bluuebunny/crossref_metadata_2025_split huggingface dataset:
On-chip brain slice stimulation: precise control of electric fields and tissue orientation
Authors: Shaner Sebastian , Lu Han , Lenz Maximilian , Garg Shreyash , Vlachos Andreas , Asplund Maria 
Published: April 2023

AbstractNon-invasive brain stimulation modalities, including transcranial direct current stimulation (tDCS), are widely used in neuroscience and clinical practice to modulate brain function and treat neuropsychiatric diseases. DC stimulation ofex vivobrain tissue slices has been a method used to understand mechanisms imparted by tDCS. However, delivering spatiotemporally uniform direct current electric fields (dcEFs) that have precisely engineered magnitudes and are also exempt from toxic electrochemical by-products are both significant limitations in conventional experimental setups. As a consequence, bioelectronic dose-response interrelations, the role of EF orientation, and the biomechanisms of prolonged or repeated stimulation over several days all remain not well understood. Here we developed a platform with fluidic, electrochemical, and magnetically-induced spatial control. Fluidically, the chamber geometrically confines precise dcEF delivery to the enclosed brain slice and allows for tissue recovery in order to monitor post-stimulation effects. Electrochemically, conducting hydrogel electrodes mitigate stimulation-induced faradaic reactions typical of commonly-used metal electrodes. Magnetically, we applied ferromagnetic substrates beneath the tissue and used an external permanent magnet to enablein siturotational control in relation to the dcEF. By combining the microfluidic chamber with live-cell calcium imaging and electrophysiological recordings, we showcased the potential to study the acute and lasting effects of dcEFs with the potential of providing multi-session stimulation. This on-chip bioelectronic platform presents a modernized yet simple solution to electrically stimulate explanted tissue by offering more environmental control to users, which unlocks new opportunities to conduct thorough brain stimulation mechanistic investigations.Graphical abstract
Hippocampus and Striatum Showed Distinct Contributions to Longitudinal Changes in Value-Based Learning in Middle Childhood
Authors: Falck Johannes , Zhang Lei , Raffington Laurel , Mohn Johannes J. , Triesch Jochen , Heim Christine , Shing Yee Lee 
Published: April 2023

AbstractThe hippocampal-dependent memory system and striatal-dependent memory system modulate reinforcement learning depending on feedback timing in adults, but their contributions during development remain unclear. In a 2-year longitudinal study, 6-to-7-year-old children performed a reinforcement learning task in which they received feedback immediately or with a short delay following their response. Children’s learning was found to be sensitive to feedback timing modulations in their reaction time and inverse temperature parameter, which quantifies value-guided decision-making. They showed longitudinal improvements towards more optimal value-based learning, and their hippocampal volume showed protracted maturation. Better delayed model-derived learning covaried with larger hippocampal volume longitudinally, in line with the adult literature. In contrast, a larger striatal volume in children was associated with both better immediate and delayed model-derived learning longitudinally. These findings show, for the first time, an early hippocampal contribution to the dynamic development of reinforcement learning in middle childhood, with neurally less differentiated and more cooperative memory systems than in adults.
NAD+metabolism is a key modulator of bacterial respiratory epithelial infections
Authors: Klabunde Björn , Wesener André , Bertrams Wilhelm , Beinborn Isabell , Paczia Nicole , Surmann Kristin , Blankenburg Sascha , Wilhelm Jochen , Serrania Javier , Knoops Kèvin , Elsayed Eslam M. , Laakmann Katrin , Jung Anna Lena , Kirschbaum Andreas , Mraheil Mobarak Abu , Becker Anke , Völker Uwe , Vollmeister Evelyn , Benedikter Birke J. , Schmeck Bernd 
Published: April 2023

1.SummaryLower respiratory tract infections caused byStreptococcusOpneumoniae (Spn)are a leading cause of death globally. Here we investigate the bronchial epithelial response toSpninfection on a transcriptomic, proteomic and metabolic level. We found the NAD+salvage pathway to be dysregulated upon infection in a cell line model, primary human lung tissue andin vivoin rodents, leading to a reduced production of NAD+. Knockdown of NAD+salvage enzymes (NAMPT, NMNAT1) increased bacterial replication. NAD+treatment ofSpninhibited its growth while growth of other respiratory pathogens improved. Boosting NAD+production increased NAD+levels in immortalized and primary cells and decreased bacterial replication upon infection. NAD+treatment ofSpndysregulated the bacterial metabolism and reduced intrabacterial ATP. Enhancing the bacterial ATP metabolism abolished the antibacterial effect of NAD+. Thus, we identified the NAD+salvage pathway as an antibacterial cascade inSpninfections, predicting a novel antibacterial mechanism of NAD+.
Validation of Tau Antibodies for Use in Western Blotting and Immunohistochemistry
Authors: Ellis Michael J. , Lekka Christiana , Tulmin Hanna , O’Brien Darragh P. , Dhayal Shalinee , Zeissler Marie-Louise , Knudsen Jakob G. , Kessler Benedikt M. , Morgan Noel G. , Todd John A. , Richardson Sarah J. , Stefana M. Irina 
Published: April 2023

AbstractBackgroundThe microtubule-associated protein Tau has attracted diverse and increasing research interest, with Tau being mentioned in the title/abstract of nearly 34,000 PubMed-indexed publications to date. To accelerate studies into Tau biology, the characterisation of its multiple proteoforms, including disease-relevant post-translational modifications (PTMs), and its role in neurodegeneration, a multitude of Tau-targeting antibodies have been developed, with hundreds of distinct antibody clones currently available for purchase. Nonetheless, concerns over antibody specificity and limited understanding of the performance of many of these reagents has hindered research.MethodsWe have employed a range of techniques in combination with samples of murine and human origin to characterise the performance and specificity of 53 commercially-available Tau antibodies by Western blot, and a subset of these, 35 antibodies, in immunohistochemistry.ResultsContinued expression of residual protein was found in presumptive Tau “knockout” human cells and further confirmed through mass-spectrometry proteomics, providing evidence of Tau isoforms generated by exon skipping. Importantly, many total and isoform-specific antibodies failed to detect this residual Tau, as well as Tau expressed at low, endogenous levels, thus highlighting the importance of antibody choice. Our data further reveal that the binding of several “total” Tau antibodies, which are assumed to detect Tau independently of post-translational modifications, was partially inhibited by phosphorylation. Many antibodies also displayed non-specific cross-reactivity, with some total and phospho-Tau antibodies cross-reacting with MAP2 isoforms, while the “oligomer-specific” T22 antibody detected monomeric Tau on Western blot. Regardless of their specificity, with one exception, the phospho-Tau antibodies tested were found to not detect the unphosphorylated protein.ConclusionsWe identify Tau antibodies across all categories (total, PTM-dependent and isoform-specific) that can be employed in Western blot and/or immunohistochemistry applications to reliably detect even low levels of Tau expression with high specificity. This is of particular importance for studying Tau in non-neuronal cells and peripheral tissues, as well as for the confident validation of knockout cells and/or animal models. This work represents an extensive resource that serves as a point of reference for future studies. Our findings may also aid in the re-interpretation of existing data and improve reproducibility of Tau research.
A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling
Authors: Kang Sun Woo Sophie , Cunningham Rory P. , Miller Colin B. , Brown Lauryn A. , Cultraro Constance M. , Harned Adam , Narayan Kedar , Hernandez Jonathan , Jenkins Lisa M. , Lobanov Alexei , Cam Maggie , Porat-Shliom Natalie 
Published: April 2023

AbstractIn the liver, mitochondria are exposed to different concentrations of nutrients due to their spatial positioning across the periportal (PP) and pericentral (PC) axis. How these mitochondria sense and integrate these signals to respond and maintain homeostasis is not known. Here, we combined intravital microscopy, spatial proteomics, and functional assessment to investigate mitochondrial heterogeneity in the context of liver zonation. We found that PP and PC mitochondria are morphologically and functionally distinct; beta-oxidation was elevated in PP regions, while lipid synthesis was predominant in the PC mitochondria. In addition, comparative phosphoproteomics revealed spatially distinct patterns of mitochondrial composition and potential regulation via phosphorylation. Acute pharmacological modulation of nutrient sensing through AMPK and mTOR shifted mitochondrial phenotypes in the PP and PC regions, linking nutrient gradients across the lobule and mitochondrial heterogeneity. This study highlights the role of protein phosphorylation in mitochondrial structure, function, and overall homeostasis in hepatic metabolic zonation. These findings have important implications for liver physiology and disease.
Elevated temperature alters microbial communities, but not decomposition rates, during three years of in-situ peat decomposition
Authors: Roth Spencer , Griffiths Natalie A. , Kolka Randall K. , Oleheiser Keith C. , Carrell Alyssa A. , Klingeman Dawn M. , Seibert Angela , Chanton Jeffrey P. , Hanson Paul J. , Schadt Christopher W. 
Published: April 2023

AbstractPeatlands store approximately one-third of the global terrestrial carbon and are historically considered carbon sinks due to primary production outpacing microbial decomposition of organic matter. Climate change has the potential to alter the rate at which peatlands store or release carbon, and results from the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment have shown net losses of organic matter and increased greenhouse gas production from a boreal peatland in response to whole-ecosystem warming. In this study, we utilized the SPRUCE sites to investigate how warming and elevated CO2impact peat microbial communities and peat soil decomposition. We deployed peat soil decomposition ladders across warming and CO2treatment enclosures for three years, after which we characterized bacterial, archaeal, and fungal communities through amplicon sequencing and measured peat mass and compositional changes across four depth increments. Microbial diversity and community composition were significantly impacted by soil depth, temperature, and CO2treatment. Bacterial/archaeal α-diversity increased significantly with increasing temperature, and fungal α-diversity was significantly lower under elevated CO2treatment. Trans-domain microbial networks showed higher complexity (nodes, edges, degree, betweenness centrality) of microbial communities in decomposition ladders from warmed enclosures, and the number of highly connected, hub taxa within the networks was positively correlated with temperature. Methanogenic hubs were identified in the networks constructed from the warmest enclosures, indicating increased importance of methanogenesis in response to warming. Microbial community responses were not however reflected in measures of peat soil decomposition, as warming and elevated CO2had no significant short-term effects on soil mass loss or composition. Regardless of treatment, on average only 4.5% of the original soil mass was lost after three years and variation between replicates was high, potentially masking treatment effects. Many previous studies from the SPRUCE experiment have shown that warming is accelerating organic-matter decomposition and CO2and CH4production, and our results suggest that these changes may be driven by warming-induced shifts in microbial communities.
Four additional natural 7-deazaguanine derivatives in phages and how to make them
Authors: Cui Liang , Balalkundu Seetharamsingh , Liu Chuanfa , Ye Hong , Hourihan Jacob , Rausch Astrid , Hauß Christopher , Nilsson Emelie , Hoetzinger Matthias , Holmfeldt Karin , Zhang Weijia , Martinez-Alvarez Laura , Peng Xu , Tremblay Denise , Moinau Sylvain , Solonenko Natalie , Sullivan Matthew B. , Lee Yan-Jiun , Mulholland Andrew , Weigele Peter , de Crécy-Lagard Valérie , Dedon Peter C. , Hutinet Geoffrey 
Published: April 2023

ABSTRACTBacteriophages and bacteria are engaged in a constant arms race, continually evolving new molecular tools to survive one another. To protect their genomic DNA from restriction enzymes, the most common bacterial defence systems, double-stranded DNA phages have evolved complex modifications that affect all four bases. This study focuses on modifications at position 7 of guanines. Eight derivatives of 7-deazaguanines were identified, including four previously unknown ones: 2’-deoxy-7-(methylamino)methyl-7-deazaguanine (mdPreQ1), 2’-deoxy-7-(formylamino)methyl-7-deazaguanine (fdPreQ1), 2’-deoxy-7-deazaguanine (dDG), and 2’-deoxy-7-carboxy-7-deazaguanine (dCDG). These modifications are inserted in DNA by a guanine transglycosylase named DpdA. Three subfamilies of DpdA had been previously characterized: bDpdA, DpdA1, and DpdA2. Two additional subfamilies were identified in this work: DpdA3, which allows for complete replacement of the guanines, and DpdA4, which is specific to archaeal viruses. Transglycosylases have now been identified in all phages and viruses carrying 7-deazaguanine modifications, indicating that the insertion of these modifications is a post-replication event. Three enzymes were predicted to be involved in the biosynthesis of these newly identified DNA modifications: 7-carboxy-7-deazaguanine decarboxylase (DpdL), dPreQ1formyltransferase (DpdN), and dPreQ1methyltransferase (DpdM), which was experimentally validated and harbors a unique fold not previously observed for nucleic acid methylases.
Disturbance increases functional diversity but decreases phylogenetic diversity of an arboreal tropical ant community
Authors: Hoenle Philipp O. , Plowman Nichola S. , Matos-Maraví Pável , Bello Francesco de , Bishop Tom R. , Libra Martin , Idigel Cliffson , Rimandai Maling , Klimes Petr 
Published: April 2023

AbstractTropical rainforest canopies host a highly diverse arthropod fauna, which contribute to ecosystem function through their functional (FD) and phylogenetic diversity (PD). While a lot of previous research has documented the severe negative impacts of disturbance on the FD and PD of ground invertebrate communities, our understanding of arboreal counterparts is limited.Here, we studied the effects of forest disturbance on an ecologically important invertebrate group, the ants, in a lowland rainforest in New Guinea. We exhaustively sampled 4000 m2area of a primary and a secondary forest for canopy ants. We report > 2800 occurrences of 128 ant species in 852 trees, one of the most comprehensive arboreal collections to date.To test how ant PD and FD differ between the two forests, we constructed the ant species-level community phylogeny and measured 10 functional traits. Furthermore, we assessed by data exclusion the influence of species which were not nesting in individual trees (visitors) or only nesting (nesters), and of non-native species on FD and PD values. We expected that disturbance would decrease FD and PD in tree dwelling ants. We hypothesized that traits in primary forests would be more overdispersed due to the greater availability of ecological niches, while secondary forests would have stronger trait clustering due to a a stronger habitat filtering caused by more extreme microclimate.Primary forests had higher species richness and PD than secondary forest. Surprisingly, we found higher FD in secondary forest. This pattern was robust even if we decoupled functional and phylogenetic signals or if non-native ant species were excluded from the data. Visitors did not contribute strongly to FD, but they increased PD. Community trait means further corroborate the functional distinctiveness of arboreal ants among secondary and primary forest, with almost all traits being impacted by disturbance and forest succession.We conclude that the most plausible explanation is increased competition among closely related ant species in the secondary forest, which drives trait divergence. In the primary forest, abiotic habitat filters leads to more similar morphology and thus lower FD of phylogenetically more diverse ant assemblages.
CRISPR/Cas9 screen identifies KRAS-induced COX-2 as a driver of immunotherapy resistance in lung cancer
Authors: Boumelha Jesse , de Castro Andrea , Bah Nourdine , Cha Hongui , de Carné Trécesson Sophie , Rana Sareena , Anastasiou Panayiotis , Mugarza Edurne , Moore Christopher , Goldstone Robert , East Phil , Litchfield Kevin , Lee Se-Hoon , Molina-Arcas Miriam , Downward Julian 
Published: April 2023

ABSTRACTOncogenic KRAS impairs anti-tumour immune responses, but effective strategies to combine KRAS inhibitors and immunotherapies have so far proven elusive. In vivo CRISPR-Cas9 screening in an immunogenic murine lung cancer model identifies mechanisms by which oncogenic KRAS promotes immune evasion, most notably expression of immunosuppressive cyclooxygenase-2 (COX-2) in cancer cells. Oncogenic KRAS was a potent inducer of COX-2 in both mouse and human lung cancer which was suppressed using KRAS inhibitors. COX-2 acting via prostaglandin E2 (PGE2) promotes resistance to immune checkpoint blockade (ICB) in both mouse and human lung adenocarcinoma. Targeting COX-2/PGE2 remodelled the tumour microenvironment by inducing pro-inflammatory polarisation of myeloid cells and influx of activated cytotoxic CD8+ T cells, which increased the efficacy of ICB. Restoration of COX-2 expression contributed to tumour relapse after prolonged KRAS inhibition. We propose testing COX-2/PGE2 pathway inhibitors in combination with KRAS G12C inhibition or ICB in patients with KRAS-mutant lung cancer.
Colorectal cancer as a model for biological evolution
Authors: Ledda Marco , Pluchino Alessandro , Ragusa Marco 
Published: April 2023

AbstractComplexity in cancer research has led to the creation of powerful analytical tools for helping experimentalin vivoandin vitromethods. These tools range from systems of differential equations resolved in computer simulations, to lattice models and agent-based models (ABMs). These analytical methods are focused on studying cell behavior and dynamic cell populations. Among these, those that are increasingly used are ABMs because they can incorporate multi-scale features ranging from the individual up to the population level, mixing rules based on mathematical and conceptual parameters, and combining statistical/population assumptions with individual heterogeneity. In this work, we present an ABM that simulates tumor progression in a colonic crypt, with the aim of providing an experimentalin silicoenvironment for testing results achieved in traditional lab research, and developing alternative scenarios of tumor development. As the first part of an ongoing project, the long-term goal is to reproduce and study, the general evolutionary mechanisms of a biological system.
Different behavioural profiles between invasive and native nudibranchs: means for invasion success?
Authors: Macali Armando , Ferretti Sara , Scozzafava Serena , Carere Claudio 
Published: April 2023

AbstractBehaviour is predicted to be a primary determinant of the success of the invasion process during the early phases of colonization. Comparing sympatric invaders and native species may provide a good approach to unravel behavioural traits involved in an invasion process. In this study, we carried out an experimental simulation of the introduction and the establishment phase into a new environment and assessed the expression of activity, alertness and habituation in a non-indigenous Mediterranean population of the South African nudibranchGodiva quadricolorcomparing its profiles with those of the sympatric nativeCratena peregrinaandCaloria quatrefagesi. Individuals of these three species were subjected to three behavioural tests: spontaneous activity, carried out in the introduction phase (immediately after sampling) and after a week of acclimatization; alert test, in which a potential threat was simulated by means of a tactile stimulus; habituation test, where the same alert test stimulus was repeated five times at thirty- minute intervals. Native nudibranch had repeatable traits, although with species differences perhaps related to their different ecological niches. The comparison with the invasive species highlighted its low repeatability in activity levels, suggesting higher plasticity, a strong tendency to locomotor activity, and a marked sensitization in the habituation test. Such traits could play an important and active role in the ongoing invasion process.
Interspecies blastocyst complementation generates functional rat cell-derived forebrain tissues in mice
Authors: Huang Jia , He Bingbing , Yang Xiali , Long Xin , Wei Yinghui , Gao Yanxia , Fang Yuan , Ying Wenqin , Wang Zikang , Li Chao , Zhou Yingsi , Li Shuaishuai , Shi Linyu , Guo Fan , Zhou Haibo , Yang Hui , Wu Jun 
Published: April 2023

SUMMARYInterspecies organogenesis via blastocyst complementation provides a unique platform to study development in an evolutionarily context and holds potential to overcome world-wide organ shortages1. By using this technique, rat pancreas, thymus, heart, and eye tissues have been generated in mice2–4. To date, however, xeno-generation of brain tissues has not been achieved through blastocyst complementation. Here, we developed an optimized one-step blastocyst complementation strategy based on C-CRISPR5, which facilitated rapid screening of candidate genes to support blastocyst complementation. Among the seven WNT pathway-related genes selected for targeting, onlyDkk1orHesx1deficiency supported forebrain complementation by blastocyst injection of mouse embryonic stem cells (mESCs). Further, injecting rat ESCs (rESCs) into mouse blastocysts deficient forHesx1but notDkk1supported the development of adult chimeric forebrains comprised a large proportion of rat cells that were structurally and functionally similar to the mouse forebrains. Our analysis revealed that the rESC-derived forebrains developed along the spatial-temporal trajectory with the mouse forebrains rather than rat forebrains, but gene expression profiles of rESC-derived nerve cells surprisingly maintained the characteristics of the rat cells. We noted that the chimeric rate gradually decreased as development progressed, suggesting xenogeneic barriers during mid-to-late prenatal development. Interspecies forebrain complementation opens the door for studying evolutionarily conserved and divergent mechanisms underlying brain development and cognitive function. The C-CRIPSR based IBC strategy developed here holds great potential to broaden the study and application of interspecies organogenesis.