bluuebunny/crossref_metadata_2025_split huggingface dataset:
Posttranscriptional tuning of gene expression over a large dynamic range in synthetic tobacco chloroplast operons
Authors: Yu Qiguo , Tungsuchat-Huang Tarinee , Ioannou Alexander , Barkan Alice , Maliga Pal 
Published: January 2024

ABSTRACTAchieving balanced gene expression within synthetic operons requires a spectrum of expression levels. Here we investigate the expression ofgfpreporter gene in tobacco chloroplasts, guided by variants of the plastidatpH5’ UTR, which harbors a binding site for PPR10, a protein that activatesatpHat the post-transcriptional level. Our findings reveal that endogenous tobacco PPR10 confers distinct levels of reporter activation when coupled with the tobacco and maizeatpH5’ UTRs in different design contexts. Notably, high GFP expression was not coupled to stabilization of monocistronicgfptranscripts in dicistronic reporter lines, adding to the evidence that PPR10 activates translation via a mechanism that is independent of its stabilization of monocistronic transcripts. Furthermore, the incorporation of a tRNA upstream of the UTR nearly abolishesgfpmRNA (and GFP protein), resulting in a substantial reduction in GFP accumulation. When combined with a mutantatpH5’ UTR, the tRNA leads to an exceptionally low level of transgene expression. Collectively, this approach allows for tuning reporter gene expression across a wide range, spanning from 0.02% to 25% of the total soluble cellular protein (TSP). These findings highlight the toolbox available for plastid synthetic biology applications requiring multigene expression at varying levels.
Cell envelope structural and functional contributions to antibiotic resistance inBurkholderia cenocepacia
Authors: Hogan Andrew M , Motnenko Anna , Rahman A S M Zisanur , Cardona Silvia T 
Published: January 2024

AbstractAntibiotic activity is limited by the physical construction of the Gram-negative cell envelope. Species of theBurkholderia cepaciacomplex (Bcc) are known as intrinsically multidrug-resistant opportunistic pathogens with low permeability cell envelopes. Here, we re-examined a previously performed chemical-genetic screen of barcoded transposon mutants inB. cenocepaciaK56-2, focusing on cell envelope structural and functional processes. We identified structures mechanistically important for resistance to singular and multiple antibiotic classes. For example, the polymeric O-antigen was important for resistance to cationic antibiotics, while defects in peptidoglycan precursor synthesis specifically increased susceptibility to cycloserine and revealed a new putative amino acid racemase. Susceptibility to novobiocin, avibactam, and the LpxC inhibitor, PF-04753299, was linked to the BpeAB-OprB efflux pump, suggesting these drugs are substrates for this pump inB. cenocepacia. Additionally, disruption of the periplasmic disulfide bond formation system caused pleiotropic defects on outer membrane integrity and β-lactamase activity. Our findings highlight the layering of resistance mechanisms in the structure and function of the cell envelope. Consequently, we point out processes that can be targeted for developing antibiotic potentiators.ImportanceThe Gram-negative cell envelope is a double-layered physical barrier that protects cells from extracellular stressors, such as antibiotics. TheBurkholderiacell envelope is known to contain additional modifications that reduce permeability. We investigatedBurkholderiacell envelope factors contributing to antibiotic resistance from a genome-wide view by re-examining data from a transposon mutant library exposed to an antibiotic panel. We identified susceptible phenotypes for defects in structures and functions in the outer membrane, periplasm, and cytoplasm. Overall, we show that resistance linked to the cell envelope is multifaceted and provides new targets for the development of antibiotic potentiators.
Hippocampus oxytocin signaling promotes prosocial eating in rats
Authors: Rea Jessica J. , Liu Clarissa M. , Hayes Anna M.R. , Bashaw Alexander G. , Schwartz Grace , Ohan Rita , Décarie-Spain Léa , Kao Alicia E. , Klug Molly E. , Phung Kenneth J. , Waldow Alice I. , Wood Ruth I. , Kanoski Scott E. 
Published: January 2024

ABSTRACTThe hypothalamic neuropeptide oxytocin (OT) influences both food intake and social behavior. Given that food preference and consumption are heavily affected by social factors in mammals, it is critical to understand the extent that OT’s role in regulating these two fundamental behaviors is interconnected. Here we evaluated the role of OT signaling in the dentate gyrus of the dorsal hippocampus (HPCd), a brain region recently linked with eating and social memory, on food preference and consumption in rats under conditions that vary with regards to social presence and conspecific familiarity. Results from neuropharmacological and virogenetic knockdown approaches reveal that HPCd OT signaling promotes eating in the presence of a familiar but not an unfamiliar conspecific. Additionally, HPCd OT receptor signaling is required for the social transmission of food preference. These findings collectively identify the HPCd as a novel substrate where oxytocin synergistically influences eating and social behaviors.
Single-cell transcriptional dynamics in a living vertebrate
Authors: Eck Elizabeth , Moretti Bruno , Schlomann Brandon H. , Bragantini Jordão , Lange Merlin , Zhao Xiang , VijayKumar Shruthi , Valentin Guillaume , Loureiro Cristina , Soroldoni Daniele , Royer Loïc A. , Oates Andrew C. , Garcia Hernan G. 
Published: January 2024

AbstractThe ability to quantify transcriptional dynamics in individual cells via live imaging has revolutionized our understanding of gene regulation. However, such measurements are lacking in the context of vertebrate embryos. We addressed this deficit by applying MS2-MCP mRNA labeling to the quantification of transcription in zebrafish, a model vertebrate. We developed a platform of transgenic organisms, light sheet fluorescence microscopy, and optimized image analysis that enables visualization and quantification of MS2 reporters. We used these tools to obtain the first single-cell, real-time measurements of transcriptional dynamics of the segmentation clock. Our measurements challenge the traditional view of smooth clock oscillations and instead suggest a model of discrete transcriptional bursts that are organized in space and time. Together, these results highlight how measuring single-cell transcriptional activity can reveal unexpected features of gene regulation and how this data can fuel the dialogue between theory and experiment.
Human cytomegalovirus deploys molecular mimicry to recruit VPS4A to sites of virus assembly
Authors: Butt Benjamin G. , Fischer Daniela , Rep Alison R. , Schauflinger Martin , Read Clarissa , Böck Thomas , Hirner Manuel , Graham Stephen C. , von Einem Jens 
Published: January 2024

AbstractThe AAA-type ATPase VPS4 is recruited by proteins of the endosomal sorting complex required for transport III (ESCRT-III) to catalyse membrane constriction and membrane fission. VPS4A accumulates at the cytoplasmic viral assembly complex (cVAC) of cells infected with human cytomegalovirus (HCMV), the site where nascent virus particles obtain their membrane envelope. Here we show that VPS4A is recruited to the cVAC via interaction with pUL71. Sequence analysis, deep-learning structure prediction, molecular dynamics and mutagenic analysis identify a short peptide motif in the C-terminal region of pUL71 that is necessary and sufficient for the interaction with VPS4A. This motif is predicted to bind the same groove of the N-terminal VPS4A Microtubule-Interacting and Trafficking (MIT) domain as the Type 2 MIT-Interacting Motif (MIM2) of cellular ESCRT-III components, and this viral MIM2-like motif (vMIM2) is conserved across β-herpesvirus pUL71 homologues. However, recruitment of VPS4A by pUL71 is dispensable for HCMV morphogenesis or replication and the function of the conserved vMIM2 during infection remains enigmatic. VPS4-recruitment via a vMIM2 represents a previously unknown mechanism of molecular mimicry in viruses, extending previous observations that herpesviruses encode proteins with structural and functional homology to cellular ESCRT-III components.
CDC5L surveils cellular stress responses and stress granule formation through transcriptional repression
Authors: Qian Beituo , Li Shunyi , Duan Yongjia , Qiu Feng , Hu Rirong , Yue Wenkai , Cui Jihong , Wang Qiangqiang , Li Wanjin , Fang Yanshan 
Published: January 2024

ABSTRACTCells have evolved a variety of mechanisms to respond to stress, such as activating the PERK– eIF2α pathway and forming stress granules (SGs). It is important that these mechanisms are inducted only when necessary and exerted at appropriate levels, to prevent spontaneous or excessive activation of stress responses. However, the mechanisms by which cells keep the stress response programs in check are elusive. In this study, we discovered that downregulation ofCell Division Cycle 5 Like(CDC5L) causes spontaneous SG formation in the absence of any stress, which is independent of its known functions in the cell cycle or the PRP19 complex. Instead, we found that CDC5L binds to thePERKpromoter through its DNA-binding domains and repressesPERKmRNA transcription. As a result, it negatively regulates the abundance of PERK protein and the phosphorylation levels of eIF2α, thereby suppressing the PERK–eIF2α signaling pathway and preventing undesirable SG assembly. Further RNA-sequencing (seq) and chromatin immunoprecipitation (ChIP)-seq analyses reveal a dual function of CDC5L in gene transcription: it acts as a transcriptional activator in cell cycle control but as a repressor in cellular stress responses. Finally, we show that the loss ofCDC5Ldecreases cell viability and fly survival under mild stress conditions. Together, our findings demonstrate a previously unknown role and mechanism of CDC5L in the surveillance of cellular stress through transcriptional repression, which serves as a gatekeeper for the stress response programs such as the PERK–eIF2α pathway and SG formation.Significance statementCells need to respond to stress promptly for survival. Meanwhile, it is equally important to prevent spontaneous or excessive activation of stress response programs when no stress or only minor stress is present. Here, we reveal that the DNA/RNA-binding protein CDC5L represses the transcription of a cluster of stress response genes includingPERK. In doing so, CDC5L suppresses the PERK-eIF2α pathway and prevents spontaneous SG assembly. Downregulation ofCDC5Lreleases the restraint on these genes, resulting in an exaggerated response to stress and decreased viability in both cell and fly models. Taken together, this study demonstrates the existence of a gatekeeper mechanism that surveils the stress response programs and highlights the crucial role of CDC5L-mediated transcriptional repression in this regulation.
Age differences in functional connectivity track dedifferentiation of category representations
Authors: Pauley Claire , Zeithamova Dagmar , Sander Myriam C. 
Published: January 2024

AbstractWith advancing age, the distinctiveness of neural representations of information declines. While the finding of this so-called ‘age-related neural dedifferentiation’ in category-selective neural regions is well-described, the contribution of age-related changes in network organization to dedifferentiation is unknown. Here, we asked whether age differences in a) whole-brain network segregation (i.e., network dedifferentiation) and b) functional connectivity to category-selective neural regions are related to regional dedifferentiation of categorical representations. Younger and older adults viewed blocks of face and house stimuli in the fMRI scanner. We found an age-related decline in neural distinctiveness for faces in the fusiform gyrus (FG) and for houses in the parahippocampal gyrus (PHG). Functional connectivity analyses revealed age-related dedifferentiation of global network structure as well as age differences in connectivity between the FG and early visual cortices. Interindividual correlations demonstrated that regional distinctiveness was related to network segregation. Together, our findings suggest that dedifferentiation of categorical representations may be linked to age-related reorganization of functional networks.HighlightsCategory representations are less distinctive, or dedifferentiated, in older adultsHere, we linked age differences in functional connectivity to dedifferentiationAge-related declines in network segregation were linked to dedifferentiation
NeoCOMM: A Neocortical Neuroinspired Computational Model for the Reconstruction and Simulation of Epileptiform Events
Authors: Al Harrach Mariam , Yochum Maxime , Ruffini Giulio , Bartolomei Fabrice , Benquet Pascal , Wendling Fabrice 
Published: January 2024

AbstractUnderstanding the pathophysiological dynamics which underline interictal epileptiform events (IEEs) such as epileptic spikes, spike-and-waves or High-frequency oscillations (HFOs) is of major importance in the context of neocortical refractory epilepsy, as it paves the way for the development of novel therapies. Typically, these events are detected in local field potential (LFP) recordings obtained through depth electrodes during pre-surgical investigations. Although essential, the underlying pathophysiological mechanisms for the generation of these epileptic neuromarkers remain unclear. The aim of this paper is to propose a novel neurophysiologically relevant reconstruction of the neocortical microcircuitry in the context of epilepsy. This reconstruction intends to facilitate the analysis of a comprehensive set of parameters encompassing physiological, morphological, and biophysical aspects that directly impact the generation and recording of different IEEs. Accordingly, a novel microscale computational model of an epileptic neocortical column was introduced. This model incorporates the intricate multilayered structure of the cortex and allows for the simulation of realistic interictal epileptic signals. The proposed model was validated through comparisons with real IEEs recorded using intracranial stereo-electroencephalography (SEEG) signals from both humans and animals. Using the model, the user can recreate epileptiform patterns observed in different species (human, rodent, and mouse) and study the intracellular activity associated with these patterns. Our model allowed us to unravel the relationship between glutamatergic and GABAergic synaptic transmission of the epileptic neural network and the type of generated IEE. Moreover, sensitivity analyses allowed for the exploration of the pathophysiological parameters responsible for the transitions between these events. Finally, the presented modeling framework also provides an Electrode Tissue Model (ETI) that adds realism to the simulated signals and offers the possibility of studying their sensitivity to the electrode characteristics. The model (NeoCoMM) presented in this work can be of great use in different applications since it offers anin silicoframework for sensitivity analysis and hypothesis testing. It can also be used as a starting point for more complex studies.
The intrinsically disordered N-terminus of SUMO1 is an intramolecular inhibitor of SUMO1 interactions
Authors: Richter Sebastian M. , Jin Fan , Ritterhoff Tobias , Fergin Aleksandra , Maurer Eric , Frank Andrea , Daube Michael , Hajnal Alex , Klevit Rachel , Gräter Frauke , Flotho Annette , Melchior Frauke 
Published: January 2024

SUMMARYUbiquitin-related proteins of the SUMO family are reversibly attached to thousands of proteins in eukaryotic cells. Many SUMO substrates, effectors and enzymes carry short motifs (SIMs) that mediate low affinity interactions with SUMO proteins. How specificity is achieved in target selection, SUMO paralogue choice and SUMO-dependent interactions is largely unknown. A unique but poorly understood feature of SUMO proteins is their intrinsically disordered N-terminus. We reveal a function for N-termini of human,C. elegans,and yeast SUMO proteins as intramolecular inhibitors of SUMO- SIM interactions. Mutational analyses, NMR spectroscopy, and Molecular Dynamics simulations indicate that SUMO’s N-terminus can inhibit SIM binding by fast and fuzzy interactions with SUMO‘s core. Deletion of theC. elegansSUMO1 N-terminus leads to p53-dependent apoptosis during germline development, indicating an important role in DNA damage repair. Our findings reveal a mechanism of disorder-based autoinhibition that contributes to the specificity of SUMOylation and SUMO-dependent interactions.
Behavioural Investigations of Psilocybin in Animals 1962-2021: A Scoping Review
Authors: Shore Ron , Dobson Kat , Thomson Nina , Barnim Nigel , Bergman Hailey , Rideout Katie , McKeown Sandra , Olmstead Mary C. , Goldie Craig , Dumont Eric 
Published: January 2024

AbstractBackground and AimsPsilocybin is a psychedelic drug that may hold promise for a wide range of human health conditions, yet the identification of therapeutic processes and mechanisms of action remains exploratory. We conducted a scoping review on pre-clinical behavioural investigations of psilocybin in non-human animals to help determine the behavioural effects of psilocybin in non-human animals, to identify studies completed, behavioural tests employed, and what dosing modalities had been studied.MethodsA librarian-conducted literature search was performed using predefined key terms and search criteria and additional searching was conducted by reviewers, using electronic databases, grey literature sources, and reference lists of relevant articles or reviews. The final search updated occurred in October, 2021. Studies were reviewed, screened and selected against an a priori protocol using Covidence software by multiple reviewers with results plotted across the Research Domains Criteria construct.ResultsFrom 4124 records identified by database searching, 260 publications were subjected to full-text review with 77 studies included in this scoping review, published between 1962-2021. The preponderance of studies (n=64) investigated behavioural outcomes in rodents. Only 43 studies (55.8%) reported on housing conditions, and seventeen studies (22.1%) failed to report sample size. All studies reported behavioural outcomes following drug administration, with fifty-one studies (66.2%) using psilocybin, thirty studies (42.9%) psilocin, four studies (5.2%) administering whole mushroom extracts (WME), and a further eight studies investigating both psilocybin and psilocin and one study reporting the effects of both psilocin and WME. One hundred and thirty distinct behavioural investigations using fifty different behavioral paradigms were identified. Few adverse events were reported, and even exceedingly high doses were apparently well tolerated.ConclusionWith seventy-seven publications spanning close to sixty years, there is huge variation in study design and quality. Overall psilocybin presents a unique and strong safety profile with no evidence of biological toxicity, is characterized by unique time and dose-dependent effects, and its pattern of drug action is significantly context and training-sensitive. Data suggest putative effects of psilocybin include acute arousal, dose-dependent sedation, reductions in fear conditioning at low doses, reduced aggression, improved valence, acute disruption of working memory, the rescuing of deficits from chronic stress, and improved learning when combined with repeated environmental exposure after resolution of drug effect.
Revisiting soil fungal biomarkers and conversion factors: Interspecific variability in phospholipid fatty acids, ergosterol and rDNA copy numbers
Authors: Camenzind T , Haslwimmer H , Rillig MC , Ruess L , Finn DR , Tebbe CC , Hempel S , Marhan S 
Published: January 2024

AbstractThe abundances of fungi and bacteria in soil are used as simple predictors for carbon dynamics, and represent widely available microbial traits. Soil biomarkers serve as quantitative estimates of these microbial groups, though not quantifying microbial biomass per se. The accurate conversion to microbial carbon pools, and an understanding of its comparability among soils is therefore needed. We refined conversion factors for classical fungal biomarkers, and evaluated the application of quantitative PCR (qPCR, rDNA copies) as a biomarker for soil fungi. Based on biomarker contents in pure fungal cultures of 30 isolates, combined with available references, we propose average conversion factors of 95.3 g fungal C g−1ergosterol, 32.0 mg fungal C µmol−1PLFA 18:2ω6,9 and 0.264 pg fungal C ITS1 DNA copy−1. As expected, interspecific variability was most pronounced in rDNA copies, though qPCR results showed the least phylogenetic bias. A modeling approach based on exemplary agricultural soils further supported the hypothesis that high diversity in soil buffers against biomarker variability, whereas also phylogenetic biases impact the accuracy of comparisons in biomarker estimates. Our analyses suggest that qPCR results cover the fungal community in soil best, though with a variability only partly offset in highly diverse soils. PLFA 18:2ω6,9 and ergosterol represent accurate biomarkers to quantify Ascomycota and Basidiomycota. To conclude, the ecological interpretation and coverage of biomarker data prior to their application in global models is important, where the combination of different biomarkers may be most insightful.
Clusters of lineage-specific genes are anchored by ZNF274 in repressive perinucleolar compartments
Authors: Begnis Martina , Duc Julien , Offner Sandra , Grun Delphine , Sheppard Shaoline , Rosspopoff Olga , Trono Didier 
Published: January 2024

ABSTRACTLong known as the site of ribosome biogenesis, the nucleolus is increasingly recognized for its role in shaping 3D genome organization. Still, the mechanisms governing the targeting of selected regions of the genome to nucleolus-associated domains (NADs) remain enigmatic. Here we reveal the essential role of ZNF274, a SCAN-bearing member of the Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFP) family, in sequestering lineage-specific gene clusters within NADs. Ablation of ZNF274 triggers transcriptional activation across entire genomic neighborhoods – encompassing, among others, protocadherin and KZFP-encoding genes – with loss of repressive chromatin marks, altered 3D genome architecture andde novoCTCF binding. Mechanistically, ZNF274 anchors target DNA sequences at the nucleolus and facilitates their compartmentalization via a previously uncharted function of the SCAN domain. Our findings illuminate the mechanisms underlying NADs organization and suggest that perinucleolar entrapment into repressive hubs constrains the activation of tandemly arrayed genes to enable selective expression and modulate cell differentiation programs during development.