bluuebunny/crossref_metadata_2025_split huggingface dataset:
The ventral hippocampal-nucleus accumbens shell circuit drives approach decisions under social novelty and learned cue approach-avoidance conflict
Authors: Patterson Dylan P , Khan Nisma , Sassaninejad Kian , Stewart Norman R , Collins Emily , Yeates Dylan , Lee Andy CH , Ito Rutsuko 
Published: June 2024

AbstractSuccessful resolution of approach-avoidance conflict (AAC) is fundamentally important for survival, and its dysregulation is a hallmark of many neuropsychiatric disorders, and yet the underlying neural circuit mechanisms are not well elucidated. Converging human and animal research has implicated the anterior/ventral hippocampus (vHPC) as a key node in arbitrating AAC in a region-specific manner. In this study, we sought to target the vHPC CA1 projection pathway to the nucleus accumbens (NAc) to delineate its contribution to AAC decision-making, particularly in the arbitration of learned reward- and punishment signals, as well as innate signals. To this end, we used pathway-specific chemogenetics in male and female Long Evans rats to inhibit the NAc shell projecting vHPC CA1 neurons while rats underwent a test in which cues of positive and negative valence were presented concurrently to elicit AAC. Further behavioral assays of social preference and memory, reward and punishment cue processing, anxiety, and novelty processing were administered to further interrogate the conditions under which the vCA1-NAc shell pathway is recruited. Chemogenetic inhibition of the vCA1-NAc shell circuit resulted in animals exhibiting increased decision-making time and avoidance bias specifically in the face of motivational conflict, as the same behavioral phenotype was absent in separate conditioned cue preference and avoidance tests. vCA1-NAc shell inhibition also led to a reduction in seeking social interaction with a novel rat but did not alter anxiety-like behaviors. The vCA1-NAc shell circuit is therefore critically engaged in biasing decisions to approach in the face of social novelty and approach-avoidance conflict. Dysregulation of this circuit could lead to the precipitation of addictive behaviours in substance abuse, or potentiation of avoidance in situations of approach-avoidance conflict.
Levels of DNA accessibility in human sperm vary across individuals with differing reproductive parameters
Authors: Gill Mark E. , Fischer Manuel , De Geyter Christian , Peters Antoine H.F.M. 
Published: June 2024

AbstractMammalian sperm DNA is packaged in a much denser form than in somatic cells, protecting the DNA from damage and reducing the size of the nucleus to improve passage towards the oocyte. While defective sperm DNA packaging correlates with reduced fertilization rates and impaired pre-implantation embryonic development, these defects are not currently examined in standard semen analysis. Here, we adapted NicE-view, an assay that directly labels accessible DNA, for use in human sperm and applied this method including extensive image quantification to examine spermatozoa from individuals with normal conventional semen parameters but variable reproductive outcomes. We found that two sub-populations of cells differing greatly in their DNA accessibility exist within both total and motile sperm. The frequencies of these two sub-populations vary between individuals, and selection of motile sperm by swim-up generally enriches for sperm with high DNA accessibility. Individuals with high frequencies of sperm with high DNA accessibility possess decreased sperm concentrations and increased DNA nicking levels and a subset of these individuals have a history of post-fertilization embryogenic failure. NicE-view shows much clearer separation of staining levels than alternative DNA labeling approaches, and represents a valuable tool for the assessment of human sperm.
Declining Genetic Polymorphisms of the C-terminus Merozoite Surface Protein-1 Amidst IncreasedPlasmodium knowlesiTransmission in Thailand
Authors: Tapaopong Parsakorn , Chainarin Sittinont , Mala Abdulrohman , Rannarong Arnuwat , Kangkasikorn Nikom , Kusolsuk Teera , Roobsoong Wanlapa , Cui Liwang , Nguitragool Wang , Sattabongkot Jetsumon , Bantuchai Sirasate 
Published: June 2024

ABSTRACTRecent reports from Thailand reveal a substantial surge inPlasmodium knowlesicases over the past decade, with a more than eightfold increase in incidence by 2023 compared to 2018. This study investigates temporal changes in genetic polymorphism associated with the escalating transmission ofP. knowlesimalaria in Thailand over the past two decades. Twenty-fiveP. knowlesisamples collected in 2018–2023 were sequenced for the 42-kDa region ofpkmsp1and compared with 24 samples collected in 2000–2009, focusing on nucleotide diversity, natural selection, recombination rate, and population differentiation. Seven unique haplotypes were identified in recent samples, compared to 15 in earlier samples. Nucleotide and haplotype diversities were lower in recent samples (π = 0.016, Hd = 0.817) than in earlier samples (π = 0.018, Hd = 0.942). Significantly higher synonymous substitution rates were observed in both sample sets (dS– dN= 2.77 and 2.43, p < 0.05), indicating purifying selection and reduced genetic diversity over time. Additionally, 8 out of 17 mutation points were located on B-cell epitopes, suggesting an adaptive response by the parasites to evade immune recognition. Population differentiation analysis using the fixation index (Fst) revealed high genetic differentiation between parasite populations in central and southern Thailand or Malaysia. Conversely, the relatively lower Fstvalue between southern Thailand and Malaysia suggests a closer genetic relationship, possibly reflecting historical gene flow. In conclusion, our findings highlight a decline in genetic diversity and evidence of purifying selection associated with the recently increased incidence ofP. knowlesimalaria in Thailand. The minor genetic differentiation betweenP. knowlesipopulations from southern Thailand and Malaysia suggests a shared recent ancestry of these parasites and underscores the need for coordinated efforts between the two countries for the elimination ofP. knowlesi.
Phosphoglucomutase A mediated regulation of carbon flux is essential for antibiotic and disease persistence inMycobacterium tuberculosis
Authors: Sharma Taruna , Tyagi Shaifali , Pal Rahul , Kundu Jayendrajyoti , Gupta Sonu Kumar , Barik Vishawjeet , Nain Vaibhav Kumar , Pandey Manitosh , Dwivedi Prabhanjan , Panda Bhishma Narayan , Kumar Yashwant , Nanda Ranjan Kumar , Chatterjee Samrat , Pandey Amit Kumar 
Published: June 2024

AbstractThe long-term survival of Mtb mandates judicious utilization of the available resources inside the host. Uninterrupted access to host-derived nutrients holds the key to the success of Mtb. Phosphoglucomutase enzyme besides synthesizing glycogen, which serves as a nutrient reservoir, also helps modulate the carbon flux in different pathogens. Studies on the role of glycogen metabolism in disease progression, reactivation, and drug susceptibility in tuberculosis are severely lacking. To investigate this, we generated an Mtb strain (ΔpgmA) devoid of the gene that encodes for the enzyme phosphoglucomutase A (pgmA). The absence ofpgmAimpedes the ability of the pathogen to survive under nutrient-limiting and reactivation conditions. In the current study, we demonstrate that the absence of cell membrane-associated glycolipids in ΔpgmAcompromised the cell wall integrity and increased the susceptibility of ΔpgmAto various stresses. Interestingly, in comparison to the wild type, low cAMP levels in ΔpgmAimparted an enhanced growth phenotype on cholesterol. Differential gene expression and carbon flux analysis suggest that stored carbon in the form of glycogen is essential for the survival of Mtb under nutrient-limiting conditions. Finally, we demonstrate that thepgmAgene of Mtb is essential for the growth of Mtb inside the host. Overall, this study unveils the significance ofpgmA-mediated regulation of membrane glycolipids and its implication on antibiotic and disease persistence in tuberculosis. Additionally, information derived from this study will help design anti-TB strategies that are novel, short, and more efficient.
A flexible, high-throughput system for studying mRNA translation kineticsin vitroandin cellulowith HiBit technology
Authors: Ascanelli C. , Lawrence E. , Batho C. A. P. , Wilson C. H. 
Published: June 2024

AbstractHiBit is an engineered luciferase’s 11 amino acid component that can be introduced as a tag at either terminus of a protein of interest. When the LgBit component and a substrate are present, HiBit and LgBit dimerise forming a functional luciferase. The HiBit technology has been extensively used for high-throughput protein turnover studies in cells. Here, we have adapted the use of the HiBit technology to quantify mRNA translation temporallyin vitroin the rabbit reticulocyte system andin celluloin HEK293 cells constitutively expressing LgBit. The assay system can detect differences in Cap, 5’UTR, modified nucleotide composition, coding sequence optimisation and poly(A) length. Importantly, using these assays we established the optimal mRNA composition varied depending on the encoded protein of interest, highlighting the importance of screening methods tailored to the protein of interest, and not reliant on reporter proteins. Our findings demonstrated that HiBit can be easily and readily adapted to monitor mRNA translation and offers a novel and highly favourable method for the development of mRNA-based therapeutics.Graphical abstract
Metagenomic global survey and in-depth genomic analyses ofRuminococcus gnavusreveal differences across host lifestyle and health status
Authors: Nooij S. , Plomp N. , Sanders I.M.J.G. , Schout L. , van der Meulen A.E. , Terveer E.M. , Norman J.M. , Karcher N. , Larralde M.F. , Vossen R.H.A.M. , Kloet S.L. , Faber K.N. , Harmsen H.J.M. , Zeller G.F. , Kuijper E.J. , Smits W.K. , Ducarmon Q.R. 
Published: June 2024

SUMMARYRuminococcus gnavusis a highly prevalent gut bacterium (present in >90% of healthy individuals), of which increased abundance is associated with chronic inflammatory diseases, most notably Crohn’s disease. Nevertheless, its global distribution has not been investigated and little is known about intraspecies genomic variation. Through a large-scale survey of 12,791 gut metagenomes, we recapitulated known associations with metabolic diseases and inflammatory bowel disease. We uncover a higher prevalence and abundance ofR. gnavusin Westernized populations and observe relative abundances of up to 83% in newborns and infants. Next, we built a collection of existing and newly culturedR. gnavusisolates (N = 45) from both healthy individuals and Crohn’s disease patients and subjected these to PacBio circular consensus sequencing to greatly expand the number of completeR. gnavusgenomes. Analysis of these genomes as well as publicly available high quality draft genomes (total > 300 genomes) revealed multiple clades which separated Crohn’s-derived isolates from healthy-derived isolates. Functional analyses of genes predicted to constituteR. gnavusvirulence factors could not explain this separation. Bacterial GWAS revealed that Crohn’s-derived isolates were enriched in genes related to mobile elements and putative mucin foraging. Together, we present one of the largest complete genome collections of any commensal gut microbe and provide novel biological insights into the global distribution and genomic variation ofR. gnavus.
Free Amino Acids Accelerate the Time-Dependent Inactivation of Rat Liver Nucleotide Pyrophosphatase / Phosphodiesterase Enpp3 elicited by EDTA
Authors: Romero Ana , Cumplido-Laso Guadalupe , Fernández Ascensión , Moreno Javier , Canales José , Ferreira Rui , López-Gómez Juan , Ribeiro João Meireles , Costas María Jesús , Cameselle José Carlos 
Published: June 2024

AbstractNucleotide-pyrophosphatases/phosphodiesterases (NPP/PDE) are membrane or secreted Zn2+-metallohydrolases of nucleoside-5’-monophosphate derivatives. They hydrolyze, for instance, ATP and 4-nitrophenyl-dTMP, and belong to the ecto-nucleotide pyrophosphatase/phosphodiesterase (ENPP) family that contains seven members (ENPP1-ENPP7). Earlier we had shown that an NPP/PDE activity solubilized and partially purified from rat liver membranes is inactivated by EDTA in a time-dependent fashion, an effect enhanced by glycine and blocked by the 4-nitrophenyl-dTMP. Here, we extended this observation to other free amino acids. Activity assays started after different incubation lengths with EDTA provided first-order, apparent inactivation constants (ki(ap)). With the exception of cysteine (a strong inhibitor) and histidine (itself evoking a time-dependent inactivation), free amino acids themselves did not affect activity but increased ki(ap). The results are compatible with a conformational change of NPP/PDE evoked by interaction with free amino acids. The enzyme preparation was analyzed to identify what ENPP family members were present. First, the hydrolytic activity on 2’,3’-cGAMP was assayed because until very recently ENPP1 was the only mammalian enzyme known to display it. 2’,3’-cGAMP hydrolase activity was clearly detected, but mass spectrometry data obtained by LC-MS/MS gave evidence that only rat Enpp3, Enpp4 and Enpp5 were present with low abundance. This finding coincided in time with a recent publication claiming that mouse Enpp3 hydrolyzes 2’,3’-cGAMP, and that Enpp1 and Enpp3 account for all the 2’,3’-cGAMP hydrolase activity in mice. So, our results are confirmatory of Enpp3 activity towards 2’,3’-cGAMP. Finally, the effect of amino acids could be relevant to NPP/PDE actions dependent on protein-protein interactions, like the known insulin-related effects of ENPP1 and possibly ENPP3.
Highly Multiplexed Spatial Transcriptomics in Bacteria
Authors: Sarfatis Ari , Wang Yuanyou , Twumasi-Ankrah Nana , Moffitt Jeffrey R. 
Published: June 2024

AbstractSingle-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hindered by the massive density of bacterial mRNA. To overcome this challenge, we combine 1000-fold volumetric expansion with multiplexed error robust fluorescencein situhybridization (MERFISH) to create bacterial-MERFISH. This method enables high-throughput, spatially resolved profiling of thousands of operons within individual bacteria. Using bacterial-MERFISH, we dissect the response ofE. colito carbon starvation, systematically map subcellular RNA organization, and chart the adaptation of a gut commensalB. thetaiotaomicronto micron-scale niches in the mammalian colon. We envision bacterial-MERFISH will be broadly applicable to the study of bacterial single-cell heterogeneity in diverse, spatially structured, and native environments.
Energy Aware Technology Mapping of Genetic Logic Circuits
Authors: Kubaczka Erik , Gehri Maximilian , Marlhens Jérémie J. M. , Schwarz Tobias , Molderings Maik , Engelmann Nicolai , Garcia Hernan G. , Hochberger Christian , Koeppl Heinz 
Published: June 2024

AbstractEnergy and its dissipation are fundamental to all living systems, including cells. Insufficient abundance of energy carriers -as caused by the additional burden of artificial genetic circuits-shifts a cell’s priority to survival, also impairing the functionality of the genetic circuit. Moreover, recent works have shown the importance of energy expenditure in information transmission. Despite living organisms being non-equilibrium systems, non-equilibrium models capable of accounting for energy dissipation and non-equilibrium response curves are not yet employed in genetic design automation (GDA) software. To this end, we introduce Energy Aware Technology Mapping, the automated design of genetic logic circuits with respect to energy efficiency and functionality. The basis for this is an energy aware non-equilibrium steady state (NESS) model of gene expression, capturing characteristics like energy dissipation -which we link to the entropy production rate- and transcriptional bursting, relevant to eukaryotes as well as prokaryotes. Our evaluation shows that a genetic logic circuit’s functional performance and energy efficiency are disjoint optimization goals. For our benchmark, energy efficiency improves by 37.2% on average when comparing to functionally optimized variants. We discover a linear increase in energy expenditure and overall protein expression with the circuit size, where Energy Aware Technology Mapping allows for designing genetic logic circuits with the energy efficiency of circuits that are one to two gates smaller. Structural variants improve this further, while results show the Pareto dominance among structures of a single Boolean function. By incorporating energy demand into the design, Energy Aware Technology Mapping enables energy efficiency by design. This extends current GDA tools and complements approaches coping with burdenin vivo.TOC Graphic
Structural Insights into the Roles of PARP4 and NAD+in the Human Vault Cage
Authors: Lodwick Jane E. , Shen Rong , Erramilli Satchal , Xie Yuan , Roganowicz Karolina , Kossiakoff Anthony A. , Zhao Minglei 
Published: June 2024

AbstractVault is a massive ribonucleoprotein complex found across Eukaryota. The major vault protein (MVP) oligomerizes into an ovular cage, which contains several minor vault components (MVCs) and is thought to transport transiently bound “cargo” molecules. Vertebrate vaults house a poly (ADP-ribose) polymerase (known as PARP4 in humans), which is the only MVC with known enzymatic activity. Despite being discovered decades ago, the molecular basis for PARP4’s interaction with MVP remains unclear. In this study, we determined the structure of the human vault cage in complex with PARP4 and its enzymatic substrate NAD+. The structures reveal atomic-level details of the protein-binding interface, as well as unexpected NAD+-binding pockets within the interior of the vault cage. In addition, proteomics data show that human vaults purified from wild-type and PARP4-depleted cells interact with distinct subsets of proteins. Our results thereby support a model in which PARP4’s specific incorporation into the vault cage helps to regulate vault’s selection of cargo and its subcellular localization. Further, PARP4’s proximity to MVP’s NAD+-binding sites could support its enzymatic function within the vault.
Contribution of telacebec to novel drug regimens in a murine tuberculosis model
Authors: Komm Oliver D. , Tyagi Sandeep , Garcia Andrew , Almeida Deepak , Chang Yong , Lee Si-Yang , Castillo Jennie Ruelas , Converse Paul J. , Black Todd , Fotouhi Nader , Nuermberger Eric L. 
Published: June 2024

AbstractThe clinical efficacy of combination drug regimens containing the first generation diarylquinoline (DARQ) bedaquiline in the treatment of multidrug-resistant tuberculosis has validated ATP synthesis as a vulnerable pathway inMycobacterium tuberculosis. New DARQs in clinical development may be even more effective than bedaquiline, including against emerging bedaquiline-resistant strains. Telacebec (T) is a novel cytochrome bc1:aa3oxidase inhibitor that also inhibits ATP synthesis. Based on its demonstrated efficacy as a monotherapy in mice and in a phase 2a clinical trial, we used an established BALB/c mouse model of tuberculosis (TB) to test the contribution of T to novel combination therapies against two strains ofM. tuberculosis(H37Rv and HN878) in an effort to find more effective regimens. Overall, T was more effective in regimens against the HN878 strain than against the H37Rv strain, a finding that supports the greater vulnerability of the former strain to T and to genetic depletion of QcrB. Against both strains, combinations of a DARQ, clofazimine (CFZ), and T were highly bactericidal. However, only against HN878 did T contribute synergistically, whereas an antagonistic effect was observed against H37Rv. These results demonstrate the therapeutic potential of T and highlight how differences in the susceptibility ofM. tuberculosisstrains could lead to different conclusions about a drug’s potential contribution to novel drug regimens.
A test of limited transpiration traits in sorghum to improve late-season water use, photosynthesis, growth, and grain yield in the high plains of Northern Colorado
Authors: Gleason Sean M. , Stewart Jared J. , Polutchko Stephanie K. , Allen Brendan S. 
Published: June 2024

AbstractLimited transpiration (LT) traits aim to conserve early-season water to benefit late-season grain development. While theoretical and modeling efforts support LT efficacy, empirical tests directly measuring water loss from leaves and canopies are scarce. This study evaluates the performance of LT genotypes in achieving reduced early-season water use and improved late-season growth and yield in semi-arid Colorado. The research involved near-isogenic lines (NILs) derived from sorghum inbred lines, subjected to different irrigation treatments. Measurements included stomatal conductance, net CO2assimilation, and photosystem II (PSII) efficiency. Results indicate that LT genotypes did not consistently exhibit lower early-season water use or higher late-season growth compared to non-LT genotypes. Early-season water use waspositivelycorrelated with above-ground biomass, challenging the assumption that early-season water conservation can be leveraged for late-season benefits. We question the efficacy of LT traits, highlighting the physiological link between water use and carbon gain, and the potential opportunity costs of reduced early-season growth. We suggests that breeding strategies should focus on enhancing deep soil water access and maximizing carbon gain rather than merely reducing transpiration or shifting water use in arid and semi-arid environments.
SOX9 Expression in Colorectal Adenomas Improves Surveillance Colonoscopy Risk Stratification in a Bowel Screening Population
Authors: Al-Badran Sara Samir Foad , Bigley Christopher , Johnstone Mark , Ammar Aula , Winton Alexander , Hay Jennifer , Quinn Jean , Jawny Jakub , Andersen Ditte , Fisher Natalie , Dunne Philip D. , Maka Noori , Lynch Gerard , McSorley Stephen , Edwards Joanne 
Published: June 2024

ABSTRACTObjectivesAdenomas are known precursors to colorectal cancer (CRC). Current UK post-polypectomy surveillance guidelines use polyp size, numbers, and histology to stratify the risk of patients developing metachronous polyps or CRC. However, these risk guidelines suffer from poor predictive value, often leading to under/over surveillance.DesignAdenomas removed from 1257 patients at bowel screening colonoscopy were retrospectively identified to investigate mutational profile and protein expression trends associated with the detection of metachronous polyps or CRC. The presence or absence of metachronous polyps or CRC was recorded 6 months to 6 years after index polypectomy.ResultsAPCandKRASwere the most mutated genes in these patients (87% and 34% respectively), and both were significantly co-occurring with the 6th most mutated geneSOX9(17% co-occurring withAPC, p=0.047; 23% co-occurring withKRAS, p=0.012). High SOX9 cytoplasmic expression was significantly associated with the detection of metachronous polyps or CRC (HR 1.543, p=0.001) and improved high risk stratification when combined with BSG2020 guidelines versus guidelines alone (HR 2.626, p<0.0001). High cytoplasmic SOX9 alone and in combination with current guidelines was an independent predictor of metachronous polyps or CRC according to various regression models. This was validated in an independent test dataset, where high cytoplasmic expression was significantly associated with the detection of metachronous polyps or CRC (HR 1.654, p=0.012) and enhanced risk stratification when combined with BSG2020 guidelines versus guidelines alone (HR 2.473, p=0.0018).ConclusionHigh cytoplasmic SOX9 expression within adenomas is associated with shorter time to detection of metachronous polyps or CRC.