bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of prenatal synthetic glucocorticoid exposure on the adolescent brain
Authors: Magalhães Ricardo , Gonçalves Nuno , Sousa Rui , Coelho Ana , Soares-Cunha Carina , Moreira Pedro , Marques Paulo , Tuulari Jetro J , Scheinin Nora M , Karlsson Linnea , Karlsson Hasse , Sousa Nuno , Rodrigues Ana João 
Published: April 2023

AbstractSynthetic Glucocorticoids (sGC) are commonly prescribed in preterm risk pregnancies in order to improve fetal organ maturation. This administration greatly reduces perinatal and neonatal mortality and respiratory distress syndrome associated with prematurity, but preclinical evidence warns for an adverse effect of sGC in the developing brain.In this work we evaluated the long-term effects of prenatal exposure to sGC in the brain of 17 years-old adolescents using multimodal MRI. From 4607 birth registrations from Hospital de Braga - Portugal, we selected participants that were born with similar gestational age, but that were either exposed during pregnancy to sGC (n=21) or non-exposed (n=24). After obtaining a detailed clinical history, participants were subjected to an extensive neuropsychological evaluation, followed by structural and functional MRI.No differences were found in the performance on neuropsychological tests between sGC-exposed and non-exposed participants. Moreover, no differences were found in regional brain volumes. However, the sGC-exposed group presented reduced functional connectivity at rest in a network involving primarily sub-cortical, cerebellar and frontal nodes in comparison to the non-exposed group, even after controlling for confounding factors such as gestational age at birth, birth weight, and sex.Our results suggest that prenatal sGC-exposed adolescents present no significant deviations in neuropsychological performance in the dimensions that we evaluated, although they presented altered functional connectivity, highlighting the need for additional studies to understand the impact of these changes in brain functioning and in behavior.HighlightsPrenatal synthetic glucocorticoid exposure does not lead to structural changes in the adolescent brain.Adolescents prenatally exposed to synthetic glucocorticoids present altered resting state network.
Optimized husbandry and targeted gene-editing for the cnidarianNematostella vectensis
Authors: Carvalho João E. , Burtin Maxence , Detournay Olivier , Amiel Aldine R. , Röttinger Eric 
Published: April 2023

AbstractOptimized laboratory conditions for research models are crucial for the success of scientific projects. This includes the control of the entire life cycle, access to all developmental stages and maintaining stable physiological conditions. Reducing the life cycle of a research model can also enhance the access to biological material and speed up genetic tool development. Thus, we optimized the rearing conditions for the sea anemoneNematostella vectensis, a cnidarian research model to study embryonic and post-metamorphic processes, such as regeneration.We adopted a semi-automated aquaculture system forN. vectensisand developed a dietary protocol optimized for the different life stages. Thereby, we increased spawning efficiencies and post-spawning survival rates, and considerably reduced the overall life cycle down to two months. To further improve the obtention of CRISPR-Cas9 mutants, we optimized the design of sgRNAs leading to full KO animals in F0 polyps using a single sgRNA. Finally, we show that NHEJ-mediated transgene insertion is possible inN. vectensis. In sum our study provides additional resources for the scientific community that uses or will useN. vectensisas a research model.Summary statementOptimized life cycle, in combination with efficient gene-editing approaches facilitates the establishment of genetic tools inN. vectensis, an emerging model for environmental stress response, regeneration, and longevity.
The Major Histocompatibility Complex modulatesBatrachochytrium dendrobatidisandRanavirusinfections in three amphibian species
Authors: Cortazar-Chinarro M , Richter-Boix A , Halvarsson P , Palomar G , Bosch J 
Published: April 2023

ABSTRACTGenetic variation of immune genes is an important component of genetic diversity. Major histocompatibility complex (MHC) genes have been put forward as a model for studying how genetic diversity is maintained and geographically distributed in wild populations. Pathogen-mediated selection processes (i.e., heterozygosity advantage, rare-allele advantage or fluctuating selection) and demography are believed to generate and maintain the extreme diversity of MHC genes observed. However, establishing the relative importance of the different proposed mechanisms has proved extremely difficult, but heterozygote advantage is expected to be more detectable when multiple pathogens are considered simultaneously. Here, we test whether MHC diversity in three amphibian species (Ichthyosaura alpestris, Pleurodeles waltl,andPelophylax perezi) is driven by pathogen-mediated selection. We examined the relationship between the individual MHC class II exon variability with individual infection status (infected or not), infection intensity, and co-infection of two main amphibian pathogens:Batrachochytrium dendrobatidis(Bd) andRanavirussp. (Rv). We found higher MHC class II exon 2 allelic diversity inI.alpestrisandP. perezithan inP.waltlbut no significant differences in allele frequencies between infection groups. We also observed significant differences inBdinfection intensity betweenBdinfected individuals and co-infected individuals depending on the number of MHC loci that an individual carries. ForI. alpestris, we show stronger evidence for MHC associations with infection intensity and status when individuals carry specific alleles and supertypes. Our results suggest that studying the association between MHC genes and single and co-infected individuals might provide new insights into host-parasite evolution and a better understanding of evolutionary mechanisms driven by MHC diversity.
The ‘Stem’ and the ‘Workers’ of the mtDNA population of the cell. Evidence from mutational analysis
Authors: Cote-L’Heureu Auden , Franco Melissa , Maithania Yogesh N. K. , Popadin Konstantin , Woods Dori , Tilly Jonathan , Khrapko Konstantin 
Published: April 2023

AbstractEvery cell in our body contains a vibrant population of mitochondria, or, more precisely, of mitochondrial DNA molecules (mtDNAs). Just like members of any population mtDNAs multiply (by replication) and ‘die’ (i.e., are removed, either by degradation or by distribution into the sister cell in mitosis). An intriguing question is whether all mitochondria in this population are equal, especially whether some are responsible primarily for reproduction and some - for empowering the various jobs of the mitochondrion, oxidative phosphorylation in the first place. Importantly, because mtDNA is highly damaged such a separation of responsibilities could help greatly reduce the conversion of DNA damage into real inheritable mutations. An unexpected twist in the resolution of this problem has been brought about by a recent high-precision analysis of mtDNA mutations (Sanchez-Contreras et al. 2023). They discovered that certain transversion mutations, unlike more common transitions, are not accumulating with age in mice. We argue that this observation requires the existence of a permanent replicating subpopulation/lineage of mtDNA molecules, which are protected from DNA damage, a.k.a. the ‘stem’ mtDNA. This also implies the existence of its antipode i.e., the ‘worker’ mtDNA, which empowers OSPHOS, sustains damage and rarely replicates. The analysis of long HiFi reads of mtDNA performed by PacBio closed circular sequencing confirms this assertion.
Engineering Nme2Cas9 Adenine Base Editors with Improved Activity and Targeting Scope
Authors: Bamidele Nathan , Zhang Han , Dong Xiaolong , Gaston Nicholas , Cheng Haoyang , Kelly Karen , Watts Jonathan K. , Xie Jun , Gao Guangping , Sontheimer Erik J. 
Published: April 2023

AbstractNme2Cas9 has been established as a genome editing platform with compact size, high accuracy, and broad targeting range, including single-AAV-deliverable adenine base editors. Here, we have engineered Nme2Cas9 to further increase the activity and targeting scope of compact Nme2Cas9 base editors. We first used domain insertion to position the deaminase domain nearer the displaced DNA strand in the target-bound complex. These domain-inlaid Nme2Cas9 variants exhibited shifted editing windows and increased activity in comparison to the N-terminally fused Nme2-ABE. We next expanded the editing scope by swapping the Nme2Cas9 PAM-interacting domain with that of SmuCas9, which we had previously defined as recognizing a single-cytidine PAM. We used these enhancements to correct two commonMECP2mutations associated with Rett syndrome with little or no bystander editing. Finally, we validated domain-inlaid Nme2-ABEs for single-AAV deliveryin vivo.
DifferentiatingBacillus subtilisincorporates valine and methionine carbon into the backbone of specific fatty acids
Authors: Rowe Gerald E. , Perreault Jonathan 
Published: April 2023

SummarySporulation inBacillus subtilishas long been a model of cellular differentiation, many aspects of which are well understood. The early stage of this process is of particular interest, especially the interrelationship of regulatory processes with metabolism in response to environmental changes. We analyzed cellular fatty acids as their methyl esters using capillary gas chromatography coupled to mass spectrometry during the transition from vegetative growth to early sporulation phase. Measurement of changes in the content of heavy fatty acid analogs in cultures supplemented with deuterium-labeled valine or methionine, or13C-labeld valine, showed that label was incorporated into the backbone of 12-methyltridecanoic and 14-methylpentadecanoic acid, in both sporulating andΔspo0Acultures. These fatty acids were formed starting with isobutyryl-CoA apparently originating only fromL-valine-d8in cultures so supplemented. Our observations indicate that following vegetative growth a pathway exists from certain amino acids into fatty acid methylene groups, evidently passing through propionyl-CoA. This finding has the potential to deepen understanding of the metabolic basis of cellular differentiation and identify new targets for antibiotics. We also observed a significant, continuous increase in the proportion of 13-methyltetradecanoic acid in fatty acids during the same period in which the pre-spore membrane would be formed.Graphical abstract:Abbreviated SummaryEarly in at least someBacillus subtilisdifferentiation scenarios, a straight-chain metabolite derived from propionyl-CoA is incorporated into fatty acids primed with isobutyryl-CoA possibly derived from cellular protein valine. Concurrently a leucine related fatty acid increases significantly, potentially comprising the predominant pre-spore septum fatty acid component. These processes occur in conjunction with the onset of fatty acid β-oxidation and bulk protein turnover.
A cell-type-specific nitric oxide-cGMP pathway regulates proprioceptor morphology
Authors: Cohn Raphael , Kolba Natalie , Picache Jaqueline A. , Lin Nancy , Saleem Aisha , Grueber Wesley B. 
Published: April 2023

AbstractNeurons show remarkable morphological diversity facilitated by transcriptional regulation during development and fitting with their connectivity and function. Second messenger pathways mediated by cyclic 3’,5’ adenosine or guanosine monophosphate (cAMP or cGMP) may serve to integrate extrinsic signals and regulate branching and growth of neurites. We investigated the regulation of cGMP signaling in neuronal morphogenesis inDrosophilasomatosensory neurons and found cell type-specificity in expression of the enzyme soluble guanylate cyclase (sGC) in different sensory neuron classes. sGC is responsible for the production of cGMP in response to the diffusible free radical messenger nitric oxide (NO) such that different levels of sGC impart cell type-specific sensitivity to NO. Supporting a role for the NO-cGMP pathway in neuronal morphogenesis, we find that knockout of sGC or nitric oxide synthase (NOS) impacts the morphology of multidendritic proprioceptors. The homeodomain transcription factor Cut shows different levels of expression in different somatosensory neuron types and we find that Cut regulates the level of cGMP signaling via repression of sGC expression. Thus, transcription factor levels contribute to cell type diversification by regulating levels of a signaling pathway to mediate somatosensory neuron morphogenesis.
A rapid ELISA platform with no sample preparation requirement
Authors: Maganzini Nicolò , Reschke Agnes , Cartwright Alyssa , Gidi Yasser , Thompson Ian A. P. , Hariri Amani , Dory Constantin , Rosenberg-Hasson Yael , Pan Jing , Eisenstein Michael , Cornell Timothy Thomas , Soh Hyongsok Tom 
Published: April 2023

AbstractSince its invention in the 1970’s, the enzyme-linked immunosorbent assay (ELISA) has served as the “gold-standard” for blood and plasma protein biomarker quantification. However, ELISAs require significant amounts of sample preparation entailing multiple reagent additions, incubations, and washing steps, limiting their clinical usefulness in the context of diagnosis and prognosis of rapidly evolving medical conditions. In this work, we describe the ‘instant ELISA’ biosensor platform, a probe that can be exposed directly to blood or other biological samples and quantifies protein biomarkers within 15 minutes. The sensor leverages a novel affinity reagent termed ‘monolithic dual-antibody clamp’ (MDAC) which preserves the specificity, sensitivity, and generalizability of ELISA while also enabling rapid analysis of unprocessed blood and other complex matrices. Using MDAC in chicken media, we demonstrate picomolar quantification of the inflammatory marker tumor necrosis factor alpha (TNFα), as well as monocyte chemotactic protein (MCP)-1, a useful prognostic indicator of cytokine release syndrome (CRS) during chimeric antigen receptor (CAR) T-cell immunotherapy. Finally, we demonstrate MCP-1 quantification in plasma samples from patients who had undergone CAR T-cell treatment.
SPADE: Spatial Deconvolution for Domain Specific Cell-type Estimation
Authors: Lu Yingying , Chen Qin , An Lingling 
Published: April 2023

AbstractThe advent of spatial transcriptomics technology has allowed for the acquisition of gene expression profiles with multi-cellular resolution in a spatially resolved manner, presenting a new milestone in the field of genomics. However, the aggregate gene expression from heterogeneous cell types obtained by these technologies poses a significant challenge for a comprehensive delineation of cell type-specific spatial patterns. Here, we propose SPADE (SPAtial DEconvolution), an in-silico method designed to address this challenge by incorporating spatial patterns during cell type decomposition. SPADE utilizes a combination of single-cell RNA sequencing data, spatial location information, and histological information to computationally estimate the proportion of cell types present at each spatial location. In our study, we showcased the effectiveness of SPADE by conducting analyses on synthetic data. Our results indicated that SPADE was able to successfully identify cell type-specific spatial patterns that were not previously identified by existing deconvolution methods. Furthermore, we applied SPADE to a real-world dataset analyzing the developmental chicken heart, where we observed that SPADE was able to accurately capture the intricate processes of cellular differentiation and morphogenesis within the heart. Specifically, we were able to reliably estimate changes in cell type compositions over time, which is a critical aspect of understanding the underlying mechanisms of complex biological systems. These findings underscore the potential of SPADE as a valuable tool for analyzing complex biological systems and shedding light on their underlying mechanisms. Taken together, our results suggest that SPADE represents a significant advancement in the field of spatial transcriptomics, providing a powerful tool for characterizing complex spatial gene expression patterns in heterogeneous tissues.
Sensory neurons couple arousal and foraging decisions inC. elegans
Authors: Scheer Elias , Bargmann Cornelia I. 
Published: April 2023

ABSTRACTForaging animals optimize feeding decisions by adjusting both common and rare behavioral patterns. Here, we characterize the relationship between an animal’s arousal state and a rare decision to leave a patch of bacterial food. Using long-term tracking and behavioral state classification, we find that food leaving decisions inC. elegansare coupled to arousal states across multiple timescales. Leaving emerges probabilistically over minutes from the high arousal roaming state, but is suppressed during the low arousal dwelling state. Immediately before leaving, animals have a brief acceleration in speed that appears as a characteristic signature of this behavioral motif. Neuromodulatory mutants and optogenetic manipulations that increase roaming have a coupled increase in leaving rates, and similarly acute manipulations that inhibit feeding induce both roaming and leaving. By contrast, inactivating a set of chemosensory neurons that depend on the cGMP-gated transduction channel TAX-4 uncouples roaming and leaving dynamics. In addition,tax-4-expressing sensory neurons promote lawn-leaving behaviors that are elicited by feeding inhibition. Our results indicate that sensory neurons responsive to both internal and external cues play an integrative role in arousal and foraging decisions.
Transcriptomic analysis during fruit development of the oil palm revealed specific isozymes related to starch metabolism that control oil yield
Authors: Apriyanto Ardha , Compart Julia , Fettke Joerg 
Published: April 2023

AbstractThe oil palm (Elaeis guineensisJacq.) produces a large amount of oil from the fruit. A recent study has shown that starch metabolism is essential for oil synthesis in fruit-producing species. Therefore, we detected gene expression changes related to starch metabolism genes throughout the maturity stages of oil palm fruit with different oil yields. Gene expression profiles were examined with three different oil yields (low, medium, and high) at six fruit development phases (4, 8, 12, 16, 20, and 22 weeks after pollination). Using RNA-seq analysis, we successfully identified and analyzed differentially expressed genes in oil palm mesocarps during development. The results showed that the transcriptome profile for each developmental phase was unique. Additionally, we found that starch synthesis and degradation occurred during fruit development and influenced oil production. Sucrose flux to the mesocarp tissue, rapid starch turnover, and high glycolytic activity have been identified as critical factors for oil production in oil palms. For starch metabolism and the glycolytic pathway, we identified specific enzyme isoforms (isozymes) that may control the oil production. This study provides valuable information for creating new high-oil-yielding palm varieties via breeding programs or genome editing approaches.
Nociception in chicken embryos, Part II: Embryonal development of electroencephalic neuronal activityin ovoas a prerequisite for nociception
Authors: Kollmansperger Sandra , Anders Malte , Werner Julia , Saller Anna M. , Weiss Larissa , Süß Stephanie C. , Reiser Judith , Schneider Gerhard , Schusser Benjamin , Baumgartner Christine , Fenzl Thomas 
Published: April 2023

AbstractChicken culling is forbidden in Germany since 2022, male/female selection and male elimination must be brought to an embryonic status prior to the onset of nociception. The present study evaluated the ontogenetic point when noxious stimuli potentially could be perceived/processed in the brainin ovo.EEG-recordings from randomized hyperpallial brain sites were recordedin ovoand noxious stimuli were applied. Temporal and spectral analyses of the EEG were performed.The onset of physiological neuronal signals could be determined at developmental day 13. ERP/ERSP/ITC analysis did not reveal phase-locked nociceptive responses.Although no central nociceptive responses were documented, adequate EEG-responses to noxious stimuli from other brain areas cannot be excluded. The extreme stress impact on the embryo during the recording may overwrite the perception of noniceptive stimuli. The results suggest developmental day 13 as the earliest embryonal stage being able to receive and process nociceptive stimuli.
All-in-one AAV-delivered epigenome-editing platform:proof-of-conceptand therapeutic implications for neurodegenerative disorders
Authors: Kantor Boris , Odonovan Bernadette , Rittiner Joseph , Hodgson Dellila , Lindner Nicholas , Guerrero Sophia , Dong Wendy , Zhang Austin , Chiba-Falek Ornit 
Published: April 2023

AbstractSafely and efficiently controlling gene expression is a long-standing goal of biomedical research, and the recently discovered bacterial CRISPR/Cas system can be harnessed to create powerful tools for epigenetic editing. Current state-of-the-art systems consist of a deactivated-Cas9 nuclease (dCas9) fused to one of several epigenetic effector motifs/domains, along with a guide RNA (gRNA) which defines the genomic target. Such systems have been used to safely and effectively silence or activate a specific gene target under a variety of circumstances. Adeno-associated vectors (AAVs) are the therapeutic platform of choice for the delivery of genetic cargo; however, their small packaging capacity is not suitable for delivery of large constructs, which includes most CRISPR/dCas9-effector systems. To circumvent this, many AAV-based CRISPR/Cas tools are delivered in two pieces, from two separate viral cassettes. However, this approach requires higher viral payloads and usually is less efficient. Here we develop a compact dCas9-based repressor system packaged within a single, optimized AAV vector. The system uses a smaller dCas9 variant derived fromStaphylococcus aureus(Sa). A novel repressor was engineered by fusing the small transcription repression domain (TRD) from MeCP2 with the KRAB repression domain. The final dSaCas9-KRAB-MeCP2(TRD) construct can be efficiently packaged, along with its associated gRNA, into AAV particles. Using reporter assays, we demonstrate that the platform is capable of robustly and sustainably repressing the expression of multiple genes-of-interest, bothin vitroandin vivo. Moreover, we successfully reduced the expression of ApoE, the stronger genetic risk factor for late onset Alzheimer’s disease (LOAD). This new platform will broaden the CRISPR/dCas9 toolset available for transcriptional manipulation of gene expression in research and therapeutic settings.