, finding differences in the spatial spread of excitatory influence across regions. Our findings suggest that the structure of local networks differs across the cortical processing hierarchy, and these differences should be considered in circuit models of processes such as decision-making and working memory.
CDKN1B(p27kip1) enhances drug tolerant persister CTCs by restricting polyploidy following mitotic inhibitors
Authors: Horwitz Elad , Dubash Taronish D. , Szabolcs Annamaria , Wittner Ben S. , Kreuzer Johannes , Morris Robert , Bardia Aditya , Chirn Brian , Wiley Devon , Che Dante , Russel Hunter C. , Herrera Lopez Xcanda Ixchel , Fox Douglas B. , Antmen Ezgi , Ting David T. , Haas Wilhelm , Sade-Feldman Moshe , Maheswaran Shyamala , Haber Daniel A.
Published: February 2024

The mitotic inhibitor docetaxel (DTX) is often used to treat endocrine-refractory metastatic breast cancer, but initial responses are mitigated as patients eventually have disease progression. Using a cohort ofex vivocultures of circulating tumor cells (CTCs) from patients with heavily pretreated breast cancer (n=18), we find two distinct patterns of DTX susceptibility, independent of clinical treatment history. In CTCs cultured from some patients, treatment with a single dose of DTX results in complete cell killing, associated with accumulation of non-viable polyploid (≥8N) cells arising from endomitosis. In others, a transient viable drug-tolerant persister (DTP) population emerges, ultimately enabling renewed proliferation of CTCs with preserved parental cell ploidy and DTX sensitivity. In these CTC cultures, efficient cell cycle exit generates a ≤4N drug-tolerant state dependent onCDKN1B(p27Kip1). Exposure to DTX triggers stabilization of CDKN1B through AKT-mediated phosphorylation at serine 10. Suppression ofCDKN1Breduces the number of persister CTCs, increases ≥8N mitotic cells and abrogates regrowth after DTX exposure. Thus, CDKN1B-mediated suppression of endomitosis contributes to a reversible persister state following mitotic inhibitors in patient-derived treatment refractory breast cancer cells.

Summary in bullets

Transient DTX tolerant persister cells emerge in some patient-derived cultured CTCs.

DTX-tolerant persisters restrict endoreduplication and polyploidy through CDKN1 (p27kip1).

DTX exposure induces CDKN1B stabilization through AKT mediated phosphorylation at serine 10.

Suppression of polyploidy underlies a drug tolerant persister state specific to mitotic inhibitors.
RomX, a novel prokaryotic regulator, links the response receiver domain of RomR with GTP-bound MglA for establishingMyxococcus xanthuspolarity
Authors: Chakraborty Sukanya , Gayathri Pananghat
Published: February 2024

Cell polarity specification and reversals are distinctive features of motility of the soil bacteriumMyxococcus xanthus. The bacterial small Ras-like GTPase, MglA, serves as a key player orchestrating these polarity oscillations. RomR, a response regulator, along with its partner RomX, has been identified to function as a guanine nucleotide exchange factor (GEF) for MglA, crucial for its polar recruitment. In this study, we determine the crystal structure of RomX, a protein of a hitherto unknown fold. RomX consists of a three-helix bundle, identified to be the same fold as the stalk domain of atlastin, a member of the dynamin family of GTPases. From our structure-based sequence analysis for proteins of a similar fold, we observe the co-occurrence of the RomX fold with response receiver domains in several bacterial response regulators. Based on mutational analysis and affinity measurements, we conclude that the helix-1 of RomX mediates the interaction with MglA-GTP, while helix-3 of RomX interacts with the RomR N-terminal receiver (REC) domain. We demonstrate that the binding between MglA and RomX is exclusively in the presence of GTP. The absence of additional stimulation of RomX GEF activity in the presence of RomR-REC supports the mutually exclusive interface on RomX for RomR and MglA interaction. Collectively, our findings validate the positioning of RomX between MglA and RomR-REC, providing insights into the concerted action of the RomR/RomX complex at both poles in driving MglA localization within polarized cells.
Age-dependent miR156-targetedSPLsare required for extrafloral nectary development inPassifloraspp
Authors: Soares Jéssica Ribeiro , Robledo Kerly Jessenia Moncaleano , de Souza Vinicius Carius , Dias Lana Laene Lima , Silva Lázara Aline Simões , da Silveira Emerson Campos , da Silva Souza Claudinei , Sousa Elisandra Silva , Sodrzeieski Pedro Alexandre , Sarmiento Yoan Camilo Guzman , de Matos Elyabe Monteiro , Falcão Thais Castilho de Arruda , Fialho Lilian da Silva , Guimarães Valéria Monteze , Viccini Lyderson Facio , Pierdona Flaviani Gabriela , Romanel Elisson , Fouracre Jim , Otoni Wagner Campos , Nogueira Fabio Tebaldi Silveira
Published: February 2024

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Passion flower extrafloral nectaries (EFNs) protrude from adult leaves and facilitate mutualistic interactions with insects, but how age cues control EFN establishment remains poorly understood.

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Here, we combined genetic and molecular studies to investigate how leaf development and EFN patterning are regulated through the age-dependent miR156-SQUAMOSA PROMOTER BINDING PROTEIN LIKE(SPL) module in two EFN-containingPassifloraspecies with distinct leaf shapes.

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Low levels of miR156 correlate with leaf maturation and EFN formation inPassiflora edulis and P. cincinnata. Consistently, overexpression of miR156 (miR156-OE), which leads to low levels ofSPLs, affected leaf ontogeny and EFN development in both species. Laminar EFNs were underdeveloped and less abundant in bothP. edulis and P. cincinnatamiR156-OE leaves. Importantly, the ecological relationships established by EFNs and their sugar profiles were negatively regulated by high levels of miR156. Moreover, transcriptome analysis of young leaf primordia revealed that miR156-targetedSPLsmay be required for proper expression of leaf and EFN development- associated genes inP. edulis and P. cincinnata.

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Our work provides the first evidence that the highly conserved miR156/SPLmodule regulates EFN development in an age-dependent manner and that the program responsible for EFN development is closely associated with the heteroblastic developmental program of the EFN-bearing leaves.
Saccharomyces cerevisiaeRev7 promotes non-homologous end-joining by blocking Mre11 nuclease and Rad50’s ATPase activities and homologous recombination
Authors: Badugu Sugith , Dhyani Kshitiza M. , Thakur Manoj , Muniyappa Kalappa
Published: February 2024

Recent studies have shown that, in human cancer cells, the tetrameric Shieldin complex (comprising REV7, SHLD1, SHLD2, and SHLD3) facilitates non-homologous end-joining (NHEJ) while blocking homologous recombination (HR). Surprisingly, several eukaryotic species lack SHLD1, SHLD2 and SHLD3 orthologs, suggesting that Rev7 may leverage an alternative mechanism to regulate the double-strand break (DSB) repair pathway choice. Exploring this hypothesis, we discovered thatSaccharomyces cerevisiaeRev7 physically interacts with the Mre11-Rad50-Xrs2 (MRX) subunits, impedes G-quadruplex DNA synergised-HU-induced toxicity and facilitates NHEJ, while antagonizing HR. Notably, we reveal that a 42-amino acid C-terminal fragment of Rev7 binds to the subunits of MRX complex, protectsrev7Δcells from G-quadruplex DNA-HU-induced toxicity, and promotes NHEJ by blocking HR. By comparison, the N-terminal HORMA domain, a conserved protein–protein interaction module, was dispensable. We further show that the full-length Rev7 impedes Mre11 nuclease and Rad50’s ATPase activities without affecting the latter’s ATP-binding ability. Combined, these results provide unanticipated insights into the functional interaction between the MRX subunits and Rev7 and highlight a mechanism by which Rev7 facilitates DSB repair via NHEJ, and attenuation of HR, by blocking Mre11 nuclease and Rad50’s ATPase activities inS. cerevisiae.

IMPACT STATEMENT

The mechanisms steering DNA double-strand break repair pathway choice is a topic of intense investigation, but remains incompletely understood. Our findings suggest that yeast Rev7 promotes DSB repair via NHEJ and inhibits homologous recombination by blocking Mre11 nuclease and Rad50’s ATPase activities.
On the Role of VP3-PI3P Interaction in Birnavirus Endosomal Membrane Targeting
Authors: Zanetti Flavia A. , Fernández Ignacio , Baquero Eduard , Guardado-Calvo Pablo , Ferrino-Iriarte Andres , Dubois Sarah , Morel Etienne , Alfonso Victoria , Aguilera Milton O. , Celayes María E. , Polo Luis M. , Suhaiman Laila , Galassi Vanesa V. , Chiarpotti María V. , Allende Carolina , Rodríguez Javier M. , Castón José R. , Lijavetzky Diego , Taboga Oscar , Colombo María I. , Del Pópolo Mario G. , Rey Félix A. , Delgui Laura R.
Published: February 2024

Birnaviruses are a group of double-stranded RNA (dsRNA) viruses infecting birds, fish and insects. Early endosomes (EE) constitute the platform for viral replication. Here, we study the mechanism of birnaviral targeting of EE membranes. Using the Infectious Bursal Disease Virus (IBDV) as a model, we validate that the viral protein 3 (VP3) binds to phosphatidylinositol-3-phosphate (PI3P) present in EE membranes. We identify the domain of VP3 involved in PI3P-binding, named P2 and localized in the core of VP3, and establish the critical role of the arginine at position 200 (R200), conserved among all known birnaviruses. Mutating R200abolishes viral replication. Moreover, we propose a two-stage modular mechanism for VP3 association with EE. Firstly, the carboxy-terminal region of VP3 adsorbs on the membrane, and then the VP3 core reinforces the membrane engagement by specifically binding PI3P through its P2 domain, additionally promoting PI3P accumulation.

Significance Statement

Birnaviruses are a family of viruses unique among the group of dsRNA viruses. Here, we show that VP3 seizes the endosomes by anchoring to the PI3P lipids in the luminal side of the EE membrane, in order to organize the viral replication factory. We propose a two-stage modular mechanism for VP3 association with PI3P-enriched EE. The significance of this work resides in the biochemical and biophysical insights on the mechanism of association of VP3 with EE and its role in the viral life cycle, which represents a substantial contribution toward understanding the replication strategy of these “non-canonical” viruses.
Integrated multi-omics analysis ofKlebsiella pneumoniaerevealed the discrepancy in flavonoid effect against strain growth between Rutin and Luteolin
Authors: Wang Zhibin , Shen Wanxia , Li Yuejiao , Wang Xiaoyun , Xu Guofeng , Yuan Xiefang , Tang Hongmei , Ma Ning , Zhong Xiaolin , Wang Xing
Published: February 2024

The emergence of drug resistant pathogenic bacteria is increasingly challenging conventional antibiotics. Plant derived flavonoids are always considered as potential alternatives to antibiotics due to their antimicrobial properties. However, the molecular mechanisms by which flavonoids inhibit pathogenic microorganisms’ growth are not fully understood. In order to better understand the inhibitory mechanism of flavonoids, two flavonoids were used to incubateKlebsiella pneumoniaeATCC700603. After incubation for 4 hours, both the metabolomic and transcriptomic analysis were performed. In present study, 5,483 genes and 882 metabolites were measured. Compared to wild control, the Rutin and Luteolin induced 507 and 374 differentially expressed genes (DEGs), respectively. However, the number of differential abundant metabolites (DAMs) were the same. The correlation between DEGs and DAMs were studied. The top 10 correlated DEGs and DAMs were identified in each comparative groups. Our results showed that, compared to Luteolin, Rutin induced the accumulation of metabolites and suppressed genes’ expression. Our results provided an explanation for the disparate effects of two flavonoids and demonstrated the inhibitory mechanism of Rutin on strain growth.
The MYCN 5′ UTR as a therapeutic target in neuroblastoma
Authors: Volegova Marina P , Brown Lauren E , Banerjee Ushashi , Dries Ruben , Sharma Bandana , Kennedy Alyssa , Porco John A. , George Rani E
Published: February 2024

Tumor cell amplification of the MYCN transcription factor is seen in half of patients with high-risk neuroblastoma, where it functions as an oncogenic driver associated with metastatic disease and poor survival. Yet, direct targeting of MYCN has been met with little success, prompting efforts to inhibit its expression at multiple levels. MYCN-amplified neuroblastoma cells have an increased requirement for protein synthesis to meet the overwhelming transcriptional burden imposed by oncogenic MYCN. Here, we take advantage of this vulnerability to interrogate the therapeutic potential of inhibiting the activity of the eukaryotic translation initiation factor 4A1 (eIF4A1), an RNA-helicase responsible for resolving structural barriers such as polypurine preponderance within 5′ untranslated regions (UTRs). We observed that eIF4A1 is a key regulator of transcript-specific mRNA recruitment in MYCN-overexpressing neuroblastomas and MYCN-associated transcripts rank highly in polypurine-rich 5′ UTR sequences, the majority of which have critical roles in cell proliferation. Using CMLD012824, a novel synthetic amidino-rocaglate (ADR) derivative, we demonstrate selectively increased eIF4A1 affinity for polypurine-rich 5′ UTRs, including the MYCN mRNA, leading to translation inhibition and cytotoxicity in human neuroblastoma cell lines and animal models. Through ribosome profiling and PAR-CLIP analysis, we show that ADR-mediated clamping of eIF4A1 onto mRNA spans the full lengths of target transcripts, whereas translational inhibition is mediated selectively through 5′ UTR binding. Both cap-dependent and cap-independent translation of MYCN are disrupted, pointing to the ability of CMLD012824 to disrupt non-canonical translation initiation. Our studies provide insights into the functional role of eIF4A1 in meeting the increased protein synthesis demands of MYCN-amplified neuroblastoma and suggest that its disruption may be therapeutically beneficial in this disease.
Cellular heterogeneity in the developing forebrain masks transcriptional outcomes and principles ofEvf2enhancer lncRNA-Dlx5/6UCE-gene guidance
Authors: Li Edward , Chakraborty Abhijit , Kohtz Sara J. , Cajigas Ivelisse , Shiau Fion , Vassar Robert J. , Clark Brian S. , Kohtz Jhumku D.
Published: February 2024

During mouse embryonic brain development, theEvf2ultraconserved enhancer (UCE) lncRNA guides the Dlx5/6UCE to ∼129 sites across chr6. However, previous work identified only 4 transcriptionally regulated targets associated withEvf2-Dlx5/6UCE enhancer-gene guided sites (EGGs), raising questions about the significance of the majority ofEvf2-EGGs. Here, single cell transcriptomics (scRNAseq) shows thatEvf2-EGGs on chr6 coincide with subpopulation-specificEvf2transcriptional targets, revealing far greater alignment between EGGs and transcriptional targets than previously reported. Surprisingly, subpopulation-specificEvf2regulated gene networks in embryonic progenitors predict adult synaptic and seizure defects.Evf2regulation of EGGs to gene bodies (GB, Dlx5/6UCE locations within ±5kb of the target gene) divides chr6 into short-range (<10Mb distant), highly activated genes, and long/super-long-range (10-129Mb), moderately repressed genes. Clustering ofEvf2transcriptionally regulated chr6 targets in populations whereEvf2is first activated supports thatEvf2-EGG transcriptional effects can occur from EGG shifts as far as 3Mb, uncoupling enhancer shift distance and transcriptional direction from transcriptional outcome.Evf2RNA binding sites (RBSs) divide chr6 into 4 major regions, consistent with a role for RBS chromosomal spacing in long-and super-long-range EGG selectivity. Surprisingly, 95% of 147 RBSs genome-wide potentially form inter-chromosomal DNA loops.Evf2-regulated combinatorial recruitment ofEvf2-ribonucleoproteins at EGGs and RBSs, together with effects on homeodomain transcription factor DNA motif recognition, support a novel model of lncRNA directed multi-modal EGG selectivity during intra- and inter-chromosomal gene regulation.
Price structure of traded honey, pollen and wax linked to winter survival of a honey bee colony
Authors: Kohli Mathieu
Published: February 2024

We consider the contribution of both honey and pollen to winter survival of a bee colony in order to assess how valuable both these commodities are from the bees’ perspective. In turn, this leads us to a method to help beekeepers evaluate the marketprice of honey and pollen.
C. elegansLIN-66 mediates EIF-3.G-dependent protein translation via a cold-shock domain
Authors: Blazie Stephen M. , Fortunati Daniel , Zhao Yan , Jin Yishi
Published: February 2024

Protein translation initiation is a complex and conserved process involving many proteins acting in concert. The eukaryotic initiation factor 3 (eIF3) complex is essential for the assembly of the pre-initiation complex that scans and positions mRNA at the initiation codon. eIF3 complex consists of 13 subunits. In addition to their essential roles in general translation initiation, emerging studies suggest that individual subunits of eIF3 can provide specialized functions in response to specific stimuli. We have previously reported that a gain-of-function (gf) mutation in the G subunit ofC. eleganseIF3 complex,eif-3.g(gf),selectively modulates protein translation in the ventral cord cholinergic motor neurons. Here, through unbiased genetic suppressor screening, we have identified thelin-66gene that mediates theeif-3.g(gf)-dependent protein translation in the motor neurons. LIN-66 is previously reported to be a nematode-specific protein composed of largely low complexity amino acid sequences with unknown functional domains. We combined bioinformatic analysis within vivofunctional dissection and identified a cold-shock domain in LIN-66 to be critical for its function. In the cholinergic motor neurons, LIN-66 shows somatic cytoplasmic localization and close association with EIF-3.G. The low complexity amino acid sequences of LIN-66 modulate its subcellular pattern. Cold-shock-domains are known to interact with RNA and have broad functions in RNA metabolism and protein translation. We propose that LIN-66 mediates stimuli-dependent protein translation by facilitating the interaction of mRNAs with EIF-3.G.
Effects of time-dependent ATP consumption caused by neuron firing on ATP concentrations in synaptic boutons containing and lacking a stationary mitochondrion
Authors: Kuznetsov Andrey V.
Published: February 2024

The precise mechanism behind the absence of a stationary mitochondrion in approximately half of presynaptic release sites in axons, and how these sites lacking a stationary mitochondrion receive ATP, is not fully understood. This paper presents a mathematical model designed to simulate the transient ATP concentration in presynapticen passantboutons. The model is utilized to investigate how the ATP concentration responds to increased ATP demand during neuronal firing in boutons with a stationary mitochondrion and those without one. The analysis suggests that neuron firing may cause oscillations in the ATP concentrations, with peak-to-peak amplitudes ranging from 0.06% to 5% of their average values. However, this does not deplete boutons lacking a mitochondrion of ATP; for physiologically relevant values of model parameters, their concentration remains approximately 3.75 times higher than the minimum concentration required for synaptic activity. The variance in average ATP concentrations between boutons containing a stationary mitochondrion and those lacking one ranges from 0.3% to 0.8%, contingent on the distance between the boutons. The model indicates that diffusion-driven ATP transport is rapid enough to adequately supply ATP molecules to boutons lacking a stationary mitochondrion.
Streptococcus pneumoniaeaugments circadian clock gene expression in zebrafish cells
Authors: Fénero Camila Morales , Sacksteder Raina E. , Kimmey Jacqueline M.
Published: February 2024

The circadian clock is a highly coordinated, cell-autonomous process that regulates the daily internal rhythms of biological organisms. Circadian clocks have been identified in various organisms, including mammals, invertebrates, cyanobacteria, and plants. The zebrafish (Danio rerio) is a practical model for studying the vertebrate circadian clock due to its small size, ease of manipulation, gene tractability, and direct light responsiveness. Several studies have revealed that bacterial, viral, and parasitic infections can impact the expression of circadian genes in mammals. While some evidence suggests that this may also be the case in zebrafish, no studies have investigated the direct effects of bacterial exposure on the zebrafish clock. Here, using zebrafish Z3 cells, we show that exposure to heat-killedStreptococcus pneumoniae(HK-Spn) can augment the expression of core repressive factors, includingper1b, per2, per3,andcry1a. Further investigation demonstrated that HK-Spn induces the production of reactive oxygen species (ROS) in Z3 cells and that the addition of NAC, a ROS antioxidant, blocks Spn-mediated induction ofper2,cry1a, andper3. Additionally, HK-Spn augmented the expression oftefaandtefb,an effect NAC suppressed. These results suggest the involvement of a ROS-dependent pathway in the augmentation ofper2,cry1a, and per3by HK-Spn. Moreover, the activation oftefaandtefbby HK-Spn represents promising new targets for further investigation of the regulation of these genes.
Testing the evolutionary potential of an alpine plant: Phenotypic plasticity in response to growth temperature far outweighs parental environmental effects and other genetic causes of variation
Authors: Arnold Pieter A. , Wang Shuo , Notarnicola Rocco F. , Nicotra Adrienne B. , Kruuk Loeske E. B.
Published: February 2024

Phenotypic plasticity and rapid evolution are fundamental processes by which organisms can maintain their function and fitness in the face of environmental changes. Here we quantified the plasticity and evolutionary potential of an alpine herbWahlenbergia ceracea. Utilising its mixed-mating system, we generated outcrossed and self-pollinated families that were grown in either cool or warm environments, and that had parents that had also been grown in either cool or warm environments. We then analysed the contribution of environmental and genetic factors to variation in a range of phenotypic traits including phenology, leaf mass per area, photosynthetic function, thermal tolerance, and reproductive fitness. The strongest effect was that of current growth temperature, indicating strong phenotypic plasticity. All traits except thermal tolerance were plastic, whereby warm-grown plants flowered earlier, grew larger, produced more reproductive stems compared to cool-grown plants. Flowering onset and biomass were heritable and under selection, with early flowering and larger plants having higher relative fitness. There was little evidence for transgenerational plasticity, maternal effects, or genotype-by-environment interactions. Inbreeding delayed flowering and reduced reproductive fitness and biomass. Overall, we found thatW. ceraceahas the capacity to respond rapidly to climate warming via plasticity, and the potential for evolutionary change.

Highlight

We found strong plasticity to growth environment in many phenotypic traits, but little effect of parental environment, revealing capacity to respond rapidly to climate warming, and potential for evolutionary change.
Augmentation of DNA exonuclease TREX1 in macrophages as a therapy for cardiac ischemic injury
Authors: Ibrahim Ahmed Gamal-Eldin , Ciullo Alessandra , Miyamoto Kazutaka , Liao Ke , Jones Xaviar M. , Yamaguchi Shukuro , Li Chang , Rannou Alice , Nawaz Asma , Morris Ashley , Tsi Kara , Marbán Cristina H. , Lee Jamie , Manriquez Nancy , Hong Yeojin , Kumar Arati Naveen , Dawkins James F. , Rogers Russell G. , Marbán Eduardo
Published: February 2024

Noncoding RNAs (ncRNAs) are increasingly recognized as bioactive. Here we report the development of TY1, a synthetic ncRNA bioinspired by a naturally-occurring human small Y RNA with immunomodulatory properties. TY1 upregulates TREX1, an exonuclease that rapidly degrades cytosolic DNA. In preclinical models of myocardial infarction (MI) induced by ischemia/reperfusion, TY1 reduced scar size. The cardioprotective effect of TY1 was abrogated by prior depletion of macrophages and mimicked by adoptive transfer of macrophages exposed either to TY1 or TREX1. Inhibition of TREX1 in macrophages blocked TY1 cardioprotection. Consistent with a central role for TREX1, TY1 attenuated DNA damage in the post-MI heart. This novel mechanism—pharmacologic upregulation of TREX1 in macrophages—establishes TY1 as the prototype for a new class of ncRNA drugs with disease-modifying bioactivity.

One Sentence Summary

Upregulation of three prime exonuclease, TREX1, in macrophages enhances tissue repair post myocardial infarction.
Sarcomeric SRX:DRX Equilibrium in Alport and LDLR/P407 Mouse Models of HFpEF
Authors: Kamiar Ali , Williams Monique , Capcha Jose M. , Kazmierczak Katarzyna , Liang Jingsheng , Lopaschuk Gary D. , Webster Keith A , Szczesna-Cordary Danuta , Shehadeh Lina A
Published: February 2024

Cardiac myosin energetic states that regulate heart contractility define interactions of myosin cross-bridges with actin-containing thin filaments have been functionally linked with the pathology of hypertrophic cardiomyopathy (HCM). In particular, the balance between the disordered relaxed (DRX) and super relaxed (SRX) states that correlate respectively with enhanced force and energy conservation significantly determine myocardial performance and energy utilization. Compelling evidence suggests that a balanced SRX and DRX states proportion is a prerequisite for long-term cardiac health. Whereas roles for altered SRX: DRX proportions in HCM have been studied in depth, the mechanics of sarcomeric dysfunction and SRX: DRX proportions have not been reported in models of acquired heart failure (HF) including HF with preserved ejection fraction (HFpEF). Here, we quantified SRX andDRX myosin populations in two mouse models of HFpEF, including Alport and LDLR/P407 mice that represent cardiorenal/hypertensive and cardiometabolic/hyperlipidemic mouse models of HFpEF, respectively. We report significant changes in the SRX:DRX in both HFpEF mouse models, with an increased DRX state associated with Alport mice and a stabilized SRX state associated with LDLR/P407 mice. These findings correlate respectively with the hypercontractility and metabolic dysregulation with bradycardia phenotypes.
Peptide Amphiphiles Hitchhike on Endogenous Biomolecules for Enhanced Cancer Imaging and Therapy
Authors: Fischer Jared M. , Stewart Morgan , Dai Mingchong , Drennan Samuel , Holland Samantha , Quentel Arnaud , Sabuncu Sinan , Kingston Benjamin R. , Dengos Isabel , Xiang Li , Bonic Karla , Goncalves Florian , Yi Xin , Ranganathan Srivathsan , Branchaud Bruce P. , Muldoon Leslie L. , Barajas Ramon F. , Yildirim Adem
Published: February 2024

The interactions of nanomaterials with biomolecules in vivo determine their biological fate. Here, we show that a self-assembled peptide amphiphile nanostructure (namely SA-E) dynamically interacts with endogenous biomolecules and takes advantage of naturally occurring processes to target a broad range of solid tumors. Upon in vivo administration, self-assembled nanostructures of SA-E disassemble and reassemble with lipoproteins in circulation. Hitchhiking on lipoproteins prolongs the blood circulation of SA-E and allows it to cross endothelial barriers through transcytosis. At the tumor site, SA-E internalizes into cancer cells by mainly interacting with lipid-raft domains on cell membranes. By exploiting these endogenous interactions, SA-E demonstrated high tumor accumulation with extended retention in various xenograft, syngeneic, patient-derived xenograft, or transgenic mouse and rat models. In addition, SA-E enabled the effective delivery of highly potent chemotherapy to breast and glioma tumors with reduced side effects. With its simple and modular design and universal tumor accumulation mechanism, SA-E represents a promising platform for broad applications in cancer imaging and therapy.
Plant Root Expansion Microscopy (ROOT-ExM): A streamlined super resolution method for plants
Authors: Grison Magali S. , Maucort Guillaume , Dumazel Amandine , Champelovier Dorian , Boutté Yohann , Fernández-Monreal Mónica , Bayer Emmanuelle M.
Published: February 2024

Expansion microscopy (ExM) has revolutionized biological imaging by physically enlarging samples, surpassing the light diffraction limit and enabling nanoscale visualization using standard microscopes. While extensively employed across a wide range of biological samples, its application to plant tissues is sparse. In this work, we present ROOT-ExM, an expansion method suited for stiff and intricate multicellular plant tissues, focusing on the primary root of Arabidopsis thaliana. ROOT-ExM achieves isotropic expansion with a fourfold increase in resolution, enabling super-resolution microscopy comparable to STimulated Emission Depletion (STED) microscopy. Labelling is achieved through immunolocalization, compartment-specific dyes, and native fluorescence preservation, while N-Hydroxysuccinimide (NHS) ester-dye conjugates reveal the ultrastructural context of cells alongside specific labelling. We successfully applied ROOT-ExM to image various cellular structures, including the Golgi apparatus, the endoplasmic reticulum, the cytoskeleton, and wall-embedded structures such as plasmodesmata. When combined with lattice light sheet microscopy (LLSM), ROOT-ExM achieves 3D quantitative analysis of nanoscale cellular process, revealing increased vesicular fusion in close proximity of the cell plate during cell division. Achieving super-resolution fluorescence imaging in plant biology remains a formidable challenge. Our findings underscore that ROOT-ExM provides a remarkable, cost-effective solution to this challenge, paving the way for unprecedented insights into plant cellular subcellular architecture.

One sentence summary

ROOT-ExM achieves super-resolution expansion microscopy in plants