bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptive responding to stimulus-outcome associations requires noradrenergic transmission in the medial prefrontal cortex
Authors: Piccin Alessandro , Plat Hadrien , Wolff Mathieu , Coutureau Etienne 
Published: December 2023

AbstractA dynamic environment, such as the one we inhabit, requires organisms to continuously update their knowledge of the setting. While the prefrontal cortex is recognized for its pivotal role in regulating such adaptive behavior, the specific contributions of each prefrontal area remain elusive. In the current work, we investigated the direct involvement of two major prefrontal subregions, the medial prefrontal cortex (mPFC) and the ventrolateral orbitofrontal cortex (vlOFC), in updating Pavlovian stimulus-outcome (S-O) associations following contingency degradation. Specifically, animals had to learn that a specific cue, previously fully predicting the delivery of a specific reward, was no longer a reliable predictor. First, we found that chemogenetic inhibition of mPFC, but not of vlOFC, neurons altered the rats’ ability to adaptively respond to degraded and non-degraded cues. Next, given the growing evidence pointing at noradrenaline (NA) as a main neuromodulator of adaptive behavior, we decided to investigate the possible involvement of NA projections to the two subregions in this higher-order cognitive process. Employing a pair of novel retrograde vectors, we traced NA projections from the locus coeruleus (LC) to both structures and observed an equivalent yet relatively segregated amount of inputs. Then, we showed that chemogenetic inhibition of NA projections to the mPFC, but not to the vlOFC, also impaired the rats’ ability to adaptively respond to the degradation procedure. Altogether, our findings provide important evidence of functional parcellation within the prefrontal cortex and point at mPFC-NA as key for updating Pavlovian S-O associations.Significant statementThe ability to update stimulus-outcome (S-O) associations is a key adaptive behavior, essential for surviving in an ever-changing environment. The prefrontal cortex is well-known for playing a key role in this process. The discrete contribution of each prefrontal subregion and of different neurotransmitters, however, remains unclear. In the current study, we show that inhibiting medial prefrontal (mPFC), but not ventrolateral orbitofrontal cortex (vlOFC), neurons impairs the rats’ ability to update S-O associations following contingency degradation. Moreover, we demonstrate that discrete noradrenergic projections to the two subregions exist and that inhibiting the ones projecting to the mPFC, but not to the vlOFC, once again impairs the rats’ behavior, thereby implying a substantial contribution of noradrenaline in orchestrating this higher-order cognitive process.
Concurrent representations of reinstated and transformed memories and their modulation by reward
Authors: Schultz Heidrun , Stoffregen Hanna , Dabas Aroma , Alcobendas María , Benoit Roland G. 
Published: December 2023

AbstractAn integral part of episodic retrieval is the reinstatement of neural activity that was present in the medial temporal lobe during encoding. However, neural memory representations do not remain static. Consolidation promotes the transformation of representations that are specific to individual episodes towards more generalized representations that reflect commonalities across episodes. Moreover, reward has been shown to augment episodic memory by enhancing consolidation, and it may accelerate the transformation of neural memory representations. We investigated this account with n=40 human participants using fMRI and an associative memory task. They encoded pictures of objects, each with one of four recurring scenes. Two scenes led to high reward, two led to low reward. The next day, participants encountered the objects again and retrieved the scenes from memory. Using representational similarity analysis, we demonstrate that retrieval is concurrently accompanied by the reinstatement of original neural representations and the activation of transformed, more generalized memories. Specifically, the parahippocampal cortex reinstates scene-specific patterns from the encoding phase during successful retrieval. In contrast, activity patterns in the medial prefrontal cortex and anterior hippocampus reflect transformed memories: They become more similar to each other for memories sharing the same scene, independent of memory success. Importantly, high reward enhances memory transformation in the anterior hippocampus. The brain thus maintains complementary memory representations: An episodic representation that resembles the original encoding pattern, and a generalized representation that summarizes commonalities across memories - in part for particularly valuable information.
In vivosingle-molecule imaging of RecB reveals efficient repair of DNA damage in Escherichia coli
Authors: Lepore Alessia , Thédié Daniel , McLaren Lorna , Azeroglu Benura , Pambos Oliver J. , Kapanidis Achillefs N. , Karoui Meriem El 
Published: December 2023

AbstractEfficient DNA repair is crucial for maintaining genome integrity and ensuring cell survival. InEscherichia coli, RecBCD plays a crucial role in processing DNA ends following a DNA double-strand break (DSB) to initiate repair by homologous recombination. While RecBCD has been extensively studiedin vitro, less is known about how it contributes to rapid and efficient repair in living bacteria. Here, we perform single-molecule microscopy to investigate DNA repair in real-time inE. coli. We quantify RecB single-molecule mobility and monitor the induction of the DNA damage response (SOS response) in individual cells. We show that RecB binding to broken DNA ends leads to efficient repair without SOS induction. In contrast, in a RecB mutant with modified activities leading to the activation of an alternative repair pathway, repair is less efficient and leads to high SOS induction. Our findings reveal how subtle alterations in RecB activity profoundly impact the efficiency of DNA repair inE. coli.
Calcium binding site in AA10 LPMO fromVibrio choleraesuggests modulating effects during environment survival and infection
Authors: Montserrat-Canals Mateu , Bjerregard-Andersen Kaare , Sørensen Henrik Vinter , Cordara Gabriele , Vaaje-Kolstad Gustav , Krengel Ute 
Published: December 2023

AbstractDespite major efforts towards its eradication, cholera remains a major health and economic burden in many developing countries. Between outbreaks, the bacterium responsible for the disease,Vibrio cholerae, survives in aquatic environmental reservoirs, where it commonly forms biofilms,e.g., on zooplankton.N-acetyl glucosamine binding protein A (GbpA) is an adhesin that binds to the chitinaceous surface of zooplankton and breaks its dense crystalline packing thanks to its lytic polysaccharide monooxygenase (LPMO) activity, which providesV. choleraewith nutrients. In addition, GbpA is an important colonization factor associated with bacterial pathogenicity, allowing the binding to mucins in the host intestine. Here, we report the discovery of a cation-binding site in proximity of the GbpA active site, which allows Ca2+, Mg2+or K+to bind close to its carbohydrate-binding surface. In addition to the X-ray crystal structures, we explored how the presence of ions affects the stability of the protein, compared the new GbpA LPMO structures to those of other LPMOs, and discussed the relevance of our discovery for bacterial survival. Calcium ions, abundant in natural sources of chitin, have been found to have the strongest effect on GbpA stability. Our findings suggest aV. cholerae-specific cation-binding site in GbpA that may fine-tune activity and binding to the different substrates during environmental survival and host infection.
RNA-sequencing reveals strong predominance ofTHRAsplicing isoform 2 in the developing and adult human brain
Authors: Graceffo Eugenio , Opitz Robert , Megges Matthias , Krude Heiko , Schuelke Markus 
Published: December 2023

AbstractThyroid hormone receptor alpha (THRα) is a nuclear hormone receptor that binds triiodothyronine (T3) and acts as an important transcription factor in development, metabolism and reproduction. THRαhas in mammals two major splicing isoforms, THRα1 and THRα2. The better characterized isoform, THRα1, is a transcriptional stimulator of genes involved in cell metabolism and growth. The less well characterized isoform, THRα2, lacks the Ligand Binding Domain (LBD) and is thought to act as an inhibitor of THRα1 action. The ratio of THRα1 to THRα2 splicing isoforms is therefore critical for transcriptional regulation in different tissues and during development. However, the expression patterns of both isoforms have not been studied in healthy human tissues or in the developing brain. Given the lack of commercially available isoform-specific antibodies, we addressed this question by analyzing four bulk RNA-sequencing datasets and two scRNA-sequencing datasets to determine the RNA expression levels of humanTHRA1andTHRA2transcripts in healthy adult tissues and in the developing brain. We demonstrate how 10X Chromium scRNA-seq datasets can be used to perform splicing-sensitive analyses of isoforms that differ at the 3’-end. In all datasets, we discovered a strong predominance ofTHRA2transcripts at all investigated stages of human brain development and in the central nervous system from healthy human adults.
A cell-free system for functional studies of small membrane proteins
Authors: Jiang Shan , Çelen Gülce , Glatter Timo , Niederholtmeyer Henrike , Yuan Jing 
Published: December 2023

AbstractNumerous small proteins have been discovered across all domains of life, among which many are hydrophobic and predicted to localize to the cell membrane. Based on a few that are well-studied, small membrane proteins are regulators involved in various biological processes, such as cell signaling, nutrient transport, drug resistance, and stress response. However, the function of most identified small membrane proteins remains elusive. Their small size and hydrophobicity make protein production challenging, hindering function discovery. Here, we combined a cell-free system with lipid sponge droplets and synthesized small membrane proteinsin vitro. Lipid sponge droplets contain a dense network of lipid bilayers, which accommodates and extracts newly synthesized small membrane proteins from the aqueous surroundings. Using small bacterial membrane proteins MgrB, SafA, and AcrZ as proof of principle, we showed that thein vitroproduced membrane proteins were functionally active, for example, modulating the activity of their target kinase as expected. The cell-free system produced small membrane proteins, including one from human, up to micromolar concentrations, indicating its high level of versatility and productivity. Furthermore, AcrZ produced in this system was used successfully forin vitroco-immunoprecipitations to identify interaction partners. This work presents a robust alternative approach for producing small membrane proteins, which opens a door to their function discovery in different domains of life.ImportanceSmall membrane proteins are shown to be involved in various biological processes in all domains of life and “can no longer be ignored”. Due to their small size and hydrophobicity, functional investigation of small membrane proteins is challenging. In this work, we present a simple, versatile, cell-free approach for synthesizing small membrane proteinsin vitro. We show that the small membrane proteins produced with our system are functional and in sufficient amounts for downstream target discoveries. Furthermore, our approach may uncover additional regulatory functions of small membrane proteins studied with conventional methods. Our work provides a robust alternative workflow for functional studies, which opens up new possibilities to advance our understanding of small membrane protein biology.
DNA nicks in both leading and lagging strand templates can trigger break-induced replication
Authors: Xu Yuanlin , Laksir Yassine , Morrow Carl A. , Taylor Kezia , Tsiappourdhi Costas , Collins Patrick , Jia Su , Andreadis Christos , Whitby Matthew C. 
Published: December 2023

AbstractEncounters between replication forks and unrepaired single-strand DNA breaks (SSBs) generate single-ended double-strand breaks (seDSBs) that can later become double-ended (deDSBs) through fork convergence. seDSBs can be repaired by break-induced replication (BIR), which is a highly mutagenic pathway that is thought to be repsonsible for many of the mutations and genome rearrangements that drive cancer development. However, the frequency of BIR’s deployment and its ability to be triggered by both leading and lagging template strand SSBs was unclear. Using site- and strand-specific SSBs generated by nicking enzymes, including CRISPR-Cas9n, we demonstrate that leading and lagging template strand SSBs in fission yeast are typically converted into deDSBs that are repaired primarily by error-free homologous recombination. However, both types of SSB can also trigger BIR, and the frequency of these events increases when the converging fork is delayed and the non-homologous end joining protein Ku70 is deleted.
Probability of stealth multiplets in sample-multiplexing for droplet-based single-cell analysis
Authors: Nakaki Fumio , Sharpe James 
Published: December 2023

AbstractBackgroundRecent advances in sample-multiplexing droplet-based single-cell RNA sequencing (mx-scRNA-seq) enable us to evaluate large numbers of different samples or experiments simultaneously by reducing the occurrence of undetectable multiplets, that is, the droplets that capture multiple cells. However, the probability of potential multiplets in mx-scRNA-seq is yet to be quantitatively examined.ResultsWe developed a simple theoretical model to predict four classes of possible multiplets in mx-scRNA-seq: Homogeneous stealth, partial stealth, multilabelled, and unlabelled. We estimated the probability of each class and have found that the partial tsealth multiplet, which has been overlooked, may sub-stantially affect the whole data when the labelling process is suboptimal. Next, we illustrated their presence in actual mx-scRNA-seq datasets when the sample labelling was suboptimal. In addition, we found that choosing a suitable sample-demultiplexing algorithm was critical to circumvent the partial stealth multiplets.ConclusionOur results show the necessity of optimising the labelling procedure and offer a theoretical basis to estimate the probability of each type of multiplets to ensure the integrity of mx-scRNA-seq.
EGFR-dependent actomyosin patterning coordinates morphogenetic movements between tissues
Authors: Clarke D. Nathaniel , Martin Adam C. 
Published: December 2023

AbstractThe movements that give rise to the body’s structure are powered by cell shape changes and rearrangements that are coordinated at supracellular scales. How such cellular coordination arises and integrates different morphogenetic programs is unclear. Using quantitative imaging, we found a complex pattern of adherens junction (AJ) levels in the ectoderm prior to gastrulation onset inDrosophila. AJ intensity exhibited a double- sided gradient, with peaks at the dorsal midline and ventral neuroectoderm. We show that this dorsal-ventral AJ pattern is regulated by epidermal growth factor (EGF) signaling and that this signal is required for ectoderm cell movement during mesoderm invagination and axis extension. We identify AJ levels and junctional actomyosin as downstream effectors of EGFR signaling. Overall, our study demonstrates a mechanism of coordination between tissue folding and convergent extension that facilitates embryo-wide gastrulation movements.
Increased HIF-2α Activity in the Nucleus Pulposus Causes Intervertebral Disc Degeneration in the Aging Mouse Spine
Authors: Johnston Shira N. , Tsingas Maria , Ain Rahatul , Barve Ruteja A. , Risbud Makarand V. 
Published: December 2023

ABSTRACTHypoxia-inducible factors (HIFs) are essential to the homeostasis of hypoxic tissues. Although HIF-2α, is expressed in nucleus pulposus (NP) cells, consequences of elevated HIF-2 activity on disc health remains unknown. We expressed HIF-2α with proline to alanine substitutions (P405A;P531A) in the Oxygen-dependent degradation domain (HIF-2αdPA) in the NP tissue using an inducible, nucleus pulposus-specific K19CreERTallele to study HIF-2α function in the adult intervertebral disc. Expression of HIF-2α in NP impacted disc morphology, as evident from small but significantly higher scores of degeneration in NP of 24-month-old K19CreERT; HIF-2αdPA(K19-dPA) mice. Noteworthy, comparisons of grades within each genotype between 14 months and 24 months indicated that HIF-2α overexpression contributed to more pronounced changes than aging alone. The annulus fibrosus (AF) compartment in the 14-month-old K19-dPA mice exhibited lower collagen turnover and Fourier transform-infrared (FTIR) spectroscopic imaging analyses showed changes in the biochemical composition of the 14-and 24-month-old K19-dPA mice. Moreover, there were changes in aggrecan, chondroitin sulfate, and COMP abundance without alterations in NP phenotypic marker CA3, suggesting the overexpression of HIF-2α had some impact on matrix composition but not the cell phenotype. Mechanistically, the global transcriptomic analysis showed enrichment of differentially expressed genes in themes closely related to NP cell function such as cilia, SLIT/ROBO pathway, and HIF/Hypoxia signaling at both 14- and 24-months. Together, these findings underscore the role of HIF-2α in the pathogenesis of disc degeneration in the aged spine.
Emergence of synchronised growth oscillations in filamentous fungi
Authors: Prakash Praneet , Jiang Xue , Richards Luke , Schofield Zoe , Schafer Patrick , Polin Marco , Soyer Orkun S. , Asally Munehiro 
Published: December 2023

AbstractSoil fungi are important decomposers of organic matter and play crucial roles in the biogeochemical cycles in the soil. Many species of fungi grow in the form of branched networks. While there have been investigations on the growth and architecture of the fungal networks, their growth dynamics in space and time is still not fully understood. In this study, we monitor the growth dynamics of the plant-promoting filamentous fungusSerendipita indicafor several days in a controlled environment within a microfluidic channel. We find that this species displays synchronized growth oscillations with the onset of sporulation and at a period of 3 hours. Quantifying this experimental synchronisation of oscillatory dynamics, we show that the synchronisation can be captured by the nearest neighbour Kuramoto model. Our analysis suggested the existence of millimetre-scale cell-cell communication across the fungi network. The microfluidic setup presented in this work may aid the future characterization of the molecular mechanisms of the cell-cell communication, which could in turn be exploited in order to control fungi growth and reproductive sporulation in soil and plant health management.
De novodesign of drug-binding proteins with predictable binding energy and specificity
Authors: Lu Lei , Gou Xuxu , Tan Sophia K , Mann Samuel I. , Yang Hyunjun , Zhong Xiaofang , Gazgalis Dimitrios , Valdiviezo Jesús , Jo Hyunil , Wu Yibing , Diolaiti Morgan E. , Ashworth Alan , Polizzi Nicholas F. , DeGrado William F. 
Published: December 2023

AbstractThe de novo design of small-molecule-binding proteins has seen exciting recent progress; however, the ability to achieve exquisite affinity for binding small molecules while tuning specificity has not yet been demonstrated directly from computation. Here, we develop a computational procedure that results in the highest affinity binders to date with predetermined relative affinities, targeting a series of PARP1 inhibitors. Two of four designed proteins bound with affinities ranging from < 5 nM to low μM, in a predictable manner. X-ray crystal structures confirmed the accuracy of the designed protein-drug interactions. Molecular dynamics simulations informed the role of water in binding. Binding free-energy calculations performed directly on the designed models are in excellent agreement with the experimentally measured affinities, suggesting that the de novo design of small-molecule-binding proteins with tuned interaction energies is now feasible entirely from computation. We expect these methods to open many opportunities in biomedicine, including rapid sensor development, antidote design, and drug delivery vehicles.One Sentence SummaryWe use informatic sampling to design low nM drug-binding proteins, and physics-based calculations to accurately predict affinities.
COVID-19-induced changes to food consumption and perceived well-being among low-income consumers in Trinidad and Tobago
Authors: Pacheco Barney G. , Pacheco Marvin H. 
Published: December 2023

PurposeThe global impact of the COVID-19 pandemic has been well documented, but there is still limited insight into the complex interaction of factors that determine its longer-term effects on the most vulnerable sectors of society. The current study therefore develops an integrated conceptual framework to investigate how consumers' fear of mortality and the perceived risk of severe illness associated with COVID-19 act as critical determinants of consumer food choices and perceived well-being.Design/methodology/approachAn online survey was utilized to collect data from a sample of 407 adult, low-income consumers across Trinidad and Tobago. The PROCESS macro was used to empirically test the hypothesized relationships in a moderated mediation model.FindingsThe results confirm that an increase in the perceived risk of severe illness has a significant negative effect on the consumption of healthy foods and perceived well-being. Moreover, consumers' choice of healthy foods mediates the negative relationship between consumers' perceived risk of severe COVID-19 illness and subjective well-being. Finally, the negative relationship between perceived risk of illness and healthy food choice weakens as an individual's fear of pandemic-related mortality increases.Originality/valueThis research integrates multiple related theoretical constructs to provide a more nuanced understanding of the lingering impact that risk perceptions and fear have on consumer food choices and associated well-being among a vulnerable Caribbean population. The changes identified have important implications for researchers interested in consumer food preferences as well as policymakers seeking to promote a healthy lifestyle among individuals coping with psychologically stressful circumstances.
The rationale for affirmative action (AA) being overturned by SCOTUS: an informational perspective of its pros and cons for the American dream
Authors: Mujtaba Bahaudin Ghulam 
Published: December 2023

PurposeThis paper aims to provide a historical overview of AA, its purpose and benefits, the legal rationale for the SCOTUS ruling and what it means for colleges and the workplace regarding equitable opportunities for minority groups (which include women, Blacks, Hispanics, Asians and other low-income populations), as they aim for the “American dream”.Design/methodology/approachSCOTUS decision and rationale, along with literature.FindingsThe race-based affirmative action (AA) precedent was recently overturned by the Supreme Court of the United States (SCOTUS) in the case of Students for Fair Admission (SFFA), Inc. vs President and Fellows of Harvard College/University of North Carolina. SCOTUS ruled that race cannot be a specific basis for college admission. In other words, public and private colleges and universities will no longer be able to consider “race” as a factor in deciding which qualified applicants should be admitted to enhance the diversity of their student body.Originality/valueThis is an original analysis.