bluuebunny/crossref_metadata_2025_split huggingface dataset:
IRF1 regulates self-renewal and stress-responsiveness to support hematopoietic stem cell maintenance
Authors: Rundberg Nilsson Alexandra , Xian Hongxu , Shalapour Shabnam , Cammenga Jörg , Karin Michael 
Published: January 2023

ABSTRACTInflammatory mediators induce emergency myelopoiesis and cycling of adult hematopoietic stem cells (HSCs) through incompletely understood mechanisms. To suppress the unwanted effects of inflammation and preserve its beneficial outcomes, the mechanisms by which inflammation affects hematopoiesis need to be fully elucidated. Rather than focusing on specific inflammatory stimuli, we here investigated the role of transcription factor Interferon (IFN) regulatory factor 1 (IRF1), which receives input from several inflammatory signaling pathways. We identify IRF1 as a master HSC regulator. IRF1 loss impairs HSC self-renewal, increases stress-induced cell cycle activation, and confers apoptosis resistance. Transcriptomic analysis revealed an aged, inflammatory signature devoid of IFN signaling with reduced megakaryocytic/erythroid priming and antigen presentation in IRF1-deficient HSCs. Finally, we conducted IRF1-based AML patient stratification to identify groups with distinct proliferative, survival and differentiation features, overlapping with our murine HSC results. Our findings position IRF1 as a pivotal regulator of HSC preservation and stress-induced responses.
Gradual change of cortical representations with growing visual expertise for synthetic shapes
Authors: Kakaei Ehsan , Braun Jochen 
Published: January 2023

AbstractVisual expertise for particular categories of objects (e.g., birds, mushrooms, minerals, and so on) is known to enhance cortical responses in parts of the ventral occipitotemporal cortex. How is such additional expertise integrated into the prior cortical representation of life-long cumulative visual experience? To address this question, we record multivariate BOLD responses to synthetic visual objects and track changes in pairwise distance as initially unfamiliar objects gradually become familiar (‘representational similarity analysis’, RSA).We find view-independent responses to synthetic shapes (i.e., an invariant representation) in large parts of the ventral occipitotemporal cortex, including the primary visual cortex. Surprisingly, the quality of representation is already high even when shapes are still unfamiliar. As shapes become familiar with repeated viewing, this quality remains high, but representational geometry shifts with more experience. For visually similar shapes that are not repeated and therefore remain unfamiliar, the representation degrades and becomes progressively marginalized.We conclude that, at least for highly dissimilar synthetic shapes, functional imaging responses can reveal detailed representational geometry at the level of exemplars, as well as gradual changes in this geometry due to experience and learning.
Nature Forest Reserves in Tanzania and their importance for conservation
Authors: Ract Claire , Burgess Neil D. , Dinesen Lars , Sumbi Peter , Malugu Isaac , Latham Julia , Anderson Lucy , Gereau Roy E. , de Lima Marcelo Gonçalves , Akida Amina , Nashanda Evarist , Lyatuu Gertrude , Platts Phil , Rovero Francesco 
Published: January 2023

AbstractSince 1997 Tanzania has undertaken a process to identify and declare a network of Nature Forest Reserves (NFRs) with high biodiversity values, mainly from within its existing portfolio of national Forest Reserves, but with some new extensions. In recent years this expansion has accelerated, with ten NFRs declared since 2015. The current network of 19 existing NFRs covered 918,212 hectares by the end of 2020 (with an additional three reserves covering 34,862 hectares in the process of being declared). The coverage by NFRs of Tanzanian habitat types has increased to include the main forest types, wet, seasonal, and dry, and includes wetlands and grasslands. This has led to more than a doubling of the coverage of species ranges of vertebrates by the NFR network. Declared and proposed reserves now contain at least 178 of Tanzania’s 242 endemic vertebrate species, of which over 50% are threatened with extinction, and 553 Tanzanian endemic plant taxa (species, subspecies, and varieties), of which 61.3% are threatened. NFRs also support 41 single site endemic vertebrate species and 76 single site endemic plant taxa. Time series data show that NFR management effectiveness is increasing, especially where donor funds are available. Tourism, diversified revenue generation and investment schemes are required to create a network of economically self-sustaining NFRs able to conserve critical biodiversity values. Improved management and investment have reduced some threats in recent years, but ongoing challenges include illegal logging, charcoal production, firewood, pole cutting, hunting, fire, wildlife trade, and the unpredictable impacts of climate change.
Enhancing additive series relay intercropping of grass pea (Lathyrus sativus L.) with low land rice (Oryza sativa L.) in North-Western Ethiopia: A farmer’s indigenous knowledge
Authors: Assefa Endeshew , Bitew Yayeh 
Published: January 2023

AbstractIn Ethiopia the facts of farmer’s indigenous knowledge based cropping system has been rarely investigated through research. A field experiment was conducted during 2021/2022 main cropping season at Fogera plain with the objective of examining the effect of additive series relay intercropping of grass pea with lowland rice on the grain yield of the component crops and production efficiency of the cropping system. The experiment consisted of a factorial combination of four seed proportion of grass pea (SPGP) (25%, 50%, 75% and 100% of the recommended seed rate of sole grass pea) relay intercropped with full seed rate of rice in four Rice: Grass pea spatial arrangements (SA) (1:1, 2:1, 3:1 and their mixed relay intercropping system). The treatments were arranged in Randomized Complete Block Design with three replications. Data on grain yield of the component crops were collected and analyzed using SAS-JMP-16 software. Results revealed that SPGP and SA had no significant effect on rice. The highest grain yield of grass pea was obtained when 25% SPGP was relay intercropped with rice in 1:3 SA (5.10 t ha-1). Maximum production efficiency in terms of total land output yield (9. 89 t ha-1) and land use efficiency (ATER =1.33), net benefit (33, 5176.79 Birr ha-1), marginal rate of return (21,428%) and positive monetary advantage index with lower competitive ratio was obtained when 50% SPGP was relay intercropped with rice in 1:3 SA. Thus, this mixture seems contributing in the development of sustainable crop production with a limited use of external inputs. Rice intercropping with other staple legume crops under residual soil moisture needs to be tested across locations and years to intensify the production efficiency and profitability of the cropping system.
Two avianPlasmodiumspecies trigger different transcriptional responses on their vectorCulex pipiens
Authors: Garrigós M , Ylla G , Martínez-de la Puente J , Figuerola J , Ruiz-López MJ 
Published: January 2023

AbstractMalaria is a mosquito-borne disease caused by protozoans of the genusPlasmodiumthat affects both humans and wildlife. The fitness consequences of infections by avian malaria are well known in birds, however, little information exists on its impact on mosquitoes. Here we study howCulex pipiensmosquitoes transcriptionally respond to infection by two differentPlasmodiumspecies,P. relictumandP. cathemerium, differing in their virulence (mortality rate) and transmissibility (parasite presence in exposed mosquitoes’ saliva). We study the mosquito response to the infection at three critical stages of parasite development: formation of ookinetes at 24 hours post-infection (hpi), the release of sporozoites into the hemocoel at 10 days post-infection (dpi), and storage of sporozoites in the salivary glands at 21dpi. For each time point, we characterized the gene expression of mosquitoes infected with eachP. relictumandP. cathemeriumand mosquitoes fed on an uninfected bird and, subsequently, compared their transcriptomic responses. Differential gene expression analysis showed most of the transcriptomic changes occurred during the early infection stage (24 hpi), especially when comparingP. relictumandP. cathemeriuminfected mosquitoes. Differentially expressed genes in mosquitoes infected with each species were related mainly to the immune response, trypsin, and other serine-proteases metabolism. We conclude that these differences in response may partly play a role in the differential virulence and transmissibility previously observed inP. relictumandP. cathemeriuminCx. pipiens.
Quantitative comparison between aMRI and DENSE for the assessment of brain tissue motion
Authors: Adams Ayodeji L. , Terem Itamar , Champagne Allen , Holdsworth Samantha J. , Zwanenburg Jaco J. M. 
Published: January 2023

AbstractPurposeAmplified MRI (aMRI) holds potential for assessing brain tissue motion and strain, using images acquired from readily-available sequences. However, image registration is necessary to extract displacements from the motion-amplified images, which may limit its accuracy. We aimed to separately assess the errors from imperfections in the aMRI amplification, and errors from the registration algorithm, using a semi-synthetic approach.MethodsGround truth brain tissue motion was derived from smoothed Displacement Encoding with Stimulated Echoes (DENSE) measurements acquired at 7T (8 subjects). Those were then applied to a still sagittal anatomical balanced-SSFP image to obtain a DENSE-animated MRI series to which aMRI (amplification factor 10) was applied. DENSE-amplified MRI series served as a reference (Damp-MRI; amplification factor, 10). Amplified displacements were extracted from aMRI and Damp-MRI using a common registration algorithm. Linear regression was used to estimate the amplification and r2agreement of the amplified displacements relative to the ground truth.ResultsThe estimated amplification was consistently lower for aMRI-derived displacements (range: [4.9±0.3 5.7±0.3]) than for Damp-MRI measurements (range: [6.7±0.5 7.7±0.5]). Nevertheless, the spatial, temporal and average characteristics of brain tissue motion derived from aMRI were comparable to the ground truth for Anterior-Posterior and Feet-Head displacements: (group averaged r2≥0.84), as were the Damp-MRI derived displacements (r2≥0.88). When aMRI was applied to in-vivo cine-bSSFP images and compared to the ground truth, the results were less favorable, highlighting the need for artefact-free images.ConclusionThese results strengthen the potential of aMRI as a tool for semi-quantitative assessment of brain tissue motion in disease.
Static and dynamic functional connectomes represent largely similar information
Authors: Matkovič Andraž , Anticevic Alan , Murray John D. , Repovš Grega 
Published: January 2023

AbstractFunctional connectivity (FC) of blood-oxygen-level-dependent (BOLD) fMRI time series can be estimated using methods that differ in sensitivity to the temporal order of time points (static vs. dynamic) and the number of regions considered in estimating a single edge (bivariate vs. multivariate). Previous research suggests that dynamic FC explains variability in FC fluctuations and behavior beyond static FC. Our aim was to systematically compare methods on both dimensions. We compared five FC methods: Pearson’s/full correlation (static, bivariate), lagged correlation (dynamic, bivariate), partial correlation (static, multivariate) and multivariate AR model with and without self-connections (dynamic, multivariate). We compared these methods by (i) assessing similarities between FC matrices, (ii) by comparing node centrality measures, and (iii) by comparing the patterns of brain-behavior associations. Although FC estimates did not differ as a function of sensitivity to temporal order, we observed differences between the multivariate and bivariate FC methods. The dynamic FC estimates were highly correlated with the static FC estimates, especially when comparing group-level FC matrices. Similarly, there were high correlations between the patterns of brain-behavior associations obtained using the dynamic and static FC methods. We conclude that the dynamic FC estimates represent information largely similar to that of the static FC.
The possible role of lipid bilayer properties in the evolutionary disappearance of betaine lipids in seed plants
Authors: Bolik Stéphanie , Schlaich Alexander , Mukhina Tetiana , Amato Alberto , Bastien Olivier , Schneck Emanuel , Demé Bruno , Jouhet Juliette 
Published: January 2023

ABSTRACTPhosphate is vital for plant and algae growth, yield, and survival, but in most environments, it is poorly available. To cope with phosphate starvation, photosynthetic organisms used their phospholipids as a phosphate reserve. In microalgae, betaine lipids replace phospholipids whereas, in higher plants, betaine lipid synthesis is lost, driving plants to other strategies. The aim of this work was to evaluate to what extent betaine lipids and PC lipids share physicochemical properties and could thus substitute each other. Using neutron diffraction and molecular dynamics simulations of two synthetic lipids, dipalmitoylphosphatidylcholine (DPPC) and dipalmitoyl-diacylglyceryl-N,N,N-trimethylhomoserine (DP-DGTS), we show that DP-DGTS bilayers are thicker, more rigid, and mutually more repulsive than DPPC bilayers. The different properties and hydration response of PC and DGTS provide an explanation for the diversity of betaine lipids observed in marine organisms and for their disappearance in seed plants.
A conserved family of immune effectors cleaves cellular ATP upon viral infection
Authors: Rousset Francois , Yirmiya Erez , Nesher Shahar , Brandis Alexander , Mehlman Tevie , Itkin Maxim , Malitsky Sergey , Millman Adi , Melamed Sarah , Sorek Rotem 
Published: January 2023

SummaryDuring viral infection, cells can deploy immune strategies that deprive viruses of molecules essential for their replication. In this study, we report a family of immune effectors in bacteria which, in response to phage infection, degrade cellular ATP and dATP by cleaving the N-glycosidic bond between the adenine and sugar moieties. These ATP nucleosidase effectors are widely distributed within multiple bacterial defense systems including CBASS, prokaryotic argonautes and NLR-like proteins, and we show that degradation of (d)ATP during infection halts phage propagation and aborts infection. By analyzing homologs of the immune ATP nucleosidase domain, we discover and characterize Detocs, a new family of bacterial defense systems with a two-component phosphotransfer signaling architecture. The immune ATP nucleosidase domain is also encoded within a diverse set of eukaryotic proteins that have immune-like architectures, and we show biochemically that these eukaryotic homologs preserve the ATP nucleosidase activity. Our findings suggest that ATP and dATP degradation is a cell-autonomous innate immune strategy conserved across the tree of life.
Intraspecific competition for a nest and its implication for the fitness of relocating ant colonies
Authors: Halder Eshika , Annagiri Sumana 
Published: January 2023

AbstractCompetitive interaction is important in structuring species composition of a habitat. Several studies have been conducted on intraspecific competition but little is known in the context of the goal-oriented task of colony relocation. Current study examines how relocating colonies respond when the new nest is a limiting resource. Examining this competition across equal sized colonies (n=17) and unequal sized colonies (n=14), we found that most trails had a clear outcome with one of the colony’s occupying the new nest, while 25% of colonies merged. Larger colonies had a significantly higher chance of occupying the new nest and outcompeted the smaller colonies in most of the cases. Colonies that had lower latency to discover and more explorers had a significantly higher chance of gaining control of the new nest and interesting the level of aggression shown by both the competing colonies was comparable. Spatio-temporal analysis of the aggression revealed that the area surrounding the old, new nest and the time at which transportation occurs has higher levels of aggression. While both the competing colonies stole pupa from each other, the mean number of successful stealing by the larger colonies was 8 times larger than smaller colonies while stealing was comparable between similar sized colonies. Relocating colonies experienced significantly more mortality as compared to controls and competition for the new nest imposed additional mortality on losing colonies over the short time. Due to the potential merging of colonies, incorporation of stolen brood and increased mortality, the overall fitness of the colonies is likely to be negatively impacted due to intraspecific competition for a new nest.
Tau in cerebrospinal fluid induces neuronal hyperexcitability and alters hippocampal theta oscillations
Authors: Brown Jessica , Camporesi Elena , Lantero-Rodriguez Juan , Olsson Maria , Wang Alice , Medem Blanca , Zetterberg Henrik , Blennow Kaj , Karikari Thomas K. , Wall Mark , Hill Emily 
Published: January 2023

AbstractAlzheimer’s disease (AD) and other tauopathies are characterized by the aggregation of tau into soluble and insoluble forms (including tangles and neuropil threads). In humans, a fraction of both phosphorylated and non-phosphorylated N-terminal to mid-domain tau species, including the aggregated forms, are secreted into cerebrospinal fluid (CSF). Some of these CSF tau species can be measured as diagnostic and prognostic biomarkers, starting from early stages of disease. While in animal models of AD pathology, soluble tau aggregates have been shown to disrupt neuronal function, it is unclear whether the tau species present in CSF will modulate neural activity. Here, we have developed and applied a novel approach to examine the electrophysiological effects of CSF from patients with a tau-positive biomarker profile. The method involves incubation of acutely-isolated wild-type mouse hippocampal brain slices with small volumes of diluted human CSF, followed by a suite of electrophysiological recording methods to evaluate their effects on neuronal function from single cells through to the network level. Comparison of the toxicity profiles of the same CSF samples, with and without immuno-depletion for tau, has enabled a pioneering demonstration that CSF-tau potently modulates neuronal function. We demonstrate that CSF-tau mediates an increase in neuronal excitability in single cells. We then observed, at the network level, increased input-output responses and enhanced paired-pulse facilitation as well as an increase in long-term potentiation. Finally, we show that CSF-tau modifies the generation and maintenance of hippocampal theta oscillations, which have important roles in learning and memory and are known to be altered in AD patients. Together, we describe a novel method for screening human CSF-tau to understand functional effects on neuron and network activity, which could have far-reaching benefits in understanding tau pathology, thus allowing for the development of better targeted treatments for tauopathies in the future.Graphic Abstract
Intestinal Paneth cell differentiation relies on asymmetric regulation of Wnt signaling by Daam1/2
Authors: Colozza Gabriele , Lee Heetak , Merenda Alessandra , Wu Szu-Hsien Sam , Català-Bordes Andrea , Radaszkiewicz Tomasz W. , Jordens Ingrid , Lee Ji-Hyun , Bamford Aileen-Diane , Farnhammer Fiona , Low Teck Yew , Maurice Madelon M. , Bryja Vítězslav , Kim Jihoon , Koo Bon-Kyoung 
Published: January 2023

AbstractThe mammalian intestine is one of the most rapidly self-renewing tissues, driven by actively cycling stem cells residing at the crypt bottom1,2. Together with stromal cells, Paneth cells form a major element of the niche microenvironment that provides various growth factors to orchestrate intestinal stem cell homeostasis, such as Wnt33. With 19 family members, different Wnt ligands can selectively activate β-catenin dependent (canonical) or independent (non-canonical) signaling4,5. Here, we report that Dishevelled-associated activator of morphogenesis 1 (Daam1) and its paralogue Daam2 asymmetrically regulate canonical and non-canonical Wnt (Wnt/PCP) signaling, and their function is required for Paneth cell progenitor differentiation. We found that Daam1/2 interacts with the Wnt antagonist Rnf43, and Daam1/2 double knockout stimulates canonical Wnt signaling by preventing Rnf43-dependent endo-lysosomal degradation of the ubiquitinated Wnt receptor, Frizzled (Fzd). Moreover, single-cell RNA sequencing analysis revealed that Paneth cell differentiation is impaired by Daam1/2 depletion, as a result of defective Wnt/PCP signaling. Taken together, we identified Daam1/2 as an unexpected hub molecule coordinating both canonical and non-canonical Wnt signaling, the regulation of which is fundamental for specifying an adequate number of Paneth cells while maintaining intestinal stem cell homeostasis.
Maternal and intrauterine influences on feto-placental growth are accompanied by sexually dimorphic changes in placental mitochondrial respiration, and metabolic signalling pathways
Authors: Salazar-Petres Esteban , Pereira-Carvalho Daniela , Lopez-Tello Jorge , Sferruzzi-Perri Amanda Nancy 
Published: January 2023

AbstractAdverse maternal environments such as small size, malnutrition and metabolic conditions are known to influence fetal growth outcomes. Similarly, fetal growth and metabolic alterations may alter the intrauterine environment and affect all fetuses in multiple gestations/litter bearing species. The placenta is the site of convergence between signals derived from the mother and the developing fetus/es. Its functions are fuelled by energy generated by mitochondrial oxidative phosphorylation (OXPHOS). The aim of this study was to delineate the role of an altered maternal and/or fetal/intrauterine environment in feto-placental growth and placental mitochondrial energetic capacity. To address this, in mice we used disruptions of the gene encoding phosphoinositol 3-kinase (PI3K) p110α, a growth and metabolic regulator to perturb the maternal and/or fetal/intrauterine environment and study the impact on wildtype conceptuses. We found that feto-placental growth was modified by a perturbed maternal and intrauterine environment, and effects were most evident for wildtype males compared to females. However, placental mitochondrial complex I+II OXPHOS and total electron transport system (ETS) capacity were similarly reduced for both fetal sexes, yet reserve capacity was additionally decreased in males in response to the maternal and intrauterine perturbations. These were also sex-dependant differences in the placental abundance of mitochondrial-related proteins (e.g. citrate synthase, ETS complexes), and activity of growth/metabolic signalling pathways (AKT and MAPK) with maternal and intrauterine alterations. Our findings thus identify that the mother and intrauterine environment provided by littermates, modulate feto-placental growth, and placental bioenergetics and metabolic signalling in a manner dependent on fetal sex. This may have relevance for understanding the pathways leading to reduced fetal growth, particularly in the context of suboptimal maternal environments and multiple gestations/litter bearing species.