bluuebunny/crossref_metadata_2025_split huggingface dataset:
MS Binding Assays with UNC0642 as reporter ligand for the MB327 binding site of the nicotinic acetylcholine receptor
Authors: Nitsche Valentin , Höfner Georg , Kaiser Jesko , Gertzen Christoph G.W. , Seeger Thomas , Niessen Karin V. , Steinritz Dirk , Worek Franz , Gohlke Holger , Paintner Franz F. , Wanner Klaus T. 
Published: November 2023

AbstractIntoxications with organophosphorus compounds (OPCs) based chemical warfare agents and insecticides may result in a detrimental overstimulation of muscarinic and nicotinic acetylcholine receptors evolving into a cholinergic crisis leading to death due to respiratory failure. In the case of the nicotinic acetylcholine receptor (nAChR), overstimulation leads to a desensitization of the receptor, which cannot be pharmacologically treated so far. Still, compounds interacting with the MB327 binding site of the nAChR like the bispyridinium salt MB327 have been found to re-establish the functional activity of the desensitized receptor. Only recently, a series of quinazoline derivatives with UNC0642 as one of the most prominent representatives has been identified to address the MB327 binding site of the nAChR as well. In the present study, MS Binding Assays utilizing UNC0642 as a reporter ligand have been established. Thus, the binding of UNC0642 towardsTorpedo-nAChR has been characterized in MS saturation and competition experiments. According to the results, UNC0642 addresses the MB327 binding site of theTorpedo-nAChR. This conclusion is further supported by the outcome ofex vivostudies performed with poisoned rat diaphragm muscles as well as byin silicostudies predicting the binding mode of the most affine analog UNC0646 in the recently proposed binding site of MB327 (MB327-PAM-1). The new MS Binding Assays based on the commercially available reporter ligand UNC0642 as one of the most affine ligands for the MB327 binding site are a potent and valuable alternative to established assays.
Vaccinia virus infection induces concurrent alterations in host chromatin architecture, accessibility, and gene expression
Authors: Venu Vrinda , Roth Cullen , Adikari Samantha H. , Small Eric M. , Starkenburg Shawn R. , Sanbonmatsu Karissa Y. , Steadman Christina R. 
Published: November 2023

AbstractGenomic DNA folds into complex configurations that produce particular local and global structures thought to profoundly impact genome function. To understand the dynamic nature of this relationship, we investigated the extent of host chromatin structural and functional changes in response to a viral agent. We performed comprehensive assessments of host architecture (Hi-C), accessibility (ATAC-seq), and gene expression (RNA-seq) in a paired manner in response to attenuated vaccinia (smallpox) virus. Over time, infection significantly increased long-range intra-chromosomal interactions and decreased chromatin accessibility. Fine-scale accessibility changes were independent of broad-scale chromatin compartment exchange, which increased (up to 12% of the genome) over time, underscoring potential independent mechanisms for global and local chromatin reorganization. The majority of differentially expressed genes, including those downregulated in immune responses, had concurrent alterations in local accessibility and loop domain restructuring. Increased B compartmentalization, intra-chromosomal interactions, and decreased inter-chromosomal interactions and chromatin accessibility together indicate that infection converts the host genome into a more condensed state with nearly equal bidirectional differential gene expression. These changes in host chromatin features may have implications for developing efficacious anti-viral countermeasures. Overall, our empirical data provides evidence of orchestrated concurrent alterations in chromatin architecture, accessibility, and gene expression in response to infection, further reinforcing the notion of coordinated structure-function dynamics of the genome.
Promoter capture drives the emergence of proto-genes inEscherichia coli
Authors: uz-Zaman Md. Hassan , D’Alton Simon , Barrick Jeffrey E. , Ochman Howard 
Published: November 2023

AbstractThe phenomenon ofde novogene birth—the emergence of genes from non-genic sequences—has received considerable attention due to the widespread occurrence of genes that are unique to particular species or genomes. Most instances ofde novogene birth have been recognized through comparative analyses of genome sequences in eukaryotes, despite the abundance of novel, lineage-specific genes in bacteria and the relative ease with which bacteria can be studied in an experimental context. Here, we explore the genetic record of theEscherichia coliLong-Term Evolution Experiment (LTEE) for changes indicative of “proto-genic” phases of new gene birth in which non-genic sequences evolve stable transcription and/or translation. Over the time-span of the LTEE, non-genic regions are frequently transcribed, translated and differentially expressed, thereby serving as raw material for new gene emergence. Most proto-genes result either from insertion element activity or chromosomal translocations that fused pre-existing regulatory sequences to regions that were not expressed in the LTEE ancestor. Additionally, we identified instances of proto-gene emergence in which a previously unexpressed sequence was transcribed after formation of an upstream promoter. Tracing the origin of the causative mutations, we discovered that most occurred early in the history of the LTEE, often within the first 20,000 generations, and became fixed soon after emergence. Our findings show that proto-genes emerge frequently within evolving populations, persist stably, and can serve as potential substrates for new gene formation.
Exploring Pre-Exposure Prophylaxis (PrEP) modality preferences among Black cisgender women attending family planning clinics in Chicago
Authors: Johnson Amy K. , Ott Emily , Friedman Eleanor E. , Moore Amy , Alvarez Isa , Pandiani Agustina , Desmarais Catherine , Haider Sadia 
Published: November 2023

ABSTRACTBackgroundDespite Pre-exposure prophylaxis’s (PrEP) demonstrated effectiveness, Black cisgender women continue to be at an elevated risk for HIV acquisition and uptake of daily oral PrEP is low in this population in the US. As advancements in PrEP delivery options continue, it is important to understand women’s acceptability of these additional options, specifically Black cisgender women, in order to inform uptake and adherence among this population at increased need of HIV prevention options.SettingA cross-sectional survey among Black cisgender women ages 13-45 (inclusive) attending women’s health clinics in Chicago, IL, prior to the approval of CAB-LA.MethodsDescriptive statistics were used to describe the sample and bivariate analysis was used to detect differences between categorical and outcome variables using chi-square test. Responses to open-ended questions were thematically coded to explore Black cisgender women’s attitudes and preferences between the three methods of PrEP delivery including: vaginal ring, long-acting injectable, and a combined method that would prevent both pregnancy and HIV.ResultsIn total, 211 cisgender women and adolescents responded to the survey. Both injections and combination pills were popular among participants, with 64.5% and 67.3% expressing interest in these forms of PrEP, respectively. The least popular method was the vaginal ring option, with 75.4% of respondents indicating that they would not consider using this modality. Overall, responses were not statistically different between the two surveys administered (Chi square p-values for injection PrEP method 0.66, combination PrEP method 0.93, and ring PrEP method 0.66) suggesting that the popularity of each method was not dependent on clinic location or age of participants.ConclusionThis research provides important insights into the preferences and attitudes of different PrEP modalities among Black cisgender women. As different modalities continue to be approved for use among cisgender women, more research is needed to investigate the acceptability and preferences of these different modalities in order to improve uptake and adherence among this population.
Lateral hypothalamic GABAergic neurons encode alcohol memories
Authors: Alonso-Lozares Isis , Wilbers Pelle , Asperl Lina , Teijsse Sem , van der Neut Charlotte , Schetters Dustin , van Mourik Yvar , McDonald Allison J. , Heistek Tim , Mansvelder Huibert D. , De Vries Taco J. , Marchant Nathan J. 
Published: November 2023

SummaryIn alcohol use disorder the alcohol memories persist during abstinence, and exposure to stimuli associated with alcohol use can lead to relapse. This highlights the importance of investigating the neural substrates underlying not only relapse, but also encoding and expression of alcohol memories. GABAergic neurons in the Lateral Hypothalamus (LH- GABA) have been shown to be critical for food-cue memories and motivation, however the extent to which this role extends to alcohol-cue memories and motivations remains unexplored. In this study, we aimed to describe how alcohol related memories are encoded and expressed in LH GABAergic neurons. Our first step was to monitor LH-GABA calcium transients during acquisition, extinction, and reinstatement of an alcohol-cue memory using fiber photometry. We trained the rats on a Pavlovian conditioning task where one conditioned stimulus (CS+) predicted alcohol (20% EtOH) and another conditioned stimulus (CS-) had no outcome. We then extinguished this association through non-reinforced presentations of the CS+ and CS-, finally in two different groups we measured relapse under non-primed and alcohol primed induced reinstatement. Our results show that initially both cues caused increased LH-GABA activity, and after learning only the alcohol-cue increased LH-GABA activity. After extinction this activity decreases, and we found no differences in LH- GABA activity during reinstatement in either group. Next, inhibited LH-GABA neurons with optogenetics to show that activity of these neurons is necessary for the formation of an alcohol-cue associations. These findings suggest that LH-GABA might be involved in attentional processes modulated by learning.
Divergent outcomes of SAK3, a T-type calcium channel enhancer, in two luminal-A type breast cancer cell lines: T-47D and MCF7
Authors: Dinesh Yashashwini Subbamanda , Subramanian Tharunika , Zinzuvadia Aarushi K , Maturana Andres D , Bhargava Anamika 
Published: November 2023

AbstractVoltage-gated calcium channels have emerged as promising targets in breast cancer. Breast cancer cell lines are widely used as experimental models. In our pursuit to explore the potential of augmenting T-type voltage-gated calcium channels as a therapeutic approach for breast cancer, we made an unexpected discovery: similar breast cancer subtype cell lines exhibited varying responses to SAK3, a T-type voltage-gated calcium channel enhancer, in terms of proliferation and intracellular calcium levels. In presenting these contrasting findings here, we aim to underscore the importance of exercising caution and validating results obtained from cell lines by cross-referencing them with other cell lines or models.
De novoSequencing and Whole Transcriptome Analysis for Biosynthesis Pathway of Diosgenin inPedalium murexL.: A Medicinal herb
Authors: Tyagi Parul , Ranjan Rajiv 
Published: November 2023

ABSTRACTTranscriptome-based investigations of candidate genes, critical pathways, and gene regulation in non- model species have been transformed by high-throughput RNA sequencing in different studies.Pedalium murexL. is one of the most important annual medicinal herbs of thePedaliaceaefamily. Because of its anti-inflammatory, antioxidant, antimicrobial, and anticancerous properties,P. murexis widely used in traditional medicine to treat gonorrhoea, leucorrhoea, urinary disorders, gastrointestinal tract disorders, cough, and asthma. Steroidal diosgenin is the major bioactive compound ofP. murex. However, transcriptional technologies have yet to be used to study the steroid diosgenin biosynthetic pathway of this herb. In this study, we performed a whole transcriptomic analysis of the root, fruit, and leaf tissues ofP. murexwith three biological replicates and obtained ∼6.77 Gb of clean raw data. A total of 148871 unigenes were assembled with an average length of N50 and 1167 bp. Putative functions could be annotated to 75198 unigenes based on a BLASTX search against the NR, Uniprot, KEGG, Pfam, GO, and COG databases. Most of the unigenes related to steroidal diosgenin backbone biosynthesis were up- regulated in the root, fruit and leaf, except for the MVD gene in the leaf. qRT-PCR further verified the differential expression analysis of selected genes. It shows the highest homology withSesamum indicum, Handroanthus impetiginosus, Erythranthe guttata, Oleaeuropaeavar. sylvestris,andDorcoceras hygrometricum. A total of 21026 unigenes of transcription factors were assembled into transcription factor families. A total of 8760 unigenes of SSR were assembled. The transcriptome data presented here will make it easier to study the functional genomics of steroidal diosgenin biosynthesis and to change the genes ofP. murexto make it more diosgenin.
Macromolecule modelling for improved metabolite quantification using short echo time brain1H MRS at 3 T and 7 T: The PRaMM Model
Authors: Dell’Orco Andrea , Riemann Layla Tabea , Ellison Stephen L. R. , Aydin Semiha , Göschel Laura , Tietze Anna , Scheel Michael , Fillmer Ariane 
Published: November 2023

AbstractPurposeTo improve reliability of metabolite quantification at both, 3 T and 7 T, we propose a novel parametrized macromolecules quantification model (PRaMM) for brain1H MRS, in which the ratios of macromolecule peak intensities are used as soft constraints.MethodsFull- and metabolite-nulled spectra were acquired in three different brain regions with different ratios of grey and white matter from six healthy volunteers, at both 3 T and 7 T. Metabolite-nulled spectra were used to identify highly correlated macromolecular signal contributions and estimate the ratios of their intensities. These ratios were then used as soft constraints in the proposed PRaMM model for quantification of full spectra. The PRaMM model was validated by comparison with a single component macromolecule model and a macromolecule subtraction technique. Moreover, the influence of the PRaMM model on the repeatability and reproducibility compared to those other methods was investigated.ResultsThe developed PRaMM model performed better than the two other approaches in all three investigated brain regions. Several estimates of metabolite concentration and their Cramér-Rao lower bounds were affected by the PRaMM model reproducibility, and repeatability of the achieved concentrations were tested by evaluating the method on a second repeated acquisitions dataset. While the observed effects on both metrics were not significant, the fit quality metrics were improved for the PRaMM method (p≤0.0001). Minimally detectable changes are in the range 0.5 – 1.9 mM and percent coefficients of variations are lower than 10% for almost all the clinically relevant metabolites. Furthermore, potential overparameterization was ruled out.ConclusionHere, the PRaMM model, a method for an improved quantification of metabolites was developed, and a method to investigate the role of the MM background and its individual components from a clinical perspective is proposed.
ADEVO: Proof-of-concept of Adenovirus Directed EVOlution by random peptide display on the fiber knob
Authors: Sallard Erwan , Fischer Julian , Beaude Nissai , Affes Arsalene , Ehrke-Schulz Eric , Zhang Wenli , Westhaus Adrian , Cabanes-Creus Marti , Lisowski Leszek , Ruszics Zsolt , Ehrhardt Anja 
Published: November 2023

ABSTRACTDirected evolution of viral vectors involves the generation of randomized libraries followed by artificial selection of improved variants. Directed evolution only yielded limited results in adenovirus vector (AdV) development until now, mainly due to insufficient complexities of randomized libraries.Clinical applications of AdVs as gene therapy or oncolytic vectors are still hampered by the predetermined tropism of natural types. To overcome this challenge, we hypothesized that the technology of randomized peptide insertions on the capsid surface can be incorporated into the AdV bioengineering toolbox for vector retargeting. Here we developed Adenovirus Directed EVOlution (ADEVO) protocols based on fiber knob peptide display.As a proof-of-concept, HAdV-C5-derived libraries were constructed following three distinct protocols and selected on A549-DCAR cells that lack the HAdV-C5 primary receptor, with the goal of identifying variants able to infect and lyse these tumor cells more efficiently. All protocols enabled the construction of high complexity libraries with up to 9.6x10^5 unique variants, an approximate 100-fold improvement compared to previously published AdV libraries. After selection, the most enriched variants did not display enhanced infectivity but rather more efficient replication and cell lysis. This warrants investigations into potential unsuspected involvement of the fiber protein in adenovirus replication.GRAPHICAL ABSTRACT
Vagus nerve mediated liver-brain axis is a major regulator of the metabolic landscape in the liver
Authors: Brito Camila Fatima , Fonseca Roberta Cristelli , Rodrigues-Ribeiro Lucas , Vaz Bruna Fernandes , Tofani Gabriel Sousa Silva , Diniz Ariane Barros , Fernandes Paola , Nunes Núbia Alexandre Melo , Pessoa Rafaela Miranda , Oliveira Amanda Carla Clemente , Cardoso Valbert Nascimento , Fernandes Simone Odília Antunes , Oliveira Maristela Poletini , Alvarez-Leite Jacqueline Isaura , Menezes Gustavo Batista , Ferreira Adaliene Versiani M , Gorshkov Vladimir , Kjeldsen Frank , Verano-Braga Thiago , Oliveira André Gustavo 
Published: November 2023

AbstractBackgroundThe liver serves as a major energetic reservoir for other tissues and its metabolic function is controlled by humoral and neural factors. The vagus nerve innervating the gastrointestinal tract plays an important role in regulating peripheral metabolism and energy expenditure. Although the liver receives vagus nerve fibers, the impact of this circuitry in the regulation of hepatic metabolism is still poorly understood.MethodsHerein, we used a combination of quantitative proteomics andin vivoimaging techniques to investigate the impact of the vagus nerve on liver metabolism.ResultsVagus nerve shapes the metabolic framework of the liver, as surgical ablation (vagotomy; VNX) of this circuitry led to a significant alteration of the hepatic proteome landscape. Differential protein expression and pathway enrichment analyses showed that glycolytic and fatty acid biosynthesis were increased following VNX, whereas β-oxidation was decreased. This metabolic shift facilitated lipid accumulation in hepatocytes. Furthermore, VNX worsened liver steatosis following high-carbohydrate or high-fat dietary challenges.ConclusionsThis study describes the liver-brain axis mediated by the vagus nerve as an important regulator of the hepatic metabolic landscape.HighlightsVagus nerve is a novel regulator of the hepatic metabolic landscape.Ablation of vagus nerve neural circuit by vagotomy resulted in a metabolic shift towards glycolysis and fatty acid biosynthesis.Lipid accumulation was increased in vagotomized mice fed with a standard diet.Liver steatosis was increased following dietary challenges with high-carbohydrate or high-fat diets.Vagus nerve can be a promising new target for NAFLD treatment.
A Genome Sequence for the Threatened Whitebark Pine
Authors: Neale David B. , Zimin Aleksey V. , Meltzer Amy , Bhattarai Akriti , Amee Maurice , Corona Laura Figueroa , Allen Brian J. , Puiu Daniela , Wright Jessica , Torre Amanda R. De La , McGuire Patrick E. , Timp Winston , Salzberg Steven L. , Wegrzyn Jill L. 
Published: November 2023

AbstractWhitebark pine (WBP,Pinus albicaulis) is a white pine of subalpine regions in western contiguous US and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR,Cronartium ribicola) and additional threats from mountain pine beetle (Dendroctonus ponderosae), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration. With deep-coverage Illumina short-reads of haploid megametophyte tissue and Oxford Nanopore long-reads of diploid needle tissue, followed by a hybrid, multistep assembly approach, we produced a final assembly containing 27.6 Gbp of sequence in 92,740 contigs (N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gbp). Approximately 87.2% (24.0 Gbp) of total sequence was placed on the twelve WBP chromosomes. Annotation yielded 25,362 protein-coding genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the greatest variation in resistance to WPBR among the North American white pines. Candidate genes for quantitative resistance include disease resistance genes known as nucleotide-binding leucine-rich-repeat receptors (NLRs). A combination of protein domain alignments and direct genome scanning was employed to fully describe the three subclasses of NLRs (TNL, CNL, RNL). Our high-quality reference sequence and annotation provide a marked improvement in NLR identification compared to previous assessments that leveraged de novo assembled transcriptomes.
Adaptive IRE1 Signaling Elicits T Cell Metabolic Remodeling and Tumor Control
Authors: Riesenberg Brian P. , Gandy Evelyn J. , Kennedy Andrew S. , Hunt Elizabeth G. , Hurst Katie E. , Sedlacek Elise L. , Gao Peng , Emanuele Michael J. , Modliszewski Jennfier , Green Jarred M. , Milner Justin J. , Wiseman R. Luke , Thaxton Jessica E. 
Published: November 2023

SummaryThe efficacy of cancer immunotherapies is limited by the metabolic instability of the tumor microenvironment (TME) that disables T cell antitumor immunity. Metabolic imbalances within the TME are sensed and responded to by stress sensors of the endoplasmic reticulum (ER) unfolded protein response (UPR). The UPR comprises three integrated signaling pathways harboring both adaptive and deleterious phases based on the extent and duration of cell stress. Here, we elucidate the differential contributions of adaptive and deleterious signaling downstream of the UPR IRE1 pathway in T cell-regulated tumor control. T cells in murine and patient cancers experience persistent ER stress, leading to hyperactive IRE1 signaling that limits tumor control. However, amplifying the adaptive arm of the IRE1 UPR serves to eliminate mitochondrial toxicity and protect T cells from chronic ER stress, yielding robust tumor engraftment and long-term tumor immunity. Our findings establish the UPR’s essential protective role in antitumor immunity.