bluuebunny/crossref_metadata_2025_split huggingface dataset:
Context-dependent acetylation of the virulence regulator PhoP accounts for carbon-source specific intracellular growth program ofMycobacterium tuberculosis
Authors: Paul Partha , Mehta Khushboo , Ujjainiya Rajat , Bamniya Bhanwar , Thakur Bhuwaneshwar , Goar Harsh , Sarkar Dibyendu 
Published: January 2024

ABSTRACTMycobacterium tuberculosisPhoP is essential for intracellular survival and virulence of the tubercle bacilli. Genetic evidences coupled with biochemical studies uncover that PhoP affects various aspects ofM. tuberculosispathophysiology including pH sensing during intracellular adaptation and carbon source utilization. Building on this observation, herein we report essentiality of thephoPlocus in carbon-source specific mycobacterial growth. Further, our results on mycobacterial growth in the presence of different carbon sources suggest accumulation of acetyl CoA, a metabolic intermediate which acetylates major transcription factors. To explore the mechanism, we examinedin vivoacetylation of PhoP, and our results suggest a link between acetylation of PhoP and mycobacterial carbon source utilization. Using a genetic screening, we identified PhoP-specific mycobacterial acetylases. Our two major findings that (a) acidic conditions of growth inhibit PhoP acetylation, which represses PhoP regulon by interfering with DNA binding activity of the regulator and (b) mycobacteria expressing acetylation-defective PhoP shows growth inhibition, together suggest a role of acetylation on mycobacterial growth via carbon-source utilization. These results have implications on intracellular survival and growth program of mycobacteria under varying environmental cues.
Chikungunya Virus Release is Reduced by TIM-1 Receptors Through Binding of Envelope Phosphatidylserine
Authors: Reyes Ballista Judith M. , Hoover Ashley J. , Noble Joseph T. , Acciani Marissa D. , Miazgowicz Kerri L. , Harrison Sarah A. , Tabscott Grace Andrea L. , Duncan Avery , Barnes Don N. , Jimenez Ariana R. , Brindley Melinda A. 
Published: January 2024

AbstractT-cell immunoglobin and mucin domain protein-1 (TIM-1) mediates entry of Chikungunya virus (CHIKV) into some mammalian cells through the interaction with envelope phospholipids. While this interaction enhances entry, TIM has been shown to tether newly formed HIV and Ebola virus particles, limiting their efficient release. In this study, we investigate the ability of surface receptors such as TIM-1 to sequester newly budded virions on the surface of infected cells. We established a luminescence reporter system to produce Chikungunya viral particles that integrate nano-luciferase and easily quantify viral particles. We found that TIM-1 on the surface of host cells significantly reduced CHIKV release efficiency in comparison to other entry factors. Removal of cell surface TIM-1 through direct cellular knock-out or altering the cellular lipid distribution enhanced CHIKV release. Over the course of infection, CHIKV was able to counteract the tethering effect by gradually decreasing the surface levels of TIM-1 in a process that appears to be mediated by the nonstructural protein 2. This study highlights the importance of phosphatidylserine receptors in mediating not only the entry of CHIKV but also its release and could aid in developing cell lines capable of enhanced vaccine production.ImportanceChikungunya virus (CHIKV) is an enveloped alphavirus transmitted by the bites of infectious mosquitoes. Infection with CHIKV results in the development of fever, joint pain, and arthralgia that can become chronic and last for months after infection. Prevention of this disease is still highly focused on vector control strategies. In December 2023, a new live attenuated vaccine against CHIKV was approved by the FDA. We aimed to study the cellular factors involved in CHIKV egress, to better understand CHIKV’s ability to efficiently infect and spread among a wide variety of cell lines. We found that TIM-1 receptors can significantly abrogate CHIKV’s ability to efficiently exit infected cells. This information can be beneficial for maximizing viral particle production in laboratory settings and during vaccine manufacturing.
An experimental census of retrons for DNA production and genome editing
Authors: Khan Asim G. , Rojas-Montero Matías , González-Delgado Alejandro , Lopez Santiago C. , Fang Rebecca F. , Shipman Seth L. 
Published: January 2024

ABSTRACTRetrons are bacterial immune systems that use reverse transcribed DNA as a detector of phage infection. They are also increasingly deployed as a component of biotechnology. For genome editing, for instance, retrons are modified so that the reverse transcribed DNA (RT-DNA) encodes an editing donor. Retrons are commonly found in bacterial genomes; thousands of unique retrons have now been predicted bioinformatically. However, only a small number have been characterized experimentally. Here, we add substantially to the corpus of experimentally studied retrons. We synthesized >100 previously untested retrons to identify the natural sequence of RT-DNA they produce, quantify their RT-DNA production, and test the relative efficacy of editing using retron-derived donors to edit bacterial genomes, phage genomes, and human genomes. We add 62 new empirically determined, natural RT-DNAs, which are not predictable from the retron sequence alone. We report a large diversity in RT-DNA production and editing rates across retrons, finding that top performing editors outperform those used in previous studies, and are drawn from a subset of the retron phylogeny.
Analysis of Methicillin Resistance inStaphylococcus AureusSepsis Using TDbasedUFE
Authors: Watanabe S. , Taguchi Y-h. 
Published: January 2024

ABSTRACTscATAC-seq explains chromatin accessibility at cell-type resolution. Accordingly, this process is crucial for advancing our understanding of pathology and disease states. However, annotated data from scATAC-seq are both extensive and sparse; thus, conducting multidimensional analyses under multiple conditions is a challenging task. TDbasedUFE is a valuable tool for analyzing scATAC-seq data as it can extract genes in an unsupervised manner under multiple conditions based on tensor decomposition. We analyzed scATAC-seq data from the peripheral blood mononuclear cells of patients with sepsis infected withS. aureususing TDbasedUFE.We extracted genes that exhibited different responses in methicillin-resistant (MSSA) and methicillin-sensitiveS. aureus(MSSA) strains in sepsis for each cell type. Subsequently, we searched for studies containing gene sets similar to the extracted genes and predicted their functions. We also constructed protein-protein interactions (PPIs) for the extracted genes, defined hub proteins as central to the interactions based on degrees and clustering coefficients, and investigated the functions of these hub proteins. The genes of interest were abundant across all cell types, ranging from 710 to 1,372 genes. The functions of the extracted genes were predicted to be associated with several diseases or physiological substances. The hub proteins identified from the PPI analysis were mainly related to the ribosome, and their functions were associated with protein synthesis. These results highlight the suitability of TDbasedUFE for the analysis of scATAC-seq data. The functions of the genes identified in this study may provide insights into new promising therapeutic approaches, considering the distinction between methicillin resistance andS. aureussepsis.
Exploring the changing association between parental and adolescent fruit and vegetable intakes, from age 10 to 30 years
Authors: Braune Tanya , Adams Prof Jean , Winpenny Dr Eleanor M. 
Published: January 2024

AbstractBackgroundAdolescence is a pivotal developmental stage, where escalating rates of overweight and obesity have raised concerns about diet quality and its association with adverse health outcomes. Parents are known to have considerable influence on childhood diet, but how this influence changes as adolescents mature is unknown. This study investigates the association between parental fruit and vegetable (FV) intake and adolescent FV consumption, exploring how this changes across adolescence and when children leave home.MethodsAdolescents aged 10-30 years (n=12,805) from the UK Household Longitudinal Study (UKHLS), and their parents, reported FV intakes every 2 years. Multilevel linear regression models were fitted to assess associations between parental and adolescent FV intakes, investigating interactions with age and living arrangement, and adjusting for sociodemographic covariates.ResultsParental FV intake was positively associated with adolescent FV intake (β=0.20 [95%CI:0.19,0.22] portions/day), with the strength of this association lowest during early adolescence (10-14 years) and peaking at 17-18 years (β=0.30 [95%CI: 0.27,0.33] portions/day). When adolescents no longer lived in the parental home, the association of parental FV intake with their own FV consumption decreased, but a positive association was maintained up to age 30 years.ConclusionsOur findings emphasise the enduring effect of parental modelling on dietary choices, highlighting the potential for interventions to promote increased FV intake, acknowledging the lasting influence of parental diet, even beyond the confines of the parental home.
Induction of NASH in theNwd1−/−mouse liver via SERCA2-dependent endoplasmic reticulum stress
Authors: Yamada Seiya , Nakadate Kazuhiko , Mizukoshi Tomoya , Kawakami Kiyoharu , Kobayashi Ryosuke , Horii Takuro , Hatada Izuho , Sakakibara Shin-ichi 
Published: January 2024

AbstractThe endoplasmic reticulum (ER) stores Ca2+and plays crucial roles in protein folding, lipid transfer, and it’s perturbations trigger an ER stress. In the liver, chronic ER stress is involved in the pathogenesis of nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH). Previous studies revealed that dysfunction of sarco/endoplasmic reticulum calcium ATPase (SERCA2), a key regulator of Ca2+transport from the cytosol to the ER, is associated with the induction of ER stress and lipid droplet formation. We previously identified NACHT and WD repeat domain-containing protein 1 (Nwd1), which is localized in the ER and mitochondria. However, the physiological significance of Nwd1 outside the central nervous system remains unclear. In this study, we revealed thatNwd1knockout mice exhibited pathological manifestations comparable to NASH. Nwd1 interacts with SERCA2 near ER membranes.Nwd1−/−livers exhibited reduced SERCA2 ATPase activity and a smaller Ca2+pool in the ER, leading to an exacerbated state of ER stress. These findings highlight the importance of SERCA2 activity mediated by Nwd1 in the pathogenesis of NASH.HighlightsNwd1−/−mice exhibited NASH-like liver steatosis.Elevated ER stress, fibrosis, and pyroptosis were observed inNwd1−/−livers.Nwd1 interacts with SERCA2, an ER membrane Ca2+ pump.Nwd1−/−livers exhibited reduced SERCA2 activity and smaller Ca2+ pools in the ER.
An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion inSaccharomyces cerevisiae
Authors: Ridenour John B. , Donczew Rafal 
Published: January 2024

ABSTRACTAccurate regulation of gene transcription by RNA polymerase II is essential for the growth and development of eukaryotic cells. Although significant progress has been made in understanding the mechanisms that regulate transcription, many questions remain unanswered. Defining the direct effects of transcriptional regulators is critically important to answering these questions. An effective approach for identifying the direct targets of transcriptional regulators is combining rapid protein depletion and quantification of newly transcribed RNA. The auxin-inducible degron (AID) system and thiol (SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) are powerful methods to rapidly degrade a target protein and directly quantify newly transcribed RNA, respectively. Both methods have been widely applied to study transcriptional regulation. To address unresolved questions in transcription, we engineered an end-to-end workflow inSaccharomyces cerevisiaeto deplete proteins of interest using the AID system and measure newly transcribed RNA using SLAM-seq. We provide a step-by-step protocol to support rapid implementation and demonstrate that the workflow can help define the direct effects of transcriptional regulators using the BET proteins Bdf1 and Bdf2 as a test case. This workflow will help address outstanding questions underlying the molecular basis of transcription and other biological processes inS. cerevisiaeand other systems.
Synthetic integrin antibodies discovered by yeast display reveal αV subunit pairing preferences with β subunits
Authors: Hao Yuxin , Yan Jiabin , Fraser Courtney , Jiang Aiping , Anuganti Murali , Zhang Roushu , Lloyd Kenneth , Jardine Joseph , Coppola Jessica , Meijers Rob , Li Jing , Springer Timothy A. 
Published: January 2024

AbstractEight of the 24 integrin heterodimers bind to the tripeptide Arg-Gly-Asp (RGD) motif in their extracellular ligands, and play essential roles in cell adhesion, migration, and homeostasis. Despite similarity in recognizing the RGD motif and some redundancy, these integrins can selectively recognize RGD-containing ligands including fibronectin, vitronectin, fibrinogen, nephronectin and the prodomain of the transforming growth factors to fulfill specific functions in cellular processes. Subtype-specific antibodies against RGD-binding integrins are desirable for investigating their specific functions. In this study, we discovered 11 antibodies that exhibit high specificity and affinity towards integrins αVβ3, αVβ5, αVβ6, αVβ8, and α5β1 from a synthetic yeast-displayed Fab library. Of these, 6 are function-blocking antibodies containing an R(G/L/T) D motif in their CDR3 sequences. We report antibody binding specificity, kinetics, and binding affinity for purified integrin ectodomains as well as intact integrins on the cell surface. We further employed these antibodies to reveal binding preferences of the αV subunit for its 5 β-subunit partners: β6=β8>β3>β1=β5.
Zebrafish live imaging reveals a surprisingly small percentage of spinal cord motor neurons die during early development
Authors: Jia Hao , Yang Hongmei , Luo Kathy Qian 
Published: January 2024

AbstractIt is widely accepted that large numbers of neurons die during the early development of vertebrates; however, the tracking of this dying process in live animals remains challenging. Here, we generated sensor zebrafish achieving live imaging of motor neuron apoptosis at single- cell resolution. Using these sensor zebrafish, we observed for the first time that in an apoptotic motor neuron, caspase-3 activation occurred quickly within 5-6 min and at the same time between the cell body and axon. Interestingly, we found that only a surprisingly small percentage of spinal cord motor neurons died during zebrafish early development, which is quite different from the generally believed massive motor neuron death occurred in the embryonic stage of chicks, mice, rats, and humans. We also observed that most of the apoptotic bodies of dead motor neurons were not colocalized with macrophages. These sensor zebrafish can serve as powerful tools to study motor neuron apoptosisin vivo.
“From Nutritional Patterns to Behavior: High-Fat Diet Influences on Inhibitory Control, Brain Gene Expression and Metabolomics in Rats”
Authors: Ruiz-Sobremazas Diego , Abreu Ana Cristina , Prados-Pardo Ángeles , Martín-González Elena , Isabel Tristán Ana , Fernández Ignacio , Moreno Margarita , Mora Santiago 
Published: January 2024

AbstractBackgroundImpulsive and compulsive behaviors are associated with inhibitory control deficits. Diet plays a pivotal role in normal development, impacting both physiology and behavior. However, the specific effects of high-fat diets (HFD) on inhibitory control have not received adequate attention.ObjectivesThis study aimed to explore how exposure to an HFD from postnatal day (PND) 33 to PND77 affects impulsive and compulsive behaviors.MethodsThe experiment involved 40 Wistar rats, half of which were male and subjected to the HFD or Chow diets. Several tasks were employed to assess behavior, including the Variable Delay to Signal (VDS), the Five Choice Serial Reaction Time Task (5-CSRTT), the Delay Discounting Task (DDT), and the Rodent Gambling Task (rGT). Genetic analyses were performed on the frontal cortex, and metabolomics and fatty acid profiles were examined using stool samples collected on PND298.ResultsThe study revealed that rats exposed to the HFD exhibited heightened impulsivity in the VDS and in the 5-CSRTT, suggesting an increase in motor impulsivity. Notably, no significant effect was observed in the DDT. Surprisingly, the HFD-exposed group demonstrated reduced levels of impulsive-like behaviors, and a different decision making, in the rGT. Furthermore, abnormal gene regultation linked to brain plasticity and dopamine were identified in the frontal cortex. Metabolomics analysis of stool samples, collected in adulthood, indicated lower levels of fatty acids.DiscussionThese results suggest that HFD exposure during adolescence may create a lasting vulnerability to inhibitory control deficits, specifically in terms of motor impulsivity, and in gene expression as well as in metabolomics profile.
FBM: Freestanding bilayer microscope for single-molecule imaging of membrane proteins
Authors: Pérez-Mitta Gonzalo , Sezgin Yeliz , Wang Weiwei , MacKinnon Roderick 
Published: January 2024

AbstractIntegral membrane proteins (IMPs) constitute a large fraction of organismal proteomes, playing fundamental roles in physiology and disease. Despite their importance, the mechanisms underlying dynamic features of IMPs, such as anomalous diffusion, protein-protein interactions, and protein clustering, remain largely unknown due to the high complexity of cell membrane environments. Available methods forin vitrostudies are insufficient to study IMP dynamics systematically. This publication introduces the Freestanding-Bilayer Microscope (FBM), which combines the advantages of freestanding bilayers with single-particle tracking. The FBM, based on planar lipid bilayers, enables the study of IMP dynamics with single-molecule resolution and unconstrained diffusion. This paper benchmarks the FBM against total internal reflection fluorescence (TIRF) imaging on supported bilayers and is used here to estimate ion channel open probability and to examine the diffusion behavior of an ion channel in phase- separated bilayers. The FBM emerges as a powerful tool to examine membrane protein/lipid organization and dynamics to understand cell membrane processes.
Artificial Sweeteners in US-Marketed Oral Nicotine Pouch Products: Correlation with Nicotine Contents and Effects on Product Preference
Authors: Jabba Sairam V. , Silinski Peter , Yang Alicia Y. , Ouyang Wenyi , Jordt Sven E. 
Published: January 2024

AbstractIntroductionArtificial sweeteners are listed as ingredients of oral nicotine pouches (ONPs), a new product category with rapidly growing market share. The exact sweetener contents of ONPs remain unknown. Artificial sweeteners in ONPs may facilitate initiation and encourage consumption behavior.Aims and MethodsArtificial sweetener contents in major US-marketed ONP brands (Zyn, on!, Velo) were determined by Liquid Chromatography-Mass Spectrometry (LC-MS). Sweetener effects during the initiation of ONP consumption were modeled in single- and two-bottle tests, offering mice ONP extracts calibrated to contain nicotine levels similar to saliva of people who use smokeless tobacco. To examine the contribution of sweet taste perception, consumption behavior was compared between wild-type mice and mice deficient in the sweet taste receptor (Tas1r2−/−).ResultsAcesulfame-K was detected in on!, Zyn and Velo ONPs (∼0.3-0.9 mg/pouch), including products marketed as “Unflavored” or “Flavor ban approved”. In Velo ONPs, sweetened with sucralose (0.6-1.2 mg/pouch), higher nicotine strength products contained higher sucralose levels. Tas1r2−/−mice consumed less ONP extracts than wild-type mice in both sexes. ONP extracts with both higher nicotine and sweetener strengths were tolerated by wild-type mice, but produced stronger aversion in Tas1r2−/−mice.ConclusionsONPs contain significant amounts of artificial sweeteners, with some brands adding more sweetener to ONPs with higher nicotine strengths. Artificial sweeteners, at levels present in ONPs, increase nicotine consumption. Increasing sweetener contents facilitates consumption of ONPs with higher nicotine strengths. Sweetness is a key determinant of ONP use initiation, likely reducing the aversive sensory effects of nicotine and other ONP constituents.ImplicationsArtificial sweeteners such as acesulfame-K or sucralose reduce aversion and facilitate initiation and continued consumption of ONPs. The marketing of some artificially sweetened ONPs as “Unflavored” of “Flavor ban-approved” suggests that the tobacco industry rejects sweet taste as a determinant for the presence of a characterizing flavor. Sweetness as imparted by artificial sweeteners in tobacco products needs to be addressed by regulators as a component of a characterizing flavor, with the aim to reduce product appeal and initiation by never users, and especially youth attracted to sweet flavors.
Early dynamics of excitation and inhibition maintain late frequency tuning in auditory cortex
Authors: Reid Ashlan P. , Zador Anthony M. , Hromádka Tomáš 
Published: January 2024

AbstractIn the auditory cortex the onset of a tone evokes time-varying excitation and inhibition. However, the role of early inhibition in shaping the temporal properties of tone-evoked responses has not been fully characterized. By using Archaerhodopsin-3 (Arch) to photo-suppress the activity of the parvalbumin-expressing (PV) class of inhibitory interneurons, we manipulated the early component of tone-evoked inhibition. We find that early inhibition directly controls the output gain of the response, reducing the number of spikes proportionately across all frequencies. However, by controlling early activity, transient inhibition prevents late excitation and spiking for non-optimal frequencies. Thus, transient tone-evoked inhibition plays a critical long-lasting role in shaping response properties in the auditory cortex.
A new genetically tractable non-vertebrate system to study complete camera-type eye regeneration
Authors: Accorsi Alice , Pardo Brenda , Ross Eric , Corbin Timothy J. , McClain Melainia , Weaver Kyle , Delventhal Kym , Morrison Jason A. , McKinney Mary Cathleen , McKinney Sean A. , Sánchez Alvarado Alejandro 
Published: January 2024

ABSTRACTCamera-type eyes are complex sensory organs susceptible to irreversible damage. Their repair is difficult to study due to the paucity of camera-type eye regeneration models. Identifying a genetically tractable organism with the ability to fully regenerate complete camera-type eyes would help overcome this difficulty. Here, we introduce the apple snailPomacea canaliculata, capable of full regeneration of camera-type eyes even after complete resection. We defined anatomical components ofP. canaliculataeyes and genes expressed during crucial steps of their regeneration. By exploiting the unique features of this organism, we successfully established the first stable mutant lines in apple snails. Our studies revealed that, akin to humans,pax6is indispensable for eye development in apple snails, establishing this as a research organism to unravel the mechanisms of camera-type eye regeneration. This work expands our understanding of complex sensory organ regeneration and offers new ways to explore this process.