bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatially Resolved Transcriptomics for Evaluation of Intracranial Vessels in a Rabbit Model: Proof of Concept
Authors: Zabriskie Matthew S. , Cooke Daniel L. , Wang Chuanzhuo , Alexander Matthew D. 
Published: February 2022

AbstractBackgroundBetter understanding of vessel biology and vascular pathophysiology is needed to improve understanding of cerebrovascular disorders. Tissue from diseased vessels can offer the best data. Rabbit models can be effective for studying intracranial vessels, filling gaps resulting from difficulties acquiring human tissue. Spatially-resolved transcriptomics (SRT) in particular hold promise for studying such models as they build on RNA sequencing methods, augmenting such data with histopathology.MethodsRabbit brains with intact arteries were flash frozen, cryosectioned, and stained with H&E to confirm adequate inclusion of intracranial vessels before proceeding with tissue optimization and gene expression analysis using the Visium SRT platform. SRT results were analyzed with k-means clustering analysis, and differential gene expression was examined, comparing arteries to veins.ResultsCryosections were successfully mounted on Visium proprietary slides. Quality control thresholds were met. Optimum permeabilization was determined to be 24 minutes for the tissue optimization step. In analysis of SRT data, k-means clustering distinguished vascular tissue from parenchyma. When comparing gene expression traits, the most differentially expressed genes were those found in smooth muscle cells. These genes were more commonly expressed in arteries compared to veins.ConclusionsIntracranial vessels from model rabbits can be processed and analyzed with the Visium SRT platform. Face validity is found in the ability of SRT data to distinguish vessels from parenchymal tissue and differential expression analysis accurately distinguishing arteries from veins. SRT should be considered for future animal model investigations into cerebrovascular diseases.
Selective integration of diverse taste inputs within a single taste modality
Authors: Deere Julia U. , Sarkissian Arvin A. , Yang Meifeng (Maia) , Uttley Hannah A. , Santana Nicole Martinez , Nguyen Lam , Ravi Kaushiki , Devineni Anita V. 
Published: February 2022

ABSTRACTA fundamental question in sensory processing is how different channels of sensory input are processed to regulate behavior. Different input channels may converge onto common downstream pathways to drive the same behaviors, or they may activate separate pathways to regulate distinct behaviors. We investigated this question in theDrosophilabitter taste system, which contains diverse bitter-sensing cells residing in different taste organs. First, we optogenetically activated subsets of bitter neurons within each organ. These subsets elicited broad and highly overlapping behavioral effects, suggesting that they converge onto common downstream pathways, but we also observed behavioral differences that argue for biased convergence. Consistent with these results, transsynaptic tracing revealed that bitter neurons in different organs connect to overlapping downstream pathways with biased connectivity. We investigated taste processing in one type of second-order bitter neuron that projects to the higher brain. These neurons integrate input from multiple organs and regulate specific taste-related behaviors. We then traced downstream circuits, providing the first glimpse into taste processing in the higher brain. Together, these results reveal that different bitter inputs are selectively integrated early in the circuit, enabling the pooling of information, while the circuit then diverges into multiple pathways that may have different roles.
Identification of Catechins Binding Pockets in Monomeric Aβ42Through Ensemble Docking and MD Simulations
Authors: Firouzi Rohoullah , Sowlati-Hashjin Shahin , Chávez-García Cecilia , Ashouri Mitra , Karimi-Jafari Mohammad Hossein , Karttunen Mikko 
Published: February 2022

AbstractThe assembly of the Amyloid-βpeptide (Aβ) into toxic oligomers and fibrils is associated with Alzheimer’s disease and dementia. Therefore, disrupting amyloid assembly by direct targeting of the Aβmonomeric form with small molecules or antibodies is a promising therapeutic strategy. However, given the dynamic nature of Aβ, standard computational tools cannot be easily applied for high-throughput structure-based virtual screening in drug discovery projects. In the current study, we propose a computational pipeline – in the framework of the ensemble docking strategy – to identify catechins’ binding pockets in monomeric Aβ42. It is shown that both hydrophobic aromatic interactions and hydrogen bonding are crucial for the binding of catechins to Aβ42. Also, it has been found that all the studied ligands, especially theEGCG, can act as potent inhibitors against amyloid aggregation by blocking the central hydrophobic region of the Aβ. Our findings are evaluated and confirmed with multi-microsecond MD simulations. Finally, it is suggested that our proposed pipeline, with low computational cost in comparison with MD simulations, is a suitable approach for the virtual screening of ligand libraries against Aβ.
The interplay between developmental stage and environment underlies the adaptive effect of a natural transposable element insertion
Authors: Merenciano Miriam , González Josefa 
Published: February 2022

ABSTRACTEstablishing causal links between adaptive mutations and their ecologically relevant phenotypes is key to understanding the process of adaptation, a central goal in evolutionary biology that is also relevant for conservation biology, medicine and agriculture. Although progress has been made, the number of causal adaptive mutations identified so far is still limited as gene by gene, and gene by environment interactions, among others, complicates linking genetic variation with its fitness–related effects. Transposable elements, often ignored in the quest for the genetic basis of adaptive evolution, are known to be a genome-wide source of regulatory elements across organisms that at times can lead to adaptive phenotypes. In this work, we combine gene expression, in vivo reporter assays, CRISPR/Cas9 genome editing, and survival experiments to characterize in detail the molecular and phenotypic consequences of a natural Drosophila melanogaster transposable element insertion: the roo solo-LTR FBti0019985. This transposable element provides an alternative promoter to the transcription factor Lime, involved in cold- and immune-stress responses. We found that the effect of FBti0019985 on Lime expression depends on the interplay between the developmental stage and the environmental conditions. We further establish a causal link between the presence of FBti0019985 and increased survival to cold- and immune-stress. Our results exemplify how several developmental stages and environmental conditions need to be considered to characterize the molecular and functional effects of a genetic variant, and add to the growing body of evidence that transposable elements can induce complex mutations with ecologically relevant effects.
CELLoGeNe - an Energy Landscape Framework for Logical Networks Controlling Cell Decisions
Authors: Andersson Emil , Sjö Mattias , Kaji Keisuke , Olariu Victor 
Published: February 2022

AbstractExperimental and computational efforts are constantly made to elucidate mechanisms controlling cell fate decisions during development and cell reprogramming. One powerful method is to consider cell commitment and reprogramming as movements in an energy landscape. Here, we develop CELLoGeNe (Computation of Energy Landscapes of Logical Gene Networks), which maps Boolean implementation of gene regulatory networks (GRNs) into energy landscapes. CELLoGeNe removes inadvertent symmetries in the energy landscapes normally arising from standard Boolean operators. Furthermore, CELLoGeNe provides a tool for visualising multi-dimensional energy landscapes and a platform to stochastically probe and analyse the shapes of the computed landscapes corresponding to the epigenetic landscapes for development and reprogramming. We demonstrate CELLoGeNe on a GRN governing maintenance and self-renewal of pluripotency, identifying attractors experimentally validated. We also apply CELLoGeNe on a network controlling reprogramming from mouse embryonic fibroblast (MEF) to induced pluripotent stem cells (iPSCs) where we identify potential roadblocks as attractors. CELLoGeNe is a general framework that can be applied to various biological systems offering a broad picture of intracellular dynamics otherwise inaccessible with existing methods.
Isocitrate dehydrogenase 3b is required for spermiogenesis but dispensable for retinal degeneration
Authors: Zhu Siyan , Huang Jiancheng , Xu Rong , Wang Yekai , Wan Yiming , McNeel Rachel , Parker Edward , Kolson Douglas , Yam Michelle , Webb Bradley , Zhao Chen , Du Jianhai 
Published: February 2022

AbstractIsocitrate dehydrogenase 3 (IDH3), a key enzyme in mitochondrial tricarboxylic acid (TCA) cycle, catalyzes the decarboxylation of isocitrate into α-ketoglutarate (αKG), converting NAD+ into NADH. We have found that IDH3 β subunit (IDH3B) is essential for IDH3 activity in multiple tissues. Loss of Idh3b in mice causes substantial accumulation of the isocitrate and its precursors in the TCA cycle, particularly in the testes, whereas the levels of the downstream metabolites remain unchanged or slightly increased. The Idh3b-knockout (KO) mice have normal visual function without retinal degeneration. However, the male KO mice are infertile. Loss of Idh3b causes energetic deficit and disrupts the biogenesis of acrosome and flagellum, resulting in spermiogenesis arrestment in sperm cells. Together, we demonstrate IDH3B controls its substrate levels in the TCA cycle and it is required for sperm mitochondrial metabolism and spermiogenesis, highlighting the importance of the tissue-specific function of the ubiquitous TCA cycle.
Dissecting aggregation and seeding dynamics of α-Syn polymorphs using the phasor approach to FLIM
Authors: Tittelmeier Jessica , Druffel-Augustin Silke , Alik Ania , Melki Ronald , Nussbaum-Krammer Carmen 
Published: February 2022

AbstractSynucleinopathies are a heterogenous group of neurodegenerative diseases characterized by the progressive accumulation of pathological α-synuclein (α-Syn). The importance of structural polymorphism of α-Syn assemblies for distinct synucleinopathies and their progression is increasingly recognized. However, the underlying mechanisms are poorly understood. Here we use fluorescence lifetime imaging microscopy (FLIM) to investigate seeded aggregation of α-Syn in a biosensor cell line. We show that conformationally distinct α-Syn polymorphs exhibit characteristic fluorescence lifetimes. FLIM further revealed that α-Syn polymorphs were differentially processed by cellular clearance pathways, yielding fibrillar species with increased seeding capacity. Thus, FLIM is not only a powerful tool to distinguish different amyloid structures, but also to monitor the dynamic process of amyloid remodeling by the cellular environment. Our data suggest that the accumulation of highly seeding competent degradation products for particular polymorphs may account for accelerated disease progression in some patients.
The GTPase Activity of the Double FYVE Domain Containing Protein 1 (DFCP1) Regulates Lipid Droplet Metabolism
Authors: Ismail V.A. , Naismith T. , Kast D.J. 
Published: February 2022

SummaryLipid droplets (LDs) are transient lipid storage organelles that can be readily tapped to resupply cells with energy or lipid building blocks, and therefore play a central role in cellular metabolism. However, the molecular factors and underlying mechanisms that regulate the growth and degradation of LDs are poorly understood. It has emerged that LD metabolism is sensitive to the autophagy- and LD-associated protein Double FYVE Domain Containing Protein 1 (DFCP1), however, little is known about DFCP1’s roles in autophagy and LD metabolism. Here, we show that DFCP1 contains a novel GTPase domain that regulates LD size by controlling the assembly of DFCP1 onto LDs in response to changes in nutrient availability. Specifically, we show that DFCP1 accumulation on LDs is independent of PI3P-binding, but requires a combination of the ER-binding domain and a unique GTPase domain. This novel GTPase domain possesses a low basal GTP turnover rate and has the ability to dimerize. Furthermore, mutations in the DFCP1 that either impact GTP hydrolysis or dimerization, result in changes in the accumulation of DFCP1 on LDs, as well as in changes in LD density and size. Importantly, the magnitude of these changes depends on the nutritional status of the cell. Collectively, our findings indicate that DFCP1 is a GTP-dependent metabolic sensor capable of modulating cellular storage of free fatty acids.
Ethylene Insensitive 3-Like 2 (EIL2) is a Brassicaceae-specific transcriptional regulator involved in fine-tuning ethylene-dependent hypocotyl elongation, lateral root formation and flowering time in Arabidopsis thaliana
Authors: Houben Maarten , Vaughan-Hirsch John , Mou Wangshu , Van de Poel Bram 
Published: February 2022

AbstractEthylene signaling directs a pleiotropy of developmental processes in plants. In Arabidopsis, ethylene signaling converges at the master transcription factor Ethylene Insensitive 3 (EIN3), which has five homologs, EIN3-like 1-5 (EIL1-5). EIL1 is most characterized and operates similar as EIN3, while EIL3-5 are not involved in ethylene signaling. EIL2 remains less investigated. Our phylogenetic analysis revealed that EIL2 homologs are only retrieved in the Brassicaceae family, suggesting EIL2 diverged to have specific functions in the mustard family. By characterizing eil2 mutants, we found that EIL2 is involved in regulating ethylene-specific developmental processes in Arabidopsis thaliana, albeit in a more subtle way compared to EIN3/EIL1. EIL2 steers ethylene-triggered hypocotyl elongation in light-grown seedlings and it is involved in lateral root formation. Furthermore, EIL2 takes part in regulating flowering time as eil2 mutants flower on average one day earlier and have fewer leaves. A pEIL2:EIL2:GFP translational reporter line revealed that EIL2 protein abundance is restricted to the stele of young developing roots. EIL2 expression, and not EIL2 protein stability, is regulated by ethylene in an EIN3/EIL1-dependent way. Despite EIL2 taking part in several developmental processes, the precise upstream and downstream regulation of this ethylene- and Brassicaceae-specific transcription factor remains to be elucidated.HighlightEIL2 is an ethylene-dependent transcription factor that evolved exclusively in the mustard family and operates downstream from EIN3/EIL1. EIL2 is involved in fine-tuning hypocotyl elongation, lateral root formation and flowering time in Arabidopsis thaliana.
A systems biology approach to elucidate the post-translational regulome of coronary artery disease
Authors: Sharma Ankit , Ghatge Madankumar , Deshpande Vrushali , Vangala Rajani Kanth 
Published: February 2022

AbstractCoronary Artery Disease is a major killer in India and world at large but the molecular regulators which modulate clinically relevant pathways are not completely understood. This study was aimed at identifying essential post-translational modifications (PTM) regulome network and its master regulator modulating the CAD associated pathways. 995 CAD associated genes were taken from InCardiome database (www.tri-incardiome.org) were analyzed for all possible PTMs. Two important interdependent molecular processes which define the function of a protein are protein-protein interactions and PTMs of which PTMs play regulatory role. Using PTMCode2 we evaluated the co-evolving amino acid residues for important PTMs and found that serine-serine phosphorylation is highly represented combinatorial regulator in these set of proteins. Furthermore, in the CAD associated pathways we again found that serine phosphorylation was dominant player in all the processes of atherosclerosis. In order to identify the master regulator kinase, we further assessed the kinome network associated with CAD and identified 5 most important kinases namely GSK3B, PRKCA, PRKCD, SRC and PRKACA which might modulate clinically important pathways. GSK3B with the highest network parameters (node degree and betweenness centrality) was identified as master regulator and 1 U/l increase of phsophoGSK3B (on a log scale) increased the odds ratio (OR) by 4.07 fold (AUC 0.620) and 6.27 fold (AUC 0.752) upon addition of conventional risk factors (CRFs).
Rtt109 promotes nucleosome replacement ahead of the replicating fork
Authors: Jonas Felix , Yaakov Gilad , Barkai Naama 
Published: February 2022

AbstractDNA replication perturbs chromatin by triggering the eviction, replacement and incorporation of nucleosomes. How this dynamic is orchestrated in time and space is poorly understood. Here, we apply a recently established sensor for histone exchange to follow the time-resolved histone H3 exchange profile in budding yeast cells undergoing synchronous replication. We find that new histones are incorporated not only behind, but also ahead of the replication fork. We provide evidence that Rtt109, the S phase-specific acetyltransferase, stabilizes nucleosomes behind the fork, but promotes H3 replacement ahead of the fork. Unexpectedly, increased replacement ahead of the fork is independent of the primary Rtt109 acetylation target H3K56, and rather results from Rtt109 activity towards the H3 N-terminus. Our results suggest that selective incorporation of differentially modified H3s behind and ahead of the replication fork results in opposing effects on histone exchange, which may contribute to genome stability by overcoming replication-associated challenges.
Validation of a colorimetric LAMP to detect Loxosceles experimental envenomation
Authors: Fernandes Luana Paula , Rocha Marcele Neves , Duarte Clara Guerra , Minozzo João Carlos , do Monte-Neto Rubens L. , Felicori Liza F. 
Published: February 2022

AbstractDiagnostic tests for brown spider accidents are unavailable and impact treatment decisions, increasing costs and patient risks. In this work, we used for the first time a fast, simple, and visual method based on the loop-mediated isothermal amplification assay (LAMP) to detect Loxosceles envenomation. Using the DNA from L. similis legs, we observed a high sensitivity using this test since as low as 0.32 pg of DNA could be detected. This pH-dependent colorimetric assay was 64 times more sensitive than PCR to detect spider DNA. The test was specific for Loxosceles once no cross-reaction was observed when testing DNA from different agents that cause similar dermonecrotic injuries. The test allowed the detection of Loxosceles intermedia DNA from hair, serum, and swab samples obtained from experimentally-envenomed rabbit within 72 h. The method sensitivity varied according to the sample and the collection time, reaching 100% sensitivity in serum and hair, respectively, 1 h and 24 h after the experimental envenomation. Due to its ease of execution, speed, sensitivity, and specificity, LAMP presents an excellent potential for identifying Loxosceles spp. envenomation. This can reduce the burden on the Health System and the morbidity for the patient by implementing the appropriate therapy immediately.In addition, this work opens up the perspective to other venomous animal accident identification using LAMP.Highlights*Using 28S primers it was possible to identify L. similis’ DNA with high sensitivity;*LAMP was 62-fold more sensitive than PCR and detected as low as 0.32 pg of DNA;*LAMP detected L. intermedia DNA from hair, serum, and exudate from experimentally-envenomed rabbits;*LAMP presents an excellent potential for identifying Loxosceles spp. envenomation.
Screening for functional regulatory variants in open chromatin using GenIE-ATAC
Authors: Cooper Sarah , Schwartzentruber Jeremy , Coomber Eve L , Wu Qianxin , Bassett Andrew 
Published: February 2022

AbstractUnderstanding the effects of genetic variation in gene regulatory elements is crucial to interpreting genome function. This is particularly pertinent for the hundreds of thousands of disease-associated variants identified by GWAS, which frequently sit within gene regulatory elements but whose functional effects are often unknown. Current methods are limited in their scalability and ability to assay regulatory variants in their endogenous context, independently of other tightly linked variants. Here we present a new medium-throughput screening system: genome engineering based interrogation of enhancers assay for transposase accessible chromatin (GenIE-ATAC), that measures the effect of individual variants on chromatin accessibility in their endogenous genomic and chromatin context. We employ this assay to screen for the effects of regulatory variants in human induced pluripotent stem cells, validating a subset of causal variants, and extend our software package (rgenie) to analyse these new data. We demonstrate that this methodology can be used to understand the impact of defined deletions and point mutations within transcription factor binding sites. We thus establish GenIE-ATAC as a method to screen for the effect of gene regulatory element variation, allowing identification and prioritisation of causal variants from GWAS for functional follow-up and understanding the mechanisms of regulatory element function.
Linear DNA amplicons as a novel cancer vaccine strategy
Authors: Conforti Antonella , Salvatori Erika , Lione Lucia , Compagnone Mirco , Pinto Eleonora , Shorrock Clay , Hayward James A. , Sun Yuhua , Liang Ben Minghwa , Palombo Fabio , Viscount Brian , Aurisicchio Luigi 
Published: February 2022

AbstractDNA-based vaccines represent a simple, safe and promising strategy for harnessing the immune system to fight infectious diseases as well as various forms of cancer and thus are considered an important tool in the cancer immunotherapy toolbox. Nonetheless, the manufacture of plasmid DNA vaccines has several drawbacks, including long lead times and the need to remove impurities from bacterial cultures. Here we report the development of polymerase chain reaction (PCR)-produced amplicon expression vectors as DNA vaccines and their in vivo application to elicit antigen-specific immune responses in animal cancer models. Amplicons encoding tumor-associated-antigens, such as telomerase reverse transcriptase or neoantigens expressed by murine tumor cell lines were able to elicit antigen-specific immune responses and proved to significantly impact tumor growth when administered in combination with immune-checkpoint inhibitors (ICIs). These results strongly support the further exploration of the use of PCR-based amplicons as an innovative immunotherapeutic approach to cancer treatment.